*HEADER    RNA                                     06-APR-04   1SZY              
*TITLE     SOLUTION STRUCTURE OF ITALY1 ("INITIATOR TRNA ANTICODON               
*TITLE    2 LOOP FROM YEAST"), AN UNMODIFIED 21-NT RNA WITH THE                  
*TITLE    3 SEQUENCE OF THE ANTICODON STEM-LOOP OF YEAST INITIATOR TRNA          
*COMPND    MOL_ID: 1;                                                            
*COMPND   2 MOLECULE: 5'-                                                        
*COMPND   3 R(P*GP*GP*CP*AP*GP*GP*GP*CP*UP*CP*AP*UP*AP*AP*CP*CP*CP*UP*G          
*COMPND   4 P*CP*C)-3';                                                          
*COMPND   5 CHAIN: A;                                                            
*COMPND   6 ENGINEERED: YES                                                      
*SOURCE    MOL_ID: 1;                                                            
*SOURCE   2 SYNTHETIC: YES                                                       
*KEYWDS    INITIATOR TRNA ANTICODON LOOP                                         
*EXPDTA    NMR                                                                   
*AUTHOR    D.C.SCHWEISGUTH, P.B.MOORE                                            
*REVDAT   1   20-APR-04 1SZY    0                                                

!RNA PARAMETER FILE 'FRAMEOWRK' FROM PARALLHDG.DNA AND ATOM NAMES
! AND HEAVY ATOM PARAMETERS FROM DNA-RNA.PARAM
!INCLUDES ALL NONEXCHANGEABLE HYDROGEN TERMS FOR BOND, ANGLE, AND
!IMPROPERS WITH ENERGY CONSTANT VARIABLES: $kchbond, $kchangle, AND $kchimpr.
!BOND, ANGLE, AND IMPROPERS WERE ESTIMATED FROM VALUES FROM THE STANDARD 
!NUCLEOTIDES OF INSIGHTII 95.0 (BIOSYM/MOLECULAR SIMULATIONS).
!CREATED 2/24/96-- JASON P. RIFE AND PETER B. MOORE
! DNA-RNA-ALLATOM.PARAM

!set echo=off message=off end

evaluate ($kchbond = 2000) 
evaluate ($kchangle  = 1000)
evaluate ($kchimpr = 1000)


!the generic bonds were taken from param11.dna with 3*kq
BOND  C5R  OH       876.000    1.4300     ! 5' end
BOND  C5D  OH       876.000    1.4300     ! 5' end
BOND  C3R  OH       876.000    1.4300     ! 3' end
BOND  C3D  OH       876.000    1.4300     ! 3' end
BOND  O2R  HO      1350.000    0.9572

!Phos.  - combined RNA/DNA statistics used 
!                      kq       x_eq       sigma
BOND  P    O1P     1489.209    1.485      ! 0.015  Phos
BOND  P    O2P     1489.209    1.485      ! 0.015  P
BOND  P    O5R     3350.720    1.593      ! 0.010  P
BOND  P    OH      3350.720    1.593      ! 0.010  P ! For 5pho patch
BOND  P    O3R     2326.889    1.607      ! 0.012  P

!Sugars
!RNA statistics
BOND  O5R  C5R     1709.551    1.425      ! 0.014  Sugar
BOND  C5R  C4R     1982.674    1.510      ! 0.013  S
BOND  C4R  C3R     2769.190    1.524      ! 0.011  S
BOND  C3R  C2R     2769.190    1.525      ! 0.011  S
BOND  C2R  C1R     3350.720    1.528      ! 0.010  S
BOND  O4R  C1R     2326.888    1.414      ! 0.012  S
BOND  O4R  C4R     2326.888    1.453      ! 0.012  S
BOND  O3R  C3R     1982.674    1.423      ! 0.013  S
BOND  C2R  O2R     1982.674    1.413      ! 0.013  S

!DNA statistics
BOND  O5R  C5D     1709.551    1.427      ! 0.014  Sugar
BOND  C5D  C4D     5235.500    1.511      ! 0.008  S
BOND  C4D  C3D     3350.720    1.528      ! 0.010  S
BOND  C3D  C2D     3350.720    1.518      ! 0.010  S
BOND  C2D  C1D     1709.551    1.521      ! 0.014  S
BOND  O4D  C1D     1982.674    1.420      ! 0.013  S
BOND  O4D  C4D     2769.190    1.446      ! 0.011  S
BOND  O3R  C3D     1982.674    1.431      ! 0.013  S

!hydrogen/carbon
BOND  C4R  H       $kchbond   1.09               
BOND  C3R  H       $kchbond   1.09               
BOND  C2R  H       $kchbond   1.09              
BOND  C1R  H       $kchbond   1.09               
BOND  C5R  H       $kchbond   1.09               

BOND  C4D  H       $kchbond   1.09               
BOND  C3D  H       $kchbond   1.09               
BOND  C2D  H       $kchbond   1.09              
BOND  C1D  H       $kchbond   1.09               
BOND  C5D  H       $kchbond   1.09               

!Bases
!base specific bonds taken from param11.dna , 3*kq
BOND  O2U  HO      1350.000    0.957      ! UR
BOND  HN   NNA     1416.000    1.010      ! URA
BOND  HN   N1T     1416.000    1.010      ! Infer.
BOND  HN   N1C     1416.000    1.010
BOND  HN   N9G     1416.000    1.010
BOND  HN   N9A     1416.000    1.010
BOND  HN   N3U     1416.000    1.010
BOND  HN   N3T     1416.000    1.010
BOND  H2   N2      1416.000    1.010
BOND  H2   N4C     1416.000    1.010
BOND  H2   N2G     1416.000    1.010
BOND  H2   N6A     1416.000    1.010

BOND  HO   OH      1350.000    0.960      ! PARAM7 (IR stretch 3400 cm-1)

!Base sugar joint bonds (scale from sugar)
!                      kq       x_eq       sigma
BOND  C1R  N1T     1709.551    1.473      ! 0.014  Base
BOND  C1R  N1U     4136.691    1.469      ! 0.009  B
BOND  C1R  N1C     2326.889    1.470      ! 0.012  B
BOND  C1R  N9G     4136.691    1.459      ! 0.009  B
BOND  C1R  N9A     3350.720    1.462      ! 0.010  B

BOND  C1D  N1T     1709.551    1.473      ! 0.014  B   !DNA
BOND  C1D  N1U     4136.691    1.469      ! 0.009  B
BOND  C1D  N1C     2326.889    1.470      ! 0.012  B
BOND  C1D  N9G     4136.691    1.459      ! 0.009  B
BOND  C1D  N9A     3350.720    1.462      ! 0.010  B

!cytosine                      kq          x_eq  sigma
BOND       C2C    ON          1370.370    1.240 !0.009  B
BOND       C4C    N4C         1370.370    1.335 !0.009  B
BOND       N1C    C2C         1110.000    1.397 !0.010  B
BOND       N1C    C6C         3083.333    1.367 !0.006  B
BOND       C2C    NC          1734.375    1.353 !0.008  B
BOND       NC     C4C         2265.306    1.335 !0.007  B
BOND       C4C    C5C         1734.375    1.425 !0.008  B
BOND       C5C    C6C         1734.375    1.339 !0.008  B
BOND       C5C    H           $kchbond    1.09               
BOND       C6C    H           $kchbond    1.09               

!thymine
BOND       N1T    C2T         1734.375    1.376 !0.008  B
BOND       C2T    N3T         1734.375    1.373 !0.008  B
BOND       N3T    C4T         1734.375    1.382 !0.008  B
BOND       C4T    C5T         1370.370    1.445 !0.009  B
BOND       C5T    C6T         2265.306    1.339 !0.007  B
BOND       C6T    N1T         2265.306    1.378 !0.007  B
BOND       C2T    ON          1734.375    1.220 !0.008  B
BOND       C4T    ON          1370.370    1.228 !0.009  B
BOND       C5T    CC3E        3083.333    1.496 !0.006  B
BOND       C6T    H           $kchbond    1.09               
BOND       CC3E   H           $kchbond    1.09               

!adenine
BOND       NC     C2A         1370.370    1.339 !0.009  B
BOND       C2A    N3A         1370.370    1.331 !0.009  B
BOND       N3A    C4A         3083.333    1.344 !0.006  B
BOND       C4A    C5A         2265.306    1.383 !0.007  B
BOND       C5A    C6A         1370.370    1.406 !0.009  B
BOND       C6A    NC          2265.306    1.351 !0.007  B
BOND       C5A    N7A         3083.333    1.388 !0.006  B
BOND       N7A    C8A         2265.306    1.311 !0.007  B
BOND       C8A    N9A         1734.375    1.373 !0.008  B
BOND       N9A    C4A         3083.333    1.374 !0.006  B
BOND       C6A    N6A         1734.375    1.335 !0.008  B
BOND       C8A    H           $kchbond    1.08               
BOND       C2A    H           $kchbond    1.09               

!guanine
BOND       NNA    C2G         1734.375    1.373 !0.008  B
BOND       C2G    N3G         1734.375    1.323 !0.008  B
BOND       N3G    C4G         2265.306    1.350 !0.007  B 
BOND       C4G    C5G         2265.306    1.379 !0.007  B
BOND       C5G    C6G         1110.000    1.419 !0.010  B 
BOND       C6G    NNA         2265.306    1.391 !0.007  B 
BOND       C5G    N7G         3083.333    1.388 !0.006  B 
BOND       N7G    C8G         3083.333    1.305 !0.006  B 
BOND       C8G    N9G         2265.306    1.374 !0.007  B 
BOND       N9G    C4G         1734.375    1.375 !0.008  B
BOND       C2G    N2G         1110.000    1.341 !0.010  B
BOND       C6G    O6G         1370.370    1.237 !0.009  B
BOND       C8G    H           $kchbond    1.08               

!uracil
BOND       C2U    ON          1370.370    1.219 !0.009  B
BOND       C4U    ON          1734.375    1.232 !0.008  B
BOND       N1U    C2U         1370.370    1.381 !0.009  B
BOND       N1U    C6U         1370.370    1.375 !0.009  B
BOND       C2U    N3U         2265.306    1.373 !0.007  B
BOND       N3U    C4U         1370.370    1.380 !0.009  B
BOND       C4U    C5U         1370.370    1.431 !0.009  B
BOND       C5U    C6U         1370.370    1.337 !0.009  B
BOND       C5U    H           $kchbond    1.09               
BOND       C6U    H           $kchbond    1.09               

!Phos.
!the ANGLe s were taken from param11.dna with 3*kq
ANGLe       HO     OH     C5R        139.500  107.300 
ANGLe       HO     O5R    C5R        139.500  107.300 
ANGLe       HO     OH     C5D        139.500  107.300 
ANGLe       HO     O5R    C5D        139.500  107.300 
ANGLe       HO     O3R    P          139.500  107.300
ANGLe       HO     OH   P          139.500  107.300 ! For 5pho patch 
ANGLe       HO     O2R    C2R        139.500  107.300 
ANGLe       OH     P      O3R        144.300  102.600 !
ANGLe       OH     P      O5R        144.300  102.600 !
ANGLe       OH     P      O1P        296.700  108.230 !
ANGLe       OH     P      O2P        296.700  108.230 !
ANGLe       OH     C5R    C4R        210.000  112.000 ! 
ANGLe       OH     C5D    C4D        210.000  112.000 ! 
ANGLe       C4D    C3D    OH         139.500  111.000 ! 
ANGLe       C4R    C3R    OH         139.500  111.000 ! 
ANGLe       C2D    C3D    OH         139.500  111.000 ! 
ANGLe       C2R    C3R    OH         139.500  111.000 ! 
ANGLe       C3R    OH     HO         139.500  107.300 !
ANGLe       C3D    OH     HO         139.500  107.300 !

!Phos.  - combined RNA/DNA statistics used 
!                                      kq      x_eq  sigma
ANGLe       O1P    P      O2P       1337.074  119.600 !1.5 P 
ANGLe       O5R    P      O1P        357.719  108.100 !2.9 P
ANGLe       O5R    P      O2P        412.677  108.300 !2.7 P 
ANGLe       O3R    P      O5R        833.356  104.000 !1.9 P 
ANGLe       O2P    P      O3R        293.791  108.300 !3.2 P
ANGLe       O1P    P      O3R        293.791  107.400 !3.2 P 

ANGLe       O5R    C5R    C4R       1534.906  110.200 !1.4 P 
ANGLe       P      O5R    C5R       1175.163  120.900 !1.6 P 
ANGLe       P      O3R    C3R       2089.178  119.700 !1.2 P

ANGLe       O5R    C5D    C4D       1534.906  110.200 !1.4 P !DNA
ANGLe       P      O5R    C5D       1175.163  120.900 !1.6 P
ANGLe       P      O3R    C3D       2089.178  119.700 !1.2 P

!Sugars
!RNA statistics
!                                      kq      x_eq  sigma
ANGLe       O4R    C4R    C3R        561.212  105.500 !1.4 S
ANGLe       C5R    C4R    C3R        488.878  115.500 !1.5 S
ANGLe       C5R    C4R    O4R        561.212  109.200 !1.4 S
ANGLe       C1R    O4R    C4R       1357.996  109.600 !0.9 S
ANGLe       C4R    C3R    C2R       1099.976  102.700 !1.0 S
ANGLe       C3R    C2R    C1R       1357.996  101.500 !0.9 S
ANGLe       O4R    C1R    C2R        561.212  106.400 !1.4 S
ANGLe       N1T    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       N1C    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       N1U    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       N9G    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       N9A    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       O4R    C1R    N1T       1099.976  108.200 !1.0 S
ANGLe       O4R    C1R    N1C       1099.976  108.200 !1.0 S
ANGLe       O4R    C1R    N1U       1099.976  108.200 !1.0 S
ANGLe       O4R    C1R    N9A       1099.976  108.200 !1.0 S
ANGLe       O4R    C1R    N9G       1099.976  108.200 !1.0 S
ANGLe       C1R    C2R    O2R        357.719  110.600 !2.9 S scale from phos.
ANGLe       C3R    C2R    O2R        357.719  113.300 !2.9 S scale from phos.
ANGLe       C4R    C3R    O3R        445.032  110.500 !2.6 S scale from phos.
ANGLe       C2R    C3R    O3R        383.726  111.000 !2.8 S scale from phos.

!DNA statistics
ANGLe       O4D    C4D    C3D       1099.976  105.600 !1.0 S
ANGLe       C5D    C4D    C3D        488.878  114.700 !1.5 S
ANGLe       C5D    C4D    O4D        429.678  109.400 !1.6 S
ANGLe       C1D    O4D    C4D        650.874  109.700 !1.3 S
ANGLe       C4D    C3D    C2D       1099.976  103.200 !1.0 S
ANGLe       C3D    C2D    C1D        650.874  102.700 !1.3 S
ANGLe       O4D    C1D    C2D        909.071  106.100 !1.1 S
ANGLe       N1T    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       N1C    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       N1U    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       N9G    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       N9A    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       O4D    C1D    N1T       1357.996  107.800 !0.9 S
ANGLe       O4D    C1D    N1C       1357.996  107.800 !0.9 S
ANGLe       O4D    C1D    N1U       1357.996  107.800 !0.9 S
ANGLe       O4D    C1D    N9A       1357.996  107.800 !0.9 S
ANGLe       O4D    C1D    N9G       1357.996  107.800 !0.9 S
ANGLe       C4D    C3D    O3R        621.574  110.300 !2.2 S scale from phos.
ANGLe       C2D    C3D    O3R        412.677  110.600 !2.7 S scale from phos.

!Ribose terms involving non-exchageables
ANGLe       OH     C5R    H         $kchangle     109.83      
ANGLe       O5R    C5R    H         $kchangle     109.83      
ANGLe       H      C5R    H         $kchangle     109.11      
ANGLe       C4R    C5R    H         $kchangle     109.11      
ANGLe       C5R    C4R    H         $kchangle     107.93      
ANGLe       H      C4R    C3R       $kchangle     107.13      
ANGLe       H      C4R    O4R       $kchangle     113.74      
ANGLe       H      C3R    C4R       $kchangle     111.35      
ANGLe       H      C3R    O3R       $kchangle     105.87      
ANGLe       H      C3R    OH        $kchangle     105.87      
ANGLe       H      C3R    C2R       $kchangle     112.27      
ANGLe       H      C2R    C3R       $kchangle     111.41      
ANGLe       H      C2R    O2R       $kchangle     113.07      
ANGLe       H      C2R    C1R       $kchangle     112.38      
ANGLe       H      C1R    C2R       $kchangle     111.95      
ANGLe       H      C1R    N1C       $kchangle     107.70      
ANGLe       H      C1R    N1U       $kchangle     107.70      
ANGLe       H      C1R    N9A       $kchangle     107.70      
ANGLe       H      C1R    N9G       $kchangle     107.70      
ANGLe       H      C1R    O4R       $kchangle     106.86      

!Deoxyribose terms involving non-exchageables
!
ANGLe       OH     C5D    H         $kchangle     109.70      
ANGLe       O5R    C5D    H         $kchangle     109.70      
ANGLe       H      C5D    H         $kchangle     109.17      
ANGLe       C4D    C5D    H         $kchangle     109.17      
ANGLe       C5D    C4D    H         $kchangle     107.78      
ANGLe       H      C4D    C3D       $kchangle     106.91      
ANGLe       H      C4D    O4D       $kchangle     112.98      
ANGLe       H      C3D    C4D       $kchangle     111.16      
ANGLe       H      C3D    O3R       $kchangle     109.34      
ANGLe       H      C3D    OH        $kchangle     109.34      
ANGLe       H      C3D    C2D       $kchangle     111.98      
ANGLe       H      C2D    C3D       $kchangle     111.36      
ANGLe       H      C2D    H         $kchangle     107.52      
ANGLe       H      C2D    C1D       $kchangle     112.29      
ANGLe       H      C1D    C2D       $kchangle     110.94      
ANGLe       H      C1D    N1C       $kchangle     108.25      
ANGLe       H      C1D    N1U       $kchangle     108.25 
ANGLe       H      C1D    N1T       $kchangle     108.25      
ANGLe       H      C1D    N9A       $kchangle     108.25      
ANGLe       H      C1D    N9G       $kchangle     108.25     
ANGLe       H      C1D    O4D       $kchangle     107.95      

!Bases
!cytosine                            kq       x_eq   sigma
ANGLe       C6C    N1C    C2C       2277.447  120.300 !0.40 B
ANGLe       N1C    C2C    NC         743.656  119.200 !0.70 B
ANGLe       C2C    NC     C4C       1457.566  119.900 !0.50 B
ANGLe       NC     C4C    C5C       2277.447  121.900 !0.40 B
ANGLe       C4C    C5C    C6C       1457.566  117.400 !0.50 B
ANGLe       C5C    C6C    N1C       1457.566  121.000 !0.50 B
ANGLe       N1C    C2C    ON        1012.199  118.900 !0.60 B
ANGLe       NC     C2C    ON         743.656  121.900 !0.70 B
ANGLe       NC     C4C    N4C        743.656  118.000 !0.70 B
ANGLe       C5C    C4C    N4C        743.656  120.200 !0.70 B
ANGLe       C6C    N1C    C1R        763.873  120.800 !1.20 B scale from sugar
ANGLe       C2C    N1C    C1R        909.071  118.800 !1.10 B scale from sugar
ANGLe       C6C    N1C    C1D        763.873  120.800 !1.20 B !DNA
ANGLe       C2C    N1C    C1D        909.071  118.800 !1.10 B
ANGLe       C4C    N4C    H2         105.000  120.000 !from param11.dna, 3*keq 
ANGLe       H2     N4C    H2         105.000  120.000 
ANGLe       N1C    C6C    H         $kchangle  119.63          
ANGLe       C5C    C6C    H         $kchangle  119.36          
ANGLe       C4C    C5C    H         $kchangle  121.54          
ANGLe       C6C    C5C    H         $kchangle  121.54          

!thymine                            kq        x_eq    sigma
ANGLe       C6T    N1T    C2T       1457.566  121.300 !0.50 B
ANGLe       N1T    C2T    N3T       1012.199  114.600 !0.60 B
ANGLe       C2T    N3T    C4T       1012.199  127.200 !0.60 B
ANGLe       N3T    C4T    C5T       1012.199  115.200 !0.60 B
ANGLe       C4T    C5T    C6T       1012.199  118.000 !0.60 B
ANGLe       C5T    C6T    N1T       1012.199  123.700 !0.60 B
ANGLe       N1T    C2T    ON         569.362  123.100 !0.80 B
ANGLe       N3T    C2T    ON        1012.199  122.300 !0.60 B
ANGLe       N3T    C4T    ON        1012.199  119.900 !0.60 B
ANGLe       C5T    C4T    ON         743.656  124.900 !0.70 B
ANGLe       C4T    C5T    CC3E      1012.199  119.000 !0.60 B
ANGLe       C6T    C5T    CC3E      1012.199  122.900 !0.60 B
ANGLe       C6T    N1T    C1R        488.878  120.400 !1.50 B scale from sugar
ANGLe       C2T    N1T    C1R        429.678  118.200 !1.60 B scale from sugar
ANGLe       C6T    N1T    C1D        488.878  120.400 !1.50 B !DNA
ANGLe       C2T    N1T    C1D        429.678  118.200 !1.60 B
ANGLe       C2T    N3T    HN         105.000  116.500  !from param11.dna, 3*keq 
ANGLe       C4T    N3T    HN         105.000  116.500  
ANGLe      C5T    CC3E   H         $kchangle  109.50
ANGLe       H      CC3E   H         $kchangle  109.44
ANGLe       N1T    C6T    H         $kchangle  119.52          
ANGLe       C5T    C6T    H         $kchangle  119.52          

!adenine                            kq        x_eq    sigma
ANGLe       C6A    NC     C2A       1012.199  118.600 !0.60 B
ANGLe       NC     C2A    N3A       1457.566  129.300 !0.50 B
ANGLe       C2A    N3A    C4A       1457.566  110.600 !0.50 B
ANGLe       N3A    C4A    C5A        743.656  126.800 !0.70 B
ANGLe       C4A    C5A    C6A       1457.566  117.000 !0.50 B
ANGLe       C5A    C6A    NC        1457.566  117.700 !0.50 B
ANGLe       C4A    C5A    N7A       1457.566  110.700 !0.50 B
ANGLe       C5A    N7A    C8A       1457.566  103.900 !0.50 B
ANGLe       N7A    C8A    N9A       1457.566  113.800 !0.50 B
ANGLe       C8A    N9A    C4A       2277.447  105.800 !0.40 B
ANGLe       N9A    C4A    C5A       2277.447  105.800 !0.40 B
ANGLe       N3A    C4A    N9A        569.362  127.400 !0.80 B
ANGLe       C6A    C5A    N7A        743.656  132.300 !0.70 B
ANGLe       NC     C6A    N6A       1012.199  118.600 !0.60 B
ANGLe       C5A    C6A    N6A        569.362  123.700 !0.80 B
ANGLe       C8A    N9A    C1R        339.499  127.700 !1.80 B scale from sugar
ANGLe       C4A    N9A    C1R        339.499  126.300 !1.80 B scale from sugar
ANGLe       C8A    N9A    C1D        339.499  127.700 !1.80 B !DNA
ANGLe       C4A    N9A    C1D        339.499  126.300 !1.80 B
ANGLe       C6A    N6A    H2         105.000  120.000  !from param11.dna, 3*keq 
ANGLe       H2     N6A    H2         105.000  120.000
ANGLe       N7A    C8A    H         $kchangle  123.16          
ANGLe       N9A    C8A    H         $kchangle  123.16          
ANGLe       NC     C2A    H         $kchangle  115.54          
ANGLe       N3A    C2A    H         $kchangle  115.54          

!guanine                             kq        x_eq    sigma
ANGLe       C6G    NNA    C2G       1012.199  125.100 !0.60 B
ANGLe       NNA    C2G    N3G       1012.199  123.900 !0.60 B
ANGLe       C2G    N3G    C4G       1457.566  111.900 !0.50 B
ANGLe       N3G    C4G    C5G       1457.566  128.600 !0.50 B
ANGLe       C4G    C5G    C6G       1012.199  118.800 !0.60 B
ANGLe       C5G    C6G    NNA       1457.566  111.500 !0.50 B
ANGLe       C4G    C5G    N7G       2277.447  110.800 !0.40 B
ANGLe       C5G    N7G    C8G       1457.566  104.300 !0.50 B
ANGLe       N7G    C8G    N9G       1457.566  113.100 !0.50 B
ANGLe       C8G    N9G    C4G       2277.447  106.400 !0.40 B
ANGLe       N9G    C4G    C5G       2277.447  105.400 !0.40 B
ANGLe       N3G    C4G    N9G       1012.199  126.000 !0.60 B
ANGLe       C6G    C5G    N7G       1012.199  130.400 !0.60 B
ANGLe       NNA    C2G    N2G        449.866  116.20  !0.90 B
ANGLe       N3G    C2G    N2G        743.656  119.900 !0.70 B
ANGLe       NNA    C6G    O6G       1012.199  119.900 !0.60 B
ANGLe       C5G    C6G    O6G       1012.199  128.600 !0.60 B
ANGLe       C8G    N9G    C1R        650.874  127.000 !1.30 B scale from sugar
ANGLe       C4G    N9G    C1R        650.874  126.500 !1.30 B scale from sugar
ANGLe       C8G    N9G    C1D        650.874  127.000 !1.30 B !DNA
ANGLe       C4G    N9G    C1D        650.874  126.500 !1.30 B
ANGLe       C2G    N2G    H2         105.000  120.000  !from param11.dna, 3*keq 
ANGLe       H2     N2G    H2         105.000  120.000
ANGLe       C2G    NNA    HN         105.000  119.300
ANGLe       C6G    NNA    HN         105.000  119.300
ANGLe       N7G    C8G    H         $kchangle  122.91          
ANGLe       N9G    C8G    H         $kchangle  122.91          

!uracile                             kq        x_eq    sigma
ANGLe       C6U    N1U    C2U       1012.199  121.000 !0.60 B
ANGLe       N1U    C2U    N3U       1012.199  114.900 !0.60 B
ANGLe       C2U    N3U    C4U       1012.199  127.000 !0.60 B
ANGLe       N3U    C4U    C5U       1012.199  114.600 !0.60 B
ANGLe       C4U    C5U    C6U       1012.199  119.700 !0.60 B
ANGLe       C5U    C6U    N1U       1457.566  122.700 !0.50 B
ANGLe       N1U    C2U    ON         743.656  122.800 !0.70 B
ANGLe       N3U    C2U    ON         743.656  122.200 !0.70 B
ANGLe       N3U    C4U    ON         743.656  119.400 !0.70 B
ANGLe       C5U    C4U    ON        1012.199  125.900 !0.60 B
ANGLe       C6U    N1U    C1R        561.212  121.200 !1.40 B
ANGLe       C2U    N1U    C1R        763.872  117.700 !1.20 B
ANGLe       C6U    N1U    C1D        561.212  121.200 !1.40 B !DNA
ANGLe       C2U    N1U    C1D        763.872  117.700 !1.20 B
ANGLe       C4U    ON     HO         105.000  120.000 !from param11.dna, 3*keq 
ANGLe       C2U    N3U    HN         105.000  116.500 
ANGLe       C4U    N3U    HN         105.000  116.500  
ANGLe       N1U    C6U    H         $kchangle  119.38          
ANGLe       C5U    C6U    H         $kchangle  119.38          
ANGLe       C4U    C5U    H         $kchangle  119.56          
ANGLe       C6U    C5U    H         $kchangle  119.56          
{
!Dihedrals from param11.dna (included for terminal residues)

!DIHEdral    X    C2R  C3R  X      4.50 3    0.000
!DIHEdral    X    C4R  C3R  X      4.50 3    0.000
!DIHEdral    X    C2R  C1R  X      4.50 3    0.000
!DIHEdral    X    C5R  O5R  X      1.50 3    0.000
!DIHEdral    X    C3R  O3R  X      1.50 3    0.000
DIHEdral    X    C3R  OH   X      1.50 3    0.000
DIHEdral    X    C5R  OH   X      1.50 3    0.000
!DIHEdral    X    C2R  O2R  X      1.50 3    0.000
!DIHEdral    X    O5R  P    X      2.25 3    0.000
DIHEdral    X    OH   P    X      2.25 3    0.000
!DIHEdral    OH   C5R  C4R  O4R    4.50 3    0.000
!DIHEdral    OH   C5R  C4R  C3R    4.50 3    0.000 ! gamma
!DIHEdral    C3R  O3R  P    OH     2.25 3    0.000 ! added by infer
!DIHEdral    C3R  O3R  P    OH     2.25 2    0.000 ! ATB, 7-SEP-84
DIHEdral    C5R  O5R  P    OH     2.25 3    0.000 ! added by infer
!DIHEdral    C5R  O5R  P    OH     2.25 2    0.000 ! ATB, 7-SEP-84

!DIHEdral    X    C2D  C3D  X      4.50 3    0.000
!DIHEdral    X    C4D  C3D  X      4.50 3    0.000  !DNA
!DIHEdral    X    C2D  C1D  X      4.50 3    0.000
!DIHEdral    X    C5D  O5R  X      1.50 3    0.000
!DIHEdral    X    C3D  O3R  X      1.50 3    0.000
DIHEdral    X    C3D  OH   X      1.50 3    0.000
DIHEdral    X    C5D  OH   X      1.50 3    0.000
!DIHEdral    OH   C5D  C4D  O4D    4.50 3    0.000
!DIHEdral    OH   C5D  C4D  C3D    4.50 3    0.000
!DIHEdral    C3D  O3R  P    OH     2.25 3    0.000
!DIHEdral    C3D  O3R  P    OH     2.25 2    0.000
DIHEdral    C5D  O5R  P    OH     2.25 3    0.000
!DIHEdral    C5D  O5R  P    OH     2.25 2    0.000
}{
!Base hydrogen DIHEdrals taken from param11.dna
DIHEdral    X    C2G  N2G  X     18.0  2  180.000
DIHEdral    X    C6A  N6A  X     18.0  2  180.000
!DIHEdral    X    C6A  N4C  X     18.00 2  180.000
DIHEdral    X    C4C  N4C  X     18.00 2  180.000
}
!IMPRopers to keep the two purine rings parallel:
!guanine
IMPRoper    C8G  C4G  C5G  NNA  250.0  2  180.000
IMPRoper    C8G  C5G  C4G  C2G  250.0  2  180.000
IMPRoper    N3G  C4G  C5G  N7G  250.0  2  180.000
IMPRoper    C6G  C5G  C4G  N9G  250.0  2  180.000
!adenine
IMPRoper    C8A  C4A  C5A  N9A  250.0  2  180.000 ! WYE AND PATCHED RESIDUES
IMPRoper    C8A  C5A  C4A  C2A  250.0  2  180.000
IMPRoper    C8A  C4A  C5A  NC   250.0  2  180.000 
IMPRoper    N3A  C4A  C5A  N7A  250.0  2  180.000
IMPRoper    C6A  C5A  C4A  N9A  250.0  2  180.000


!other base specific non-exch hydrogen IMPRopers
IMPRoper    H    C4C  C6C  C5C  $kchimpr    0    0.000
IMPRoper    H    N1C  C5C  C6C  $kchimpr    0    0.000
IMPRoper    H    C4U  C6U  C5U  $kchimpr    0    0.000
IMPRoper    H    N1U  C5U  C6U  $kchimpr    0    0.000
IMPRoper    H    N1T  C5T  C6T  $kchimpr    0    0.000
IMPRoper    H    N7A  N9A  C8A  $kchimpr    0    0.000
IMPRoper    H    NC   N3A  C2A  $kchimpr    0    0.000
IMPRoper    H    N7G  N9G  C8G  $kchimpr    0    0.000

!Impropers for ribose chirality
IMPRoper    H    C2R  O4R  N9A    $kchimpr    0    -65.000!C1R
IMPRoper    H    C2R  O4R  N9G    $kchimpr    0    -65.000!C1R
IMPRoper    H    C2R  O4R  N1C    $kchimpr    0    -65.000!C1R
IMPRoper    H    C2R  O4R  N1U    $kchimpr    0    -65.000!C1R
IMPRoper    H    C2R  O4R  N1T    $kchimpr    0    -65.000!C1R

IMPRoper    H    C3R  C1R  O2R    $kchimpr    0    65.000!C2R
IMPRoper    H    C4R  C2R  O3R    $kchimpr    0    60.300!C3R 
IMPRoper    H    C4R  C2R  OH     $kchimpr    0    60.300!C3R; TERMINAL RES 
IMPRoper    H    C5R  C3R  O4R    $kchimpr    0    70.300!C4R 
IMPRoper    H    O5R  H    C4R    $kchimpr    0    72.000!C5R; 
IMPRoper    H    OH   H    C4R    $kchimpr    0    72.000!C5R; TERMINAL RES
!Impropers for deoxyribose chirality
IMPRoper    H    C2D  O4D  N9A    $kchimpr    0    -65.280!C1D
IMPRoper    H    C2D  O4D  N9G    $kchimpr    0    -65.280!C1D
IMPRoper    H    C2D  O4D  N1C    $kchimpr    0    -65.280!C1D
IMPRoper    H    C2D  O4D  N1T    $kchimpr    0    -65.280!C1D

IMPRoper    H    C3D  H    C1D    $kchimpr    0    -73.500!C2D
IMPRoper    H    C4D  C2D  O3R    $kchimpr    0    62.660!C3D 
IMPRoper    H    C4D  C2D  OH     $kchimpr    0    62.660!C3D; TERMINAL RES 
IMPRoper    H    C5D  C3D  O4D    $kchimpr    0    70.220!C4D 
IMPRoper    H    O5R  H    C4D    $kchimpr    0    71.430!C5D; 
IMPRoper    H    OH   H    C4D    $kchimpr    0    71.430!C5D; TERMINAL RES

{
!Phos.  - periodical potentials from combined RNA/DNA statistics
!                                 kq       x_eq       (sigma in parenthesis)
DIHEdral    O3R  P    O5R  C5R    1.41 3   24     ! alpha !P (20.3)
DIHEdral    P    O5R  C5R  C4R    3.45 0  178     ! beta  !P (13.0)
DIHEdral    O5R  C5R  C4R  C3R   12.24 3   18     ! gamma !S (6.9)
DIHEdral    O5R  C5R  C4R  O4R   24.28 3   14.1   !       !S (4.9)
DIHEdral    C4R  C3R  O3R  P      7.88 0 -153     ! eps   !P (8.6)
DIHEdral    C3R  O3R  P    O5R    1.75 3   33     ! zeta  !P (18.3)

DIHEdral    O3R  P    O5R  C5D    1.41 3    6.0 !DNA
DIHEdral    P    O5R  C5D  C4D    3.45 0  183.5
DIHEdral    O5R  C5D  C4D  C3D   12.42 3   18.3
DIHEdral    O5R  C5D  C4D  O4D   24.28 3   14.1
DIHEdral    C4D  C3D  O3R  P      7.88 0  214.0
DIHEdral    C3D  O3R  P    O5R    1.75 3    0.3

!Phos.  - discrete values from combined RNA/DNA statistics
!                                 kq       x_eq       (sigma in parenthesis)
!DIHEdral    O3R  P    O5R  C5R    6.07 0  285.3   ! (9.8)  alpha1 !P
!DIHEdral    O3R  P    O5R  C5R    3.98 0   81.1   ! (12.1) alpha2;alpha3=180.
!DIHEdral    P    O5R  C5R  C4R    3.44 0  183.5   ! (13.0) beta   !P
!DIHEdral    O5R  C5R  C4R  C3R   17.94 0   52.5   ! (5.7)  gamma1 !S
!DIHEdral    O5R  C5R  C4R  C3R   14.23 0  179.4   ! (6.4)  gamma2 !S
!DIHEdral    O5R  C5R  C4R  C3R    3.85 0  292.9   ! (12.3) gamma3 !S
!DIHEdral    C4R  C3R  O3R  P      7.88 0  214.0   ! (8.6)  eps    !P
!DIHEdral    C3R  O3R  P    O5R   25.30 0  289.2   ! (4.8)  zeta1  !P 
!DIHEdral    C3R  O3R  P    O5R    2.85 0   80.7   ! (14.3) zeta2;zeta3=180.
}{
!Sugars
! c3'-endo conformation as the default for for RNA, c2'-endo for DNA,
!RNA statistics, C3'-endo
DIHEdral    C5R  C4R  C3R  O3R  30.12 0   81.1   ! delta ! c3'-endo S (4.4)
DIHEdral    O4R  C4R  C3R  O3R  33.10 0  201.8   !  4.2  ! c3'-endo S  
DIHEdral    O4R  C1R  C2R  C3R  24.28 0  335.4   !  4.9  ! c3'-endo S
DIHEdral    C1R  C2R  C3R  C4R  74.36 0   35.9   !  2.8  ! c3'-endo S
DIHEdral    C2R  C3R  C4R  O4R  60.67 0  324.7   !  3.1  ! c3'-endo S
DIHEdral    C3R  C4R  O4R  C1R  22.42 0   20.5   !  5.1  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  C2R  15.67 0    2.8   !  6.1  ! c3'-endo S
DIHEdral    C5R  C4R  C3R  C2R  60.67 0  204.0   !  3.1  ! c3'-endo S
DIHEdral    O3R  C3R  C2R  O2R  28.79 0   44.3   !  4.5  ! c3'-endo S   
DIHEdral    C4R  O4R  C1R  N1T  13.80 0  241.4   !  6.5  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  N1C  13.80 0  241.4   !  6.5  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  N1U  13.80 0  241.4   !  6.5  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  N9G  13.80 0  241.4   !  6.5  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  N9A  13.80 0  241.4   !  6.5  ! c3'-endo S

!RNA c3'-endo sugar base joint torsions  (combined RNA/DNA statistics used)
DIHEdral    O4R  C1R  N1T  C2T  13.38 0  195.7   !  6.6  ! c3'-endo S
DIHEdral    O4R  C1R  N1C  C2C  13.38 0  195.7   !  6.6  ! c3'-endo S
DIHEdral    O4R  C1R  N1U  C2U  13.38 0  195.7   !  6.6  ! c3'-endo S
DIHEdral    O4R  C1R  N9A  C4A   2.97 0  193.3   ! 14.0  ! c3'-endo S
DIHEdral    O4R  C1R  N9G  C4G   2.97 0  193.3   ! 14.0  ! c3'-endo S

!DNA statistics (c2'-endo)
DIHEdral    C5D  C4D  C3D  O3R   36.44 0  145.2   ! delta ! c2'-endo S (4.0)
DIHEdral    O4D  C1D  C2D  C3D   24.28 0   32.8   !  4.9  ! c2'-endo S 
DIHEdral    O4D  C4D  C3D  O3R   31.53 0  265.8   !  4.3  ! c2'-endo S 
DIHEdral    C1D  C2D  C3D  C4D   44.99 0  326.9   !  3.6  ! c2'-endo S
DIHEdral    C2D  C3D  C4D  O4D   28.79 0   22.6   !  4.5  ! c2'-endo S
DIHEdral    C3D  C4D  O4D  C1D   15.67 0  357.7   !  6.1  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  C2D   14.69 0  340.7   !  6.3  ! c2'-endo S
DIHEdral    C5D  C4D  C3D  C2D   34.68 0  262.0   !  4.1  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N1T   12.99 0  217.7   !  6.7  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N1C   12.99 0  217.7   !  6.7  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N1U   12.99 0  217.7   !  6.7  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N9G   12.99 0  217.7   !  6.7  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N9A   12.99 0  217.7   !  6.7  ! c2'-endo S

!DNA c2'-endo sugar base joint torsions  (combined RNA/DNA statistics used)
DIHEdral    O4D  C1D  N1T  C2T    1.72 0  229.8   ! 18.4  ! c2'-endo S   
DIHEdral    O4D  C1D  N1C  C2C    1.72 0  229.8   ! 18.4  ! c2'-endo S   
DIHEdral    O4D  C1D  N1U  C2U    1.72 0  229.8   ! 18.4  ! c2'-endo S   
DIHEdral    O4D  C1D  N9A  C4A    1.00 0  237.0   ! 24.3  ! c2'-endo S   
DIHEdral    O4D  C1D  N9G  C4G    1.00 0  237.0   ! 24.3  ! c2'-endo S   

!---------------------------------------------------------------------------
!In the case of c3'-endo conformation, the following DIHEdrals are provided
!to overwrite the c2'-endo DIHEdrals

!RNA statistics (c2'-endo)
!DIHEdral    C5R  C4R  C3R  O3R   24.28 0  147.3   ! delta ! c2'-endo S (4.9)
!DIHEdral    O4R  C1R  C2R  C3R   50.43 0   35.2   !  3.4  ! c2'-endo S 
!DIHEdral    O4R  C4R  C3R  O3R   20.75 0  268.1   !  5.3  ! c2'-endo S 
!DIHEdral    C1R  C2R  C3R  C4R   74.36 0  324.6   !  2.8  ! c2'-endo S
!DIHEdral    C2R  C3R  C4R  O4R   31.53 0   24.2   !  4.3  ! c2'-endo S
!DIHEdral    C3R  C4R  O4R  C1R   17.94 0  357.7   !  5.7  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  C2R   21.56 0  339.2   !  5.2  ! c2'-endo S
!DIHEdral    C5R  C4R  C3R  C2R   34.68 0  263.4   !  4.1  ! c2'-endo S
!DIHEdral    O3R  C3R  C2R  O2R   33.05 0  319.7   !  4.2  ! c2'-endo S   
!DIHEdral    C4R  O4R  C1R  N1T   19.27 0  216.6   !  5.5  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  N1C   19.27 0  216.6   !  5.5  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  N1U   19.27 0  216.6   !  5.5  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  N9G   19.27 0  216.6   !  5.5  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  N9A   19.27 0  216.6   !  5.5  ! c2'-endo S

!RNA c2'-endo sugar base joint torsions  (combined RNA/DNA statistics used) 
!DIHEdral    O4R  C1R  N1T  C2T    1.72 0  229.8   ! 18.4  ! c2'-endo S   
!DIHEdral    O4R  C1R  N1C  C2C    1.72 0  229.8   ! 18.4  ! c2'-endo S   
!DIHEdral    O4R  C1R  N1U  C2U    1.72 0  229.8   ! 18.4  ! c2'-endo S   
!DIHEdral    O4R  C1R  N9A  C4A    1.00 0  237.0   ! 24.3  ! c2'-endo S   
!DIHEdral    O4R  C1R  N9G  C4G    1.00 0  237.0   ! 24.3  ! c2'-endo S   

!DNA statistics, c3'-endo (insuficient data, RNA values used)
!DIHEdral    C5D  C4D  C3D  O3R  30.12 0   81.1   ! delta ! c3'-endo S (4.4)
!DIHEdral    O4D  C4D  C3D  O3R  33.10 0  201.8   !  4.2  ! c3'-endo S  
!DIHEdral    O4D  C1D  C2D  C3D  24.28 0  335.4   !  4.9  ! c3'-endo S
!DIHEdral    C1D  C2D  C3D  C4D  74.36 0   35.9   !  2.8  ! c3'-endo S
!DIHEdral    C2D  C3D  C4D  O4D  60.67 0  324.7   !  3.1  ! c3'-endo S
!DIHEdral    C3D  C4D  O4D  C1D  22.42 0   20.5   !  5.1  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  C2D  15.67 0    2.8   !  6.1  ! c3'-endo S
!DIHEdral    C5D  C4D  C3D  C2D  60.67 0  204.0   !  3.1  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N1T  13.80 0  241.4   !  6.5  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N1C  13.80 0  241.4   !  6.5  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N1U  13.80 0  241.4   !  6.5  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N9G  13.80 0  241.4   !  6.5  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N9A  13.80 0  241.4   !  6.5  ! c3'-endo S

!DNA c3'-endo sugar base joint torsions  (combined RNA/DNA statistics used)
!DIHEdral    O4D  C1D  N1T  C2T  13.38 0  195.7   !  6.6  ! c3'-endo S
!DIHEdral    O4D  C1D  N1C  C2C  13.38 0  195.7   !  6.6  ! c3'-endo S
!DIHEdral    O4D  C1D  N1U  C2U  13.38 0  195.7   !  6.6  ! c3'-endo S
!DIHEdral    O4D  C1D  N9A  C4A   2.97 0  193.3   ! 14.0  ! c3'-endo S
!DIHEdral    O4D  C1D  N9G  C4G   2.97 0  193.3   ! 14.0  ! c3'-endo S
!---------------------------------------------------------------------------
!---------------------------------------------------------------------------
}
!Impropers taken from param11.dna , 3*kq
IMPRoper    C5R  X    X    C2R   94.5  0   35.260
IMPRoper    C5R  X    X    C1R   94.5  0   35.260
IMPRoper    OH   X    X    C3R   94.5  0   35.260
IMPRoper    OH   X    X    C4R   94.5  0   35.260
IMPRoper    OH   X    X    C1R   94.5  0   35.260
IMPRoper    O3R  X    X    C3R   94.5  0   35.260
IMPRoper    O5R  X    X    C1R   94.5  0   35.260
IMPRoper    O2R  X    X    C2R   94.5  0   35.260
IMPRoper    C4R  O5R  C1R  N1T   94.5  0   35.260
IMPRoper    C4R  O5R  C1R  N1C   94.5  0   35.260
IMPRoper    C4R  O5R  C1R  N9G   94.5  0   35.260
IMPRoper    C4R  O5R  C1R  N9A   94.5  0   35.260
IMPRoper    C5R  O4R  C3R  C4R   94.5  0   35.260  
IMPRoper    N1T  C2R  O4R  C1R   94.5  0   35.260  
IMPRoper    N1C  C2R  O4R  C1R   94.5  0   35.260
IMPRoper    N9A  C2R  O4R  C1R   94.5  0   35.260  
IMPRoper    N9G  C2R  O4R  C1R   94.5  0   35.260  
IMPRoper    C4R  O5R  C1R  N1U   94.5  0   35.260
IMPRoper    N1U  C2R  O4R  C1R   94.5  0   35.260  

IMPRoper    C5D  X    X    C2D   94.5  0   35.260  !DNA
IMPRoper    C5D  X    X    C1D   94.5  0   35.260
IMPRoper    OH   X    X    C3D   94.5  0   35.260
IMPRoper    OH   X    X    C4D   94.5  0   35.260
IMPRoper    OH   X    X    C1D   94.5  0   35.260
IMPRoper    O3R  X    X    C3D   94.5  0   35.260
IMPRoper    O5R  X    X    C1D   94.5  0   35.260
IMPRoper    C4D  O5R  C1D  N1T   94.5  0   35.260
IMPRoper    C4D  O5R  C1D  N1C   94.5  0   35.260
IMPRoper    C4D  O5R  C1D  N9G   94.5  0   35.260
IMPRoper    C4D  O5R  C1D  N9A   94.5  0   35.260
IMPRoper    C5D  O4D  C3D  C4D   94.5  0   35.260  
IMPRoper    N1T  C2D  O4D  C1D   94.5  0   35.260  
IMPRoper    N1C  C2D  O4D  C1D   94.5  0   35.260
IMPRoper    N9A  C2D  O4D  C1D   94.5  0   35.260  
IMPRoper    N9G  C2D  O4D  C1D   94.5  0   35.260  
IMPRoper    C4D  O5R  C1D  N1U   94.5  0   35.260
IMPRoper    N1U  C2D  O4D  C1D   94.5  0   35.260  

!the following impropers were taken from param11x.dna
!the higher kq was used to enforce the ring planarity 
!cytosine
IMPRoper    C4C  X    X    ON  2400.0  0    0.000
IMPRoper    C4C  X    X    N1C  250.0  0    0.000
IMPRoper    C6C  X    X    NC   250.0  0    0.000
IMPRoper    C4C  X    X    N2  2400.0  0    0.000
IMPRoper    C2C  X    X    ON  2400.0  0    0.000
!infer
IMPRoper    C1R  C2C  C6C  N1C 2400.0  0    0.000
IMPRoper    C1D  C2C  C6C  N1C 2400.0  0    0.000
IMPRoper    N4C  NC   C5C  C4C 2400.0  0    0.000
IMPRoper    C2C  NC   C4C  C5C  250.0  0    0.000
IMPRoper    C5C  C6C  N1C  C2C  250.0  0    0.000
IMPRoper    H2   C4C  H2   N4C  250.0  0    0.000
IMPRoper    C5C  C4C  N4C  H2  2000.0  0    0.000

!uracil
IMPRoper    C4U  X    X    ON  2400.0  0    0.000
IMPRoper    C4U  X    X    N1U  250.0  0    0.000
IMPRoper    C6U  X    X    N3U  250.0  0    0.000
IMPRoper    C4U  X    X    N2  2400.0  0    0.000
IMPRoper    C2U  X    X    ON  2400.0  0    0.000
IMPRoper    C1R  C2U  C6U  N1U 2400.0  0    0.000
IMPRoper    C1D  C2U  C6U  N1U 2400.0  0    0.000
IMPRoper    ON   N3U  C5U  C4U  250.0  0    0.000
IMPRoper    C2U  N3U  C4U  C5U  250.0  0    0.000
IMPRoper    C5U  C6U  N1U  C2U  250.0  0    0.000
IMPRoper    H2   C4U  H2   ON   250.0  0    0.000
IMPRoper    HN   C2U  C4U  N3U  250.0  0    0.000

!thymidine
IMPRoper    C4T  X    X    ON  2400.0  0    0.000
IMPRoper    C4T  X    X    N1T  250.0  0    0.000
IMPRoper    C6T  X    X    N3T  250.0  0    0.000
IMPRoper    C4T  X    X    N2  2400.0  0    0.000
IMPRoper    C2T  X    X    ON  2400.0  0    0.000
IMPRoper    C1R  C2T  C6T  N1T 2400.0  0    0.000
IMPRoper    C1D  C2T  C6T  N1T 2400.0  0    0.000
IMPRoper    ON   N3T  C5T  C4T  250.0  0    0.000
IMPRoper    C2T  N3T  C4T  C5T  250.0  0    0.000
IMPRoper    C5T  C6T  N1T  C2T  250.0  0    0.000
IMPRoper    H2   C4T  H2   ON   250.0  0    0.000
IMPRoper    CC3E C4T  C6T  C5T  250.0  0    0.000

!infer
IMPRoper    HN   C2T  C4T  N3T  250.0  0    0.000

! The ring-spanning impropers have been left out.
!adenine
IMPRoper    N2A  N3A  NC   C2A  250.0  0    0.000
IMPRoper    H2   C2A  H2   N2A  250.0  0    0.000
IMPRoper    C4A  C5A  N7A  C8A  250.0  0    0.000
IMPRoper    C5A  C4A  N9A  C8A  250.0  0    0.000
IMPRoper    C4A  X    X    NC   250.0  0    0.000
IMPRoper    C2A  X    X    N9A  250.0  0    0.000
IMPRoper    C2A  X    X    C5A  250.0  0    0.000
IMPRoper    C6A  C5A  C4A  N3A  250.0  0    0.000
IMPRoper    C5A  X    X    N9A  250.0  0    0.000
IMPRoper    C6A  X    X    N6A 2400.0  0    0.000
IMPRoper    H2   X    X    N6A  250.0  0    0.000

!infer
IMPRoper    C1R  C4A  C8A  N9A 2400.0  0    0.000
IMPRoper    C1D  C4A  C8A  N9A 2400.0  0    0.000
IMPRoper    N9A  C4A  C5A  N7A  250.0  0    0.000
IMPRoper    N7A  C8A  N9A  C4A  250.0  0    0.000
IMPRoper    N3A  C2A  NC   C6A  250.0  0    0.000
IMPRoper    C5A  C6A  N6A  H2  2000.0  0    0.000

! The ring-spanning impropers have been left out.
!guanine
IMPRoper    C4G  C5G  N7G  C8G  250.0  0    0.000
IMPRoper    C5G  C4G  N9G  C8G  250.0  0    0.000
IMPRoper    C4G  X    X    NNA  250.0  0    0.000
IMPRoper    C2G  X    X    N9G  250.0  0    0.000
IMPRoper    C2G  X    X    C5G  250.0  0    0.000
IMPRoper    C6G  C5G  C4G  N3G  250.0  0    0.000
IMPRoper    C5G  X    X    N9G  250.0  0    0.000
IMPRoper    C6G  X    X    O6G 2400.0  0    0.000
IMPRoper    C2G  X    X    N2G 2400.0  0    0.000

!infer
IMPRoper    C1R  C4G  C8G  N9G 2400.0  0    0.000
IMPRoper    C1D  C4G  C8G  N9G 2400.0  0    0.000
IMPRoper    N9G  C4G  C5G  N7G  250.0  0    0.000
IMPRoper    N7G  C8G  N9G  C4G  250.0  0    0.000
IMPRoper    N3G  C2G  NNA  C6G  250.0  0    0.000
IMPRoper    H2   H2   C2G  N2G  250.0  0    0.000
IMPRoper    HN   C2G  C6G  NNA 2000.0  0    0.000
IMPRoper    N3G  C2G  N2G  H2  2000.0  0    0.000

!                   Lennard-Jones parameters
!                                       ------1-4-------
!                  epsilon   sigma       epsilon   sigma
!                 (Kcal/mol)   (A)      (Kcal/mol) (A)
! Taken from Rossky Karplus and Rahman BIOPOLY (1979)
! 0.05 ADDED TO RADII TO IMPRoperOVE ON NUCL.ACID STACKING/LN
!
!                  eps     sigma       eps(1:4) sigma(1:4)
NONBonded  C5R     0.0900   3.2970      0.0900   3.2970
NONBonded  C1R     0.0900   3.2970      0.0900   3.2970
NONBonded  C2R     0.0900   3.2970      0.0900   3.2970
NONBonded  C3R     0.0900   3.2970      0.0900   3.2970
NONBonded  C4R     0.0900   3.2970      0.0900   3.2970

NONBonded  C5D     0.0900   3.2970      0.0900   3.2970  !DNA
NONBonded  C1D     0.0900   3.2970      0.0900   3.2970
NONBonded  C2D     0.0900   3.2970      0.0900   3.2970
NONBonded  C3D     0.0900   3.2970      0.0900   3.2970
NONBonded  C4D     0.0900   3.2970      0.0900   3.2970

NONBonded  HN      0.0045   2.6160      0.0045   2.6160
NONBonded  H2      0.0045   1.6040      0.0045   1.6040
NONBonded  H       0.0045   2.6160      0.0045   2.6160 
!
! give it the same as th Hn from RKR
NONBonded  HO      0.0045   1.6040      0.0045   1.6040 

!
! THIS STILL IS AN EXTENDED ATOM
NONBonded  O3R      0.2304   2.7290      0.2304   2.7290
NONBonded  O4R      0.2304   2.7290      0.2304   2.7290
NONBonded  O4D      0.2304   2.7290      0.2304   2.7290
NONBonded  O5R      0.2304   2.7290      0.2304   2.7290
NONBonded  O1P      0.2304   2.7290      0.2304   2.7290
NONBonded  O2P      0.2304   2.7290      0.2304   2.7290
NONBonded  P        0.5849   3.3854      0.5849   3.3854

!bases
NONBonded  CN      0.0900   3.2970      0.0900   3.2970
NONBonded  C2      0.0900   3.2970      0.0900   3.2970
NONBonded  C3      0.0900   3.2970      0.0900   3.2970
NONBonded  CB      0.0900   3.2970      0.0900   3.2970
NONBonded  CE      0.0900   3.2970      0.0900   3.2970
NONBonded  CH      0.0900   3.2970      0.0900   3.2970

NONBonded  N2      0.1600   2.8591      0.1600   2.8591
NONBonded  N3U     0.1600   2.8591      0.1600   2.8591
NONBonded  N3T     0.1600   2.8591      0.1600   2.8591
NONBonded  NNA     0.1600   2.8591      0.1600   2.8591
NONBonded  NB      0.1600   2.8591      0.1600   2.8591
NONBonded  NC      0.1600   2.8591      0.1600   2.8591

NONBonded  NH2E    0.1600   3.0291      0.1600   3.0291
NONBonded  NS      0.1600   2.8591      0.1600   2.8591
NONBonded  N1T     0.1600   2.8591      0.1600   2.8591
NONBonded  N1C     0.1600   2.8591      0.1600   2.8591
NONBonded  N9A     0.1600   2.8591      0.1600   2.8591
NONBonded  N9G     0.1600   2.8591      0.1600   2.8591
NONBonded  N1U     0.1600   2.8591      0.1600   2.8591
NONBonded  ON      0.2304   2.7290      0.2304   2.7290
NONBonded  O2R     0.2304   2.7290      0.2304   2.7290
NONBonded  OH      0.2304   2.5508      0.2304   2.5508
NONBonded  SD      0.3515   2.6727      0.3515   2.6727  ! G U E S S
NONBonded  O2      0.2304   2.7290      0.2304   2.7290 

! NEW
NONBonded  C6C      0.0900   3.2970      0.0900   3.2970
NONBonded  C5C      0.0900   3.2970      0.0900   3.2970
NONBonded  C4C      0.0900   3.2970      0.0900   3.2970
NONBonded  C2C      0.0900   3.2970      0.0900   3.2970
NONBonded  C6U      0.0900   3.2970      0.0900   3.2970
NONBonded  C5U      0.0900   3.2970      0.0900   3.2970
NONBonded  C4U      0.0900   3.2970      0.0900   3.2970
NONBonded  C2U      0.0900   3.2970      0.0900   3.2970
NONBonded  C8A      0.0900   3.2970      0.0900   3.2970
NONBonded  C6A      0.0900   3.2970      0.0900   3.2970
NONBonded  C5A      0.0900   3.2970      0.0900   3.2970
NONBonded  C4A      0.0900   3.2970      0.0900   3.2970
NONBonded  C2A      0.0900   3.2970      0.0900   3.2970
NONBonded  C8G      0.0900   3.2970      0.0900   3.2970
NONBonded  C6G      0.0900   3.2970      0.0900   3.2970
NONBonded  C5G      0.0900   3.2970      0.0900   3.2970
NONBonded  C4G      0.0900   3.2970      0.0900   3.2970
NONBonded  C2G      0.0900   3.2970      0.0900   3.2970
NONBonded  C6T      0.0900   3.2970      0.0900   3.2970
NONBonded  C5T      0.0900   3.2970      0.0900   3.2970
NONBonded  C4T      0.0900   3.2970      0.0900   3.2970
NONBonded  C2T      0.0900   3.2970      0.0900   3.2970
NONBonded  N4C      0.1600   2.8591      0.1600   2.8591
NONBonded  O4U      0.2304   2.7290      0.2304   2.7290
NONBonded  N7G      0.1600   2.8591      0.1600   2.8591
NONBonded  N3G      0.1600   2.8591      0.1600   2.8591
NONBonded  N2G      0.1600   2.8591      0.1600   2.8591
NONBonded  N3A      0.1600   2.8591      0.1600   2.8591
NONBonded  N7A      0.1600   2.8591      0.1600   2.8591
NONBonded  N6A      0.1600   2.8591      0.1600   2.8591
NONBonded  O6G      0.2304   2.7290      0.2304   2.7290
NONBonded  CC3E     0.0900   3.2970      0.0900   3.2970
NONBonded  N2A      0.1600   2.8591      0.1600   2.8591

! special solute-solute hydrogen bonding potential parameters
AEXP 4
REXP 6 

HAEX 4 

AAEX 2
! "all" possible combinations of HB-pairs in nucleic acids:
!  WELL DEPTHS DEEPENED BY 0.5 KCAL TO IMPROVE BASEPAIR ENERGIES /LN
!  AND DISTANCES INCREASED BY 0.05
!                   Emin      Rmin
!                (Kcal/mol)   (A)
hbond  N*   O*      -14.0       2.95
hbond  N*   N*      -14.5       3.05
hbond  O*   O*      -15.75      2.80
hbond  O*   N*      -15.50      2.90

! the following NBFIXes are for DNA-DNA hydrogen bonding 

! terms
!                                         ------1-4------
!                   A           B           A          B
!           [Kcal/(mol A^12)] [Kcal/(mol A^6)]
!
nbfix  HO   ON      0.05       0.1      0.05       0.1
nbfix  HO   O3R     0.05       0.1      0.05       0.1
nbfix  HO   O5R     0.05       0.1      0.05       0.1
nbfix  HO   OH      0.05       0.1      0.05       0.1
nbfix  HO   O2R     0.05       0.1      0.05       0.1
nbfix  HO   NC      0.05       0.1      0.05       0.1

 
nbfix  H    ON       0.05       0.1      0.05       0.1
nbfix  H    O2       0.05       0.1      0.05       0.1
nbfix  H    O5R      0.05       0.1      0.05       0.1
nbfix  H    O4R      0.05       0.1      0.05       0.1
nbfix  H    O4D      0.05       0.1      0.05       0.1
nbfix  H    O3R      0.05       0.1      0.05       0.1
nbfix  H    O2R      0.05       0.1      0.05       0.1
nbfix  H    OH       0.05       0.1      0.05       0.1
nbfix  H    N7A      0.05       0.1      0.05       0.1
nbfix  H    N7G      0.05       0.1      0.05       0.1
nbfix  H    N3A      0.05       0.1      0.05       0.1
nbfix  H    N3G      0.05       0.1      0.05       0.1


nbfix  HN   ON      0.05       0.1      0.05       0.1
nbfix  HN   O2R     0.05       0.1      0.05       0.1
nbfix  HN   OH      0.05       0.1      0.05       0.1
nbfix  HN   NC      0.05       0.1      0.05       0.1

nbfix  H2   ON      0.05       0.1      0.05       0.1
nbfix  H2   O2R     0.05       0.1      0.05       0.1
nbfix  H2   OH      0.05       0.1      0.05       0.1

nbfix  H2   NC      0.05       0.1      0.05       0.1

!set echo=off end
!RNA PARAMETER FILE 'FRAMEOWRK' FROM PARALLHDG.DNA AND ATOM NAMES
! AND HEAVY ATOM PARAMETERS FROM DNA-RNA.PARAM
!INCLUDES ALL NONEXCHANGEABLE HYDROGEN TERMS FOR BOND, ANGLE, AND
!IMPROPERS WITH ENERGY CONSTANT VARIABLES: $kchbond, $kchangle, AND $kchimpr.
!BOND, ANGLE, AND IMPROPERS WERE ESTIMATED FROM VALUES FROM THE STANDARD 
!NUCLEOTIDES OF INSIGHTII 95.0 (BIOSYM/MOLECULAR SIMULATIONS).
!CREATED 2/24/96-- JASON P. RIFE AND PETER B. MOORE
REMARK DNA-RNA-ALLATOM.PARAM

set echo=off message=off end

evaluate ($kchbond = 2000) 
evaluate ($kchangle  = 1000)
evaluate ($kchimpr = 1000)


!the generic bonds were taken from param11.dna with 3*kq
BOND  C5R  OH       876.000    1.4300     ! 5' end
BOND  C5D  OH       876.000    1.4300     ! 5' end
BOND  C3R  OH       876.000    1.4300     ! 3' end
BOND  C3D  OH       876.000    1.4300     ! 3' end
BOND  O2R  HO      1350.000    0.9572

!Phos.  - combined RNA/DNA statistics used 
!                      kq       x_eq       sigma
BOND  P    O1P     1489.209    1.485      ! 0.015  Phos
BOND  P    O2P     1489.209    1.485      ! 0.015  P
BOND  P    O5R     3350.720    1.593      ! 0.010  P
BOND  P    OH      3350.720    1.593      ! 0.010  P ! For 5pho patch
BOND  P    O3R     2326.889    1.607      ! 0.012  P

!Sugars
!RNA statistics
BOND  O5R  C5R     1709.551    1.425      ! 0.014  Sugar
BOND  C5R  C4R     1982.674    1.510      ! 0.013  S
BOND  C4R  C3R     2769.190    1.524      ! 0.011  S
BOND  C3R  C2R     2769.190    1.525      ! 0.011  S
BOND  C2R  C1R     3350.720    1.528      ! 0.010  S
BOND  O4R  C1R     2326.888    1.414      ! 0.012  S
BOND  O4R  C4R     2326.888    1.453      ! 0.012  S
BOND  O3R  C3R     1982.674    1.423      ! 0.013  S
BOND  C2R  O2R     1982.674    1.413      ! 0.013  S

!DNA statistics
BOND  O5R  C5D     1709.551    1.427      ! 0.014  Sugar
BOND  C5D  C4D     5235.500    1.511      ! 0.008  S
BOND  C4D  C3D     3350.720    1.528      ! 0.010  S
BOND  C3D  C2D     3350.720    1.518      ! 0.010  S
BOND  C2D  C1D     1709.551    1.521      ! 0.014  S
BOND  O4D  C1D     1982.674    1.420      ! 0.013  S
BOND  O4D  C4D     2769.190    1.446      ! 0.011  S
BOND  O3R  C3D     1982.674    1.431      ! 0.013  S

!hydrogen/carbon
BOND  C4R  H       $kchbond   1.09               
BOND  C3R  H       $kchbond   1.09               
BOND  C2R  H       $kchbond   1.09              
BOND  C1R  H       $kchbond   1.09               
BOND  C5R  H       $kchbond   1.09               

BOND  C4D  H       $kchbond   1.09               
BOND  C3D  H       $kchbond   1.09               
BOND  C2D  H       $kchbond   1.09              
BOND  C1D  H       $kchbond   1.09               
BOND  C5D  H       $kchbond   1.09               

!Bases
!base specific bonds taken from param11.dna , 3*kq
BOND  O2U  HO      1350.000    0.957      ! UR
BOND  HN   NNA     1416.000    1.010      ! URA
BOND  HN   N1T     1416.000    1.010      ! Infer.
BOND  HN   N1C     1416.000    1.010
BOND  HN   N9G     1416.000    1.010
BOND  HN   N9A     1416.000    1.010
BOND  HN   N3U     1416.000    1.010
BOND  HN   N3T     1416.000    1.010
BOND  H2   N2      1416.000    1.010
BOND  H2   N4C     1416.000    1.010
BOND  H2   N2G     1416.000    1.010
BOND  H2   N6A     1416.000    1.010

BOND  HO   OH      1350.000    0.960      ! PARAM7 (IR stretch 3400 cm-1)

!Base sugar joint bonds (scale from sugar)
!                      kq       x_eq       sigma
BOND  C1R  N1T     1709.551    1.473      ! 0.014  Base
BOND  C1R  N1U     4136.691    1.469      ! 0.009  B
BOND  C1R  N1C     2326.889    1.470      ! 0.012  B
BOND  C1R  N9G     4136.691    1.459      ! 0.009  B
BOND  C1R  N9A     3350.720    1.462      ! 0.010  B

BOND  C1D  N1T     1709.551    1.473      ! 0.014  B   !DNA
BOND  C1D  N1U     4136.691    1.469      ! 0.009  B
BOND  C1D  N1C     2326.889    1.470      ! 0.012  B
BOND  C1D  N9G     4136.691    1.459      ! 0.009  B
BOND  C1D  N9A     3350.720    1.462      ! 0.010  B

!cytosine                      kq          x_eq  sigma
BOND       C2C    ON          1370.370    1.240 !0.009  B
BOND       C4C    N4C         1370.370    1.335 !0.009  B
BOND       N1C    C2C         1110.000    1.397 !0.010  B
BOND       N1C    C6C         3083.333    1.367 !0.006  B
BOND       C2C    NC          1734.375    1.353 !0.008  B
BOND       NC     C4C         2265.306    1.335 !0.007  B
BOND       C4C    C5C         1734.375    1.425 !0.008  B
BOND       C5C    C6C         1734.375    1.339 !0.008  B
BOND       C5C    H           $kchbond    1.09               
BOND       C6C    H           $kchbond    1.09               

!thymine
BOND       N1T    C2T         1734.375    1.376 !0.008  B
BOND       C2T    N3T         1734.375    1.373 !0.008  B
BOND       N3T    C4T         1734.375    1.382 !0.008  B
BOND       C4T    C5T         1370.370    1.445 !0.009  B
BOND       C5T    C6T         2265.306    1.339 !0.007  B
BOND       C6T    N1T         2265.306    1.378 !0.007  B
BOND       C2T    ON          1734.375    1.220 !0.008  B
BOND       C4T    ON          1370.370    1.228 !0.009  B
BOND       C5T    CC3E        3083.333    1.496 !0.006  B
BOND       C6T    H           $kchbond    1.09               
BOND       CC3E   H           $kchbond    1.09               

!adenine
BOND       NC     C2A         1370.370    1.339 !0.009  B
BOND       C2A    N3A         1370.370    1.331 !0.009  B
BOND       N3A    C4A         3083.333    1.344 !0.006  B
BOND       C4A    C5A         2265.306    1.383 !0.007  B
BOND       C5A    C6A         1370.370    1.406 !0.009  B
BOND       C6A    NC          2265.306    1.351 !0.007  B
BOND       C5A    N7A         3083.333    1.388 !0.006  B
BOND       N7A    C8A         2265.306    1.311 !0.007  B
BOND       C8A    N9A         1734.375    1.373 !0.008  B
BOND       N9A    C4A         3083.333    1.374 !0.006  B
BOND       C6A    N6A         1734.375    1.335 !0.008  B
BOND       C8A    H           $kchbond    1.08               
BOND       C2A    H           $kchbond    1.09               

!guanine
BOND       NNA    C2G         1734.375    1.373 !0.008  B
BOND       C2G    N3G         1734.375    1.323 !0.008  B
BOND       N3G    C4G         2265.306    1.350 !0.007  B 
BOND       C4G    C5G         2265.306    1.379 !0.007  B
BOND       C5G    C6G         1110.000    1.419 !0.010  B 
BOND       C6G    NNA         2265.306    1.391 !0.007  B 
BOND       C5G    N7G         3083.333    1.388 !0.006  B 
BOND       N7G    C8G         3083.333    1.305 !0.006  B 
BOND       C8G    N9G         2265.306    1.374 !0.007  B 
BOND       N9G    C4G         1734.375    1.375 !0.008  B
BOND       C2G    N2G         1110.000    1.341 !0.010  B
BOND       C6G    O6G         1370.370    1.237 !0.009  B
BOND       C8G    H           $kchbond    1.08               

!uracil
BOND       C2U    ON          1370.370    1.219 !0.009  B
BOND       C4U    ON          1734.375    1.232 !0.008  B
BOND       N1U    C2U         1370.370    1.381 !0.009  B
BOND       N1U    C6U         1370.370    1.375 !0.009  B
BOND       C2U    N3U         2265.306    1.373 !0.007  B
BOND       N3U    C4U         1370.370    1.380 !0.009  B
BOND       C4U    C5U         1370.370    1.431 !0.009  B
BOND       C5U    C6U         1370.370    1.337 !0.009  B
BOND       C5U    H           $kchbond    1.09               
BOND       C6U    H           $kchbond    1.09               

!Phos.
!the ANGLe s were taken from param11.dna with 3*kq
ANGLe       HO     OH     C5R        139.500  107.300 
ANGLe       HO     O5R    C5R        139.500  107.300 
ANGLe       HO     OH     C5D        139.500  107.300 
ANGLe       HO     O5R    C5D        139.500  107.300 
ANGLe       HO     O3R    P          139.500  107.300
ANGLe       HO     OH   P          139.500  107.300 ! For 5pho patch 
ANGLe       HO     O2R    C2R        139.500  107.300 
ANGLe       OH     P      O3R        144.300  102.600 !
ANGLe       OH     P      O5R        144.300  102.600 !
ANGLe       OH     P      O1P        296.700  108.230 !
ANGLe       OH     P      O2P        296.700  108.230 !
ANGLe       OH     C5R    C4R        210.000  112.000 ! 
ANGLe       OH     C5D    C4D        210.000  112.000 ! 
ANGLe       C4D    C3D    OH         139.500  111.000 ! 
ANGLe       C4R    C3R    OH         139.500  111.000 ! 
ANGLe       C2D    C3D    OH         139.500  111.000 ! 
ANGLe       C2R    C3R    OH         139.500  111.000 ! 
ANGLe       C3R    OH     HO         139.500  107.300 !
ANGLe       C3D    OH     HO         139.500  107.300 !

!Phos.  - combined RNA/DNA statistics used 
!                                      kq      x_eq  sigma
ANGLe       O1P    P      O2P       1337.074  119.600 !1.5 P 
ANGLe       O5R    P      O1P        357.719  108.100 !2.9 P
ANGLe       O5R    P      O2P        412.677  108.300 !2.7 P 
ANGLe       O3R    P      O5R        833.356  104.000 !1.9 P 
ANGLe       O2P    P      O3R        293.791  108.300 !3.2 P
ANGLe       O1P    P      O3R        293.791  107.400 !3.2 P 

ANGLe       O5R    C5R    C4R       1534.906  110.200 !1.4 P 
ANGLe       P      O5R    C5R       1175.163  120.900 !1.6 P 
ANGLe       P      O3R    C3R       2089.178  119.700 !1.2 P

ANGLe       O5R    C5D    C4D       1534.906  110.200 !1.4 P !DNA
ANGLe       P      O5R    C5D       1175.163  120.900 !1.6 P
ANGLe       P      O3R    C3D       2089.178  119.700 !1.2 P

!Sugars
!RNA statistics
!                                      kq      x_eq  sigma
ANGLe       O4R    C4R    C3R        561.212  105.500 !1.4 S
ANGLe       C5R    C4R    C3R        488.878  115.500 !1.5 S
ANGLe       C5R    C4R    O4R        561.212  109.200 !1.4 S
ANGLe       C1R    O4R    C4R       1357.996  109.600 !0.9 S
ANGLe       C4R    C3R    C2R       1099.976  102.700 !1.0 S
ANGLe       C3R    C2R    C1R       1357.996  101.500 !0.9 S
ANGLe       O4R    C1R    C2R        561.212  106.400 !1.4 S
ANGLe       N1T    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       N1C    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       N1U    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       N9G    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       N9A    C1R    C2R        429.678  113.400 !1.6 S
ANGLe       O4R    C1R    N1T       1099.976  108.200 !1.0 S
ANGLe       O4R    C1R    N1C       1099.976  108.200 !1.0 S
ANGLe       O4R    C1R    N1U       1099.976  108.200 !1.0 S
ANGLe       O4R    C1R    N9A       1099.976  108.200 !1.0 S
ANGLe       O4R    C1R    N9G       1099.976  108.200 !1.0 S
ANGLe       C1R    C2R    O2R        357.719  110.600 !2.9 S scale from phos.
ANGLe       C3R    C2R    O2R        357.719  113.300 !2.9 S scale from phos.
ANGLe       C4R    C3R    O3R        445.032  110.500 !2.6 S scale from phos.
ANGLe       C2R    C3R    O3R        383.726  111.000 !2.8 S scale from phos.

!DNA statistics
ANGLe       O4D    C4D    C3D       1099.976  105.600 !1.0 S
ANGLe       C5D    C4D    C3D        488.878  114.700 !1.5 S
ANGLe       C5D    C4D    O4D        429.678  109.400 !1.6 S
ANGLe       C1D    O4D    C4D        650.874  109.700 !1.3 S
ANGLe       C4D    C3D    C2D       1099.976  103.200 !1.0 S
ANGLe       C3D    C2D    C1D        650.874  102.700 !1.3 S
ANGLe       O4D    C1D    C2D        909.071  106.100 !1.1 S
ANGLe       N1T    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       N1C    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       N1U    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       N9G    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       N9A    C1D    C2D        488.878  114.200 !1.5 S
ANGLe       O4D    C1D    N1T       1357.996  107.800 !0.9 S
ANGLe       O4D    C1D    N1C       1357.996  107.800 !0.9 S
ANGLe       O4D    C1D    N1U       1357.996  107.800 !0.9 S
ANGLe       O4D    C1D    N9A       1357.996  107.800 !0.9 S
ANGLe       O4D    C1D    N9G       1357.996  107.800 !0.9 S
ANGLe       C4D    C3D    O3R        621.574  110.300 !2.2 S scale from phos.
ANGLe       C2D    C3D    O3R        412.677  110.600 !2.7 S scale from phos.

!Ribose terms involving non-exchageables
ANGLe       OH     C5R    H         $kchangle     109.83      
ANGLe       O5R    C5R    H         $kchangle     109.83      
ANGLe       H      C5R    H         $kchangle     109.11      
ANGLe       C4R    C5R    H         $kchangle     109.11      
ANGLe       C5R    C4R    H         $kchangle     107.93      
ANGLe       H      C4R    C3R       $kchangle     107.13      
ANGLe       H      C4R    O4R       $kchangle     113.74      
ANGLe       H      C3R    C4R       $kchangle     111.35      
ANGLe       H      C3R    O3R       $kchangle     105.87      
ANGLe       H      C3R    OH        $kchangle     105.87      
ANGLe       H      C3R    C2R       $kchangle     112.27      
ANGLe       H      C2R    C3R       $kchangle     111.41      
ANGLe       H      C2R    O2R       $kchangle     113.07      
ANGLe       H      C2R    C1R       $kchangle     112.38      
ANGLe       H      C1R    C2R       $kchangle     111.95      
ANGLe       H      C1R    N1C       $kchangle     107.70      
ANGLe       H      C1R    N1U       $kchangle     107.70      
ANGLe       H      C1R    N9A       $kchangle     107.70      
ANGLe       H      C1R    N9G       $kchangle     107.70      
ANGLe       H      C1R    O4R       $kchangle     106.86      

!Deoxyribose terms involving non-exchageables
!
ANGLe       OH     C5D    H         $kchangle     109.70      
ANGLe       O5R    C5D    H         $kchangle     109.70      
ANGLe       H      C5D    H         $kchangle     109.17      
ANGLe       C4D    C5D    H         $kchangle     109.17      
ANGLe       C5D    C4D    H         $kchangle     107.78      
ANGLe       H      C4D    C3D       $kchangle     106.91      
ANGLe       H      C4D    O4D       $kchangle     112.98      
ANGLe       H      C3D    C4D       $kchangle     111.16      
ANGLe       H      C3D    O3R       $kchangle     109.34      
ANGLe       H      C3D    OH        $kchangle     109.34      
ANGLe       H      C3D    C2D       $kchangle     111.98      
ANGLe       H      C2D    C3D       $kchangle     111.36      
ANGLe       H      C2D    H         $kchangle     107.52      
ANGLe       H      C2D    C1D       $kchangle     112.29      
ANGLe       H      C1D    C2D       $kchangle     110.94      
ANGLe       H      C1D    N1C       $kchangle     108.25      
ANGLe       H      C1D    N1U       $kchangle     108.25 
ANGLe       H      C1D    N1T       $kchangle     108.25      
ANGLe       H      C1D    N9A       $kchangle     108.25      
ANGLe       H      C1D    N9G       $kchangle     108.25     
ANGLe       H      C1D    O4D       $kchangle     107.95      

!Bases
!cytosine                            kq       x_eq   sigma
ANGLe       C6C    N1C    C2C       2277.447  120.300 !0.40 B
ANGLe       N1C    C2C    NC         743.656  119.200 !0.70 B
ANGLe       C2C    NC     C4C       1457.566  119.900 !0.50 B
ANGLe       NC     C4C    C5C       2277.447  121.900 !0.40 B
ANGLe       C4C    C5C    C6C       1457.566  117.400 !0.50 B
ANGLe       C5C    C6C    N1C       1457.566  121.000 !0.50 B
ANGLe       N1C    C2C    ON        1012.199  118.900 !0.60 B
ANGLe       NC     C2C    ON         743.656  121.900 !0.70 B
ANGLe       NC     C4C    N4C        743.656  118.000 !0.70 B
ANGLe       C5C    C4C    N4C        743.656  120.200 !0.70 B
ANGLe       C6C    N1C    C1R        763.873  120.800 !1.20 B scale from sugar
ANGLe       C2C    N1C    C1R        909.071  118.800 !1.10 B scale from sugar
ANGLe       C6C    N1C    C1D        763.873  120.800 !1.20 B !DNA
ANGLe       C2C    N1C    C1D        909.071  118.800 !1.10 B
ANGLe       C4C    N4C    H2         105.000  120.000 !from param11.dna, 3*keq 
ANGLe       H2     N4C    H2         105.000  120.000 
ANGLe       N1C    C6C    H         $kchangle  119.63          
ANGLe       C5C    C6C    H         $kchangle  119.36          
ANGLe       C4C    C5C    H         $kchangle  121.54          
ANGLe       C6C    C5C    H         $kchangle  121.54          

!thymine                            kq        x_eq    sigma
ANGLe       C6T    N1T    C2T       1457.566  121.300 !0.50 B
ANGLe       N1T    C2T    N3T       1012.199  114.600 !0.60 B
ANGLe       C2T    N3T    C4T       1012.199  127.200 !0.60 B
ANGLe       N3T    C4T    C5T       1012.199  115.200 !0.60 B
ANGLe       C4T    C5T    C6T       1012.199  118.000 !0.60 B
ANGLe       C5T    C6T    N1T       1012.199  123.700 !0.60 B
ANGLe       N1T    C2T    ON         569.362  123.100 !0.80 B
ANGLe       N3T    C2T    ON        1012.199  122.300 !0.60 B
ANGLe       N3T    C4T    ON        1012.199  119.900 !0.60 B
ANGLe       C5T    C4T    ON         743.656  124.900 !0.70 B
ANGLe       C4T    C5T    CC3E      1012.199  119.000 !0.60 B
ANGLe       C6T    C5T    CC3E      1012.199  122.900 !0.60 B
ANGLe       C6T    N1T    C1R        488.878  120.400 !1.50 B scale from sugar
ANGLe       C2T    N1T    C1R        429.678  118.200 !1.60 B scale from sugar
ANGLe       C6T    N1T    C1D        488.878  120.400 !1.50 B !DNA
ANGLe       C2T    N1T    C1D        429.678  118.200 !1.60 B
ANGLe       C2T    N3T    HN         105.000  116.500  !from param11.dna, 3*keq 
ANGLe       C4T    N3T    HN         105.000  116.500  
ANGLe      C5T    CC3E   H         $kchangle  109.50
ANGLe       H      CC3E   H         $kchangle  109.44
ANGLe       N1T    C6T    H         $kchangle  119.52          
ANGLe       C5T    C6T    H         $kchangle  119.52          

!adenine                            kq        x_eq    sigma
ANGLe       C6A    NC     C2A       1012.199  118.600 !0.60 B
ANGLe       NC     C2A    N3A       1457.566  129.300 !0.50 B
ANGLe       C2A    N3A    C4A       1457.566  110.600 !0.50 B
ANGLe       N3A    C4A    C5A        743.656  126.800 !0.70 B
ANGLe       C4A    C5A    C6A       1457.566  117.000 !0.50 B
ANGLe       C5A    C6A    NC        1457.566  117.700 !0.50 B
ANGLe       C4A    C5A    N7A       1457.566  110.700 !0.50 B
ANGLe       C5A    N7A    C8A       1457.566  103.900 !0.50 B
ANGLe       N7A    C8A    N9A       1457.566  113.800 !0.50 B
ANGLe       C8A    N9A    C4A       2277.447  105.800 !0.40 B
ANGLe       N9A    C4A    C5A       2277.447  105.800 !0.40 B
ANGLe       N3A    C4A    N9A        569.362  127.400 !0.80 B
ANGLe       C6A    C5A    N7A        743.656  132.300 !0.70 B
ANGLe       NC     C6A    N6A       1012.199  118.600 !0.60 B
ANGLe       C5A    C6A    N6A        569.362  123.700 !0.80 B
ANGLe       C8A    N9A    C1R        339.499  127.700 !1.80 B scale from sugar
ANGLe       C4A    N9A    C1R        339.499  126.300 !1.80 B scale from sugar
ANGLe       C8A    N9A    C1D        339.499  127.700 !1.80 B !DNA
ANGLe       C4A    N9A    C1D        339.499  126.300 !1.80 B
ANGLe       C6A    N6A    H2         105.000  120.000  !from param11.dna, 3*keq 
ANGLe       H2     N6A    H2         105.000  120.000
ANGLe       N7A    C8A    H         $kchangle  123.16          
ANGLe       N9A    C8A    H         $kchangle  123.16          
ANGLe       NC     C2A    H         $kchangle  115.54          
ANGLe       N3A    C2A    H         $kchangle  115.54          

!guanine                             kq        x_eq    sigma
ANGLe       C6G    NNA    C2G       1012.199  125.100 !0.60 B
ANGLe       NNA    C2G    N3G       1012.199  123.900 !0.60 B
ANGLe       C2G    N3G    C4G       1457.566  111.900 !0.50 B
ANGLe       N3G    C4G    C5G       1457.566  128.600 !0.50 B
ANGLe       C4G    C5G    C6G       1012.199  118.800 !0.60 B
ANGLe       C5G    C6G    NNA       1457.566  111.500 !0.50 B
ANGLe       C4G    C5G    N7G       2277.447  110.800 !0.40 B
ANGLe       C5G    N7G    C8G       1457.566  104.300 !0.50 B
ANGLe       N7G    C8G    N9G       1457.566  113.100 !0.50 B
ANGLe       C8G    N9G    C4G       2277.447  106.400 !0.40 B
ANGLe       N9G    C4G    C5G       2277.447  105.400 !0.40 B
ANGLe       N3G    C4G    N9G       1012.199  126.000 !0.60 B
ANGLe       C6G    C5G    N7G       1012.199  130.400 !0.60 B
ANGLe       NNA    C2G    N2G        449.866  116.20  !0.90 B
ANGLe       N3G    C2G    N2G        743.656  119.900 !0.70 B
ANGLe       NNA    C6G    O6G       1012.199  119.900 !0.60 B
ANGLe       C5G    C6G    O6G       1012.199  128.600 !0.60 B
ANGLe       C8G    N9G    C1R        650.874  127.000 !1.30 B scale from sugar
ANGLe       C4G    N9G    C1R        650.874  126.500 !1.30 B scale from sugar
ANGLe       C8G    N9G    C1D        650.874  127.000 !1.30 B !DNA
ANGLe       C4G    N9G    C1D        650.874  126.500 !1.30 B
ANGLe       C2G    N2G    H2         105.000  120.000  !from param11.dna, 3*keq 
ANGLe       H2     N2G    H2         105.000  120.000
ANGLe       C2G    NNA    HN         105.000  119.300
ANGLe       C6G    NNA    HN         105.000  119.300
ANGLe       N7G    C8G    H         $kchangle  122.91          
ANGLe       N9G    C8G    H         $kchangle  122.91          

!uracile                             kq        x_eq    sigma
ANGLe       C6U    N1U    C2U       1012.199  121.000 !0.60 B
ANGLe       N1U    C2U    N3U       1012.199  114.900 !0.60 B
ANGLe       C2U    N3U    C4U       1012.199  127.000 !0.60 B
ANGLe       N3U    C4U    C5U       1012.199  114.600 !0.60 B
ANGLe       C4U    C5U    C6U       1012.199  119.700 !0.60 B
ANGLe       C5U    C6U    N1U       1457.566  122.700 !0.50 B
ANGLe       N1U    C2U    ON         743.656  122.800 !0.70 B
ANGLe       N3U    C2U    ON         743.656  122.200 !0.70 B
ANGLe       N3U    C4U    ON         743.656  119.400 !0.70 B
ANGLe       C5U    C4U    ON        1012.199  125.900 !0.60 B
ANGLe       C6U    N1U    C1R        561.212  121.200 !1.40 B
ANGLe       C2U    N1U    C1R        763.872  117.700 !1.20 B
ANGLe       C6U    N1U    C1D        561.212  121.200 !1.40 B !DNA
ANGLe       C2U    N1U    C1D        763.872  117.700 !1.20 B
ANGLe       C4U    ON     HO         105.000  120.000 !from param11.dna, 3*keq 
ANGLe       C2U    N3U    HN         105.000  116.500 
ANGLe       C4U    N3U    HN         105.000  116.500  
ANGLe       N1U    C6U    H         $kchangle  119.38          
ANGLe       C5U    C6U    H         $kchangle  119.38          
ANGLe       C4U    C5U    H         $kchangle  119.56          
ANGLe       C6U    C5U    H         $kchangle  119.56          

!Dihedrals from param11.dna (included for terminal residues)

DIHEdral    X    C2R  C3R  X      4.50 3    0.000
DIHEdral    X    C4R  C3R  X      4.50 3    0.000
DIHEdral    X    C2R  C1R  X      4.50 3    0.000
DIHEdral    X    C5R  O5R  X      1.50 3    0.000
DIHEdral    X    C3R  O3R  X      1.50 3    0.000
DIHEdral    X    C3R  OH   X      1.50 3    0.000
DIHEdral    X    C5R  OH   X      1.50 3    0.000
DIHEdral    X    C2R  O2R  X      1.50 3    0.000
DIHEdral    X    O5R  P    X      2.25 3    0.000
DIHEdral    X    OH   P    X      2.25 3    0.000
DIHEdral    OH   C5R  C4R  O4R    4.50 3    0.000
DIHEdral    OH   C5R  C4R  C3R    4.50 3    0.000 ! gamma
DIHEdral    C3R  O3R  P    OH     2.25 3    0.000 ! added by infer
DIHEdral    C3R  O3R  P    OH     2.25 2    0.000 ! ATB, 7-SEP-84
DIHEdral    C5R  O5R  P    OH     2.25 3    0.000 ! added by infer
DIHEdral    C5R  O5R  P    OH     2.25 2    0.000 ! ATB, 7-SEP-84

DIHEdral    X    C2D  C3D  X      4.50 3    0.000
DIHEdral    X    C4D  C3D  X      4.50 3    0.000  !DNA
DIHEdral    X    C2D  C1D  X      4.50 3    0.000
DIHEdral    X    C5D  O5R  X      1.50 3    0.000
DIHEdral    X    C3D  O3R  X      1.50 3    0.000
DIHEdral    X    C3D  OH   X      1.50 3    0.000
DIHEdral    X    C5D  OH   X      1.50 3    0.000
DIHEdral    OH   C5D  C4D  O4D    4.50 3    0.000
DIHEdral    OH   C5D  C4D  C3D    4.50 3    0.000
DIHEdral    C3D  O3R  P    OH     2.25 3    0.000
DIHEdral    C3D  O3R  P    OH     2.25 2    0.000
DIHEdral    C5D  O5R  P    OH     2.25 3    0.000
DIHEdral    C5D  O5R  P    OH     2.25 2    0.000


!Base hydrogen DIHEdrals taken from param11.dna
DIHEdral    X    C2G  N2G  X     18.0  2  180.000
DIHEdral    X    C6A  N6A  X     18.0  2  180.000
DIHEdral    X    C6A  N4C  X     18.00 2  180.000
DIHEdral    X    C4C  N4C  X     18.00 2  180.000

!IMPRopers to keep the two purine rings parallel:
!guanine
IMPRoper    C8G  C4G  C5G  NNA  250.0  2  180.000
IMPRoper    C8G  C5G  C4G  C2G  250.0  2  180.000
IMPRoper    N3G  C4G  C5G  N7G  250.0  2  180.000
IMPRoper    C6G  C5G  C4G  N9G  250.0  2  180.000
!adenine
IMPRoper    C8A  C4A  C5A  N9A  250.0  2  180.000 ! WYE AND PATCHED RESIDUES
IMPRoper    C8A  C5A  C4A  C2A  250.0  2  180.000
IMPRoper    C8A  C4A  C5A  NC   250.0  2  180.000 
IMPRoper    N3A  C4A  C5A  N7A  250.0  2  180.000
IMPRoper    C6A  C5A  C4A  N9A  250.0  2  180.000


!other base specific non-exch hydrogen IMPRopers
IMPRoper    H    C4C  C6C  C5C  $kchimpr    0    0.000
IMPRoper    H    N1C  C5C  C6C  $kchimpr    0    0.000
IMPRoper    H    C4U  C6U  C5U  $kchimpr    0    0.000
IMPRoper    H    N1U  C5U  C6U  $kchimpr    0    0.000
IMPRoper    H    N1T  C5T  C6T  $kchimpr    0    0.000
IMPRoper    H    N7A  N9A  C8A  $kchimpr    0    0.000
IMPRoper    H    NC   N3A  C2A  $kchimpr    0    0.000
IMPRoper    H    N7G  N9G  C8G  $kchimpr    0    0.000

!Impropers for ribose chirality
IMPRoper    H    C2R  O4R  N9A    $kchimpr    0    -65.000!C1R
IMPRoper    H    C2R  O4R  N9G    $kchimpr    0    -65.000!C1R
IMPRoper    H    C2R  O4R  N1C    $kchimpr    0    -65.000!C1R
IMPRoper    H    C2R  O4R  N1U    $kchimpr    0    -65.000!C1R
IMPRoper    H    C2R  O4R  N1T    $kchimpr    0    -65.000!C1R

IMPRoper    H    C3R  C1R  O2R    $kchimpr    0    65.000!C2R
IMPRoper    H    C4R  C2R  O3R    $kchimpr    0    60.300!C3R 
IMPRoper    H    C4R  C2R  OH     $kchimpr    0    60.300!C3R; TERMINAL RES 
IMPRoper    H    C5R  C3R  O4R    $kchimpr    0    70.300!C4R 
IMPRoper    H    O5R  H    C4R    $kchimpr    0    72.000!C5R; 
IMPRoper    H    OH   H    C4R    $kchimpr    0    72.000!C5R; TERMINAL RES
!Impropers for deoxyribose chirality
IMPRoper    H    C2D  O4D  N9A    $kchimpr    0    -65.280!C1D
IMPRoper    H    C2D  O4D  N9G    $kchimpr    0    -65.280!C1D
IMPRoper    H    C2D  O4D  N1C    $kchimpr    0    -65.280!C1D
IMPRoper    H    C2D  O4D  N1T    $kchimpr    0    -65.280!C1D

IMPRoper    H    C3D  H    C1D    $kchimpr    0    -73.500!C2D
IMPRoper    H    C4D  C2D  O3R    $kchimpr    0    62.660!C3D 
IMPRoper    H    C4D  C2D  OH     $kchimpr    0    62.660!C3D; TERMINAL RES 
IMPRoper    H    C5D  C3D  O4D    $kchimpr    0    70.220!C4D 
IMPRoper    H    O5R  H    C4D    $kchimpr    0    71.430!C5D; 
IMPRoper    H    OH   H    C4D    $kchimpr    0    71.430!C5D; TERMINAL RES


!Phos.  - periodical potentials from combined RNA/DNA statistics
!                                 kq       x_eq       (sigma in parenthesis)
DIHEdral    O3R  P    O5R  C5R    1.41 3    6.0   ! alpha !P (20.3)
DIHEdral    P    O5R  C5R  C4R    3.45 0  183.5   ! beta  !P (13.0)
DIHEdral    O5R  C5R  C4R  C3R   12.24 3   18.3   ! gamma !S (6.9)
DIHEdral    O5R  C5R  C4R  O4R   24.28 3   14.1   !       !S (4.9)
DIHEdral    C4R  C3R  O3R  P      7.88 0  214.0   ! eps   !P (8.6)
DIHEdral    C3R  O3R  P    O5R    1.75 3    0.3   ! zeta  !P (18.3)

DIHEdral    O3R  P    O5R  C5D    1.41 3    6.0 !DNA
DIHEdral    P    O5R  C5D  C4D    3.45 0  183.5
DIHEdral    O5R  C5D  C4D  C3D   12.42 3   18.3
DIHEdral    O5R  C5D  C4D  O4D   24.28 3   14.1
DIHEdral    C4D  C3D  O3R  P      7.88 0  214.0
DIHEdral    C3D  O3R  P    O5R    1.75 3    0.3

!Phos.  - discrete values from combined RNA/DNA statistics
!                                 kq       x_eq       (sigma in parenthesis)
!DIHEdral    O3R  P    O5R  C5R    6.07 0  285.3   ! (9.8)  alpha1 !P
!DIHEdral    O3R  P    O5R  C5R    3.98 0   81.1   ! (12.1) alpha2;alpha3=180.
!DIHEdral    P    O5R  C5R  C4R    3.44 0  183.5   ! (13.0) beta   !P
!DIHEdral    O5R  C5R  C4R  C3R   17.94 0   52.5   ! (5.7)  gamma1 !S
!DIHEdral    O5R  C5R  C4R  C3R   14.23 0  179.4   ! (6.4)  gamma2 !S
!DIHEdral    O5R  C5R  C4R  C3R    3.85 0  292.9   ! (12.3) gamma3 !S
!DIHEdral    C4R  C3R  O3R  P      7.88 0  214.0   ! (8.6)  eps    !P
!DIHEdral    C3R  O3R  P    O5R   25.30 0  289.2   ! (4.8)  zeta1  !P 
!DIHEdral    C3R  O3R  P    O5R    2.85 0   80.7   ! (14.3) zeta2;zeta3=180.

!Sugars
! c3'-endo conformation as the default for for RNA, c2'-endo for DNA,
!RNA statistics, C3'-endo
DIHEdral    C5R  C4R  C3R  O3R  30.12 0   81.1   ! delta ! c3'-endo S (4.4)
DIHEdral    O4R  C4R  C3R  O3R  33.10 0  201.8   !  4.2  ! c3'-endo S  
DIHEdral    O4R  C1R  C2R  C3R  24.28 0  335.4   !  4.9  ! c3'-endo S
DIHEdral    C1R  C2R  C3R  C4R  74.36 0   35.9   !  2.8  ! c3'-endo S
DIHEdral    C2R  C3R  C4R  O4R  60.67 0  324.7   !  3.1  ! c3'-endo S
DIHEdral    C3R  C4R  O4R  C1R  22.42 0   20.5   !  5.1  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  C2R  15.67 0    2.8   !  6.1  ! c3'-endo S
DIHEdral    C5R  C4R  C3R  C2R  60.67 0  204.0   !  3.1  ! c3'-endo S
DIHEdral    O3R  C3R  C2R  O2R  28.79 0   44.3   !  4.5  ! c3'-endo S   
DIHEdral    C4R  O4R  C1R  N1T  13.80 0  241.4   !  6.5  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  N1C  13.80 0  241.4   !  6.5  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  N1U  13.80 0  241.4   !  6.5  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  N9G  13.80 0  241.4   !  6.5  ! c3'-endo S
DIHEdral    C4R  O4R  C1R  N9A  13.80 0  241.4   !  6.5  ! c3'-endo S

!RNA c3'-endo sugar base joint torsions  (combined RNA/DNA statistics used)
DIHEdral    O4R  C1R  N1T  C2T  13.38 0  195.7   !  6.6  ! c3'-endo S
DIHEdral    O4R  C1R  N1C  C2C  13.38 0  195.7   !  6.6  ! c3'-endo S
DIHEdral    O4R  C1R  N1U  C2U  13.38 0  195.7   !  6.6  ! c3'-endo S
DIHEdral    O4R  C1R  N9A  C4A   2.97 0  193.3   ! 14.0  ! c3'-endo S
DIHEdral    O4R  C1R  N9G  C4G   2.97 0  193.3   ! 14.0  ! c3'-endo S

!DNA statistics (c2'-endo)
DIHEdral    C5D  C4D  C3D  O3R   36.44 0  145.2   ! delta ! c2'-endo S (4.0)
DIHEdral    O4D  C1D  C2D  C3D   24.28 0   32.8   !  4.9  ! c2'-endo S 
DIHEdral    O4D  C4D  C3D  O3R   31.53 0  265.8   !  4.3  ! c2'-endo S 
DIHEdral    C1D  C2D  C3D  C4D   44.99 0  326.9   !  3.6  ! c2'-endo S
DIHEdral    C2D  C3D  C4D  O4D   28.79 0   22.6   !  4.5  ! c2'-endo S
DIHEdral    C3D  C4D  O4D  C1D   15.67 0  357.7   !  6.1  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  C2D   14.69 0  340.7   !  6.3  ! c2'-endo S
DIHEdral    C5D  C4D  C3D  C2D   34.68 0  262.0   !  4.1  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N1T   12.99 0  217.7   !  6.7  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N1C   12.99 0  217.7   !  6.7  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N1U   12.99 0  217.7   !  6.7  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N9G   12.99 0  217.7   !  6.7  ! c2'-endo S
DIHEdral    C4D  O4D  C1D  N9A   12.99 0  217.7   !  6.7  ! c2'-endo S

!DNA c2'-endo sugar base joint torsions  (combined RNA/DNA statistics used)
DIHEdral    O4D  C1D  N1T  C2T    1.72 0  229.8   ! 18.4  ! c2'-endo S   
DIHEdral    O4D  C1D  N1C  C2C    1.72 0  229.8   ! 18.4  ! c2'-endo S   
DIHEdral    O4D  C1D  N1U  C2U    1.72 0  229.8   ! 18.4  ! c2'-endo S   
DIHEdral    O4D  C1D  N9A  C4A    1.00 0  237.0   ! 24.3  ! c2'-endo S   
DIHEdral    O4D  C1D  N9G  C4G    1.00 0  237.0   ! 24.3  ! c2'-endo S   

!---------------------------------------------------------------------------
!In the case of c3'-endo conformation, the following DIHEdrals are provided
!to overwrite the c2'-endo DIHEdrals

!RNA statistics (c2'-endo)
!DIHEdral    C5R  C4R  C3R  O3R   24.28 0  147.3   ! delta ! c2'-endo S (4.9)
!DIHEdral    O4R  C1R  C2R  C3R   50.43 0   35.2   !  3.4  ! c2'-endo S 
!DIHEdral    O4R  C4R  C3R  O3R   20.75 0  268.1   !  5.3  ! c2'-endo S 
!DIHEdral    C1R  C2R  C3R  C4R   74.36 0  324.6   !  2.8  ! c2'-endo S
!DIHEdral    C2R  C3R  C4R  O4R   31.53 0   24.2   !  4.3  ! c2'-endo S
!DIHEdral    C3R  C4R  O4R  C1R   17.94 0  357.7   !  5.7  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  C2R   21.56 0  339.2   !  5.2  ! c2'-endo S
!DIHEdral    C5R  C4R  C3R  C2R   34.68 0  263.4   !  4.1  ! c2'-endo S
!DIHEdral    O3R  C3R  C2R  O2R   33.05 0  319.7   !  4.2  ! c2'-endo S   
!DIHEdral    C4R  O4R  C1R  N1T   19.27 0  216.6   !  5.5  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  N1C   19.27 0  216.6   !  5.5  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  N1U   19.27 0  216.6   !  5.5  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  N9G   19.27 0  216.6   !  5.5  ! c2'-endo S
!DIHEdral    C4R  O4R  C1R  N9A   19.27 0  216.6   !  5.5  ! c2'-endo S

!RNA c2'-endo sugar base joint torsions  (combined RNA/DNA statistics used) 
!DIHEdral    O4R  C1R  N1T  C2T    1.72 0  229.8   ! 18.4  ! c2'-endo S   
!DIHEdral    O4R  C1R  N1C  C2C    1.72 0  229.8   ! 18.4  ! c2'-endo S   
!DIHEdral    O4R  C1R  N1U  C2U    1.72 0  229.8   ! 18.4  ! c2'-endo S   
!DIHEdral    O4R  C1R  N9A  C4A    1.00 0  237.0   ! 24.3  ! c2'-endo S   
!DIHEdral    O4R  C1R  N9G  C4G    1.00 0  237.0   ! 24.3  ! c2'-endo S   

!DNA statistics, c3'-endo (insuficient data, RNA values used)
!DIHEdral    C5D  C4D  C3D  O3R  30.12 0   81.1   ! delta ! c3'-endo S (4.4)
!DIHEdral    O4D  C4D  C3D  O3R  33.10 0  201.8   !  4.2  ! c3'-endo S  
!DIHEdral    O4D  C1D  C2D  C3D  24.28 0  335.4   !  4.9  ! c3'-endo S
!DIHEdral    C1D  C2D  C3D  C4D  74.36 0   35.9   !  2.8  ! c3'-endo S
!DIHEdral    C2D  C3D  C4D  O4D  60.67 0  324.7   !  3.1  ! c3'-endo S
!DIHEdral    C3D  C4D  O4D  C1D  22.42 0   20.5   !  5.1  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  C2D  15.67 0    2.8   !  6.1  ! c3'-endo S
!DIHEdral    C5D  C4D  C3D  C2D  60.67 0  204.0   !  3.1  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N1T  13.80 0  241.4   !  6.5  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N1C  13.80 0  241.4   !  6.5  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N1U  13.80 0  241.4   !  6.5  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N9G  13.80 0  241.4   !  6.5  ! c3'-endo S
!DIHEdral    C4D  O4D  C1D  N9A  13.80 0  241.4   !  6.5  ! c3'-endo S

!DNA c3'-endo sugar base joint torsions  (combined RNA/DNA statistics used)
!DIHEdral    O4D  C1D  N1T  C2T  13.38 0  195.7   !  6.6  ! c3'-endo S
!DIHEdral    O4D  C1D  N1C  C2C  13.38 0  195.7   !  6.6  ! c3'-endo S
!DIHEdral    O4D  C1D  N1U  C2U  13.38 0  195.7   !  6.6  ! c3'-endo S
!DIHEdral    O4D  C1D  N9A  C4A   2.97 0  193.3   ! 14.0  ! c3'-endo S
!DIHEdral    O4D  C1D  N9G  C4G   2.97 0  193.3   ! 14.0  ! c3'-endo S
!---------------------------------------------------------------------------
!---------------------------------------------------------------------------

!Impropers taken from param11.dna , 3*kq
IMPRoper    C5R  X    X    C2R   94.5  0   35.260
IMPRoper    C5R  X    X    C1R   94.5  0   35.260
IMPRoper    OH   X    X    C3R   94.5  0   35.260
IMPRoper    OH   X    X    C4R   94.5  0   35.260
IMPRoper    OH   X    X    C1R   94.5  0   35.260
IMPRoper    O3R  X    X    C3R   94.5  0   35.260
IMPRoper    O5R  X    X    C1R   94.5  0   35.260
IMPRoper    O2R  X    X    C2R   94.5  0   35.260
IMPRoper    C4R  O5R  C1R  N1T   94.5  0   35.260
IMPRoper    C4R  O5R  C1R  N1C   94.5  0   35.260
IMPRoper    C4R  O5R  C1R  N9G   94.5  0   35.260
IMPRoper    C4R  O5R  C1R  N9A   94.5  0   35.260
IMPRoper    C5R  O4R  C3R  C4R   94.5  0   35.260  
IMPRoper    N1T  C2R  O4R  C1R   94.5  0   35.260  
IMPRoper    N1C  C2R  O4R  C1R   94.5  0   35.260
IMPRoper    N9A  C2R  O4R  C1R   94.5  0   35.260  
IMPRoper    N9G  C2R  O4R  C1R   94.5  0   35.260  
IMPRoper    C4R  O5R  C1R  N1U   94.5  0   35.260
IMPRoper    N1U  C2R  O4R  C1R   94.5  0   35.260  

IMPRoper    C5D  X    X    C2D   94.5  0   35.260  !DNA
IMPRoper    C5D  X    X    C1D   94.5  0   35.260
IMPRoper    OH   X    X    C3D   94.5  0   35.260
IMPRoper    OH   X    X    C4D   94.5  0   35.260
IMPRoper    OH   X    X    C1D   94.5  0   35.260
IMPRoper    O3R  X    X    C3D   94.5  0   35.260
IMPRoper    O5R  X    X    C1D   94.5  0   35.260
IMPRoper    C4D  O5R  C1D  N1T   94.5  0   35.260
IMPRoper    C4D  O5R  C1D  N1C   94.5  0   35.260
IMPRoper    C4D  O5R  C1D  N9G   94.5  0   35.260
IMPRoper    C4D  O5R  C1D  N9A   94.5  0   35.260
IMPRoper    C5D  O4D  C3D  C4D   94.5  0   35.260  
IMPRoper    N1T  C2D  O4D  C1D   94.5  0   35.260  
IMPRoper    N1C  C2D  O4D  C1D   94.5  0   35.260
IMPRoper    N9A  C2D  O4D  C1D   94.5  0   35.260  
IMPRoper    N9G  C2D  O4D  C1D   94.5  0   35.260  
IMPRoper    C4D  O5R  C1D  N1U   94.5  0   35.260
IMPRoper    N1U  C2D  O4D  C1D   94.5  0   35.260  

!the following impropers were taken from param11x.dna
!the higher kq was used to enforce the ring planarity 
!cytosine
IMPRoper    C4C  X    X    ON  2400.0  0    0.000
IMPRoper    C4C  X    X    N1C  250.0  0    0.000
IMPRoper    C6C  X    X    NC   250.0  0    0.000
IMPRoper    C4C  X    X    N2  2400.0  0    0.000
IMPRoper    C2C  X    X    ON  2400.0  0    0.000
!infer
IMPRoper    C1R  C2C  C6C  N1C 2400.0  0    0.000
IMPRoper    C1D  C2C  C6C  N1C 2400.0  0    0.000
IMPRoper    N4C  NC   C5C  C4C 2400.0  0    0.000
IMPRoper    C2C  NC   C4C  C5C  250.0  0    0.000
IMPRoper    C5C  C6C  N1C  C2C  250.0  0    0.000
IMPRoper    H2   C4C  H2   N4C  250.0  0    0.000
IMPRoper    C5C  C4C  N4C  H2  2000.0  0    0.000

!uracil
IMPRoper    C4U  X    X    ON  2400.0  0    0.000
IMPRoper    C4U  X    X    N1U  250.0  0    0.000
IMPRoper    C6U  X    X    N3U  250.0  0    0.000
IMPRoper    C4U  X    X    N2  2400.0  0    0.000
IMPRoper    C2U  X    X    ON  2400.0  0    0.000
IMPRoper    C1R  C2U  C6U  N1U 2400.0  0    0.000
IMPRoper    C1D  C2U  C6U  N1U 2400.0  0    0.000
IMPRoper    ON   N3U  C5U  C4U  250.0  0    0.000
IMPRoper    C2U  N3U  C4U  C5U  250.0  0    0.000
IMPRoper    C5U  C6U  N1U  C2U  250.0  0    0.000
IMPRoper    H2   C4U  H2   ON   250.0  0    0.000
IMPRoper    HN   C2U  C4U  N3U  250.0  0    0.000

!thymidine
IMPRoper    C4T  X    X    ON  2400.0  0    0.000
IMPRoper    C4T  X    X    N1T  250.0  0    0.000
IMPRoper    C6T  X    X    N3T  250.0  0    0.000
IMPRoper    C4T  X    X    N2  2400.0  0    0.000
IMPRoper    C2T  X    X    ON  2400.0  0    0.000
IMPRoper    C1R  C2T  C6T  N1T 2400.0  0    0.000
IMPRoper    C1D  C2T  C6T  N1T 2400.0  0    0.000
IMPRoper    ON   N3T  C5T  C4T  250.0  0    0.000
IMPRoper    C2T  N3T  C4T  C5T  250.0  0    0.000
IMPRoper    C5T  C6T  N1T  C2T  250.0  0    0.000
IMPRoper    H2   C4T  H2   ON   250.0  0    0.000
IMPRoper    CC3E C4T  C6T  C5T  250.0  0    0.000

!infer
IMPRoper    HN   C2T  C4T  N3T  250.0  0    0.000

! The ring-spanning impropers have been left out.
!adenine
IMPRoper    N2A  N3A  NC   C2A  250.0  0    0.000
IMPRoper    H2   C2A  H2   N2A  250.0  0    0.000
IMPRoper    C4A  C5A  N7A  C8A  250.0  0    0.000
IMPRoper    C5A  C4A  N9A  C8A  250.0  0    0.000
IMPRoper    C4A  X    X    NC   250.0  0    0.000
IMPRoper    C2A  X    X    N9A  250.0  0    0.000
IMPRoper    C2A  X    X    C5A  250.0  0    0.000
IMPRoper    C6A  C5A  C4A  N3A  250.0  0    0.000
IMPRoper    C5A  X    X    N9A  250.0  0    0.000
IMPRoper    C6A  X    X    N6A 2400.0  0    0.000
IMPRoper    H2   X    X    N6A  250.0  0    0.000

!infer
IMPRoper    C1R  C4A  C8A  N9A 2400.0  0    0.000
IMPRoper    C1D  C4A  C8A  N9A 2400.0  0    0.000
IMPRoper    N9A  C4A  C5A  N7A  250.0  0    0.000
IMPRoper    N7A  C8A  N9A  C4A  250.0  0    0.000
IMPRoper    N3A  C2A  NC   C6A  250.0  0    0.000
IMPRoper    C5A  C6A  N6A  H2  2000.0  0    0.000

! The ring-spanning impropers have been left out.
!guanine
IMPRoper    C4G  C5G  N7G  C8G  250.0  0    0.000
IMPRoper    C5G  C4G  N9G  C8G  250.0  0    0.000
IMPRoper    C4G  X    X    NNA  250.0  0    0.000
IMPRoper    C2G  X    X    N9G  250.0  0    0.000
IMPRoper    C2G  X    X    C5G  250.0  0    0.000
IMPRoper    C6G  C5G  C4G  N3G  250.0  0    0.000
IMPRoper    C5G  X    X    N9G  250.0  0    0.000
IMPRoper    C6G  X    X    O6G 2400.0  0    0.000
IMPRoper    C2G  X    X    N2G 2400.0  0    0.000

!infer
IMPRoper    C1R  C4G  C8G  N9G 2400.0  0    0.000
IMPRoper    C1D  C4G  C8G  N9G 2400.0  0    0.000
IMPRoper    N9G  C4G  C5G  N7G  250.0  0    0.000
IMPRoper    N7G  C8G  N9G  C4G  250.0  0    0.000
IMPRoper    N3G  C2G  NNA  C6G  250.0  0    0.000
IMPRoper    H2   H2   C2G  N2G  250.0  0    0.000
IMPRoper    HN   C2G  C6G  NNA 2000.0  0    0.000
IMPRoper    N3G  C2G  N2G  H2  2000.0  0    0.000

!                   Lennard-Jones parameters
!                                       ------1-4-------
!                  epsilon   sigma       epsilon   sigma
!                 (Kcal/mol)   (A)      (Kcal/mol) (A)
! Taken from Rossky Karplus and Rahman BIOPOLY (1979)
! 0.05 ADDED TO RADII TO IMPRoperOVE ON NUCL.ACID STACKING/LN
!
!                  eps     sigma       eps(1:4) sigma(1:4)
NONBonded  C5R     0.0900   3.2970      0.0900   3.2970
NONBonded  C1R     0.0900   3.2970      0.0900   3.2970
NONBonded  C2R     0.0900   3.2970      0.0900   3.2970
NONBonded  C3R     0.0900   3.2970      0.0900   3.2970
NONBonded  C4R     0.0900   3.2970      0.0900   3.2970

NONBonded  C5D     0.0900   3.2970      0.0900   3.2970  !DNA
NONBonded  C1D     0.0900   3.2970      0.0900   3.2970
NONBonded  C2D     0.0900   3.2970      0.0900   3.2970
NONBonded  C3D     0.0900   3.2970      0.0900   3.2970
NONBonded  C4D     0.0900   3.2970      0.0900   3.2970

NONBonded  HN      0.0045   2.6160      0.0045   2.6160
NONBonded  H2      0.0045   1.6040      0.0045   1.6040
NONBonded  H       0.0045   2.6160      0.0045   2.6160 
!
! give it the same as th Hn from RKR
NONBonded  HO      0.0045   1.6040      0.0045   1.6040 

!
! THIS STILL IS AN EXTENDED ATOM
NONBonded  O3R      0.2304   2.7290      0.2304   2.7290
NONBonded  O4R      0.2304   2.7290      0.2304   2.7290
NONBonded  O4D      0.2304   2.7290      0.2304   2.7290
NONBonded  O5R      0.2304   2.7290      0.2304   2.7290
NONBonded  O1P      0.2304   2.7290      0.2304   2.7290
NONBonded  O2P      0.2304   2.7290      0.2304   2.7290
NONBonded  P        0.5849   3.3854      0.5849   3.3854

!bases
NONBonded  CN      0.0900   3.2970      0.0900   3.2970
NONBonded  C2      0.0900   3.2970      0.0900   3.2970
NONBonded  C3      0.0900   3.2970      0.0900   3.2970
NONBonded  CB      0.0900   3.2970      0.0900   3.2970
NONBonded  CE      0.0900   3.2970      0.0900   3.2970
NONBonded  CH      0.0900   3.2970      0.0900   3.2970

NONBonded  N2      0.1600   2.8591      0.1600   2.8591
NONBonded  N3U     0.1600   2.8591      0.1600   2.8591
NONBonded  N3T     0.1600   2.8591      0.1600   2.8591
NONBonded  NNA     0.1600   2.8591      0.1600   2.8591
NONBonded  NB      0.1600   2.8591      0.1600   2.8591
NONBonded  NC      0.1600   2.8591      0.1600   2.8591

NONBonded  NH2E    0.1600   3.0291      0.1600   3.0291
NONBonded  NS      0.1600   2.8591      0.1600   2.8591
NONBonded  N1T     0.1600   2.8591      0.1600   2.8591
NONBonded  N1C     0.1600   2.8591      0.1600   2.8591
NONBonded  N9A     0.1600   2.8591      0.1600   2.8591
NONBonded  N9G     0.1600   2.8591      0.1600   2.8591
NONBonded  N1U     0.1600   2.8591      0.1600   2.8591
NONBonded  ON      0.2304   2.7290      0.2304   2.7290
NONBonded  O2R     0.2304   2.7290      0.2304   2.7290
NONBonded  OH      0.2304   2.5508      0.2304   2.5508
NONBonded  SD      0.3515   2.6727      0.3515   2.6727  ! G U E S S
NONBonded  O2      0.2304   2.7290      0.2304   2.7290 

! NEW
NONBonded  C6C      0.0900   3.2970      0.0900   3.2970
NONBonded  C5C      0.0900   3.2970      0.0900   3.2970
NONBonded  C4C      0.0900   3.2970      0.0900   3.2970
NONBonded  C2C      0.0900   3.2970      0.0900   3.2970
NONBonded  C6U      0.0900   3.2970      0.0900   3.2970
NONBonded  C5U      0.0900   3.2970      0.0900   3.2970
NONBonded  C4U      0.0900   3.2970      0.0900   3.2970
NONBonded  C2U      0.0900   3.2970      0.0900   3.2970
NONBonded  C8A      0.0900   3.2970      0.0900   3.2970
NONBonded  C6A      0.0900   3.2970      0.0900   3.2970
NONBonded  C5A      0.0900   3.2970      0.0900   3.2970
NONBonded  C4A      0.0900   3.2970      0.0900   3.2970
NONBonded  C2A      0.0900   3.2970      0.0900   3.2970
NONBonded  C8G      0.0900   3.2970      0.0900   3.2970
NONBonded  C6G      0.0900   3.2970      0.0900   3.2970
NONBonded  C5G      0.0900   3.2970      0.0900   3.2970
NONBonded  C4G      0.0900   3.2970      0.0900   3.2970
NONBonded  C2G      0.0900   3.2970      0.0900   3.2970
NONBonded  C6T      0.0900   3.2970      0.0900   3.2970
NONBonded  C5T      0.0900   3.2970      0.0900   3.2970
NONBonded  C4T      0.0900   3.2970      0.0900   3.2970
NONBonded  C2T      0.0900   3.2970      0.0900   3.2970
NONBonded  N4C      0.1600   2.8591      0.1600   2.8591
NONBonded  O4U      0.2304   2.7290      0.2304   2.7290
NONBonded  N7G      0.1600   2.8591      0.1600   2.8591
NONBonded  N3G      0.1600   2.8591      0.1600   2.8591
NONBonded  N2G      0.1600   2.8591      0.1600   2.8591
NONBonded  N3A      0.1600   2.8591      0.1600   2.8591
NONBonded  N7A      0.1600   2.8591      0.1600   2.8591
NONBonded  N6A      0.1600   2.8591      0.1600   2.8591
NONBonded  O6G      0.2304   2.7290      0.2304   2.7290
NONBonded  CC3E     0.0900   3.2970      0.0900   3.2970
NONBonded  N2A      0.1600   2.8591      0.1600   2.8591

! special solute-solute hydrogen bonding potential parameters
AEXP 4
REXP 6 

HAEX 4 

AAEX 2
! "all" possible combinations of HB-pairs in nucleic acids:
!  WELL DEPTHS DEEPENED BY 0.5 KCAL TO IMPROVE BASEPAIR ENERGIES /LN
!  AND DISTANCES INCREASED BY 0.05
!                   Emin      Rmin
!                (Kcal/mol)   (A)
hbond  N*   O*      -14.0       2.95
hbond  N*   N*      -14.5       3.05
hbond  O*   O*      -15.75      2.80
hbond  O*   N*      -15.50      2.90

! the following NBFIXes are for DNA-DNA hydrogen bonding 

! terms
!                                         ------1-4------
!                   A           B           A          B
!           [Kcal/(mol A^12)] [Kcal/(mol A^6)]
!
nbfix  HO   ON      0.05       0.1      0.05       0.1
nbfix  HO   O3R     0.05       0.1      0.05       0.1
nbfix  HO   O5R     0.05       0.1      0.05       0.1
nbfix  HO   OH      0.05       0.1      0.05       0.1
nbfix  HO   O2R     0.05       0.1      0.05       0.1
nbfix  HO   NC      0.05       0.1      0.05       0.1

 
nbfix  H    ON       0.05       0.1      0.05       0.1
nbfix  H    O2       0.05       0.1      0.05       0.1
nbfix  H    O5R      0.05       0.1      0.05       0.1
nbfix  H    O4R      0.05       0.1      0.05       0.1
nbfix  H    O4D      0.05       0.1      0.05       0.1
nbfix  H    O3R      0.05       0.1      0.05       0.1
nbfix  H    O2R      0.05       0.1      0.05       0.1
nbfix  H    OH       0.05       0.1      0.05       0.1
nbfix  H    N7A      0.05       0.1      0.05       0.1
nbfix  H    N7G      0.05       0.1      0.05       0.1
nbfix  H    N3A      0.05       0.1      0.05       0.1
nbfix  H    N3G      0.05       0.1      0.05       0.1


nbfix  HN   ON      0.05       0.1      0.05       0.1
nbfix  HN   O2R     0.05       0.1      0.05       0.1
nbfix  HN   OH      0.05       0.1      0.05       0.1
nbfix  HN   NC      0.05       0.1      0.05       0.1

nbfix  H2   ON      0.05       0.1      0.05       0.1
nbfix  H2   O2R     0.05       0.1      0.05       0.1
nbfix  H2   OH      0.05       0.1      0.05       0.1

nbfix  H2   NC      0.05       0.1      0.05       0.1

set echo=off end
!RNA TOPOLOGY FILE 'FRAMEWORK' FROM TOPALLHDG.DNA AND ATOM NAMES
!  FROM DNA-RNA.PARAM
!INCLUDES ALL NONEXCHANGEABLE HYDROGENS AND TERMS FOR BOND, ANGLE, AND
!IMPROPERS. NONEXCHANGEABLE HYDROGEN CHARGES WERE ASSIGNED 0.035. 
!CARBON CHARGES WERE REDUCED 0.035 FOR EACH ATTACHED HYDROGEN.
!CREATED 2/24/96-- JASON P. RIFE AND PETER B. MOORE
! DNA-RNA-ALLATOM.TOP

!set echo=false end

AUTOGENERATE  ANGLES=TRUE  END
{*==========================*}

{* DNA/RNA default masses *}

MASS   P     30.97400! phosphorus
MASS   O1P   15.99940! O in phosphate
MASS   O2P   15.99940! O in phosphate
MASS   O5R   15.99940! ester -P-O-C-
MASS   C5R   12.011! corresp. to CH2E
MASS   C4R   12.011! corresp. to CH1E
MASS   C3R   12.011! corresp. to CH1E
MASS   C2R   12.011! corresp. to CH1E
MASS   C1R   12.011! corresp. to CH1E
MASS   O4R   15.99940! ester -P-O-C-
MASS   O3R   15.99940! ester -P-O-C-
MASS   O2R   15.99940! ester -P-O-C-
MASS   OH    15.99940! corresp. to OH1

!DEOXY SUGAR
MASS   C5D   14.02700! corresp. to CH2E
MASS   C4D   13.01900! corresp. to CH1E
MASS   C3D   13.01900! corresp. to CH1E
MASS   C2D   13.01900! corresp. to CH1E
MASS   C1D   13.01900! corresp. to CH1E
MASS   O4D   15.99940! ester -P-O-C-
MASS   O5D   15.99940! 
MASS   O3D   15.99940!  

! Insert Bases
! Generic

MASS   N2    14.00670! nitrogen in -NH2
MASS   NNA   14.00670! corresp. to NH1
MASS   ON    15.99940! corresp. to O
MASS   NC    14.00670! corresp. to NR
MASS   NS    14.00670! nitrogen in ring >N-

! Insert 4 Bases
!  GUA
MASS   N9G    14.00670! nitrogen in ring >N-
MASS   C2G    12.011! (prev CE)
MASS   N3G    14.00670! (prev NC)
MASS   C4G    12.01100! (prev CB)
MASS   C5G    12.01100! (prev CB)
MASS   C6G    12.01100! (prev CN)
MASS   N7G    14.00670! (prev NB)
MASS   C8G    12.011! (prev CE)
MASS   O6G    15.99940! (prev CE)
MASS   N2G    14.00670! nitrogen in -NH2
!  ADE
MASS   N9A    14.00670! nitrogen in ring >N-
MASS   C2A    12.011! (prev CE)
MASS   N3A    14.00670! (prev NC)
MASS   C4A    12.01100! (prev CB)
MASS   C5A    12.01100! (prev CB)
MASS   C6A    12.01100! (prev CA)
MASS   N7A    14.00670! (prev NB)
MASS   C8A    12.011! (prev CE)
MASS   N6A    14.00670! nitrogen in -NH2

!  CYT
MASS   N1C    14.00670! nitrogen in ring >N-
MASS   C2C    12.01100! (prev CN)
MASS   C4C    12.01100! (prev CA)
MASS   C5C    12.011! (prev CF)
MASS   C6C    12.011! (prev CF)
MASS   N4C    14.00670! nitrogen in -NH2

!  THY
MASS   N1T    14.00670! nitrogen in ring >N-
MASS   N3T    14.00670! nitrogen in ring >N-
MASS   C2T    12.01100! (prev CN)
MASS   C4T    12.01100! (prev CN)
MASS   C5T    12.011! (prev CS)
MASS   C6T    12.011! (prev CF)
MASS   CC3E   12.01100! (prev CF)

! END

MASS   H      1.00800! non-exchangeable Hydrogens
MASS   HN     1.00800! corresp. to H
MASS   H2     1.00800! hydrogen in -NH2
MASS   HO     1.00800! hydroxy hydrogen

!  URI
MASS   N1U    14.00670! nitrogen in ring >N-
MASS   C2U    12.01100! (prev CN)
MASS   C4U    12.01100! (prev CA)
MASS   C5U    12.011! (prev CF)
MASS   C6U    12.011! (prev CF)
MASS   N3U    14.00670! 


RESIdue GUA
  GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END !JPR
  ATOM H5'' TYPE=H     CHARGE=0.035   END !JPR
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065  END
  ATOM H4'  TYPE=H     CHARGE=0.035   END !JPR
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.165   END !JPR
  ATOM H1'  TYPE=H     CHARGE=0.035   END !JPR

! Insert Base
 GROUp
  ATOM N9   TYPE=N9G   CHARGE=-0.19   END
  ATOM C4   TYPE=C4G   CHARGE=0.19    EXCLusion=( N1 )   END
 GROUp
  ATOM N3   TYPE=N3G   CHARGE=-0.35   EXCLusion=( C6 )   END    
  ATOM C2   TYPE=C2G   CHARGE=0.35    EXCLusion=( C5 )   END    
 GROUp
  ATOM N2   TYPE=N2G   CHARGE=-0.42   END    
  ATOM H21  TYPE=H2    CHARGE=0.21    END    
  ATOM H22  TYPE=H2    CHARGE=0.21    END    
 GROUp
  ATOM N1   TYPE=NNA   CHARGE=-0.26   END    
  ATOM H1   TYPE=HN    CHARGE=0.26    END    
 GROUp
  ATOM C6   TYPE=C6G   CHARGE=0.30    END    
  ATOM O6   TYPE=O6G   CHARGE=-0.30   END    
 GROUp
  ATOM C5   TYPE=C5G   CHARGE=0.02    END
  ATOM N7   TYPE=N7G   CHARGE=-0.25   END
  ATOM C8   TYPE=C8G   CHARGE=0.145   END 
  ATOM H8   TYPE=H     CHARGE=0.035   END 

!

 GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115   END
  ATOM H2'  TYPE=H     CHARGE=0.035   END  
  ATOM O2'  TYPE=O2R   CHARGE=-0.40   END    
  ATOM HO2' TYPE=HO    CHARGE=0.25    END 
 GROUP
  ATOM C3'  TYPE=C3R    CHARGE=-0.035 END
  ATOM H3'  TYPE=H      CHARGE=0.035  END 
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END

 BOND P    O1P         BOND P    O2P           BOND P    O5'    

 BOND O5'  C5'         BOND C5'  C4'           BOND C4'  O4'
 BOND C4'  C3'         BOND O4'  C1'           BOND C1'  N9
 BOND C1'  C2'         BOND N9   C4            BOND N9   C8
 BOND C4   N3          BOND C4   C5            BOND N3   C2
 BOND C2   N2          BOND C2   N1            BOND N2   H21 

 BOND N2   H22         BOND N1   H1            BOND N1   C6
 BOND C6   O6          BOND C6   C5            BOND C5   N7
 BOND N7   C8          BOND C2'  C3'           BOND C3'  O3'
 BOND C2'  O2'         BOND C8   H8
 
 BOND O2'  HO2' 
 BOND C5'  H5'         BOND C5'  H5''          BOND C4'  H4'
 BOND C3'  H3'         BOND C2'  H2'           BOND C1'  H1'
{
 DIHEdral  P    O5'  C5'  C4'        DIHEdral  O5'  C5'  C4'  O4'
 DIHEdral  O5'  C5'  C4'  C3' 
}{
 DIHEdral  C3'  C4'  O4'  C1'
 DIHEdral  C4'  O4'  C1'  C2'        DIHEdral  O4'  C1'  C2'  C3' 

 DIHEdral  C1'  C2'  C3'  C4'        DIHEdral  O4'  C4'  C3'  O3'
 DIHEdral  C5'  C4'  C3'  C2'        DIHEdral  O3'  C3'  C2'  O2'
 DIHEdral  O4'  C1'  N9   C4         
 DIHEdral  C3'  C2'  O2'  H2'
}
 
 ! 
 IMPRoper N3   C2   N2   H21         IMPRoper C1'  C4   C8   N9
 IMPRoper N9   C4   C5   N7          IMPRoper C4   C5   N7   C8
 IMPRoper C5   N7   C8   N9          IMPRoper N7   C8   N9   C4
 IMPRoper C8   N9   C4   C5          IMPRoper N2   N3   N1   C2  

 IMPRoper H1   C2   C6   N1          IMPRoper O6   N1   C5   C6
 IMPRoper C4   N3   C2   N1          IMPRoper N3   C2   N1   C6
 IMPRoper C2   N1   C6   C5          IMPRoper N1   C6   C5   C4  

 IMPRoper C6   C5   C4   N3          IMPRoper C5   C4   N3   C2
 IMPRoper H22  H21  C2   N2          
 IMPRoper H8   N7   N9   C8 

!IMPRoper to keep the two purine rings parallel:
 IMPRoper C8   C4   C5   N1          IMPRoper C8   C5   C4   C2
 IMPRoper N3   C4   C5   N7          IMPRoper C6   C5   C4   N9

!RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N9  !C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H21  N2         
 DONOr H22  N2            
 DONOr H1   N1   
 DONOr H2'  O2'

 ACCEptor O6   C6      
 ACCEptor N3  " "         
 ACCEptor O1P  P
 ACCEptor O2P  P
 ACCEptor O2'  " " 

 END {GUA}

! ---------------------------------------------------------------------

! ---------------------------------------------------------------------

RESIdue ADE
GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END 
  ATOM H5'' TYPE=H     CHARGE=0.035   END 
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065   END
  ATOM H4'  TYPE=H     CHARGE=0.035   END 
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.165   END 
  ATOM H1'  TYPE=H     CHARGE=0.035   END 

! Insert Base
 GROUp
  ATOM N9    TYPE=N9A   CHARGE=-0.19   END
  ATOM C4    TYPE=C4A   CHARGE=0.19    EXCLusion=( N1 )  END
 GROUp
  ATOM N3    TYPE=N3A   CHARGE=-0.26   EXCLusion=( C6 )  END     
  ATOM C2    TYPE=C2A   CHARGE=0.225   EXCLusion=( C5 )  END      
  ATOM H2    TYPE=H     CHARGE=0.035   END 
 GROUp
  ATOM N1    TYPE=NC    CHARGE=-0.28   END     
  ATOM C6    TYPE=C6A   CHARGE=0.28    END     
 GROUp
  ATOM N6    TYPE=N6A   CHARGE=-0.42   END     
  ATOM H61   TYPE=H2    CHARGE=0.21    END     
  ATOM H62   TYPE=H2    CHARGE=0.21    END     
 GROUp
  ATOM C5    TYPE=C5A   CHARGE=0.02    END
  ATOM N7    TYPE=N7A   CHARGE=-0.25   END
  ATOM C8    TYPE=C8A   CHARGE=0.195   END 
  ATOM H8    TYPE=H     CHARGE=0.035   END 
! END

 GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115   END
  ATOM H2'  TYPE=H     CHARGE=0.035   END 
  ATOM O2'  TYPE=O2R   CHARGE=-0.40   END    
  ATOM HO2' TYPE=HO    CHARGE=0.25    END 
 GROUP
  ATOM C3'  TYPE=C3R   CHARGE=-0.035  END
  ATOM H3'  TYPE=H     CHARGE=0.035   END 
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END

 BOND P    O1P              BOND P    O2P              BOND P    O5'
 BOND O5'  C5'              BOND C5'  C4'              BOND C4'  O4'
 BOND C4'  C3'              BOND O4'  C1'              BOND C1'  N9
 BOND C1'  C2'              BOND N9   C4               BOND N9   C8
 BOND C4   N3               BOND C4   C5               BOND N3   C2
 BOND C2   N1               BOND N1   C6               BOND C6   N6  

 BOND N6   H61              BOND N6   H62              BOND C6   C5   

 BOND C5   N7               BOND N7   C8               BOND C2'  C3'
 BOND C2'  O2'              BOND C3'  O3'
 BOND C8   H8               BOND C2   H2 
 BOND O2'  HO2'
 BOND C5'  H5'         BOND C5'  H5''          BOND C4'  H4'
 BOND C3'  H3'         BOND C2'  H2'           BOND C1'  H1'
{
 DIHEdral P   O5'  C5'  C4'              DIHEdral O5'  C5'  C4'  O4'
 DIHEdral O5'  C5'  C4'  C3'  
}{
 DIHEdral C3'  C4'  O4'  C1'
 DIHEdral C4'  O4'  C1'  C2'             DIHEdral O4'  C1'  C2'  C3' 

 DIHEdral C1'  C2'  C3'  C4'             DIHEdral O4'  C4'  C3'  O3'
 DIHEdral C5'  C4'  C3'  C2'             DIHEdral O2'  C2'  C3'  O3'
 DIHEdral O4'  C1'  N9   C4              
 DIHEdral C3'  C2'  O2'  H2'
 }
 
 !
 IMPRoper C5   C6   N6   H61             IMPRoper C1'  C4   C8   N9
 IMPRoper N9   C4   C5   N7              IMPRoper C4   C5   N7   C8  
 IMPRoper C5   N7   C8   N9              IMPRoper N7   C8   N9   C4 
 IMPRoper C8   N9   C4   C5              IMPRoper N6   N1   C5   C6  
 IMPRoper H62  C6   H61  N6              IMPRoper C4   N3   C2   N1      
 IMPRoper N3   C2   N1   C6              IMPRoper C2   N1   C6   C5
 IMPRoper N1   C6   C5   C4              IMPRoper C6   C5   C4   N3
 IMPRoper C5   C4   N3   C2              
 IMPRoper H2   N1   N3   C2              IMPRoper H8   N7   N9   C8
 ! IMPRoper to keep the two purine rings parallel:
 IMPRoper C8   C4   C5   N1              IMPRoper C8   C5   C4   C2
 IMPRoper N3   C4   C5   N7              IMPRoper C6   C5   C4   N9
 

!RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N9  !C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H61  N6             
 DONOr H62  N6             
 DONOr H2'  O2'

 ACCEptor N3 " "           
 ACCEptor N1 " "
 ACCEptor O1P  P           
 ACCEptor O2P  P
 ACCEptor O2' " "

 END {ADE}

! ---------------------------------------------------------------------

! ---------------------------------------------------------------------

RESIdue CYT
  GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END 
  ATOM H5'' TYPE=H     CHARGE=0.035   END 
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065   END
  ATOM H4'  TYPE=H     CHARGE=0.035   END 
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.165   END 
  ATOM H1'  TYPE=H     CHARGE=0.035   END 

! Insert Base

 GROUp
  ATOM N1    TYPE=N1C   CHARGE=-0.19  EXCLUSION=( C4 )  END
  ATOM C6    TYPE=C6C   CHARGE=0.155  EXCLUSION=( N3 )  END 
  ATOM H6    TYPE=H     CHARGE=0.035  END 
 GROUp
  ATOM C2    TYPE=C2C   CHARGE=0.30    EXCLUSION=( C5 )  END     
  ATOM O2    TYPE=ON    CHARGE=-0.30   END                       
 GROUp
  ATOM N3    TYPE=NC    CHARGE=-0.28   END     
  ATOM C4    TYPE=C4C   CHARGE=0.28    END     
 GROUp
  ATOM N4    TYPE=N4C   CHARGE=-0.42   END     
  ATOM H41   TYPE=H2    CHARGE=0.21    END     
  ATOM H42   TYPE=H2    CHARGE=0.21    END     
 GROUp
  ATOM C5    TYPE=C5C   CHARGE=-0.035  END !CHRG 
  ATOM H5    TYPE=H     CHARGE=0.035   END 
 GROUp

! END


GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115   END
  ATOM H2'  TYPE=H     CHARGE=0.035   END 
  ATOM O2'  TYPE=O2R   CHARGE=-0.40   END    
  ATOM HO2' TYPE=HO    CHARGE=0.25    END 
 GROUP
  ATOM C3'  TYPE=C3R   CHARGE=-0.035  END
  ATOM H3'  TYPE=H     CHARGE=0.035   END
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END

 BOND P    O1P             BOND P    O2P             BOND P    O5'
 BOND O5'  C5'             BOND C5'  C4'             BOND C4'  O4'
 BOND C4'  C3'             BOND O4'  C1'             BOND C1'  N1
 BOND C1'  C2'             BOND N1   C2              BOND N1   C6
                           BOND C2   N3              BOND N3   C4
 BOND C4   N4              BOND N4   H41             BOND N4   H42 
 BOND C2   O2
 BOND C4   C5              BOND C5   C6              BOND C2'  C3'
 BOND C3'  O3'             BOND C2'  O2'             
 BOND C6   H6              BOND C5   H5
 BOND O2'  HO2' 
 BOND C5'  H5'         BOND C5'  H5''          BOND C4'  H4'
 BOND C3'  H3'         BOND C2'  H2'           BOND C1'  H1'

{
 DIHEdral P    O5'  C5'  C4'             DIHEdral O5'  C5'  C4'  O4'
 DIHEdral O5'  C5'  C4'  C3'  
}{
 DIHEdral C3'  C4'  O4'  C1'
 DIHEdral C4'  O4'  C1'  C2'             DIHEdral O4'  C1'  C2'  C3' 

 DIHEdral C1'  C2'  C3'  C4'             DIHEdral O4'  C4'  C3'  O3'
 DIHEdral C5'  C4'  C3'  C2'             DIHEdral O2'  C2'  C3'  O3'
 DIHEdral O4'  C1'  N1   C2              
 DIHEdral C3'  C2'  O2'  H2'
 
 ! New dihedrals
 DIHEdral  C5'  C4'  C3'  O3'            DIHEdral  C4'  O4'  C1'  N1
}

 IMPRoper C5   C4   N4   H41               IMPRoper C1'  C2   C6   N1
 IMPRoper O2   N1   N3   C2                IMPRoper N4   N3   C5   C4
 IMPRoper N1   C2   N3   C4                IMPRoper C2   N3   C4   C5
 IMPRoper N3   C4   C5   C6                IMPRoper C4   C5   C6   N1
 IMPRoper C5   C6   N1   C2                IMPRoper C6   N1   C2   N3
 IMPRoper H42  C4   H41  N4               
 IMPRoper H5  C4  C6   C5                  IMPRoper  H6   N1   C5   C6
 
!RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N1  !C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H42  N4              
 DONOr H2'  O2'                
 DONOr H41  N4

 ACCEptor O2   C2           
 ACCEptor N3   " "
 ACCEptor O1P  P            
 ACCEptor O2P  P
 ACCEptor O2' " "  ! added, ATB, 8-9-84

 END {CYT}

!------------------------------------------------------------------

! ---------------------------------------------------------------------

! ---------------------------------------------------------------------

RESIdue THY
 GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END
  ATOM H5''  TYPE=H     CHARGE=0.035  END
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065   END
  ATOM H4'  TYPE=H     CHARGE=0.035   END
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.20    END
  ATOM H1'  TYPE=H     CHARGE=0.165   END

! Insert Base
 GROUp
  ATOM N1    TYPE=N1T   CHARGE=-0.19  EXCLUSION=( C4 )  END
  ATOM C6    TYPE=C6T   CHARGE=0.155  EXCLUSION=( N3 )  END
  ATOM H6    TYPE=H     CHARGE=0.035  END
 GROUp
  ATOM C2    TYPE=C2T   CHARGE=0.35   EXCLUSION=( C5 )  END     
  ATOM O2    TYPE=ON    CHARGE=-0.35  END                       
 GROUp
  ATOM N3    TYPE=N3T   CHARGE=-0.26  END      
  ATOM H3    TYPE=HN    CHARGE=0.26   END      
 GROUp
  ATOM C4    TYPE=C4T   CHARGE=0.30   END      
  ATOM O4    TYPE=ON    CHARGE=-0.30  END      
 GROUp
  ATOM C5    TYPE=C5T   CHARGE=-0.035 END
  ATOM C7    TYPE=CC3E  CHARGE=-0.070 END ! name per IUPAC-IUB recomm.
  ATOM H71   TYPE=H     CHARGE=0.035  END ! name per IUPAC-IUB recomm.
  ATOM H72   TYPE=H     CHARGE=0.035  END ! name per IUPAC-IUB recomm.
  ATOM H73   TYPE=H     CHARGE=0.035  END ! name per IUPAC-IUB recomm.

 GROUp

! END 


 GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115    END
  ATOM H2'  TYPE=H     CHARGE=0.035    END    
  ATOM O2'  TYPE=O2R   CHARGE=-0.40    END    
  ATOM HO2' TYPE=HO    CHARGE=0.25     END    
 GROUP
  ATOM C3'  TYPE=C3R   CHARGE=-0.035   END
  ATOM H3'  TYPE=H     CHARGE=0.035    END
 
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END


 BOND P    O1P               BOND P    O2P               BOND P    O5'
 BOND O5'  C5'               BOND C5'  C4'               BOND C4'  O4'
 BOND C4'  C3'               BOND O4'  C1'               BOND C1'  N1
 BOND C1'  C2'               BOND N1   C2                BOND N1   C6
 BOND C2   O2                BOND C2   N3                BOND N3   H3
 BOND N3   C4                BOND C4   O4                BOND C4   C5
 BOND C5   C7                BOND C5   C6                BOND C2'  C3'
 BOND C3'  O3'               BOND C2'  O2'               BOND O2'  H2'
 BOND O2'  HO2'       BOND C5'  H5'               BOND C5'  H5'' 
 BOND C3'  H3'       BOND C2'  H2'               BOND C1'  H1' 
 BOND C4'  H4'               BOND C7   H71               BOND C7   H72
 BOND C7   H73               BOND C6   H6
{
 DIHEdral P   O5'  C5'  C4'              DIHEdral O5'  C5'  C4'  O4'
 DIHEdral O5'  C5'  C4'  C3'  
}{
 DIHEdral C3'  C4'  O4'  C1'
 DIHEdral C4'  O4'  C1'  C2'             DIHEdral O4'  C1'  C2'  C3' 

 DIHEdral C1'  C2'  C3'  C4'             DIHEdral O4'  C4'  C3'  O3'
 DIHEdral C5'  C4'  C3'  C2'             DIHEdral O2'  C2'  C3'  O3'
 DIHEdral O4'  C1'  N1   C2              
 DIHEdral C3'  C2'  O2'  H2'
 

 ! New dihedrals
 DIHEdral  C5'  C4'  C3'  O3'            DIHEdral  C4'  O4'  C1'  N1
}

 IMPRoper O4   N3   C5   C4                IMPRoper C1'  C2   C6   N1
 IMPRoper O2   N1   N3   C2                IMPRoper C4   C5   C6   N1
 IMPRoper N1   C2   N3   C4                IMPRoper C2   N3   C4   C5
                                           IMPRoper N3   C4   C5   C6
 IMPRoper C5   C6   N1   C2                IMPRoper C6   N1   C2   N3
 IMPRoper H3   C2   C4   N3               
 IMPRoper C7   C4   C6   C5                IMPRoper  H6   N1   C5   C6
 
!RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N1 ! C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H3   N3                
 DONOr HO2' O2'

 ACCEptor O2   C2              
 ACCEptor O4   C4
 ACCEptor O1P  P               
 ACCEptor O2P  P       
 ACCEptor O2'  " " ! added, ATB, 8-9-84

 END {THY}


!------------------------------------------------------------------

RESIdue URI
GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END 
  ATOM H5'' TYPE=H     CHARGE=0.035   END 
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065   END
  ATOM H4'  TYPE=H     CHARGE=0.035   END 
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.165   END 
  ATOM H1'  TYPE=H     CHARGE=0.035   END 


 GROUp
  ATOM N1    TYPE=N1U   CHARGE=-0.19  EXCLUSION=( C4 )  END
  ATOM C6    TYPE=C6U   CHARGE=0.155  EXCLUSION=( N3 )  END 
  ATOM H6    TYPE=H     CHARGE=0.035  END 
 GROUp
  ATOM C2    TYPE=C2U   CHARGE=0.30   EXCLUSION=( C5 )  END     
  ATOM O2    TYPE=ON    CHARGE=-0.30  END                      
 GROUp
  ATOM N3    TYPE=N3U   CHARGE=-0.28  END     
  ATOM H3    TYPE=HN    CHARGE=0.26   END      
 GROUp
  ATOM C4    TYPE=C4U   CHARGE=0.28   END     
  ATOM O4    TYPE=ON    CHARGE=-0.30  END       
 GROUp
  ATOM C5    TYPE=C5U   CHARGE=-0.035 END !JPR
  ATOM H5    TYPE=H     CHARGE=0.035  END !JPR

 GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115   END
  ATOM H2'  TYPE=H     CHARGE=0.035   END ! 
  ATOM O2'  TYPE=O2R   CHARGE=-0.40   END    
  ATOM HO2'   TYPE=HO    CHARGE=0.25  END 
 GROUP
  ATOM C3'  TYPE=C3R    CHARGE=-0.035 END
  ATOM H3'  TYPE=H     CHARGE=0.035   END 
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END

 BOND P    O1P                BOND P    O2P              BOND P    O5'
 BOND O5'  C5'                BOND C5'  C4'              BOND C4'  O4'
 BOND C4'  C3'                BOND O4'  C1'              BOND C1'  N1
 BOND C1'  C2'                BOND N1   C2               BOND N1   C6
 BOND C2   O2                 BOND C2   N3               BOND N3   H3
 BOND N3   C4                 BOND C4   O4               BOND C4   C5  

 BOND C5   C6                 BOND C2'  C3'              BOND C3'  O3'
 BOND C2'  O2'                
 BOND C5  H5                  BOND C6   H6
 
 BOND O2'  HO2' 
 BOND C5'  H5'         BOND C5'  H5''          BOND C4'  H4'
 BOND C3'  H3'         BOND C2'  H2'           BOND C1'  H1'
{
 DIHEdral P   O5'  C5'  C4'              DIHEdral O5'  C5'  C4'  O4'
 DIHEdral O5'  C5'  C4'  C3'  
}{
 DIHEdral C3'  C4'  O4'  C1'
 DIHEdral C4'  O4'  C1'  C2'             DIHEdral O4'  C1'  C2'  C3' 

 DIHEdral C1'  C2'  C3'  C4'             DIHEdral O4'  C4'  C3'  O3'
 DIHEdral C5'  C4'  C3'  C2'             DIHEdral O2'  C2'  C3'  O3'
 DIHEdral O4'  C1'  N1   C2              
 DIHEdral C3'  C2'  O2'  H2'

 DIHEdral P    O3'  C3'  C2'             DIHEdral P    O3'  C3'  C4'           
 ! New dihedrals
 DIHEdral  C5'  C4'  C3'  O3'            DIHEdral  C4'  O4'  C1'  N1
}
                                            IMPRoper C1'  C2   C6   N1
 IMPRoper O2   N1   N3   C2                 IMPRoper H3   C2   C4   N3
 IMPRoper O4   N3   C5   C4                 IMPRoper N1   C2   N3   C4
 IMPRoper C2   N3   C4   C5                 IMPRoper N3   C4   C5   C6
 IMPRoper C4   C5   C6   N1                 IMPRoper C5   C6   N1   C2
 IMPRoper C6   N1   C2   N3                 
 IMPRoper H5   C4   C6   C5                 IMPRoper H6   N1   C5   C6

 !GENERAL RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N1  !C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H3   N3                    
 DONOr H2'  O2'

 ACCEptor O2   C2                
 ACCEptor O4   C4
 ACCEptor O1P  P                 
 ACCEptor O2P  P
 ACCEptor O2' " " 

 

END {URI}

!------------------------------------------------------------------
!------------------------------------------------------------------
!note: O3' and O5' will remain O3R and O5R for DNA molecules
!this is consistent with values in parameter files

PRESidue DEOX    ! Patch to make DEOXYribose of the ribose
 DELETE ATOM O2'   END
 DELETE ATOM HO2'   END
GROUP
 MODIFY  ATOM C2'  TYPE=C2D   CHARGE=-0.07    END
 MODIFY  ATOM C5'  TYPE=C5D   CHARGE=-0.07    END
 MODIFY  ATOM C4'  TYPE=C4D   CHARGE=0.065    END
 MODIFY  ATOM O4'  TYPE=O4D   CHARGE=-0.30    END
 MODIFY  ATOM C1'  TYPE=C1D   CHARGE=0.165    END
 MODIFY  ATOM C3'  TYPE=C3D   CHARGE=-0.035   END
 ADD     ATOM H2'' TYPE=H     CHARGE=0.035    END
 
 ADD BOND   C2'  H2''
 ADD ANGLE  C1'  C2'  H2'
 ADD ANGLE  C3'  C2'  H2''
 ADD ANGLE  H2'  C2'  H2''
 ADD IMPRoper   H2'  C3'  H2'' C1'! C2' chirality term
END {DEOX}

!------------------------------------------------------------------
!------------------------------------------------------------------


PRESidue 5PHO           ! 5-terminus (with phosphate)
 !                      ! should be used as "FIRST  5PHO  TAIL + * END"
 GROUp                  ! i.e. to be patched to the first RNA residue
  ADD ATOM +H5T   TYPE=HO    CHARGE=0.15    END
  ADD ATOM +O5T   TYPE=OH    CHARGE=-0.15   END
        
  ADD BOND +H5T  +O5T
  ADD BOND +O5T  +P
  ADD ANGLe +H5T  +O5T  +P
  ADD ANGLe +O5'  +P  +O5T
  ADD ANGLe +O5T  +P  +O1P
  ADD ANGLe +O5T  +P  +O2P 

!  ADD DIHEdral +O5'  +P   +O5T   +H5T
!  ADD DIHEdral +C5'  +O5'  +P    +O5T
  ADD DONOr +H5T  +O5T
END {5PHO}

!------------------------------------------------------------------


PRESidue 3TER               ! 3-terminus (without phosphate)
                            ! should be used as "LAST 3TER  HEAD - * END"
 GROUp                      ! i.e. to be patched to the last RNA residue
  MODIFY ATOM -C3'    TYPE=C3R    CHARGE=0.15    END       
  MODIFY ATOM -O3'    TYPE=OH     CHARGE=-0.40   END       
  ADD ATOM -H3T  TYPE=HO     CHARGE=0.25        END       
 !
 ADD BOND -O3'  -H3T
 ADD ANGLe -C3'  -O3'  -H3T
! ADD DIHEdral -C4'  -C3'  -O3'  -H3T
 ADD DONOr -H3T  -O3'
END {3TER}

!------------------------------------------------------------------


PRESidue 5TER        ! 5-terminus (without phosphate)
 !                   ! should be used as "FIRST  5TER  TAIL + * END"
 GROUp               ! i.e. to be patched to the first RNA residue
  ADD ATOM +H5T  TYPE=HO    CHARGE=0.25    END      
  MODIFY ATOM +O5'  TYPE=OH  CHARGE=-0.40  END      
  MODIFY ATOM +C5'  TYPE=C5R  CHARGE=0.15  END      
  DELETE ATOM +P   END
  DELETE ATOM +O1P END
  DELETE ATOM +O2P END
 !
 ADD BOND +H5T   +O5'
 ADD ANGLe +H5T   +O5'  +C5'
! ADD DIHEdral +H5T   +O5'  +C5'  +C4'
 ADD DONOr +H5T   +O5'
END {5TER}

! ---------------------------------------------------------------------
!------------------------------------------------------------------

PRESidue NUC         ! patch for nucleic acid backbone
                     ! should be used as "LINK NUC  HEAD - *  TAIL + *  END"
                     ! i.e. it links the previous RNA residue (-) with
                     ! the current one (+)
 GROUp               

  MODIFY ATOM -O3' END   !
  MODIFY ATOM +P   END   !
  MODIFY ATOM +O1P END   ! this should correctly define the electrostatic 

  MODIFY ATOM +O2P END   ! group boundary 

  MODIFY ATOM +O5' END   !
 ADD BOND -O3' +P
 ADD ANGLE -C3' -O3' +P
 ADD ANGLE -O3' +P  +O1P
 ADD ANGLE -O3' +P  +O2P
 ADD ANGLE -O3' +P  +O5'
!ADD DIHEdral -O3' +P  +O5'  +C5'   

! ADD DIHEdral -C4' -C3' -O3'  +P
! ADD DIHEdral -C3' -O3' +P   +O5'  

END {NUC}

!------------------------------------------------------------------

!set echo=true end


!RNA TOPOLOGY FILE 'FRAMEWORK' FROM TOPALLHDG.DNA AND ATOM NAMES
!  FROM DNA-RNA.PARAM
!INCLUDES ALL NONEXCHANGEABLE HYDROGENS AND TERMS FOR BOND, ANGLE, AND
!IMPROPERS. NONEXCHANGEABLE HYDROGEN CHARGES WERE ASSIGNED 0.035. 
!CARBON CHARGES WERE REDUCED 0.035 FOR EACH ATTACHED HYDROGEN.
!CREATED 2/24/96-- JASON P. RIFE AND PETER B. MOORE
REMARK DNA-RNA-ALLATOM.TOP

set echo=false end

AUTOGENERATE  ANGLES=TRUE  END
{*==========================*}

{* DNA/RNA default masses *}

MASS   P     30.97400! phosphorus
MASS   O1P   15.99940! O in phosphate
MASS   O2P   15.99940! O in phosphate
MASS   O5R   15.99940! ester -P-O-C-
MASS   C5R   12.011! corresp. to CH2E
MASS   C4R   12.011! corresp. to CH1E
MASS   C3R   12.011! corresp. to CH1E
MASS   C2R   12.011! corresp. to CH1E
MASS   C1R   12.011! corresp. to CH1E
MASS   O4R   15.99940! ester -P-O-C-
MASS   O3R   15.99940! ester -P-O-C-
MASS   O2R   15.99940! ester -P-O-C-
MASS   OH    15.99940! corresp. to OH1

!DEOXY SUGAR
MASS   C5D   14.02700! corresp. to CH2E
MASS   C4D   13.01900! corresp. to CH1E
MASS   C3D   13.01900! corresp. to CH1E
MASS   C2D   13.01900! corresp. to CH1E
MASS   C1D   13.01900! corresp. to CH1E
MASS   O4D   15.99940! ester -P-O-C-
MASS   O5D   15.99940! 
MASS   O3D   15.99940!  

! Insert Bases
! Generic

MASS   N2    14.00670! nitrogen in -NH2
MASS   NNA   14.00670! corresp. to NH1
MASS   ON    15.99940! corresp. to O
MASS   NC    14.00670! corresp. to NR
MASS   NS    14.00670! nitrogen in ring >N-

! Insert 4 Bases
!  GUA
MASS   N9G    14.00670! nitrogen in ring >N-
MASS   C2G    12.011! (prev CE)
MASS   N3G    14.00670! (prev NC)
MASS   C4G    12.01100! (prev CB)
MASS   C5G    12.01100! (prev CB)
MASS   C6G    12.01100! (prev CN)
MASS   N7G    14.00670! (prev NB)
MASS   C8G    12.011! (prev CE)
MASS   O6G    15.99940! (prev CE)
MASS   N2G    14.00670! nitrogen in -NH2
!  ADE
MASS   N9A    14.00670! nitrogen in ring >N-
MASS   C2A    12.011! (prev CE)
MASS   N3A    14.00670! (prev NC)
MASS   C4A    12.01100! (prev CB)
MASS   C5A    12.01100! (prev CB)
MASS   C6A    12.01100! (prev CA)
MASS   N7A    14.00670! (prev NB)
MASS   C8A    12.011! (prev CE)
MASS   N6A    14.00670! nitrogen in -NH2

!  CYT
MASS   N1C    14.00670! nitrogen in ring >N-
MASS   C2C    12.01100! (prev CN)
MASS   C4C    12.01100! (prev CA)
MASS   C5C    12.011! (prev CF)
MASS   C6C    12.011! (prev CF)
MASS   N4C    14.00670! nitrogen in -NH2

!  THY
MASS   N1T    14.00670! nitrogen in ring >N-
MASS   N3T    14.00670! nitrogen in ring >N-
MASS   C2T    12.01100! (prev CN)
MASS   C4T    12.01100! (prev CN)
MASS   C5T    12.011! (prev CS)
MASS   C6T    12.011! (prev CF)
MASS   CC3E   12.01100! (prev CF)

! END

MASS   H      1.00800! non-exchangeable Hydrogens
MASS   HN     1.00800! corresp. to H
MASS   H2     1.00800! hydrogen in -NH2
MASS   HO     1.00800! hydroxy hydrogen

!  URI
MASS   N1U    14.00670! nitrogen in ring >N-
MASS   C2U    12.01100! (prev CN)
MASS   C4U    12.01100! (prev CA)
MASS   C5U    12.011! (prev CF)
MASS   C6U    12.011! (prev CF)
MASS   N3U    14.00670! 


RESIdue GUA
  GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END !JPR
  ATOM H5'' TYPE=H     CHARGE=0.035   END !JPR
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065  END
  ATOM H4'  TYPE=H     CHARGE=0.035   END !JPR
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.165   END !JPR
  ATOM H1'  TYPE=H     CHARGE=0.035   END !JPR

! Insert Base
 GROUp
  ATOM N9   TYPE=N9G   CHARGE=-0.19   END
  ATOM C4   TYPE=C4G   CHARGE=0.19    EXCLusion=( N1 )   END
 GROUp
  ATOM N3   TYPE=N3G   CHARGE=-0.35   EXCLusion=( C6 )   END    
  ATOM C2   TYPE=C2G   CHARGE=0.35    EXCLusion=( C5 )   END    
 GROUp
  ATOM N2   TYPE=N2G   CHARGE=-0.42   END    
  ATOM H21  TYPE=H2    CHARGE=0.21    END    
  ATOM H22  TYPE=H2    CHARGE=0.21    END    
 GROUp
  ATOM N1   TYPE=NNA   CHARGE=-0.26   END    
  ATOM H1   TYPE=HN    CHARGE=0.26    END    
 GROUp
  ATOM C6   TYPE=C6G   CHARGE=0.30    END    
  ATOM O6   TYPE=O6G   CHARGE=-0.30   END    
 GROUp
  ATOM C5   TYPE=C5G   CHARGE=0.02    END
  ATOM N7   TYPE=N7G   CHARGE=-0.25   END
  ATOM C8   TYPE=C8G   CHARGE=0.145   END 
  ATOM H8   TYPE=H     CHARGE=0.035   END 

!

 GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115   END
  ATOM H2'  TYPE=H     CHARGE=0.035   END  
  ATOM O2'  TYPE=O2R   CHARGE=-0.40   END    
  ATOM HO2' TYPE=HO    CHARGE=0.25    END 
 GROUP
  ATOM C3'  TYPE=C3R    CHARGE=-0.035 END
  ATOM H3'  TYPE=H      CHARGE=0.035  END 
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END

 BOND P    O1P         BOND P    O2P           BOND P    O5'    

 BOND O5'  C5'         BOND C5'  C4'           BOND C4'  O4'
 BOND C4'  C3'         BOND O4'  C1'           BOND C1'  N9
 BOND C1'  C2'         BOND N9   C4            BOND N9   C8
 BOND C4   N3          BOND C4   C5            BOND N3   C2
 BOND C2   N2          BOND C2   N1            BOND N2   H21 

 BOND N2   H22         BOND N1   H1            BOND N1   C6
 BOND C6   O6          BOND C6   C5            BOND C5   N7
 BOND N7   C8          BOND C2'  C3'           BOND C3'  O3'
 BOND C2'  O2'         BOND C8   H8
 
 BOND O2'  HO2' 
 BOND C5'  H5'         BOND C5'  H5''          BOND C4'  H4'
 BOND C3'  H3'         BOND C2'  H2'           BOND C1'  H1'

 DIHEdral  P    O5'  C5'  C4'        DIHEdral  O5'  C5'  C4'  O4'
 DIHEdral  O5'  C5'  C4'  C3' 

 DIHEdral  C3'  C4'  O4'  C1'
 DIHEdral  C4'  O4'  C1'  C2'        DIHEdral  O4'  C1'  C2'  C3' 

 DIHEdral  C1'  C2'  C3'  C4'        DIHEdral  O4'  C4'  C3'  O3'
 DIHEdral  C5'  C4'  C3'  C2'        DIHEdral  O3'  C3'  C2'  O2'
 DIHEdral  O4'  C1'  N9   C4         
 DIHEdral  C3'  C2'  O2'  H2'

 
 ! 
 IMPRoper N3   C2   N2   H21         IMPRoper C1'  C4   C8   N9
 IMPRoper N9   C4   C5   N7          IMPRoper C4   C5   N7   C8
 IMPRoper C5   N7   C8   N9          IMPRoper N7   C8   N9   C4
 IMPRoper C8   N9   C4   C5          IMPRoper N2   N3   N1   C2  

 IMPRoper H1   C2   C6   N1          IMPRoper O6   N1   C5   C6
 IMPRoper C4   N3   C2   N1          IMPRoper N3   C2   N1   C6
 IMPRoper C2   N1   C6   C5          IMPRoper N1   C6   C5   C4  

 IMPRoper C6   C5   C4   N3          IMPRoper C5   C4   N3   C2
 IMPRoper H22  H21  C2   N2          
 IMPRoper H8   N7   N9   C8 

!IMPRoper to keep the two purine rings parallel:
 IMPRoper C8   C4   C5   N1          IMPRoper C8   C5   C4   C2
 IMPRoper N3   C4   C5   N7          IMPRoper C6   C5   C4   N9

!RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N9  !C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H21  N2         
 DONOr H22  N2            
 DONOr H1   N1   
 DONOr H2'  O2'

 ACCEptor O6   C6      
 ACCEptor N3  " "         
 ACCEptor O1P  P
 ACCEptor O2P  P
 ACCEptor O2'  " " 

 END {GUA}

! ---------------------------------------------------------------------

! ---------------------------------------------------------------------

RESIdue ADE
GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END 
  ATOM H5'' TYPE=H     CHARGE=0.035   END 
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065   END
  ATOM H4'  TYPE=H     CHARGE=0.035   END 
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.165   END 
  ATOM H1'  TYPE=H     CHARGE=0.035   END 

! Insert Base
 GROUp
  ATOM N9    TYPE=N9A   CHARGE=-0.19   END
  ATOM C4    TYPE=C4A   CHARGE=0.19    EXCLusion=( N1 )  END
 GROUp
  ATOM N3    TYPE=N3A   CHARGE=-0.26   EXCLusion=( C6 )  END     
  ATOM C2    TYPE=C2A   CHARGE=0.225   EXCLusion=( C5 )  END      
  ATOM H2    TYPE=H     CHARGE=0.035   END 
 GROUp
  ATOM N1    TYPE=NC    CHARGE=-0.28   END     
  ATOM C6    TYPE=C6A   CHARGE=0.28    END     
 GROUp
  ATOM N6    TYPE=N6A   CHARGE=-0.42   END     
  ATOM H61   TYPE=H2    CHARGE=0.21    END     
  ATOM H62   TYPE=H2    CHARGE=0.21    END     
 GROUp
  ATOM C5    TYPE=C5A   CHARGE=0.02    END
  ATOM N7    TYPE=N7A   CHARGE=-0.25   END
  ATOM C8    TYPE=C8A   CHARGE=0.195   END 
  ATOM H8    TYPE=H     CHARGE=0.035   END 
! END

 GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115   END
  ATOM H2'  TYPE=H     CHARGE=0.035   END 
  ATOM O2'  TYPE=O2R   CHARGE=-0.40   END    
  ATOM HO2' TYPE=HO    CHARGE=0.25    END 
 GROUP
  ATOM C3'  TYPE=C3R   CHARGE=-0.035  END
  ATOM H3'  TYPE=H     CHARGE=0.035   END 
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END

 BOND P    O1P              BOND P    O2P              BOND P    O5'
 BOND O5'  C5'              BOND C5'  C4'              BOND C4'  O4'
 BOND C4'  C3'              BOND O4'  C1'              BOND C1'  N9
 BOND C1'  C2'              BOND N9   C4               BOND N9   C8
 BOND C4   N3               BOND C4   C5               BOND N3   C2
 BOND C2   N1               BOND N1   C6               BOND C6   N6  

 BOND N6   H61              BOND N6   H62              BOND C6   C5   

 BOND C5   N7               BOND N7   C8               BOND C2'  C3'
 BOND C2'  O2'              BOND C3'  O3'
 BOND C8   H8               BOND C2   H2 
 BOND O2'  HO2'
 BOND C5'  H5'         BOND C5'  H5''          BOND C4'  H4'
 BOND C3'  H3'         BOND C2'  H2'           BOND C1'  H1'

 DIHEdral P   O5'  C5'  C4'              DIHEdral O5'  C5'  C4'  O4'
 DIHEdral O5'  C5'  C4'  C3'  

 DIHEdral C3'  C4'  O4'  C1'
 DIHEdral C4'  O4'  C1'  C2'             DIHEdral O4'  C1'  C2'  C3' 

 DIHEdral C1'  C2'  C3'  C4'             DIHEdral O4'  C4'  C3'  O3'
 DIHEdral C5'  C4'  C3'  C2'             DIHEdral O2'  C2'  C3'  O3'
 DIHEdral O4'  C1'  N9   C4              
 DIHEdral C3'  C2'  O2'  H2'
 
 
 !
 IMPRoper C5   C6   N6   H61             IMPRoper C1'  C4   C8   N9
 IMPRoper N9   C4   C5   N7              IMPRoper C4   C5   N7   C8  
 IMPRoper C5   N7   C8   N9              IMPRoper N7   C8   N9   C4 
 IMPRoper C8   N9   C4   C5              IMPRoper N6   N1   C5   C6  
 IMPRoper H62  C6   H61  N6              IMPRoper C4   N3   C2   N1      
 IMPRoper N3   C2   N1   C6              IMPRoper C2   N1   C6   C5
 IMPRoper N1   C6   C5   C4              IMPRoper C6   C5   C4   N3
 IMPRoper C5   C4   N3   C2              
 IMPRoper H2   N1   N3   C2              IMPRoper H8   N7   N9   C8
 ! IMPRoper to keep the two purine rings parallel:
 IMPRoper C8   C4   C5   N1              IMPRoper C8   C5   C4   C2
 IMPRoper N3   C4   C5   N7              IMPRoper C6   C5   C4   N9
 

!RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N9  !C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H61  N6             
 DONOr H62  N6             
 DONOr H2'  O2'

 ACCEptor N3 " "           
 ACCEptor N1 " "
 ACCEptor O1P  P           
 ACCEptor O2P  P
 ACCEptor O2' " "

 END {ADE}

! ---------------------------------------------------------------------

! ---------------------------------------------------------------------

RESIdue CYT
  GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END 
  ATOM H5'' TYPE=H     CHARGE=0.035   END 
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065   END
  ATOM H4'  TYPE=H     CHARGE=0.035   END 
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.165   END 
  ATOM H1'  TYPE=H     CHARGE=0.035   END 

! Insert Base

 GROUp
  ATOM N1    TYPE=N1C   CHARGE=-0.19  EXCLUSION=( C4 )  END
  ATOM C6    TYPE=C6C   CHARGE=0.155  EXCLUSION=( N3 )  END 
  ATOM H6    TYPE=H     CHARGE=0.035  END 
 GROUp
  ATOM C2    TYPE=C2C   CHARGE=0.30    EXCLUSION=( C5 )  END     
  ATOM O2    TYPE=ON    CHARGE=-0.30   END                       
 GROUp
  ATOM N3    TYPE=NC    CHARGE=-0.28   END     
  ATOM C4    TYPE=C4C   CHARGE=0.28    END     
 GROUp
  ATOM N4    TYPE=N4C   CHARGE=-0.42   END     
  ATOM H41   TYPE=H2    CHARGE=0.21    END     
  ATOM H42   TYPE=H2    CHARGE=0.21    END     
 GROUp
  ATOM C5    TYPE=C5C   CHARGE=-0.035  END !CHRG 
  ATOM H5    TYPE=H     CHARGE=0.035   END 
 GROUp

! END


GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115   END
  ATOM H2'  TYPE=H     CHARGE=0.035   END 
  ATOM O2'  TYPE=O2R   CHARGE=-0.40   END    
  ATOM HO2' TYPE=HO    CHARGE=0.25    END 
 GROUP
  ATOM C3'  TYPE=C3R   CHARGE=-0.035  END
  ATOM H3'  TYPE=H     CHARGE=0.035   END
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END

 BOND P    O1P             BOND P    O2P             BOND P    O5'
 BOND O5'  C5'             BOND C5'  C4'             BOND C4'  O4'
 BOND C4'  C3'             BOND O4'  C1'             BOND C1'  N1
 BOND C1'  C2'             BOND N1   C2              BOND N1   C6
                           BOND C2   N3              BOND N3   C4
 BOND C4   N4              BOND N4   H41             BOND N4   H42 
 BOND C2   O2
 BOND C4   C5              BOND C5   C6              BOND C2'  C3'
 BOND C3'  O3'             BOND C2'  O2'             
 BOND C6   H6              BOND C5   H5
 BOND O2'  HO2' 
 BOND C5'  H5'         BOND C5'  H5''          BOND C4'  H4'
 BOND C3'  H3'         BOND C2'  H2'           BOND C1'  H1'


 DIHEdral P    O5'  C5'  C4'             DIHEdral O5'  C5'  C4'  O4'
 DIHEdral O5'  C5'  C4'  C3'  

 DIHEdral C3'  C4'  O4'  C1'
 DIHEdral C4'  O4'  C1'  C2'             DIHEdral O4'  C1'  C2'  C3' 

 DIHEdral C1'  C2'  C3'  C4'             DIHEdral O4'  C4'  C3'  O3'
 DIHEdral C5'  C4'  C3'  C2'             DIHEdral O2'  C2'  C3'  O3'
 DIHEdral O4'  C1'  N1   C2              
 DIHEdral C3'  C2'  O2'  H2'
 
 ! New dihedrals
 DIHEdral  C5'  C4'  C3'  O3'            DIHEdral  C4'  O4'  C1'  N1


 IMPRoper C5   C4   N4   H41               IMPRoper C1'  C2   C6   N1
 IMPRoper O2   N1   N3   C2                IMPRoper N4   N3   C5   C4
 IMPRoper N1   C2   N3   C4                IMPRoper C2   N3   C4   C5
 IMPRoper N3   C4   C5   C6                IMPRoper C4   C5   C6   N1
 IMPRoper C5   C6   N1   C2                IMPRoper C6   N1   C2   N3
 IMPRoper H42  C4   H41  N4               
 IMPRoper H5  C4  C6   C5                  IMPRoper  H6   N1   C5   C6
 
!RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N1  !C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H42  N4              
 DONOr H2'  O2'                
 DONOr H41  N4

 ACCEptor O2   C2           
 ACCEptor N3   " "
 ACCEptor O1P  P            
 ACCEptor O2P  P
 ACCEptor O2' " "  ! added, ATB, 8-9-84

 END {CYT}

!------------------------------------------------------------------

! ---------------------------------------------------------------------

! ---------------------------------------------------------------------

RESIdue THY
 GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END
  ATOM H5''  TYPE=H     CHARGE=0.035  END
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065   END
  ATOM H4'  TYPE=H     CHARGE=0.035   END
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.20    END
  ATOM H1'  TYPE=H     CHARGE=0.165   END

! Insert Base
 GROUp
  ATOM N1    TYPE=N1T   CHARGE=-0.19  EXCLUSION=( C4 )  END
  ATOM C6    TYPE=C6T   CHARGE=0.155  EXCLUSION=( N3 )  END
  ATOM H6    TYPE=H     CHARGE=0.035  END
 GROUp
  ATOM C2    TYPE=C2T   CHARGE=0.35   EXCLUSION=( C5 )  END     
  ATOM O2    TYPE=ON    CHARGE=-0.35  END                       
 GROUp
  ATOM N3    TYPE=N3T   CHARGE=-0.26  END      
  ATOM H3    TYPE=HN    CHARGE=0.26   END      
 GROUp
  ATOM C4    TYPE=C4T   CHARGE=0.30   END      
  ATOM O4    TYPE=ON    CHARGE=-0.30  END      
 GROUp
  ATOM C5    TYPE=C5T   CHARGE=-0.035 END
  ATOM C7    TYPE=CC3E  CHARGE=-0.070 END ! name per IUPAC-IUB recomm.
  ATOM H71   TYPE=H     CHARGE=0.035  END ! name per IUPAC-IUB recomm.
  ATOM H72   TYPE=H     CHARGE=0.035  END ! name per IUPAC-IUB recomm.
  ATOM H73   TYPE=H     CHARGE=0.035  END ! name per IUPAC-IUB recomm.

 GROUp

! END 


 GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115    END
  ATOM H2'  TYPE=H     CHARGE=0.035    END    
  ATOM O2'  TYPE=O2R   CHARGE=-0.40    END    
  ATOM HO2' TYPE=HO    CHARGE=0.25     END    
 GROUP
  ATOM C3'  TYPE=C3R   CHARGE=-0.035   END
  ATOM H3'  TYPE=H     CHARGE=0.035    END
 
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END


 BOND P    O1P               BOND P    O2P               BOND P    O5'
 BOND O5'  C5'               BOND C5'  C4'               BOND C4'  O4'
 BOND C4'  C3'               BOND O4'  C1'               BOND C1'  N1
 BOND C1'  C2'               BOND N1   C2                BOND N1   C6
 BOND C2   O2                BOND C2   N3                BOND N3   H3
 BOND N3   C4                BOND C4   O4                BOND C4   C5
 BOND C5   C7                BOND C5   C6                BOND C2'  C3'
 BOND C3'  O3'               BOND C2'  O2'               BOND O2'  H2'
 BOND O2'  HO2'       BOND C5'  H5'               BOND C5'  H5'' 
 BOND C3'  H3'       BOND C2'  H2'               BOND C1'  H1' 
 BOND C4'  H4'               BOND C7   H71               BOND C7   H72
 BOND C7   H73               BOND C6   H6

 DIHEdral P   O5'  C5'  C4'              DIHEdral O5'  C5'  C4'  O4'
 DIHEdral O5'  C5'  C4'  C3'  

 DIHEdral C3'  C4'  O4'  C1'
 DIHEdral C4'  O4'  C1'  C2'             DIHEdral O4'  C1'  C2'  C3' 

 DIHEdral C1'  C2'  C3'  C4'             DIHEdral O4'  C4'  C3'  O3'
 DIHEdral C5'  C4'  C3'  C2'             DIHEdral O2'  C2'  C3'  O3'
 DIHEdral O4'  C1'  N1   C2              
 DIHEdral C3'  C2'  O2'  H2'
 

 ! New dihedrals
 DIHEdral  C5'  C4'  C3'  O3'            DIHEdral  C4'  O4'  C1'  N1


 IMPRoper O4   N3   C5   C4                IMPRoper C1'  C2   C6   N1
 IMPRoper O2   N1   N3   C2                IMPRoper C4   C5   C6   N1
 IMPRoper N1   C2   N3   C4                IMPRoper C2   N3   C4   C5
                                           IMPRoper N3   C4   C5   C6
 IMPRoper C5   C6   N1   C2                IMPRoper C6   N1   C2   N3
 IMPRoper H3   C2   C4   N3               
 IMPRoper C7   C4   C6   C5                IMPRoper  H6   N1   C5   C6
 
!RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N1 ! C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H3   N3                
 DONOr HO2' O2'

 ACCEptor O2   C2              
 ACCEptor O4   C4
 ACCEptor O1P  P               
 ACCEptor O2P  P       
 ACCEptor O2'  " " ! added, ATB, 8-9-84

 END {THY}


!------------------------------------------------------------------

RESIdue URI
GROUp
  ATOM P    TYPE=P     CHARGE=1.20    END
  ATOM O1P  TYPE=O1P   CHARGE=-0.40   END
  ATOM O2P  TYPE=O2P   CHARGE=-0.40   END
  ATOM O5'  TYPE=O5R   CHARGE=-0.36   END
 GROUp
  ATOM C5'  TYPE=C5R   CHARGE=-0.070  END
  ATOM H5'  TYPE=H     CHARGE=0.035   END 
  ATOM H5'' TYPE=H     CHARGE=0.035   END 
 GROUp
  ATOM C4'  TYPE=C4R   CHARGE=0.065   END
  ATOM H4'  TYPE=H     CHARGE=0.035   END 
  ATOM O4'  TYPE=O4R   CHARGE=-0.30   END
  ATOM C1'  TYPE=C1R   CHARGE=0.165   END 
  ATOM H1'  TYPE=H     CHARGE=0.035   END 


 GROUp
  ATOM N1    TYPE=N1U   CHARGE=-0.19  EXCLUSION=( C4 )  END
  ATOM C6    TYPE=C6U   CHARGE=0.155  EXCLUSION=( N3 )  END 
  ATOM H6    TYPE=H     CHARGE=0.035  END 
 GROUp
  ATOM C2    TYPE=C2U   CHARGE=0.30   EXCLUSION=( C5 )  END     
  ATOM O2    TYPE=ON    CHARGE=-0.30  END                      
 GROUp
  ATOM N3    TYPE=N3U   CHARGE=-0.28  END     
  ATOM H3    TYPE=HN    CHARGE=0.26   END      
 GROUp
  ATOM C4    TYPE=C4U   CHARGE=0.28   END     
  ATOM O4    TYPE=ON    CHARGE=-0.30  END       
 GROUp
  ATOM C5    TYPE=C5U   CHARGE=-0.035 END !JPR
  ATOM H5    TYPE=H     CHARGE=0.035  END !JPR

 GROUP
  ATOM C2'  TYPE=C2R   CHARGE=0.115   END
  ATOM H2'  TYPE=H     CHARGE=0.035   END ! 
  ATOM O2'  TYPE=O2R   CHARGE=-0.40   END    
  ATOM HO2'   TYPE=HO    CHARGE=0.25  END 
 GROUP
  ATOM C3'  TYPE=C3R    CHARGE=-0.035 END
  ATOM H3'  TYPE=H     CHARGE=0.035   END 
 GROUP
  ATOM O3'  TYPE=O3R   CHARGE=-0.36   END

 BOND P    O1P                BOND P    O2P              BOND P    O5'
 BOND O5'  C5'                BOND C5'  C4'              BOND C4'  O4'
 BOND C4'  C3'                BOND O4'  C1'              BOND C1'  N1
 BOND C1'  C2'                BOND N1   C2               BOND N1   C6
 BOND C2   O2                 BOND C2   N3               BOND N3   H3
 BOND N3   C4                 BOND C4   O4               BOND C4   C5  

 BOND C5   C6                 BOND C2'  C3'              BOND C3'  O3'
 BOND C2'  O2'                
 BOND C5  H5                  BOND C6   H6
 
 BOND O2'  HO2' 
 BOND C5'  H5'         BOND C5'  H5''          BOND C4'  H4'
 BOND C3'  H3'         BOND C2'  H2'           BOND C1'  H1'

 DIHEdral P   O5'  C5'  C4'              DIHEdral O5'  C5'  C4'  O4'
 DIHEdral O5'  C5'  C4'  C3'  

 DIHEdral C3'  C4'  O4'  C1'
 DIHEdral C4'  O4'  C1'  C2'             DIHEdral O4'  C1'  C2'  C3' 

 DIHEdral C1'  C2'  C3'  C4'             DIHEdral O4'  C4'  C3'  O3'
 DIHEdral C5'  C4'  C3'  C2'             DIHEdral O2'  C2'  C3'  O3'
 DIHEdral O4'  C1'  N1   C2              
 DIHEdral C3'  C2'  O2'  H2'

 DIHEdral P    O3'  C3'  C2'             DIHEdral P    O3'  C3'  C4'           
 ! New dihedrals
 DIHEdral  C5'  C4'  C3'  O3'            DIHEdral  C4'  O4'  C1'  N1

                                            IMPRoper C1'  C2   C6   N1
 IMPRoper O2   N1   N3   C2                 IMPRoper H3   C2   C4   N3
 IMPRoper O4   N3   C5   C4                 IMPRoper N1   C2   N3   C4
 IMPRoper C2   N3   C4   C5                 IMPRoper N3   C4   C5   C6
 IMPRoper C4   C5   C6   N1                 IMPRoper C5   C6   N1   C2
 IMPRoper C6   N1   C2   N3                 
 IMPRoper H5   C4   C6   C5                 IMPRoper H6   N1   C5   C6

 !GENERAL RIBOSE IMPROPERS
IMPRoper     H1'  C2'  O4'  N1  !C1'
IMPRoper     H2'  C3'  C1'  O2' !C2'
IMPRoper     H3'  C4'  C2'  O3' !C3'
IMPRoper     H4'  C5'  C3'  O4' !C4'
IMPRoper     H5'  O5'  H5'' C4' !C5'

 DONOr H3   N3                    
 DONOr H2'  O2'

 ACCEptor O2   C2                
 ACCEptor O4   C4
 ACCEptor O1P  P                 
 ACCEptor O2P  P
 ACCEptor O2' " " 

 

END {URI}

!------------------------------------------------------------------
!------------------------------------------------------------------
!note: O3' and O5' will remain O3R and O5R for DNA molecules
!this is consistent with values in parameter files

PRESidue DEOX    ! Patch to make DEOXYribose of the ribose
 DELETE ATOM O2'   END
 DELETE ATOM HO2'   END
GROUP
 MODIFY  ATOM C2'  TYPE=C2D   CHARGE=-0.07    END
 MODIFY  ATOM C5'  TYPE=C5D   CHARGE=-0.07    END
 MODIFY  ATOM C4'  TYPE=C4D   CHARGE=0.065    END
 MODIFY  ATOM O4'  TYPE=O4D   CHARGE=-0.30    END
 MODIFY  ATOM C1'  TYPE=C1D   CHARGE=0.165    END
 MODIFY  ATOM C3'  TYPE=C3D   CHARGE=-0.035   END
 ADD     ATOM H2'' TYPE=H     CHARGE=0.035    END
 
 ADD BOND   C2'  H2''
 ADD ANGLE  C1'  C2'  H2'
 ADD ANGLE  C3'  C2'  H2''
 ADD ANGLE  H2'  C2'  H2''
 ADD IMPRoper   H2'  C3'  H2'' C1'! C2' chirality term
END {DEOX}

!------------------------------------------------------------------
!------------------------------------------------------------------


PRESidue 5PHO           ! 5-terminus (with phosphate)
 !                      ! should be used as "FIRST  5PHO  TAIL + * END"
 GROUp                  ! i.e. to be patched to the first RNA residue
  ADD ATOM +H5T   TYPE=HO    CHARGE=0.15    END
  ADD ATOM +O5T   TYPE=OH    CHARGE=-0.15   END
        
  ADD BOND +H5T  +O5T
  ADD BOND +O5T  +P
  ADD ANGLe +H5T  +O5T  +P
  ADD ANGLe +O5'  +P  +O5T
  ADD ANGLe +O5T  +P  +O1P
  ADD ANGLe +O5T  +P  +O2P 

  ADD DIHEdral +O5'  +P   +O5T   +H5T
  ADD DIHEdral +C5'  +O5'  +P    +O5T
  ADD DONOr +H5T  +O5T
END {5PHO}

!------------------------------------------------------------------


PRESidue 3TER               ! 3-terminus (without phosphate)
                            ! should be used as "LAST 3TER  HEAD - * END"
 GROUp                      ! i.e. to be patched to the last RNA residue
  MODIFY ATOM -C3'    TYPE=C3R    CHARGE=0.15    END       
  MODIFY ATOM -O3'    TYPE=OH     CHARGE=-0.40   END       
  ADD ATOM -H3T  TYPE=HO     CHARGE=0.25        END       
 !
 ADD BOND -O3'  -H3T
 ADD ANGLe -C3'  -O3'  -H3T
 ADD DIHEdral -C4'  -C3'  -O3'  -H3T
 ADD DONOr -H3T  -O3'
END {3TER}

!------------------------------------------------------------------


PRESidue 5TER        ! 5-terminus (without phosphate)
 !                   ! should be used as "FIRST  5TER  TAIL + * END"
 GROUp               ! i.e. to be patched to the first RNA residue
  ADD ATOM +H5T  TYPE=HO    CHARGE=0.25    END      
  MODIFY ATOM +O5'  TYPE=OH  CHARGE=-0.40  END      
  MODIFY ATOM +C5'  TYPE=C5R  CHARGE=0.15  END      
  DELETE ATOM +P   END
  DELETE ATOM +O1P END
  DELETE ATOM +O2P END
 !
 ADD BOND +H5T   +O5'
 ADD ANGLe +H5T   +O5'  +C5'
 ADD DIHEdral +H5T   +O5'  +C5'  +C4'
 ADD DONOr +H5T   +O5'
END {5TER}

! ---------------------------------------------------------------------
!------------------------------------------------------------------

PRESidue NUC         ! patch for nucleic acid backbone
                     ! should be used as "LINK NUC  HEAD - *  TAIL + *  END"
                     ! i.e. it links the previous RNA residue (-) with
                     ! the current one (+)
 GROUp               

  MODIFY ATOM -O3' END   !
  MODIFY ATOM +P   END   !
  MODIFY ATOM +O1P END   ! this should correctly define the electrostatic 

  MODIFY ATOM +O2P END   ! group boundary 

  MODIFY ATOM +O5' END   !
 ADD BOND -O3' +P
 ADD ANGLE -C3' -O3' +P
 ADD ANGLE -O3' +P  +O1P
 ADD ANGLE -O3' +P  +O2P
 ADD ANGLE -O3' +P  +O5'
ADD DIHEdral -O3' +P  +O5'  +C5'   

 ADD DIHEdral -C4' -C3' -O3'  +P
 ADD DIHEdral -C3' -O3' +P   +O5'  

END {NUC}

!------------------------------------------------------------------

set echo=true end


README   This file

JPR topology and parameter files, March 1996

dna-rna-allatom.top JPR top file plus changes:
    Commented out remarks and set echo/message statements
    Commented out all dihedrals except alpha-gamma, epsilon, zeta (and their
 equivalents on 5' and 3' termini).
    Commented out remaining dihedrals, since they weren't helpful
dna-rna-allatom.top.old JPR top file
dna-rna-allatom.par JPR par file plus changes:
    Commented out remarks and set echo/message statements
    Commented out second definitions of terminal hydroxyl dihedrals with
 periodicity 2 (?!?)
    Commented out erroneous "DIHEdral    X    C6A  N4C  X"
    Commented out all dihedrals except alpha-gamma, epsilon, zeta (and their
 equivalents on 5' and 3' termini). Note that I commented out the amino
 dihedrals because they have no counterpart in the topology file, but
 that there are impropers which do the same job.
    Changed x_eq for backbone dihedrals to A-form angles from Sanger
    Commented out remaining dihedrals, since they weren't helpful
dna-rna-allatom.par.old JPR par file
Number of segments = 1
Number of residues = 21
segid  num res  alpha    beta   gamma     eps    zeta     chi     nu0     nu1     nu2     nu3     nu4
------ --- ---  ------ ------- ------- ------- ------- ------- ------- ------- ------- ------- -------
     A   1 GUA    0.00 -168.88   40.92 -147.66  -74.73 -157.97    1.66  -24.57   36.86  -36.92   22.21
     A   2 GUA  -58.81  173.82   43.71 -155.75  -72.41 -155.47   -0.36  -24.25   38.22  -39.48   25.07
     A   3 CYT  -63.42  178.55   48.26 -151.81  -75.88 -161.20    1.96  -25.16   37.49  -37.41   22.36
     A   4 ADE  -58.35  175.38   45.83 -152.66  -74.26 -154.76    0.57  -24.13   37.19  -37.89   23.52
     A   5 GUA  -55.22  173.78   44.73 -152.21  -74.20 -155.90   -0.86  -23.50   37.61  -39.09   25.17
     A   6 GUA  -60.11  174.36   47.15 -158.30  -70.95 -155.59    0.08  -24.67   38.52  -39.46   24.82
     A   7 GUA  -61.81  178.43   52.45 -151.57  -60.89 -156.64   -0.32  -21.55   33.92  -35.15   22.39
     A   8 CYT  -68.45 -162.99   43.90 -125.92  -85.01 -161.69   14.44  -30.25   33.72  -26.47    7.73
     A   9 URI  -37.87  161.65   39.08 -149.53  -50.59 -162.25   -1.54  -20.06   32.74  -34.66   22.80
     A  10 CYT  119.21  167.25   68.15 -116.32  -81.40 -127.59  -13.47   22.64  -22.62   15.73   -1.62
     A  11 ADE  -97.54  157.10   51.30 -169.84  -71.20 -124.34   -7.64  -17.16   33.90  -39.21   29.44
     A  12 URI  -64.22  169.84   69.80  -98.91  -93.75 -127.79  -30.44   24.14   -9.56   -7.42   23.63
     A  13 ADE  -91.56  154.78   53.07 -159.94  -70.77 -150.17   12.77  -34.71   42.35  -36.04   14.73
     A  14 ADE  -64.91  149.14   84.18 -117.45  -68.27  175.75    5.57  -28.29   39.03  -36.90   19.75
     A  15 CYT  -52.77  162.66   44.20 -151.63  -80.21 -162.89   -0.11  -24.70   38.68  -39.81   25.13
     A  16 CYT  -52.99  175.42   41.66 -148.81  -76.91 -161.01    3.84  -26.07   37.15  -36.01   20.31
     A  17 CYT  -57.88  172.14   45.46 -154.01  -77.64 -162.81    1.56  -25.61   38.60  -38.73   23.42
     A  18 URI  -53.22  176.02   42.70 -149.29  -77.46 -161.44    3.93  -26.39   37.56  -36.36   20.48
     A  19 GUA  -52.85  171.81   42.78 -153.56  -72.65 -156.43    0.60  -24.86   38.36  -39.04   24.22
     A  20 CYT  -60.61  177.86   45.73 -154.70  -74.38 -161.79    2.02  -25.27   37.63  -37.51   22.36
     A  21 CYT  -62.35  177.52   49.84    0.00    0.00 -161.13    1.80  -23.87   35.53  -35.59   21.32

! average.inp -- Computes the average structure, RMSDs from the average
! for each original structure and the rms RMSD.
! Dave Schweisguth , 1 Sep 1996
! Derived from nmr/average.inp

set seed=@xplor.seed end ! Use 'xplor -s'

set echo=off message=off end ! Normal use
!set echo=on message=all end ! Auxiliary file debugging

structure @rsf.inp end  ! Read the structure file.
parameter @XPLORLIB:toppar/dna-rna-allatom.par end

noe nres=1000 @noes.stem.inp @noes.loop.inp @base-pairs.inp end
restraints dihedral nassign=300 @dihedrals.inp end
evaluate($planarweight=50) ! AAFS' choice
restraints planar @planars.inp end

set echo=on message=all end

noe    ! Parameters for NOE effective energy term.
    ceiling=1000                      
    averaging  * cent
    potential  * square
    sqconstant * 1
    sqexponent * 2
    scale      * 100  ! Constant NOE scale throughout the protocol.
end

parameter
    nbonds
 ctonnb=9.5
 ctofnb=10.5
 cutnb=11.5
 tolerance=0.5
 rdie
 switch
 vswitch
    end
end

restraints dihedral scale=800 end

flags exclude * include bond angl dihe impr vdw elec noe cdih plan end

! Compute the mean structure.

evaluate ($nfile=9)
vector do (store1=0) (all)
vector do (store2=0) (all)
vector do (store3=0) (all)
vector do (store4=0) (all)

evaluate ($count=0)
while ($count < $nfile) loop main
    evaluate ($count=$count+1)
    evaluate ($filename="average."+encode($count)+".pdb")
    coordinates initialize end
    coordinates @@$filename
    if ($count=1) then
 coordinates copy end ! Store first structure in comparison set.
    end if
    coordinates fit end
    vector do (store1=store1+x) (all)
    vector do (store2=store2+y) (all)
    vector do (store3=store3+z) (all)
    vector do (store4=store4+x*x+y*y+z*z) (all)
end loop main

vector do (x=store1 / $nfile) (all)
vector do (y=store2 / $nfile) (all)
vector do (z=store3 / $nfile) (all)
vector do (b=sqrt(max(0,store4/$nfile-(x**2+y**2+z**2)))) (all)

! Minimize the averaged structure

minimize powell nstep=200 nprint=25 end

! Analyze and write out the averaged structure

print threshold=0.05 bonds          
evaluate ($rms_bond=$result)
evaluate ($v_bond=$violations)
print threshold=5 angles
evaluate ($rms_angl=$result)
evaluate ($v_angl=$violations)
print threshold=15 dihedrals
evaluate ($rms_dihe=$result)
evaluate ($v_dihe=$violations)
print threshold=5 impropers
evaluate ($rms_impr=$result)
evaluate ($v_impr=$violations)
print threshold=0.2 noe 
evaluate ($rms_noe=$result)
evaluate ($v_noe=$violations)
print threshold=5 cdih
evaluate ($rms_cdih=$result)
evaluate ($v_cdih=$violations)

set echo=off message=off end

display Energy:      bond $bond, angle $angl, dihedral $dihe,
display              improper $impr, NOE $noe, c-dihedral $cdih,
display              planar $plan, VdW $vdw, elec $elec, total $ener
display RMSD:        bond $rms_bond, angle $rms_angl, dihedral $rms_dihe,
display              improper $rms_impr, NOE $rms_noe, c-dihedral $rms_cdih
display Violations:  bond $v_bond, angle $v_angl, dihedral $v_dihe,
display              improper $v_impr, NOE $v_noe, c-dihedral $v_cdih

set echo=on message=all end

! b array (last column) is the rms difference from the mean

write coordinates output=average.pdb end

! Compute an overall rms difference.

coordinates copy end
evaluate ($rmsd_rmsd=0)
evaluate ($rmsd_rmsd_stem=0)
evaluate ($rmsd_rmsd_loop=0)

evaluate ($count=0)
while ($count < $nfile) loop main
    evaluate ($count=$count+1)
    evaluate ($filename="average."+encode($count)+".pdb")
    coordinates initialize end
    coordinates @@$filename
    coordinates fit end
    coordinates rms end
    evaluate ($rmsd_rmsd=$rmsd_rmsd + $result**2)
    coordinates fit selection=(residue 1:7 or residue 15:21) end
    coordinates rms selection=(residue 1:7 or residue 15:21) end
    evaluate ($rmsd_rmsd_stem=$rmsd_rmsd_stem + $result**2)
    coordinates fit selection=(residue 8:14) end
    coordinates rms selection=(residue 8:14) end
    evaluate ($rmsd_rmsd_loop=$rmsd_rmsd_loop + $result**2)
end loop main

! RMS RMSD to the average structure

evaluate ($rmsd_rmsd=sqrt($rmsd_rmsd / $nfile))
evaluate ($rmsd_rmsd_stem=sqrt($rmsd_rmsd_stem / $nfile))
evaluate ($rmsd_rmsd_loop=sqrt($rmsd_rmsd_loop / $nfile))

stop
! Base pair restraints
!
! Heavy-atom to heavy-atom distances from Saenger p. 123
! Imino and amino to bonded nitrogen distances (all 1.01) from JPR's
!    parameter file
!
! AU pair
!
! AN6-UO4 (2.95) - AN6-AH62 (1.01) = AH62-UO4 (1.94)
! AN1-UN3 (2.82) - UH3-UN3 (1.01) = AN1-UH3 (1.81)
!
! GC pair
!
! GO6-CN4 (2.91) - CH42-CN4 (1.01) = GO6-CH42 (1.90)
! GN1-CN3 (2.95) - GN1-GH1 (1.01) = GH1-CN3 (1.94)
! GN2-CO2 (2.86) - GN2-GH22 (1.01) = GH22-CO2 (1.85)

! GC

assign (resid 1 and name O6) (resid 21 and name H42) 1.90 0.1 0.1
assign (resid 1 and name H1) (resid 21 and name N3) 1.94 0.1 0.1
assign (resid 1 and name H22) (resid 21 and name O2) 1.90 0.1 0.1

! GC

assign (resid 2 and name O6) (resid 20 and name H42) 1.90 0.1 0.1
assign (resid 2 and name H1) (resid 20 and name N3) 1.94 0.1 0.1
assign (resid 2 and name H22) (resid 20 and name O2) 1.90 0.1 0.1

! CG

assign (resid 3 and name H42) (resid 19 and name O6) 1.90 0.1 0.1
assign (resid 3 and name N3) (resid 19 and name H1) 1.94 0.1 0.1
assign (resid 3 and name O2) (resid 19 and name H22) 1.90 0.1 0.1

! AU

assign (resid 4 and name H62) (resid 18 and name O4) 1.94 0.1 0.1
assign (resid 4 and name N1) (resid 18 and name H3) 1.81 0.1 0.1

! GC

assign (resid 5 and name O6) (resid 17 and name H42) 1.90 0.1 0.1
assign (resid 5 and name H1) (resid 17 and name N3) 1.94 0.1 0.1
assign (resid 5 and name H22) (resid 17 and name O2) 1.90 0.1 0.1

! GC

assign (resid 6 and name O6) (resid 16 and name H42) 1.90 0.1 0.1
assign (resid 6 and name H1) (resid 16 and name N3) 1.94 0.1 0.1
assign (resid 6 and name H22) (resid 16 and name O2) 1.90 0.1 0.1

! GC

assign (resid 7 and name O6) (resid 15 and name H42) 1.90 0.1 0.1
assign (resid 7 and name H1) (resid 15 and name N3) 1.94 0.1 0.1
assign (resid 7 and name H22) (resid 15 and name O2) 1.90 0.1 0.1
! dg.inp -- Full metric matrix distance geometry
! Dave Schweisguth , 7 May 1996
! Derived from nmr/dg_full_embed.inp

set seed=@xplor.seed end     ! Use 'xplor -s'

set echo=off message=off end     ! Normal use
!set echo=on message=all end     ! Auxiliary file debugging

structure @rsf.inp end
parameter @XPLORLIB:toppar/dna-rna-allatom.par end
! Uncomment the following to define rigid groups (which seem to do nothing)
!coordinates disposition=main @template.pdb     ! END in PDB file

noe nres=1000 @noes.stem.inp @noes.loop.inp @base-pairs.inp end
restraints dihedral nassign=300 @dihedrals.inp end

set echo=on message=all end

! Include NOE and dihedral restraints in mmdg

flags exclude * include bond angle dihe impr vdw noe cdih end
parameter nbonds repel=0.8 end end  ! Scale van der Waals radii

mmdg
!    @groups.inp      ! Uncomment to define rigid groups
        ! (which seem to do nothing)
    selection=(all)
    storebounds
end

! Loop until embedding is successful. Once usually suffices.

evaluate ($embedded="false")
while ($embedded="false") loop embed
    mmdg recallbounds end
end loop embed

! Scale coordinates by $dgscale (defined by mmdg)

vector do (x = x * $dgscale) (known)
vector do (y = y * $dgscale) (known)
vector do (z = z * $dgscale) (known)

! Regularize

flags exclude * include dg end
minimize powell nstep=100 drop=10 nprint=25 end

write coordinates output=dg.pdb end
   
stop
! dgsa.inp -- Clean up the output of dg.inp using simulated annealing
! Dave Schweisguth , 22 Jul 1996
! Derived from nmr/dgsa.inp

evaluate ($init_t=3000)  ! Temperature for constant-temperature MD
evaluate ($high_steps=6000) ! Number of steps at high temp
evaluate ($high_timestep=0.002) ! Time of each MD step at high temp
evaluate ($final_t=300)  ! Final temperature
evaluate ($cool_steps=7500) ! Number of steps for cooling
evaluate ($cool_timestep=0.002) ! Time of each MD step when cooling
evaluate ($tempstep=50)  ! Degree increment for cooling

set seed=@xplor.seed end ! Use 'xplor -s'

set echo=off message=off end ! Normal use
!set echo=on message=all end ! Auxiliary file debugging

structure @rsf.inp end
parameter @XPLORLIB:toppar/dna-rna-allatom.par end

noe nres=1000 @noes.stem.inp @noes.loop.inp @base-pairs.inp end
restraints dihedral nassign=300 @dihedrals.inp end
evaluate($planarweight=50) ! AAFS' choice
restraints planar @planars.inp end

set echo=on message=all end

vector do (fbeta=10) (all) ! Friction coeff. for MD heatbath, in 1/ps.
vector do (mass=100) (all)      ! Uniform heavy masses to speed MD.

noe    ! Parameters for NOE effective energy term.
    ceiling=1000                      
    averaging  * cent
    potential  * square
    sqconstant * 1
    sqexponent * 2
    scale      * 100  ! Constant NOE scale throughout the protocol.
end

parameter   ! Parameters for the repulsive energy term.
    nbonds
 repel=0.5  ! Initial value for repel--modified later.
 rexp=2
 irexp=2
 rcon=1
 nbxmod=-2  ! Initial value for nbxmod--modified later.
 wmin=0.01 
 cutnb=4.5
 ctonnb=2.99
 ctofnb=3
 tolerance=0.5 
    end
end

! Test for the correct enantiomer; if you want to bypass this test because
! the substructures were tested previously, simply remove the -1 from the
! next statement.      

for $image in (1 -1) loop imag

    coordinates initialize end
    coordinates @dg.pdb       ! END in PDB file
    vector do (x=x * $image) (known)
    vector identity (store1) (not known)    ! Set store1 to unknowns.
  
    ! Create local ideal geometry by template fitting;
    ! this also takes care of unknown atoms.          
       
    coordinates copy end ! Store current coordinates in comparison set.
    coordinates initialize end
    coordinates @template.pdb      ! END in PDB file
   
    set echo=off message=off end
    for $id in id (tag) loop fit     ! Loop over residue tags.  
      
 ! LSQ fitting using known coordinates.
 coordinates fit selection=(byresidue (id $id) and not store1) end

 ! Store fitted template coordinates for this residue.
 coordinates copy selection=(byresidue (id $id)) end
    
    end loop fit
    set echo=on message=all end
    
    coordinates swap end
     
    ! Minimization of bonds, VDWs, and NOEs.
    
    flags exclude * include bond vdw noe cdih plan end
    constraints interaction (all) (all) weights * 1 vdw 20 end end
    parameter nbonds nbxmod=-2 repel=0.5 end end
    restraints dihedral scale=20 end 
    minimize powell drop=10 nstep=300 nprint=10 end
    
    ! Include angles. 
    
    flags include angl end
    minimize powell drop=10 nstep=300 nprint=10 end
    
    ! Dynamics, slowly introducing dihedral and improper angles

    flags include dihe impr end
     
    evaluate ($nstep1=int($high_steps/8))   ! Dynamics runs 1, 2, 3 and 5
    evaluate ($nstep2=int($high_steps/2))   ! Dynamics run 4
    
    constraints inter (all) (all) weights * 0.1 dihe 0.05 impr 0.05 vdw 20 end end
    dynamics verlet
 nstep=$nstep1 time=$high_timestep iasvel=maxwell firstt=$init_t 
 tcoup=true tbath=$init_t nprint=100 iprfrq=0                     
    end
    
    constraints inter (all) (all) weights * 0.2 dihe 0.1 impr 0.1 vdw 20 end end
    dynamics verlet
 nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t 
 tcoup=true tbath=$init_t nprint=100 iprfrq=0                     
    end
    
    constraints inter (all) (all) weights * 0.2 dihe 0.2 impr 0.2 vdw 0.01 end end
    parameter nbonds repel=0.9 end end 
    dynamics verlet
 nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t       
 tcoup=true tbath=$init_t nprint=100 iprfrq=0                 
    end
    
    constraints inter (all) (all) weights * 0.4 dihe 0.4 impr 0.4 vdw 0.003 end end
    parameter nbonds nbxmod=-3 end end 
    dynamics verlet
 nstep=$nstep2 time=$high_timestep iasvel=current firstt=$init_t       
 tcoup=true tbath=$init_t nprint=100 iprfrq=0                 
    end
    
    constraints inter (all) (all) weights * 1 dihe 1 impr 1 vdw 0.003 end end
    dynamics verlet
 nstep=$nstep1 time=$high_timestep iasvel=current firstt=$init_t       
 tcoup=true tbath=$init_t nprint=100 iprfrq=0                 
    end
    
    if ($image=1) then
 vector do (store7=x) (all)     ! Store first image in stores.
 vector do (store8=y) (all)
 vector do (store9=z) (all)
 vector do (store4=vx) (all)
 vector do (store5=vy) (all)
 vector do (store6=vz) (all)
    end if

end loop imag

! Establish the correct handedness of the structure.
  
energy end
evaluate ($e_minus=$ener) 
coordinates copy end
vector do (x=store7) (all)
vector do (y=store8) (all)
vector do (z=store9) (all)
energy end
evaluate ($e_plus=$ener) 
if ($e_plus > $e_minus) then
    evaluate ($hand=-1)
    coordinates swap end
else
    evaluate ($hand=1)
    vector do (vx=store4) (all)
    vector do (vy=store5) (all)
    vector do (vz=store6) (all)
end if

! Increase VDW interaction and cool.

restraints dihedral scale=800 end

evaluate ($bath=$init_t)
evaluate ($ncycle=($init_t-$final_t)/$tempstep)
evaluate ($nstep=int($cool_steps/$ncycle))

evaluate ($ini_rad=0.9)
evaluate ($fin_rad=0.75)
evaluate ($radius=$ini_rad)
evaluate ($radfact=($fin_rad/$ini_rad)^(1/$ncycle))
evaluate ($ini_con=0.003)
evaluate ($fin_con=4.0)
evaluate ($k_vdw=$ini_con)
evaluate ($k_vdwfact=($fin_con/$ini_con)^(1/$ncycle))
    
evaluate ($i_cool=0)
while ($i_cool < $ncycle) loop cool

    evaluate ($i_cool=$i_cool+1)
    evaluate ($bath=$bath - $tempstep)       
    evaluate ($radius=max($fin_rad,$radius*$radfact))
    evaluate ($k_vdw=min($fin_con,$k_vdw*$k_vdwfact))
    
    parameter nbonds repel=$radius end end
    constraints interaction (all) (all) weights * 1 vdw $k_vdw end end
    dynamics verlet
 nstep=$nstep time=$cool_timestep iasvel=current firstt=$bath
 tcoup=true tbath=$bath nprint=$nstep iprfrq=0  
    end

    ! Abort condition.

    evaluate ($critical=$temp/$bath)
    if ($critical > 10) then
 display Rerun job with smaller timestep (i.e., 0.003) 
 stop
    end if

end loop cool
  
! Final minimization.

minimize powell drop=10 nstep=600 nprint=25 end

! Analyze and write out the final structure.

print threshold=0.05 bonds          
evaluate ($rms_bond=$result)
evaluate ($v_bond=$violations)
print threshold=5 angles
evaluate ($rms_angl=$result)
evaluate ($v_angl=$violations)
print threshold=15 dihedrals
evaluate ($rms_dihe=$result)
evaluate ($v_dihe=$violations)
print threshold=5 impropers
evaluate ($rms_impr=$result)
evaluate ($v_impr=$violations)
print threshold=0.2 noe 
evaluate ($rms_noe=$result)
evaluate ($v_noe=$violations)
print threshold=5 cdih
evaluate ($rms_cdih=$result)
evaluate ($v_cdih=$violations)

set echo=off message=off end

display Energy:      bond $bond, angle $angl, dihedral $dihe,
display              improper $impr, NOE $noe, c-dihedral $cdih,
display              planar $plan, VdW $vdw, total $ener
display RMSD:        bond $rms_bond, angle $rms_angl, dihedral $rms_dihe,
display              improper $rms_impr, NOE $rms_noe, c-dihedral $rms_cdih
display Violations:  bond $v_bond, angle $v_angl, dihedral $v_dihe,
display              improper $v_impr, NOE $v_noe, c-dihedral $v_cdih
display Handedness $hand, enantiomer discrimination $e_plus:$e_minus

set echo=on message=all end

write coordinates output=dgsa.pdb end
    
stop
#!/bin/csh -f
#$ -cwd -o dgsa.run.o -e dgsa.run.e -m bae -M dcs@proton.chem.yale.edu

set i=21
while ($i <= 30)
    set ii=`nawk 'BEGIN { printf "%02d", '$i' }'`

    xplor -s < dg.inp > dg.$ii.out
    xplor -s < dgsa.inp > dgsa.$ii.out
    ip 'repdb -ix -om' dg.pdb dgsa.pdb
    mv dg.pdb dg.$ii.pdb
    mv dgsa.pdb dgsa.$ii.pdb

    @ i++
end

perl -ne 'print if /^Ener/ .. /^ X-PLOR/' dgsa.??.out > dgsa.summary
perl -ne 'print if /0.2 noe/ .. /NOEPRI/' dgsa.??.out > dgsa.summary.noes
perl -ne 'print if /5 cdih/ .. /RMS deviation/' dgsa.??.out > dgsa.summary.cdih
qsub3 -q medium-phe refine.run
Energy:      bond 5.90512, angle 78.8593, dihedral 0,
             improper 10.7274, NOE 50.8731, c-dihedral 0.340015,
             planar 8.35049, VdW 140.529, total 295.585
RMSD:        bond 1.919015E-03, angle 0.635438, dihedral 0,
             improper 0.308381, NOE 2.341371E-02, c-dihedral 8.29046E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 2, c-dihedral 0
Handedness -1, enantiomer discrimination 21177.8:11441.4
 X-PLOR> 
Energy:      bond 12.8321, angle 150.851, dihedral 0,
             improper 14.3855, NOE 91.1044, c-dihedral 9.96906,
             planar 10.2854, VdW 180.643, total 470.07
RMSD:        bond 2.790835E-03, angle 0.831394, dihedral 0,
             improper 0.362285, NOE 3.133255E-02, c-dihedral 0.448907
Violations:  bond 0, angle 5, dihedral 0,
             improper 0, NOE 7, c-dihedral 0
Handedness -1, enantiomer discrimination 31528.4:5963.22
 X-PLOR> 
Energy:      bond 4.75237, angle 78.1279, dihedral 0,
             improper 10.529, NOE 31.1738, c-dihedral 0.650518,
             planar 7.79061, VdW 122.387, total 255.411
RMSD:        bond 1.68525E-03, angle 0.621372, dihedral 0,
             improper 0.304682, NOE 1.832825E-02, c-dihedral 0.114672
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness 1, enantiomer discrimination 11615.4:29287.6
 X-PLOR> 
Energy:      bond 16.2144, angle 139.035, dihedral 0,
             improper 16.912, NOE 221.524, c-dihedral 8.79085,
             planar 9.86272, VdW 173.114, total 585.453
RMSD:        bond 3.168553E-03, angle 0.804985, dihedral 0,
             improper 0.407163, NOE 4.885803E-02, c-dihedral 0.421546
Violations:  bond 0, angle 3, dihedral 0,
             improper 0, NOE 5, c-dihedral 0
Handedness -1, enantiomer discrimination 24118.3:5296.4
 X-PLOR> 
Energy:      bond 5.04972, angle 81.789, dihedral 0,
             improper 10.3322, NOE 30.145, c-dihedral 0.12704,
             planar 9.21155, VdW 124.689, total 261.344
RMSD:        bond 1.741615E-03, angle 0.639569, dihedral 0,
             improper 0.304484, NOE 1.802327E-02, c-dihedral 5.067567E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness -1, enantiomer discrimination 23846.3:6076.52
 X-PLOR> 
Energy:      bond 6.15639, angle 78.8947, dihedral 0,
             improper 9.90625, NOE 59.2593, c-dihedral 0.448364,
             planar 9.33985, VdW 125.16, total 289.165
RMSD:        bond 1.935025E-03, angle 0.6329, dihedral 0,
             improper 0.299906, NOE 2.526994E-02, c-dihedral 9.520172E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 3, c-dihedral 0
Handedness -1, enantiomer discrimination 25345.4:8051.48
 X-PLOR> 
Energy:      bond 86.898, angle 340.25, dihedral 0,
             improper 27.6642, NOE 155.902, c-dihedral 26.6771,
             planar 10.2821, VdW 702.715, total 1350.39
RMSD:        bond 7.415511E-03, angle 1.16729, dihedral 0,
             improper 0.531386, NOE 4.098759E-02, c-dihedral 0.734343
Violations:  bond 5, angle 13, dihedral 0,
             improper 0, NOE 5, c-dihedral 2
Handedness -1, enantiomer discrimination 32518.6:5894.71
 X-PLOR> 
Energy:      bond 4.77988, angle 75.1605, dihedral 0,
             improper 10.0879, NOE 28.7483, c-dihedral 0.113657,
             planar 8.82426, VdW 121.194, total 248.908
RMSD:        bond 1.671527E-03, angle 0.609677, dihedral 0,
             improper 0.29928, NOE 1.76008E-02, c-dihedral 4.793214E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness -1, enantiomer discrimination 26821.2:5609.61
 X-PLOR> 
Energy:      bond 15.3974, angle 154.177, dihedral 0,
             improper 16.6241, NOE 138.875, c-dihedral 16.2327,
             planar 9.36799, VdW 184.418, total 535.091
RMSD:        bond 3.205729E-03, angle 0.832072, dihedral 0,
             improper 0.416525, NOE 3.868456E-02, c-dihedral 0.572828
Violations:  bond 0, angle 5, dihedral 0,
             improper 0, NOE 6, c-dihedral 0
Handedness 1, enantiomer discrimination 8522:26662.2
 X-PLOR> 
Energy:      bond 13.6538, angle 151.875, dihedral 0,
             improper 14.6787, NOE 133.044, c-dihedral 4.30209,
             planar 9.2648, VdW 220.089, total 546.907
RMSD:        bond 2.893107E-03, angle 0.840282, dihedral 0,
             improper 0.382529, NOE 3.78638E-02, c-dihedral 0.294896
Violations:  bond 0, angle 5, dihedral 0,
             improper 0, NOE 7, c-dihedral 0
Handedness -1, enantiomer discrimination 31289.9:5766.53
 X-PLOR> 
Energy:      bond 5.12775, angle 76.2701, dihedral 0,
             improper 10.5905, NOE 31.4411, c-dihedral 0.489987,
             planar 7.63491, VdW 124.358, total 255.912
RMSD:        bond 1.772877E-03, angle 0.617485, dihedral 0,
             improper 0.310133, NOE 1.840667E-02, c-dihedral 9.95226E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness -1, enantiomer discrimination 24808.5:5975.32
 X-PLOR> 
Energy:      bond 5.9437, angle 78.4555, dihedral 0,
             improper 10.303, NOE 50.892, c-dihedral 0.388776,
             planar 9.63777, VdW 139.613, total 295.234
RMSD:        bond 1.924919E-03, angle 0.633099, dihedral 0,
             improper 0.294884, NOE 2.341805E-02, c-dihedral 8.86501E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 2, c-dihedral 0
Handedness -1, enantiomer discrimination 29575.2:5949.65
 X-PLOR> 
Energy:      bond 13.7255, angle 142.944, dihedral 0,
             improper 13.9402, NOE 149.468, c-dihedral 4.00317,
             planar 8.9372, VdW 176.472, total 509.49
RMSD:        bond 2.887286E-03, angle 0.820241, dihedral 0,
             improper 0.363015, NOE 4.013285E-02, c-dihedral 0.284467
Violations:  bond 0, angle 6, dihedral 0,
             improper 0, NOE 10, c-dihedral 0
Handedness -1, enantiomer discrimination 27231.3:7674.96
 X-PLOR> 
Energy:      bond 6.29757, angle 82.0422, dihedral 0,
             improper 10.1442, NOE 64.0165, c-dihedral 1.01445,
             planar 11.0051, VdW 123.987, total 298.507
RMSD:        bond 1.982593E-03, angle 0.642821, dihedral 0,
             improper 0.302042, NOE 2.626466E-02, c-dihedral 0.143201
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 3, c-dihedral 0
Handedness 1, enantiomer discrimination 8653.55:23129.6
 X-PLOR> 
Energy:      bond 6.83591, angle 103.384, dihedral 0,
             improper 17.8236, NOE 67.0964, c-dihedral 2.34858,
             planar 10.3814, VdW 155.814, total 363.684
RMSD:        bond 2.054421E-03, angle 0.70923, dihedral 0,
             improper 0.448378, NOE 2.688906E-02, c-dihedral 0.217887
Violations:  bond 0, angle 2, dihedral 0,
             improper 0, NOE 3, c-dihedral 0
Handedness -1, enantiomer discrimination 33011.4:8050.22
 X-PLOR> 
Energy:      bond 13.7119, angle 116.256, dihedral 0,
             improper 15.0779, NOE 120.966, c-dihedral 5.80054,
             planar 8.9191, VdW 177.561, total 458.293
RMSD:        bond 2.854683E-03, angle 0.740652, dihedral 0,
             improper 0.395744, NOE 3.610423E-02, c-dihedral 0.342424
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 5, c-dihedral 0
Handedness -1, enantiomer discrimination 29732.4:8804.64
 X-PLOR> 
Energy:      bond 5.00497, angle 77.3692, dihedral 0,
             improper 11.4953, NOE 33.1543, c-dihedral 0.138008,
             planar 8.78684, VdW 128.215, total 264.164
RMSD:        bond 1.745134E-03, angle 0.623485, dihedral 0,
             improper 0.336235, NOE 1.890149E-02, c-dihedral 5.281796E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness 1, enantiomer discrimination 6252.63:32002.7
 X-PLOR> 
Energy:      bond 4.46327, angle 74.0568, dihedral 0,
             improper 11.3776, NOE 29.7519, c-dihedral 0.318286,
             planar 9.74649, VdW 122.672, total 252.387
RMSD:        bond 1.638185E-03, angle 0.610755, dihedral 0,
             improper 0.328203, NOE 1.790537E-02, c-dihedral 8.021177E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness -1, enantiomer discrimination 24711.3:6059.8
 X-PLOR> 
Energy:      bond 5.26995, angle 88.9759, dihedral 0,
             improper 10.9464, NOE 32.1239, c-dihedral 0.550161,
             planar 8.28057, VdW 132.16, total 278.307
RMSD:        bond 1.799612E-03, angle 0.667412, dihedral 0,
             improper 0.322085, NOE 1.860545E-02, c-dihedral 0.105457
Violations:  bond 0, angle 1, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness -1, enantiomer discrimination 26990.8:7844.89
 X-PLOR> 
Energy:      bond 5.40724, angle 84.3604, dihedral 0,
             improper 10.2789, NOE 31.8027, c-dihedral 0.173655,
             planar 9.33801, VdW 123.567, total 264.927
RMSD:        bond 1.789621E-03, angle 0.64195, dihedral 0,
             improper 0.29987, NOE 1.851218E-02, c-dihedral 5.924798E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness -1, enantiomer discrimination 29517.3:6564.07
 X-PLOR> 
Energy:      bond 6.53166, angle 84.7209, dihedral 0,
             improper 15.532, NOE 51.1307, c-dihedral 1.31549,
             planar 8.80964, VdW 137.403, total 305.443
RMSD:        bond 1.999104E-03, angle 0.660653, dihedral 0,
             improper 0.410605, NOE 2.347291E-02, c-dihedral 0.16307
Violations:  bond 0, angle 1, dihedral 0,
             improper 0, NOE 1, c-dihedral 0
Handedness -1, enantiomer discrimination 30704:6183.34
 X-PLOR> 
Energy:      bond 5.49573, angle 85.7651, dihedral 0,
             improper 9.76151, NOE 31.3762, c-dihedral 0.823867,
             planar 8.10678, VdW 121.804, total 263.133
RMSD:        bond 1.814732E-03, angle 0.646841, dihedral 0,
             improper 0.288219, NOE 1.838765E-02, c-dihedral 0.12905
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness -1, enantiomer discrimination 28113.1:10998.6
 X-PLOR> 
Energy:      bond 5.58225, angle 77.1977, dihedral 0,
             improper 10.6323, NOE 30.1826, c-dihedral 0.232036,
             planar 8.67506, VdW 122.962, total 255.464
RMSD:        bond 1.809896E-03, angle 0.615385, dihedral 0,
             improper 0.313497, NOE 1.803451E-02, c-dihedral 6.848684E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness -1, enantiomer discrimination 25198.4:7956.69
 X-PLOR> 
Energy:      bond 5.13891, angle 85.1997, dihedral 0,
             improper 10.6193, NOE 30.3197, c-dihedral 0.2347,
             planar 9.40499, VdW 124.617, total 265.535
RMSD:        bond 1.749242E-03, angle 0.647939, dihedral 0,
             improper 0.314735, NOE 1.807543E-02, c-dihedral 6.887884E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness 1, enantiomer discrimination 10244.4:49810.6
 X-PLOR> 
Energy:      bond 4.65062, angle 73.7207, dihedral 0,
             improper 12.3936, NOE 37.0746, c-dihedral 1.11686,
             planar 9.45004, VdW 126.55, total 264.957
RMSD:        bond 1.68665E-03, angle 0.616676, dihedral 0,
             improper 0.362439, NOE 1.998777E-02, c-dihedral 0.150255
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 1, c-dihedral 0
Handedness -1, enantiomer discrimination 28125.2:5885.38
 X-PLOR> 
Energy:      bond 8.14897, angle 94.4384, dihedral 0,
             improper 14.1336, NOE 62.0362, c-dihedral 1.87612,
             planar 9.55377, VdW 145.476, total 335.663
RMSD:        bond 2.31537E-03, angle 0.672277, dihedral 0,
             improper 0.386857, NOE 2.585523E-02, c-dihedral 0.194742
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 2, c-dihedral 0
Handedness -1, enantiomer discrimination 23128.5:6021.17
 X-PLOR> 
Energy:      bond 4.64367, angle 78.113, dihedral 0,
             improper 10.4032, NOE 27.9669, c-dihedral 0.296144,
             planar 8.1771, VdW 124.128, total 253.728
RMSD:        bond 1.663E-03, angle 0.622537, dihedral 0,
             improper 0.307507, NOE 1.735993E-02, c-dihedral 7.73715E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
Handedness 1, enantiomer discrimination 8178.76:29096.5
 X-PLOR> 
Energy:      bond 6.14007, angle 81.9247, dihedral 0,
             improper 13.7242, NOE 51.7972, c-dihedral 1.54088,
             planar 9.88652, VdW 128.557, total 293.57
RMSD:        bond 1.945851E-03, angle 0.635274, dihedral 0,
             improper 0.391619, NOE 2.36254E-02, c-dihedral 0.176487
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 1, c-dihedral 0
Handedness -1, enantiomer discrimination 25525.8:6195.14
 X-PLOR> 
Energy:      bond 470.913, angle 842.622, dihedral 0,
             improper 772.189, NOE 3550.62, c-dihedral 206.649,
             planar 348.621, VdW 3649.15, total 9840.77
RMSD:        bond 2.056123E-02, angle 2.75644, dihedral 0,
             improper 3.83389, NOE 0.195604, c-dihedral 2.04383
Violations:  bond 26, angle 39, dihedral 0,
             improper 43, NOE 119, c-dihedral 6
Handedness -1, enantiomer discrimination 28050.9:9033.63
 X-PLOR> 
Energy:      bond 12.4425, angle 122.021, dihedral 0,
             improper 20.0433, NOE 90.2992, c-dihedral 9.43853,
             planar 8.7171, VdW 147.654, total 410.616
RMSD:        bond 2.709058E-03, angle 0.760379, dihedral 0,
             improper 0.490084, NOE 3.119378E-02, c-dihedral 0.436799
Violations:  bond 0, angle 1, dihedral 0,
             improper 0, NOE 4, c-dihedral 0
Handedness -1, enantiomer discrimination 40420.8:9090.39
 X-PLOR> 
X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.083
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.449
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.115
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.422
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.051
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.095
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 ========================================
 A    11   ADE  C3' 
 A    11   ADE  O3' 
 A    12   URI  P   
 A    12   URI  O5' 
 Dihedral=  -32.957  Energy=    0.020 C=    1.000 Equil=  -71.000 Delta=   -8.043
 Range=  30.000 Exponent=  2
 ========================================
 A    11   ADE  O4' 
 A    11   ADE  C1' 
 A    11   ADE  N9  
 A    11   ADE  C4  
 Dihedral= -122.877  Energy=    0.008 C=    1.000 Equil= -158.000 Delta=   -5.123
 Range=  30.000 Exponent=  2
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     2
 RMS deviation=   0.734
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.048
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.573
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.295
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.100
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.089
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.284
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.143
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.218
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.342
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.053
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.080
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.105
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.059
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.163
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.129
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.068
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.069
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.150
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.195
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.077
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.176
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 ========================================
 A    1    GUA  O4' 
 A    1    GUA  C1' 
 A    1    GUA  N9  
 A    1    GUA  C4  
 Dihedral=  167.133  Energy=    0.120 C=    1.000 Equil= -158.000 Delta=   19.867
 Range=  15.000 Exponent=  2
 ========================================
 A    2    GUA  C4' 
 A    2    GUA  C3' 
 A    2    GUA  O3' 
 A    3    CYT  P   
 Dihedral= -178.167  Energy=    0.031 C=    1.000 Equil= -153.000 Delta=   10.167
 Range=  15.000 Exponent=  2
 ========================================
 A    2    GUA  O4' 
 A    2    GUA  C1' 
 A    2    GUA  N9  
 A    2    GUA  C4  
 Dihedral= -179.338  Energy=    0.012 C=    1.000 Equil= -158.000 Delta=    6.338
 Range=  15.000 Exponent=  2
 ========================================
 A    3    CYT  P   
 A    3    CYT  O5' 
 A    3    CYT  C5' 
 A    3    CYT  C4' 
 Dihedral=  154.852  Energy=    0.020 C=    1.000 Equil=  178.000 Delta=    8.148
 Range=  15.000 Exponent=  2
 ========================================
 A    3    CYT  C4' 
 A    3    CYT  C3' 
 A    3    CYT  O3' 
 A    4    ADE  P   
 Dihedral= -175.965  Energy=    0.019 C=    1.000 Equil= -153.000 Delta=    7.965
 Range=  15.000 Exponent=  2
 ========================================
 A    21   CYT  O4' 
 A    21   CYT  C1' 
 A    21   CYT  N1  
 A    21   CYT  C2  
 Dihedral= -132.513  Energy=    0.033 C=    1.000 Equil= -158.000 Delta=  -10.487
 Range=  15.000 Exponent=  2
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     6
 RMS deviation=   2.044
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.437
X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H4' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.737 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.263  E(NOE)=   6.942
 ========================================
 set-i-atoms
          A    12   URI  H1' 
 set-j-atoms
          A    13   ADE  H8  
 R=   5.310 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.310  E(NOE)=   9.634

 NOEPRI: RMS diff. =   0.023,  #(violat.> 0.2)=     2 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.274 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.274  E(NOE)=   7.495
 ========================================
 set-i-atoms
          A    10   CYT  H6  
 set-j-atoms
          A    11   ADE  H8  
 R=   2.739 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.261  E(NOE)=   6.807
 ========================================
 set-i-atoms
          A    10   CYT  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.252 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.252  E(NOE)=   6.341
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.386 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.386  E(NOE)=  14.921
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.779 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.221  E(NOE)=   4.879
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.306 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.306  E(NOE)=   9.339
 ========================================
 set-i-atoms
          A    13   ADE  H3' 
 set-j-atoms
          A    14   ADE  H8  
 R=   3.224 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.224  E(NOE)=   4.999

 NOEPRI: RMS diff. =   0.031,  #(violat.> 0.2)=     7 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.359 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.359  E(NOE)=  12.910
 ========================================
 set-i-atoms
          A    10   CYT  H1' 
 set-j-atoms
          A    11   ADE  H8  
 R=   2.423 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.577  E(NOE)=  33.299
 ========================================
 set-i-atoms
          A    10   CYT  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.326 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.326  E(NOE)=  10.624
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.882 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.882  E(NOE)=  77.747
 ========================================
 set-i-atoms
          A    10   CYT  H4' 
 set-j-atoms
          A    11   ADE  H8  
 R=   2.293 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.707  E(NOE)=  50.038

 NOEPRI: RMS diff. =   0.049,  #(violat.> 0.2)=     5 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.668 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.332  E(NOE)=  11.043
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.309 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.309  E(NOE)=   9.568
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.222 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.222  E(NOE)=   4.929

 NOEPRI: RMS diff. =   0.025,  #(violat.> 0.2)=     3 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    10   CYT  H1' 
 set-j-atoms
          A    11   ADE  H8  
 R=   5.652 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.652  E(NOE)=  42.469
 ========================================
 set-i-atoms
          A    10   CYT  H4' 
 set-j-atoms
          A    11   ADE  H8  
 R=   5.445 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.445  E(NOE)=  19.770
 ========================================
 set-i-atoms
          A    11   ADE  H2' 
 set-j-atoms
          A    12   URI  H6  
 R=   4.557 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.557  E(NOE)=  31.038
 ========================================
 set-i-atoms
          A    12   URI  H1' 
 set-j-atoms
          A    12   URI  H4' 
 R=   2.738 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.262  E(NOE)=   6.888
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.222 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.222  E(NOE)=   4.912

 NOEPRI: RMS diff. =   0.041,  #(violat.> 0.2)=     5 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.472 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.472  E(NOE)=  22.246
 ========================================
 set-i-atoms
          A    10   CYT  H6  
 set-j-atoms
          A    10   CYT  H3' 
 R=   4.239 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.239  E(NOE)=   5.696
 ========================================
 set-i-atoms
          A    10   CYT  H1' 
 set-j-atoms
          A    11   ADE  H8  
 R=   5.446 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.446  E(NOE)=  19.863
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.357 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.357  E(NOE)=  12.754
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.318 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.318  E(NOE)=  10.120
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.492 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.492  E(NOE)=  24.247

 NOEPRI: RMS diff. =   0.039,  #(violat.> 0.2)=     6 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H1' 
 set-j-atoms
          A    10   CYT  H2' 
 R=   5.326 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.326  E(NOE)=  10.611
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.248 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.248  E(NOE)=   6.132
 ========================================
 set-i-atoms
          A    10   CYT  H6  
 set-j-atoms
          A    11   ADE  H8  
 R=   2.733 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.267  E(NOE)=   7.131
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.617 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.617  E(NOE)=  38.099
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    11   ADE  H3' 
 R=   3.313 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.313  E(NOE)=   9.801
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    12   URI  H3' 
 R=   4.320 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.320  E(NOE)=  10.257
 ========================================
 set-i-atoms
          A    12   URI  H1' 
 set-j-atoms
          A    13   ADE  H8  
 R=   5.259 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.259  E(NOE)=   6.715

 NOEPRI: RMS diff. =   0.038,  #(violat.> 0.2)=     7 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H4' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.749 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.251  E(NOE)=   6.294
 ========================================
 set-i-atoms
          A    12   URI  H1' 
 set-j-atoms
          A    13   ADE  H8  
 R=   5.316 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.316  E(NOE)=   9.968

 NOEPRI: RMS diff. =   0.023,  #(violat.> 0.2)=     2 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H1' 
 set-j-atoms
          A    10   CYT  H2' 
 R=   5.209 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.209  E(NOE)=   4.387
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.250 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.250  E(NOE)=   6.245
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.324 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.324  E(NOE)=  10.482
 ========================================
 set-i-atoms
          A    10   CYT  H4' 
 set-j-atoms
          A    11   ADE  H8  
 R=   2.790 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.210  E(NOE)=   4.408
 ========================================
 set-i-atoms
          A    11   ADE  H2  
 set-j-atoms
          A    12   URI  H1' 
 R=   5.451 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.451  E(NOE)=  20.298
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.493 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.493  E(NOE)=  24.291
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.679 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.321  E(NOE)=  10.297
 ========================================
 set-i-atoms
          A    12   URI  H3' 
 set-j-atoms
          A    13   ADE  H8  
 R=   3.437 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.437  E(NOE)=  19.067
 ========================================
 set-i-atoms
          A    14   ADE  H3' 
 set-j-atoms
          A    15   CYT  H1' 
 R=   5.206 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.206  E(NOE)=   4.263
 ========================================
 set-i-atoms
          A    11   ADE  H1' 
 set-j-atoms
          A    12   URI  H6  
 R=   2.675 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.325  E(NOE)=  10.564

 NOEPRI: RMS diff. =   0.040,  #(violat.> 0.2)=    10 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.690 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.310  E(NOE)=   9.637
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.375 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.375  E(NOE)=  14.072
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.213 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.213  E(NOE)=   4.534

 NOEPRI: RMS diff. =   0.026,  #(violat.> 0.2)=     3 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.339 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.339  E(NOE)=  11.487
 ========================================
 set-i-atoms
          A    12   URI  H4' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.762 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.238  E(NOE)=   5.641
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.331 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.331  E(NOE)=  10.960

 NOEPRI: RMS diff. =   0.027,  #(violat.> 0.2)=     3 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H6  
 set-j-atoms
          A    9    URI  H3' 
 R=   2.797 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.203  E(NOE)=   4.105
 ========================================
 set-i-atoms
          A    9    URI  H1' 
 set-j-atoms
          A    10   CYT  H2' 
 R=   5.472 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.472  E(NOE)=  22.306
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.334 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.334  E(NOE)=  11.124
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.485 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.485  E(NOE)=  23.564
 ========================================
 set-i-atoms
          A    10   CYT  H4' 
 set-j-atoms
          A    11   ADE  H8  
 R=   2.569 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.431  E(NOE)=  18.598

 NOEPRI: RMS diff. =   0.036,  #(violat.> 0.2)=     5 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.019,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.019,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.019,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.307 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.307  E(NOE)=   9.398

 NOEPRI: RMS diff. =   0.023,  #(violat.> 0.2)=     1 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.276 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.276  E(NOE)=   7.598

 NOEPRI: RMS diff. =   0.020,  #(violat.> 0.2)=     1 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H4' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.799 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.201  E(NOE)=   4.054
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.464 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.464  E(NOE)=  21.488

 NOEPRI: RMS diff. =   0.026,  #(violat.> 0.2)=     2 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.017,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.318 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.318  E(NOE)=  10.096

 NOEPRI: RMS diff. =   0.024,  #(violat.> 0.2)=     1 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    1    GUA  H1' 
 set-j-atoms
          A    1    GUA  H3' 
 R=   3.544 NOE= 3.86 (- 0.10/+ 0.10) Delta=   0.213  E(NOE)=   4.518
 ========================================
 set-i-atoms
          A    1    GUA  H1' 
 set-j-atoms
          A    1    GUA  H21 
 R=   6.100 NOE= 4.77 (- 0.10/+ 0.10) Delta=  -1.226  E(NOE)= 150.226
 ========================================
 set-i-atoms
          A    1    GUA  H1' 
 set-j-atoms
          A    1    GUA  H8  
 R=   3.346 NOE= 3.73 (- 0.10/+ 0.10) Delta=   0.281  E(NOE)=   7.870
 ========================================
 set-i-atoms
          A    1    GUA  H1' 
 set-j-atoms
          A    2    GUA  H8  
 R=   2.886 NOE= 4.32 (- 0.10/+ 0.10) Delta=   1.333  E(NOE)= 177.820
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    1    GUA  H21 
 R=   4.011 NOE= 4.70 (- 0.10/+ 0.10) Delta=   0.591  E(NOE)=  34.965
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    1    GUA  H8  
 R=   4.450 NOE= 4.15 (- 0.10/+ 0.10) Delta=  -0.201  E(NOE)=   4.035
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    2    GUA  H1' 
 R=   4.642 NOE= 4.19 (- 0.10/+ 0.10) Delta=  -0.349  E(NOE)=  12.189
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    2    GUA  H3' 
 R=   3.826 NOE= 4.26 (- 0.10/+ 0.10) Delta=   0.337  E(NOE)=  11.384
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    2    GUA  H5' 
 R=   2.590 NOE= 2.89 (- 0.10/+ 0.10) Delta=   0.200  E(NOE)=   4.007
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    2    GUA  H5''
 R=   3.803 NOE= 4.27 (- 0.10/+ 0.10) Delta=   0.365  E(NOE)=  13.293
 ========================================
 set-i-atoms
          A    1    GUA  H3' 
 set-j-atoms
          A    2    GUA  H8  
 R=   3.896 NOE= 3.02 (- 0.10/+ 0.10) Delta=  -0.772  E(NOE)=  59.523
 ========================================
 set-i-atoms
          A    1    GUA  H21 
 set-j-atoms
          A    2    GUA  H1' 
 R=   3.797 NOE= 3.25 (- 0.10/+ 0.10) Delta=  -0.442  E(NOE)=  19.519
 ========================================
 set-i-atoms
          A    1    GUA  H21 
 set-j-atoms
          A    2    GUA  H8  
 R=   3.388 NOE= 4.88 (- 0.10/+ 0.10) Delta=   1.388  E(NOE)= 192.641
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    2    GUA  H1' 
 R=   4.513 NOE= 4.21 (- 0.10/+ 0.10) Delta=  -0.208  E(NOE)=   4.328
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    2    GUA  H1  
 R=   5.138 NOE= 4.79 (- 0.10/+ 0.10) Delta=  -0.248  E(NOE)=   6.139
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    21   CYT  H1' 
 R=   3.405 NOE= 4.32 (- 0.10/+ 0.10) Delta=   0.812  E(NOE)=  66.009
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    21   CYT  H2' 
 R=   5.596 NOE= 4.67 (- 0.10/+ 0.10) Delta=  -0.829  E(NOE)=  68.735
 ========================================
 set-i-atoms
          A    1    GUA  H1  
 set-j-atoms
          A    20   CYT  H42 
 R=   5.057 NOE= 4.75 (- 0.10/+ 0.10) Delta=  -0.209  E(NOE)=   4.355
 ========================================
 set-i-atoms
          A    2    GUA  H1' 
 set-j-atoms
          A    2    GUA  H21 
 R=   5.319 NOE= 4.78 (- 0.10/+ 0.10) Delta=  -0.444  E(NOE)=  19.711
 ========================================
 set-i-atoms
          A    2    GUA  H1' 
 set-j-atoms
          A    2    GUA  H8  
 R=   3.395 NOE= 3.73 (- 0.10/+ 0.10) Delta=   0.232  E(NOE)=   5.380
 ========================================
 set-i-atoms
          A    2    GUA  H1' 
 set-j-atoms
          A    3    CYT  H6  
 R=   3.732 NOE= 4.30 (- 0.10/+ 0.10) Delta=   0.466  E(NOE)=  21.753
 ========================================
 set-i-atoms
          A    2    GUA  H2' 
 set-j-atoms
          A    2    GUA  H21 
 R=   4.295 NOE= 4.70 (- 0.10/+ 0.10) Delta=   0.307  E(NOE)=   9.404
 ========================================
 set-i-atoms
          A    2    GUA  H2' 
 set-j-atoms
          A    3    CYT  H1' 
 R=   3.446 NOE= 4.19 (- 0.10/+ 0.10) Delta=   0.646  E(NOE)=  41.732
 ========================================
 set-i-atoms
          A    2    GUA  H2' 
 set-j-atoms
          A    3    CYT  H3' 
 R=   3.924 NOE= 4.26 (- 0.10/+ 0.10) Delta=   0.239  E(NOE)=   5.704
 ========================================
 set-i-atoms
          A    2    GUA  H2' 
 set-j-atoms
          A    3    CYT  H4' 
 R=   4.004 NOE= 4.44 (- 0.10/+ 0.10) Delta=   0.338  E(NOE)=  11.393
 ========================================
 set-i-atoms
          A    2    GUA  H2' 
 set-j-atoms
          A    3    CYT  H5''
 R=   3.742 NOE= 4.27 (- 0.10/+ 0.10) Delta=   0.426  E(NOE)=  18.153
 ========================================
 set-i-atoms
          A    2    GUA  H3' 
 set-j-atoms
          A    2    GUA  H8  
 R=   3.633 NOE= 3.20 (- 0.10/+ 0.10) Delta=  -0.337  E(NOE)=  11.390
 ========================================
 set-i-atoms
          A    2    GUA  H3' 
 set-j-atoms
          A    3    CYT  H5' 
 R=   4.339 NOE= 3.96 (- 0.10/+ 0.10) Delta=  -0.281  E(NOE)=   7.880
 ========================================
 set-i-atoms
          A    2    GUA  H3' 
 set-j-atoms
          A    3    CYT  H5''
 R=   5.278 NOE= 4.91 (- 0.10/+ 0.10) Delta=  -0.270  E(NOE)=   7.267
 ========================================
 set-i-atoms
          A    2    GUA  H3' 
 set-j-atoms
          A    3    CYT  H5  
 R=   3.821 NOE= 3.31 (- 0.10/+ 0.10) Delta=  -0.407  E(NOE)=  16.550
 ========================================
 set-i-atoms
          A    2    GUA  H5''
 set-j-atoms
          A    2    GUA  H8  
 R=   4.853 NOE= 4.37 (- 0.10/+ 0.10) Delta=  -0.385  E(NOE)=  14.795
 ========================================
 set-i-atoms
          A    2    GUA  H21 
 set-j-atoms
          A    3    CYT  H1' 
 R=   3.921 NOE= 3.25 (- 0.10/+ 0.10) Delta=  -0.566  E(NOE)=  32.085
 ========================================
 set-i-atoms
          A    2    GUA  H21 
 set-j-atoms
          A    3    CYT  H6  
 R=   3.278 NOE= 4.83 (- 0.10/+ 0.10) Delta=   1.448  E(NOE)= 209.657
 ========================================
 set-i-atoms
          A    2    GUA  H21 
 set-j-atoms
          A    19   GUA  H22 
 R=   5.095 NOE= 4.57 (- 0.10/+ 0.10) Delta=  -0.424  E(NOE)=  17.951
 ========================================
 set-i-atoms
          A    2    GUA  H21 
 set-j-atoms
          A    21   CYT  H1' 
 R=   5.027 NOE= 4.49 (- 0.10/+ 0.10) Delta=  -0.434  E(NOE)=  18.814
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    3    CYT  H1' 
 R=   4.789 NOE= 4.21 (- 0.10/+ 0.10) Delta=  -0.484  E(NOE)=  23.438
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    19   GUA  H21 
 R=   5.222 NOE= 4.57 (- 0.10/+ 0.10) Delta=  -0.551  E(NOE)=  30.332
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    19   GUA  H22 
 R=   4.175 NOE= 3.56 (- 0.10/+ 0.10) Delta=  -0.510  E(NOE)=  26.012
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    19   GUA  H1  
 R=   4.515 NOE= 4.14 (- 0.10/+ 0.10) Delta=  -0.278  E(NOE)=   7.746
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    20   CYT  H1' 
 R=   5.027 NOE= 4.32 (- 0.10/+ 0.10) Delta=  -0.610  E(NOE)=  37.255
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    20   CYT  H2' 
 R=   5.331 NOE= 4.67 (- 0.10/+ 0.10) Delta=  -0.565  E(NOE)=  31.929
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    21   CYT  H1' 
 R=   4.701 NOE= 4.37 (- 0.10/+ 0.10) Delta=  -0.227  E(NOE)=   5.134
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    21   CYT  H6  
 R=   5.490 NOE= 4.96 (- 0.10/+ 0.10) Delta=  -0.429  E(NOE)=  18.374
 ========================================
 set-i-atoms
          A    2    GUA  H8  
 set-j-atoms
          A    3    CYT  H5  
 R=   4.434 NOE= 3.90 (- 0.10/+ 0.10) Delta=  -0.435  E(NOE)=  18.884
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    3    CYT  H41 
 R=   3.583 NOE= 4.35 (- 0.10/+ 0.10) Delta=   0.670  E(NOE)=  44.838
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    3    CYT  H42 
 R=   3.210 NOE= 3.75 (- 0.10/+ 0.10) Delta=   0.438  E(NOE)=  19.214
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    3    CYT  H5  
 R=   4.266 NOE= 4.95 (- 0.10/+ 0.10) Delta=   0.584  E(NOE)=  34.057
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    20   CYT  H41 
 R=   4.592 NOE= 4.02 (- 0.10/+ 0.10) Delta=  -0.470  E(NOE)=  22.097
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    20   CYT  H42 
 R=   2.886 NOE= 2.48 (- 0.10/+ 0.10) Delta=  -0.308  E(NOE)=   9.470
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    21   CYT  H41 
 R=   3.610 NOE= 4.08 (- 0.10/+ 0.10) Delta=   0.374  E(NOE)=  14.018
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    21   CYT  H42 
 R=   2.577 NOE= 3.89 (- 0.10/+ 0.10) Delta=   1.211  E(NOE)= 146.547
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    21   CYT  H5  
 R=   5.166 NOE= 4.40 (- 0.10/+ 0.10) Delta=  -0.668  E(NOE)=  44.644
 ========================================
 set-i-atoms
          A    3    CYT  H1' 
 set-j-atoms
          A    4    ADE  H5' 
 R=   4.262 NOE= 4.68 (- 0.10/+ 0.10) Delta=   0.314  E(NOE)=   9.854
 ========================================
 set-i-atoms
          A    3    CYT  H2' 
 set-j-atoms
          A    4    ADE  H1' 
 R=   3.697 NOE= 4.19 (- 0.10/+ 0.10) Delta=   0.395  E(NOE)=  15.578
 ========================================
 set-i-atoms
          A    3    CYT  H2' 
 set-j-atoms
          A    4    ADE  H4' 
 R=   4.058 NOE= 4.44 (- 0.10/+ 0.10) Delta=   0.284  E(NOE)=   8.083
 ========================================
 set-i-atoms
          A    3    CYT  H3' 
 set-j-atoms
          A    3    CYT  H5' 
 R=   4.037 NOE= 3.69 (- 0.10/+ 0.10) Delta=  -0.251  E(NOE)=   6.283
 ========================================
 set-i-atoms
          A    3    CYT  H3' 
 set-j-atoms
          A    4    ADE  H5''
 R=   5.286 NOE= 4.91 (- 0.10/+ 0.10) Delta=  -0.278  E(NOE)=   7.734
 ========================================
 set-i-atoms
          A    3    CYT  H3' 
 set-j-atoms
          A    4    ADE  H8  
 R=   3.480 NOE= 3.03 (- 0.10/+ 0.10) Delta=  -0.347  E(NOE)=  12.075
 ========================================
 set-i-atoms
          A    3    CYT  H5' 
 set-j-atoms
          A    3    CYT  H6  
 R=   3.648 NOE= 3.24 (- 0.10/+ 0.10) Delta=  -0.307  E(NOE)=   9.450
 ========================================
 set-i-atoms
          A    3    CYT  H5''
 set-j-atoms
          A    3    CYT  H6  
 R=   3.679 NOE= 4.06 (- 0.10/+ 0.10) Delta=   0.277  E(NOE)=   7.671
 ========================================
 set-i-atoms
          A    3    CYT  HO2'
 set-j-atoms
          A    4    ADE  H5' 
 R=   2.606 NOE= 2.94 (- 0.10/+ 0.10) Delta=   0.235  E(NOE)=   5.526
 ========================================
 set-i-atoms
          A    3    CYT  H41 
 set-j-atoms
          A    4    ADE  H61 
 R=   4.180 NOE= 3.57 (- 0.10/+ 0.10) Delta=  -0.514  E(NOE)=  26.424
 ========================================
 set-i-atoms
          A    3    CYT  H41 
 set-j-atoms
          A    20   CYT  H41 
 R=   4.490 NOE= 4.82 (- 0.10/+ 0.10) Delta=   0.227  E(NOE)=   5.169
 ========================================
 set-i-atoms
          A    3    CYT  H42 
 set-j-atoms
          A    19   GUA  H22 
 R=   3.308 NOE= 4.57 (- 0.10/+ 0.10) Delta=   1.159  E(NOE)= 134.276
 ========================================
 set-i-atoms
          A    3    CYT  H42 
 set-j-atoms
          A    20   CYT  H41 
 R=   3.395 NOE= 3.71 (- 0.10/+ 0.10) Delta=   0.210  E(NOE)=   4.393
 ========================================
 set-i-atoms
          A    3    CYT  H6  
 set-j-atoms
          A    4    ADE  H8  
 R=   5.172 NOE= 4.78 (- 0.10/+ 0.10) Delta=  -0.295  E(NOE)=   8.690
 ========================================
 set-i-atoms
          A    3    CYT  H5  
 set-j-atoms
          A    4    ADE  H61 
 R=   5.631 NOE= 4.82 (- 0.10/+ 0.10) Delta=  -0.710  E(NOE)=  50.443
 ========================================
 set-i-atoms
          A    4    ADE  H1' 
 set-j-atoms
          A    19   GUA  H21 
 R=   5.400 NOE= 4.49 (- 0.10/+ 0.10) Delta=  -0.806  E(NOE)=  64.893
 ========================================
 set-i-atoms
          A    4    ADE  H1' 
 set-j-atoms
          A    19   GUA  H22 
 R=   3.855 NOE= 4.37 (- 0.10/+ 0.10) Delta=   0.419  E(NOE)=  17.558
 ========================================
 set-i-atoms
          A    4    ADE  H5''
 set-j-atoms
          A    4    ADE  H8  
 R=   3.881 NOE= 4.33 (- 0.10/+ 0.10) Delta=   0.344  E(NOE)=  11.814
 ========================================
 set-i-atoms
          A    4    ADE  H62 
 set-j-atoms
          A    18   URI  H3  
 R=   2.704 NOE= 2.40 (- 0.10/+ 0.10) Delta=  -0.208  E(NOE)=   4.337
 ========================================
 set-i-atoms
          A    4    ADE  H62 
 set-j-atoms
          A    19   GUA  H1  
 R=   3.818 NOE= 4.42 (- 0.10/+ 0.10) Delta=   0.500  E(NOE)=  24.951
 ========================================
 set-i-atoms
          A    4    ADE  H61 
 set-j-atoms
          A    17   CYT  H42 
 R=   4.897 NOE= 4.58 (- 0.10/+ 0.10) Delta=  -0.218  E(NOE)=   4.773
 ========================================
 set-i-atoms
          A    4    ADE  H2  
 set-j-atoms
          A    19   GUA  H1' 
 R=   5.876 NOE= 4.66 (- 0.10/+ 0.10) Delta=  -1.118  E(NOE)= 124.923
 ========================================
 set-i-atoms
          A    5    GUA  H22 
 set-j-atoms
          A    18   URI  H1' 
 R=   4.698 NOE= 4.37 (- 0.10/+ 0.10) Delta=  -0.224  E(NOE)=   5.030
 ========================================
 set-i-atoms
          A    5    GUA  H22 
 set-j-atoms
          A    18   URI  H3  
 R=   4.524 NOE= 4.86 (- 0.10/+ 0.10) Delta=   0.236  E(NOE)=   5.548
 ========================================
 set-i-atoms
          A    18   URI  H1' 
 set-j-atoms
          A    18   URI  HO2'
 R=   3.293 NOE= 2.99 (- 0.10/+ 0.10) Delta=  -0.203  E(NOE)=   4.116
 ========================================
 set-i-atoms
          A    18   URI  H1' 
 set-j-atoms
          A    19   GUA  H5' 
 R=   5.125 NOE= 4.68 (- 0.10/+ 0.10) Delta=  -0.348  E(NOE)=  12.101
 ========================================
 set-i-atoms
          A    18   URI  HO2'
 set-j-atoms
          A    19   GUA  H4' 
 R=   4.060 NOE= 3.52 (- 0.10/+ 0.10) Delta=  -0.439  E(NOE)=  19.271
 ========================================
 set-i-atoms
          A    18   URI  H6  
 set-j-atoms
          A    19   GUA  H8  
 R=   4.374 NOE= 4.76 (- 0.10/+ 0.10) Delta=   0.287  E(NOE)=   8.218
 ========================================
 set-i-atoms
          A    19   GUA  H1' 
 set-j-atoms
          A    19   GUA  H21 
 R=   4.406 NOE= 4.78 (- 0.10/+ 0.10) Delta=   0.269  E(NOE)=   7.261
 ========================================
 set-i-atoms
          A    19   GUA  H2' 
 set-j-atoms
          A    19   GUA  H8  
 R=   3.804 NOE= 4.15 (- 0.10/+ 0.10) Delta=   0.245  E(NOE)=   5.982
 ========================================
 set-i-atoms
          A    19   GUA  H3' 
 set-j-atoms
          A    19   GUA  H8  
 R=   2.744 NOE= 3.20 (- 0.10/+ 0.10) Delta=   0.352  E(NOE)=  12.378
 ========================================
 set-i-atoms
          A    19   GUA  H4' 
 set-j-atoms
          A    20   CYT  H5' 
 R=   4.472 NOE= 4.17 (- 0.10/+ 0.10) Delta=  -0.205  E(NOE)=   4.196
 ========================================
 set-i-atoms
          A    19   GUA  H21 
 set-j-atoms
          A    19   GUA  H1  
 R=   3.165 NOE= 3.48 (- 0.10/+ 0.10) Delta=   0.215  E(NOE)=   4.643
 ========================================
 set-i-atoms
          A    19   GUA  H21 
 set-j-atoms
          A    20   CYT  H1' 
 R=   3.896 NOE= 3.25 (- 0.10/+ 0.10) Delta=  -0.541  E(NOE)=  29.262
 ========================================
 set-i-atoms
          A    19   GUA  H21 
 set-j-atoms
          A    20   CYT  H6  
 R=   5.518 NOE= 4.83 (- 0.10/+ 0.10) Delta=  -0.592  E(NOE)=  35.072
 ========================================
 set-i-atoms
          A    19   GUA  H22 
 set-j-atoms
          A    20   CYT  H1' 
 R=   4.739 NOE= 4.21 (- 0.10/+ 0.10) Delta=  -0.434  E(NOE)=  18.858
 ========================================
 set-i-atoms
          A    19   GUA  H8  
 set-j-atoms
          A    20   CYT  H5  
 R=   3.416 NOE= 3.90 (- 0.10/+ 0.10) Delta=   0.383  E(NOE)=  14.675
 ========================================
 set-i-atoms
          A    19   GUA  H1  
 set-j-atoms
          A    20   CYT  H41 
 R=   4.677 NOE= 4.35 (- 0.10/+ 0.10) Delta=  -0.224  E(NOE)=   5.022
 ========================================
 set-i-atoms
          A    19   GUA  H1  
 set-j-atoms
          A    20   CYT  H5  
 R=   5.534 NOE= 4.95 (- 0.10/+ 0.10) Delta=  -0.484  E(NOE)=  23.397
 ========================================
 set-i-atoms
          A    20   CYT  H4' 
 set-j-atoms
          A    20   CYT  HO2'
 R=   3.412 NOE= 3.78 (- 0.10/+ 0.10) Delta=   0.266  E(NOE)=   7.099
 ========================================
 set-i-atoms
          A    20   CYT  HO2'
 set-j-atoms
          A    21   CYT  H1' 
 R=   3.798 NOE= 4.15 (- 0.10/+ 0.10) Delta=   0.253  E(NOE)=   6.397
 ========================================
 set-i-atoms
          A    20   CYT  H41 
 set-j-atoms
          A    21   CYT  H42 
 R=   3.629 NOE= 4.12 (- 0.10/+ 0.10) Delta=   0.395  E(NOE)=  15.570
 ========================================
 set-i-atoms
          A    20   CYT  H41 
 set-j-atoms
          A    21   CYT  H5  
 R=   4.943 NOE= 4.47 (- 0.10/+ 0.10) Delta=  -0.368  E(NOE)=  13.507
 ========================================
 set-i-atoms
          A    20   CYT  H42 
 set-j-atoms
          A    21   CYT  H41 
 R=   2.709 NOE= 3.06 (- 0.10/+ 0.10) Delta=   0.256  E(NOE)=   6.552
 ========================================
 set-i-atoms
          A    20   CYT  H42 
 set-j-atoms
          A    21   CYT  H42 
 R=   2.604 NOE= 3.26 (- 0.10/+ 0.10) Delta=   0.560  E(NOE)=  31.341
 ========================================
 set-i-atoms
          A    20   CYT  H42 
 set-j-atoms
          A    21   CYT  H5  
 R=   4.695 NOE= 4.39 (- 0.10/+ 0.10) Delta=  -0.202  E(NOE)=   4.085
 ========================================
 set-i-atoms
          A    20   CYT  H6  
 set-j-atoms
          A    21   CYT  H6  
 R=   5.311 NOE= 4.95 (- 0.10/+ 0.10) Delta=  -0.259  E(NOE)=   6.693
 ========================================
 set-i-atoms
          A    20   CYT  H6  
 set-j-atoms
          A    21   CYT  H5  
 R=   4.365 NOE= 4.00 (- 0.10/+ 0.10) Delta=  -0.264  E(NOE)=   6.970
 ========================================
 set-i-atoms
          A    20   CYT  H5  
 set-j-atoms
          A    21   CYT  H41 
 R=   3.571 NOE= 4.05 (- 0.10/+ 0.10) Delta=   0.375  E(NOE)=  14.068
 ========================================
 set-i-atoms
          A    20   CYT  H5  
 set-j-atoms
          A    21   CYT  H5  
 R=   4.424 NOE= 3.99 (- 0.10/+ 0.10) Delta=  -0.330  E(NOE)=  10.900
 ========================================
 set-i-atoms
          A    21   CYT  H2' 
 set-j-atoms
          A    21   CYT  H6  
 R=   3.518 NOE= 4.00 (- 0.10/+ 0.10) Delta=   0.381  E(NOE)=  14.543
 ========================================
 set-i-atoms
          A    21   CYT  H3' 
 set-j-atoms
          A    21   CYT  H6  
 R=   2.615 NOE= 2.99 (- 0.10/+ 0.10) Delta=   0.273  E(NOE)=   7.433
 ========================================
 set-i-atoms
          A    21   CYT  H41 
 set-j-atoms
          A    21   CYT  H6  
 R=   4.219 NOE= 4.65 (- 0.10/+ 0.10) Delta=   0.331  E(NOE)=  10.955
 ========================================
 set-i-atoms
          A    21   CYT  H41 
 set-j-atoms
          A    21   CYT  H5  
 R=   2.000 NOE= 2.42 (- 0.10/+ 0.10) Delta=   0.325  E(NOE)=  10.532
 ========================================
 set-i-atoms
          A    21   CYT  H42 
 set-j-atoms
          A    21   CYT  H5  
 R=   3.094 NOE= 3.71 (- 0.10/+ 0.10) Delta=   0.514  E(NOE)=  26.373
 ========================================
 set-i-atoms
          A    12   URI  H4' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.770 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.230  E(NOE)=   5.289
 ========================================
 set-i-atoms
          A    12   URI  H1' 
 set-j-atoms
          A    13   ADE  H8  
 R=   5.333 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.333  E(NOE)=  11.101
 ========================================
 set-i-atoms
          A    1    GUA  O6  
 set-j-atoms
          A    21   CYT  H42 
 R=   3.005 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -1.005  E(NOE)= 101.051
 ========================================
 set-i-atoms
          A    1    GUA  H1  
 set-j-atoms
          A    21   CYT  N3  
 R=   2.953 NOE= 1.94 (- 0.10/+ 0.10) Delta=  -0.913  E(NOE)=  83.330
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    21   CYT  O2  
 R=   2.594 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -0.594  E(NOE)=  35.296
 ========================================
 set-i-atoms
          A    2    GUA  O6  
 set-j-atoms
          A    20   CYT  H42 
 R=   2.407 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -0.407  E(NOE)=  16.605
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    20   CYT  N3  
 R=   2.905 NOE= 1.94 (- 0.10/+ 0.10) Delta=  -0.865  E(NOE)=  74.850
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    20   CYT  O2  
 R=   2.902 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -0.902  E(NOE)=  81.427
 ========================================
 set-i-atoms
          A    3    CYT  H42 
 set-j-atoms
          A    19   GUA  O6  
 R=   2.764 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -0.764  E(NOE)=  58.419
 ========================================
 set-i-atoms
          A    3    CYT  N3  
 set-j-atoms
          A    19   GUA  H1  
 R=   2.323 NOE= 1.94 (- 0.10/+ 0.10) Delta=  -0.283  E(NOE)=   8.015
 ========================================
 set-i-atoms
          A    3    CYT  O2  
 set-j-atoms
          A    19   GUA  H22 
 R=   2.487 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -0.487  E(NOE)=  23.683
 ========================================
 set-i-atoms
          A    4    ADE  N1  
 set-j-atoms
          A    18   URI  H3  
 R=   2.301 NOE= 1.81 (- 0.10/+ 0.10) Delta=  -0.391  E(NOE)=  15.269

 NOEPRI: RMS diff. =   0.196,  #(violat.> 0.2)=   119 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    7    GUA  H8  
 set-j-atoms
          A    8    CYT  H6  
 R=   5.286 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.286  E(NOE)=   8.159
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.290 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.290  E(NOE)=   8.429
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.353 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.353  E(NOE)=  12.453
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.352 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.352  E(NOE)=  12.395

 NOEPRI: RMS diff. =   0.031,  #(violat.> 0.2)=     4 of    928 NOEs
# Dihedral angle constraints for ITALY2
# A-form values from Arnott and Chandrasekaran (1982) as reported by Sanger (1984)

#  alpha   beta    gamma  epsilon   zeta    chi      nu0       nu1        nu2      nu3       nu4

g  none    none    none   -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
g  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
c  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
a  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
g  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
g  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
g  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
c  -68 30  178 30  54 30  -120 120  -71 30  -158 30    3   30  -25   30   37   30  -36   30  21   30
u  -68 30  178 30  54 30  -120 120  none    -158 30    3   30  -25   30   37   30  -36   30  21   30
c  none    178 30  54 30  -120 120  none    -158 30  none none  none    none      none
a  none    178 30  none   -120 120  -71 30  -158 30  none none  none    none      none
u  -68 30  178 30  none   -120 120  none    -158 30  -21.7 30   35.2 30  -35.2 30   21.8 30   0   30
a  none    178 30  54 30  -120 120  -71 30  -158 30  none none  none    none      none
a  -68 30  178 30  54 30  -120 120  -71 30  -158 30    3   30  -25   30   37   30  -36   30  21   30
c  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
c  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
c  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
u  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
g  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
c  -68 15  178 15  54 15  -153  15  -71 15  -158 15    3   15  -25   15   37   15  -36   15  21   15
c  -68 15  178 15  54 15  none      none    -158 15    3   15  -25   15   37   15  -36   15  21   15
! g1 beta is unconstrained

! g1 gamma is unconstrained

! g1 epsilon
assign (resid 1 and name C4') (resid 1 and name C3')
       (resid 1 and name O3') (resid 2 and name P  )
       1 -153 15 2

! g1 zeta
assign (resid 1 and name C3') (resid 1 and name O3')
       (resid 2 and name P  ) (resid 2 and name O5')
       1 -71 15 2

! g1 chi
assign (resid 1 and name O4') (resid 1 and name C1')
       (resid 1 and name N9 ) (resid 1 and name C4 )
       1 -158 15 2

! g1 nu0
assign (resid 1 and name C4') (resid 1 and name O4')
       (resid 1 and name C1') (resid 1 and name C2')
       1 3 15 2

! g1 nu1
assign (resid 1 and name O4') (resid 1 and name C1')
       (resid 1 and name C2') (resid 1 and name C3')
       1 -25 15 2

! g1 nu2
assign (resid 1 and name C1') (resid 1 and name C2')
       (resid 1 and name C3') (resid 1 and name C4')
       1 37 15 2

! g1 nu3
assign (resid 1 and name C2') (resid 1 and name C3')
       (resid 1 and name C4') (resid 1 and name O4')
       1 -36 15 2

! g1 nu4
assign (resid 1 and name C3') (resid 1 and name C4')
       (resid 1 and name O4') (resid 1 and name C1')
       1 21 15 2

! g2 alpha
assign (resid 1 and name O3') (resid 2 and name P  )
       (resid 2 and name O5') (resid 2 and name C5')
       1 -68 15 2

! g2 beta
assign (resid 2 and name P  ) (resid 2 and name O5')
       (resid 2 and name C5') (resid 2 and name C4')
       1 178 15 2

! g2 gamma
assign (resid 2 and name O5') (resid 2 and name C5')
       (resid 2 and name C4') (resid 2 and name C3')
       1 54 15 2

! g2 epsilon
assign (resid 2 and name C4') (resid 2 and name C3')
       (resid 2 and name O3') (resid 3 and name P  )
       1 -153 15 2

! g2 zeta
assign (resid 2 and name C3') (resid 2 and name O3')
       (resid 3 and name P  ) (resid 3 and name O5')
       1 -71 15 2

! g2 chi
assign (resid 2 and name O4') (resid 2 and name C1')
       (resid 2 and name N9 ) (resid 2 and name C4 )
       1 -158 15 2

! g2 nu0
assign (resid 2 and name C4') (resid 2 and name O4')
       (resid 2 and name C1') (resid 2 and name C2')
       1 3 15 2

! g2 nu1
assign (resid 2 and name O4') (resid 2 and name C1')
       (resid 2 and name C2') (resid 2 and name C3')
       1 -25 15 2

! g2 nu2
assign (resid 2 and name C1') (resid 2 and name C2')
       (resid 2 and name C3') (resid 2 and name C4')
       1 37 15 2

! g2 nu3
assign (resid 2 and name C2') (resid 2 and name C3')
       (resid 2 and name C4') (resid 2 and name O4')
       1 -36 15 2

! g2 nu4
assign (resid 2 and name C3') (resid 2 and name C4')
       (resid 2 and name O4') (resid 2 and name C1')
       1 21 15 2

! c3 alpha
assign (resid 2 and name O3') (resid 3 and name P  )
       (resid 3 and name O5') (resid 3 and name C5')
       1 -68 15 2

! c3 beta
assign (resid 3 and name P  ) (resid 3 and name O5')
       (resid 3 and name C5') (resid 3 and name C4')
       1 178 15 2

! c3 gamma
assign (resid 3 and name O5') (resid 3 and name C5')
       (resid 3 and name C4') (resid 3 and name C3')
       1 54 15 2

! c3 epsilon
assign (resid 3 and name C4') (resid 3 and name C3')
       (resid 3 and name O3') (resid 4 and name P  )
       1 -153 15 2

! c3 zeta
assign (resid 3 and name C3') (resid 3 and name O3')
       (resid 4 and name P  ) (resid 4 and name O5')
       1 -71 15 2

! c3 chi
assign (resid 3 and name O4') (resid 3 and name C1')
       (resid 3 and name N1 ) (resid 3 and name C2 )
       1 -158 15 2

! c3 nu0
assign (resid 3 and name C4') (resid 3 and name O4')
       (resid 3 and name C1') (resid 3 and name C2')
       1 3 15 2

! c3 nu1
assign (resid 3 and name O4') (resid 3 and name C1')
       (resid 3 and name C2') (resid 3 and name C3')
       1 -25 15 2

! c3 nu2
assign (resid 3 and name C1') (resid 3 and name C2')
       (resid 3 and name C3') (resid 3 and name C4')
       1 37 15 2

! c3 nu3
assign (resid 3 and name C2') (resid 3 and name C3')
       (resid 3 and name C4') (resid 3 and name O4')
       1 -36 15 2

! c3 nu4
assign (resid 3 and name C3') (resid 3 and name C4')
       (resid 3 and name O4') (resid 3 and name C1')
       1 21 15 2

! a4 alpha
assign (resid 3 and name O3') (resid 4 and name P  )
       (resid 4 and name O5') (resid 4 and name C5')
       1 -68 15 2

! a4 beta
assign (resid 4 and name P  ) (resid 4 and name O5')
       (resid 4 and name C5') (resid 4 and name C4')
       1 178 15 2

! a4 gamma
assign (resid 4 and name O5') (resid 4 and name C5')
       (resid 4 and name C4') (resid 4 and name C3')
       1 54 15 2

! a4 epsilon
assign (resid 4 and name C4') (resid 4 and name C3')
       (resid 4 and name O3') (resid 5 and name P  )
       1 -153 15 2

! a4 zeta
assign (resid 4 and name C3') (resid 4 and name O3')
       (resid 5 and name P  ) (resid 5 and name O5')
       1 -71 15 2

! a4 chi
assign (resid 4 and name O4') (resid 4 and name C1')
       (resid 4 and name N9 ) (resid 4 and name C4 )
       1 -158 15 2

! a4 nu0
assign (resid 4 and name C4') (resid 4 and name O4')
       (resid 4 and name C1') (resid 4 and name C2')
       1 3 15 2

! a4 nu1
assign (resid 4 and name O4') (resid 4 and name C1')
       (resid 4 and name C2') (resid 4 and name C3')
       1 -25 15 2

! a4 nu2
assign (resid 4 and name C1') (resid 4 and name C2')
       (resid 4 and name C3') (resid 4 and name C4')
       1 37 15 2

! a4 nu3
assign (resid 4 and name C2') (resid 4 and name C3')
       (resid 4 and name C4') (resid 4 and name O4')
       1 -36 15 2

! a4 nu4
assign (resid 4 and name C3') (resid 4 and name C4')
       (resid 4 and name O4') (resid 4 and name C1')
       1 21 15 2

! g5 alpha
assign (resid 4 and name O3') (resid 5 and name P  )
       (resid 5 and name O5') (resid 5 and name C5')
       1 -68 15 2

! g5 beta
assign (resid 5 and name P  ) (resid 5 and name O5')
       (resid 5 and name C5') (resid 5 and name C4')
       1 178 15 2

! g5 gamma
assign (resid 5 and name O5') (resid 5 and name C5')
       (resid 5 and name C4') (resid 5 and name C3')
       1 54 15 2

! g5 epsilon
assign (resid 5 and name C4') (resid 5 and name C3')
       (resid 5 and name O3') (resid 6 and name P  )
       1 -153 15 2

! g5 zeta
assign (resid 5 and name C3') (resid 5 and name O3')
       (resid 6 and name P  ) (resid 6 and name O5')
       1 -71 15 2

! g5 chi
assign (resid 5 and name O4') (resid 5 and name C1')
       (resid 5 and name N9 ) (resid 5 and name C4 )
       1 -158 15 2

! g5 nu0
assign (resid 5 and name C4') (resid 5 and name O4')
       (resid 5 and name C1') (resid 5 and name C2')
       1 3 15 2

! g5 nu1
assign (resid 5 and name O4') (resid 5 and name C1')
       (resid 5 and name C2') (resid 5 and name C3')
       1 -25 15 2

! g5 nu2
assign (resid 5 and name C1') (resid 5 and name C2')
       (resid 5 and name C3') (resid 5 and name C4')
       1 37 15 2

! g5 nu3
assign (resid 5 and name C2') (resid 5 and name C3')
       (resid 5 and name C4') (resid 5 and name O4')
       1 -36 15 2

! g5 nu4
assign (resid 5 and name C3') (resid 5 and name C4')
       (resid 5 and name O4') (resid 5 and name C1')
       1 21 15 2

! g6 alpha
assign (resid 5 and name O3') (resid 6 and name P  )
       (resid 6 and name O5') (resid 6 and name C5')
       1 -68 15 2

! g6 beta
assign (resid 6 and name P  ) (resid 6 and name O5')
       (resid 6 and name C5') (resid 6 and name C4')
       1 178 15 2

! g6 gamma
assign (resid 6 and name O5') (resid 6 and name C5')
       (resid 6 and name C4') (resid 6 and name C3')
       1 54 15 2

! g6 epsilon
assign (resid 6 and name C4') (resid 6 and name C3')
       (resid 6 and name O3') (resid 7 and name P  )
       1 -153 15 2

! g6 zeta
assign (resid 6 and name C3') (resid 6 and name O3')
       (resid 7 and name P  ) (resid 7 and name O5')
       1 -71 15 2

! g6 chi
assign (resid 6 and name O4') (resid 6 and name C1')
       (resid 6 and name N9 ) (resid 6 and name C4 )
       1 -158 15 2

! g6 nu0
assign (resid 6 and name C4') (resid 6 and name O4')
       (resid 6 and name C1') (resid 6 and name C2')
       1 3 15 2

! g6 nu1
assign (resid 6 and name O4') (resid 6 and name C1')
       (resid 6 and name C2') (resid 6 and name C3')
       1 -25 15 2

! g6 nu2
assign (resid 6 and name C1') (resid 6 and name C2')
       (resid 6 and name C3') (resid 6 and name C4')
       1 37 15 2

! g6 nu3
assign (resid 6 and name C2') (resid 6 and name C3')
       (resid 6 and name C4') (resid 6 and name O4')
       1 -36 15 2

! g6 nu4
assign (resid 6 and name C3') (resid 6 and name C4')
       (resid 6 and name O4') (resid 6 and name C1')
       1 21 15 2

! g7 alpha
assign (resid 6 and name O3') (resid 7 and name P  )
       (resid 7 and name O5') (resid 7 and name C5')
       1 -68 15 2

! g7 beta
assign (resid 7 and name P  ) (resid 7 and name O5')
       (resid 7 and name C5') (resid 7 and name C4')
       1 178 15 2

! g7 gamma
assign (resid 7 and name O5') (resid 7 and name C5')
       (resid 7 and name C4') (resid 7 and name C3')
       1 54 15 2

! g7 epsilon
assign (resid 7 and name C4') (resid 7 and name C3')
       (resid 7 and name O3') (resid 8 and name P  )
       1 -153 15 2

! g7 zeta
assign (resid 7 and name C3') (resid 7 and name O3')
       (resid 8 and name P  ) (resid 8 and name O5')
       1 -71 15 2

! g7 chi
assign (resid 7 and name O4') (resid 7 and name C1')
       (resid 7 and name N9 ) (resid 7 and name C4 )
       1 -158 15 2

! g7 nu0
assign (resid 7 and name C4') (resid 7 and name O4')
       (resid 7 and name C1') (resid 7 and name C2')
       1 3 15 2

! g7 nu1
assign (resid 7 and name O4') (resid 7 and name C1')
       (resid 7 and name C2') (resid 7 and name C3')
       1 -25 15 2

! g7 nu2
assign (resid 7 and name C1') (resid 7 and name C2')
       (resid 7 and name C3') (resid 7 and name C4')
       1 37 15 2

! g7 nu3
assign (resid 7 and name C2') (resid 7 and name C3')
       (resid 7 and name C4') (resid 7 and name O4')
       1 -36 15 2

! g7 nu4
assign (resid 7 and name C3') (resid 7 and name C4')
       (resid 7 and name O4') (resid 7 and name C1')
       1 21 15 2

! c8 alpha
assign (resid 7 and name O3') (resid 8 and name P  )
       (resid 8 and name O5') (resid 8 and name C5')
       1 -68 30 2

! c8 beta
assign (resid 8 and name P  ) (resid 8 and name O5')
       (resid 8 and name C5') (resid 8 and name C4')
       1 178 30 2

! c8 gamma
assign (resid 8 and name O5') (resid 8 and name C5')
       (resid 8 and name C4') (resid 8 and name C3')
       1 54 30 2

! c8 epsilon
assign (resid 8 and name C4') (resid 8 and name C3')
       (resid 8 and name O3') (resid 9 and name P  )
       1 -120 120 2

! c8 zeta
assign (resid 8 and name C3') (resid 8 and name O3')
       (resid 9 and name P  ) (resid 9 and name O5')
       1 -71 30 2

! c8 chi
assign (resid 8 and name O4') (resid 8 and name C1')
       (resid 8 and name N1 ) (resid 8 and name C2 )
       1 -158 30 2

! c8 nu0
assign (resid 8 and name C4') (resid 8 and name O4')
       (resid 8 and name C1') (resid 8 and name C2')
       1 3 30 2

! c8 nu1
assign (resid 8 and name O4') (resid 8 and name C1')
       (resid 8 and name C2') (resid 8 and name C3')
       1 -25 30 2

! c8 nu2
assign (resid 8 and name C1') (resid 8 and name C2')
       (resid 8 and name C3') (resid 8 and name C4')
       1 37 30 2

! c8 nu3
assign (resid 8 and name C2') (resid 8 and name C3')
       (resid 8 and name C4') (resid 8 and name O4')
       1 -36 30 2

! c8 nu4
assign (resid 8 and name C3') (resid 8 and name C4')
       (resid 8 and name O4') (resid 8 and name C1')
       1 21 30 2

! u9 alpha
assign (resid 8 and name O3') (resid 9 and name P  )
       (resid 9 and name O5') (resid 9 and name C5')
       1 -68 30 2

! u9 beta
assign (resid 9 and name P  ) (resid 9 and name O5')
       (resid 9 and name C5') (resid 9 and name C4')
       1 178 30 2

! u9 gamma
assign (resid 9 and name O5') (resid 9 and name C5')
       (resid 9 and name C4') (resid 9 and name C3')
       1 54 30 2

! u9 epsilon
assign (resid 9 and name C4') (resid 9 and name C3')
       (resid 9 and name O3') (resid 10 and name P  )
       1 -120 120 2

! u9 zeta is unconstrained

! u9 chi
assign (resid 9 and name O4') (resid 9 and name C1')
       (resid 9 and name N1 ) (resid 9 and name C2 )
       1 -158 30 2

! u9 nu0
assign (resid 9 and name C4') (resid 9 and name O4')
       (resid 9 and name C1') (resid 9 and name C2')
       1 3 30 2

! u9 nu1
assign (resid 9 and name O4') (resid 9 and name C1')
       (resid 9 and name C2') (resid 9 and name C3')
       1 -25 30 2

! u9 nu2
assign (resid 9 and name C1') (resid 9 and name C2')
       (resid 9 and name C3') (resid 9 and name C4')
       1 37 30 2

! u9 nu3
assign (resid 9 and name C2') (resid 9 and name C3')
       (resid 9 and name C4') (resid 9 and name O4')
       1 -36 30 2

! u9 nu4
assign (resid 9 and name C3') (resid 9 and name C4')
       (resid 9 and name O4') (resid 9 and name C1')
       1 21 30 2

! c10 alpha is unconstrained

! c10 beta
assign (resid 10 and name P  ) (resid 10 and name O5')
       (resid 10 and name C5') (resid 10 and name C4')
       1 178 30 2

! c10 gamma
assign (resid 10 and name O5') (resid 10 and name C5')
       (resid 10 and name C4') (resid 10 and name C3')
       1 54 30 2

! c10 epsilon
assign (resid 10 and name C4') (resid 10 and name C3')
       (resid 10 and name O3') (resid 11 and name P  )
       1 -120 120 2

! c10 zeta is unconstrained

! c10 chi
assign (resid 10 and name O4') (resid 10 and name C1')
       (resid 10 and name N1 ) (resid 10 and name C2 )
       1 -158 30 2

! c10 nu0 is unconstrained

! c10 nu1 is unconstrained

! c10 nu2 is unconstrained

! c10 nu3 is unconstrained

! c10 nu4 is unconstrained

! a11 alpha is unconstrained

! a11 beta
assign (resid 11 and name P  ) (resid 11 and name O5')
       (resid 11 and name C5') (resid 11 and name C4')
       1 178 30 2

! a11 gamma is unconstrained

! a11 epsilon
assign (resid 11 and name C4') (resid 11 and name C3')
       (resid 11 and name O3') (resid 12 and name P  )
       1 -120 120 2

! a11 zeta
assign (resid 11 and name C3') (resid 11 and name O3')
       (resid 12 and name P  ) (resid 12 and name O5')
       1 -71 30 2

! a11 chi
assign (resid 11 and name O4') (resid 11 and name C1')
       (resid 11 and name N9 ) (resid 11 and name C4 )
       1 -158 30 2

! a11 nu0 is unconstrained

! a11 nu1 is unconstrained

! a11 nu2 is unconstrained

! a11 nu3 is unconstrained

! a11 nu4 is unconstrained

! u12 alpha
assign (resid 11 and name O3') (resid 12 and name P  )
       (resid 12 and name O5') (resid 12 and name C5')
       1 -68 30 2

! u12 beta
assign (resid 12 and name P  ) (resid 12 and name O5')
       (resid 12 and name C5') (resid 12 and name C4')
       1 178 30 2

! u12 gamma is unconstrained

! u12 epsilon
assign (resid 12 and name C4') (resid 12 and name C3')
       (resid 12 and name O3') (resid 13 and name P  )
       1 -120 120 2

! u12 zeta is unconstrained

! u12 chi
assign (resid 12 and name O4') (resid 12 and name C1')
       (resid 12 and name N1 ) (resid 12 and name C2 )
       1 -158 30 2

! u12 nu0
assign (resid 12 and name C4') (resid 12 and name O4')
       (resid 12 and name C1') (resid 12 and name C2')
       1 -21.7 30 2

! u12 nu1
assign (resid 12 and name O4') (resid 12 and name C1')
       (resid 12 and name C2') (resid 12 and name C3')
       1 35.2 30 2

! u12 nu2
assign (resid 12 and name C1') (resid 12 and name C2')
       (resid 12 and name C3') (resid 12 and name C4')
       1 -35.2 30 2

! u12 nu3
assign (resid 12 and name C2') (resid 12 and name C3')
       (resid 12 and name C4') (resid 12 and name O4')
       1 21.8 30 2

! u12 nu4
assign (resid 12 and name C3') (resid 12 and name C4')
       (resid 12 and name O4') (resid 12 and name C1')
       1 0 30 2

! a13 alpha is unconstrained

! a13 beta
assign (resid 13 and name P  ) (resid 13 and name O5')
       (resid 13 and name C5') (resid 13 and name C4')
       1 178 30 2

! a13 gamma
assign (resid 13 and name O5') (resid 13 and name C5')
       (resid 13 and name C4') (resid 13 and name C3')
       1 54 30 2

! a13 epsilon
assign (resid 13 and name C4') (resid 13 and name C3')
       (resid 13 and name O3') (resid 14 and name P  )
       1 -120 120 2

! a13 zeta
assign (resid 13 and name C3') (resid 13 and name O3')
       (resid 14 and name P  ) (resid 14 and name O5')
       1 -71 30 2

! a13 chi
assign (resid 13 and name O4') (resid 13 and name C1')
       (resid 13 and name N9 ) (resid 13 and name C4 )
       1 -158 30 2

! a13 nu0 is unconstrained

! a13 nu1 is unconstrained

! a13 nu2 is unconstrained

! a13 nu3 is unconstrained

! a13 nu4 is unconstrained

! a14 alpha
assign (resid 13 and name O3') (resid 14 and name P  )
       (resid 14 and name O5') (resid 14 and name C5')
       1 -68 30 2

! a14 beta
assign (resid 14 and name P  ) (resid 14 and name O5')
       (resid 14 and name C5') (resid 14 and name C4')
       1 178 30 2

! a14 gamma
assign (resid 14 and name O5') (resid 14 and name C5')
       (resid 14 and name C4') (resid 14 and name C3')
       1 54 30 2

! a14 epsilon
assign (resid 14 and name C4') (resid 14 and name C3')
       (resid 14 and name O3') (resid 15 and name P  )
       1 -120 120 2

! a14 zeta
assign (resid 14 and name C3') (resid 14 and name O3')
       (resid 15 and name P  ) (resid 15 and name O5')
       1 -71 30 2

! a14 chi
assign (resid 14 and name O4') (resid 14 and name C1')
       (resid 14 and name N9 ) (resid 14 and name C4 )
       1 -158 30 2

! a14 nu0
assign (resid 14 and name C4') (resid 14 and name O4')
       (resid 14 and name C1') (resid 14 and name C2')
       1 3 30 2

! a14 nu1
assign (resid 14 and name O4') (resid 14 and name C1')
       (resid 14 and name C2') (resid 14 and name C3')
       1 -25 30 2

! a14 nu2
assign (resid 14 and name C1') (resid 14 and name C2')
       (resid 14 and name C3') (resid 14 and name C4')
       1 37 30 2

! a14 nu3
assign (resid 14 and name C2') (resid 14 and name C3')
       (resid 14 and name C4') (resid 14 and name O4')
       1 -36 30 2

! a14 nu4
assign (resid 14 and name C3') (resid 14 and name C4')
       (resid 14 and name O4') (resid 14 and name C1')
       1 21 30 2

! c15 alpha
assign (resid 14 and name O3') (resid 15 and name P  )
       (resid 15 and name O5') (resid 15 and name C5')
       1 -68 15 2

! c15 beta
assign (resid 15 and name P  ) (resid 15 and name O5')
       (resid 15 and name C5') (resid 15 and name C4')
       1 178 15 2

! c15 gamma
assign (resid 15 and name O5') (resid 15 and name C5')
       (resid 15 and name C4') (resid 15 and name C3')
       1 54 15 2

! c15 epsilon
assign (resid 15 and name C4') (resid 15 and name C3')
       (resid 15 and name O3') (resid 16 and name P  )
       1 -153 15 2

! c15 zeta
assign (resid 15 and name C3') (resid 15 and name O3')
       (resid 16 and name P  ) (resid 16 and name O5')
       1 -71 15 2

! c15 chi
assign (resid 15 and name O4') (resid 15 and name C1')
       (resid 15 and name N1 ) (resid 15 and name C2 )
       1 -158 15 2

! c15 nu0
assign (resid 15 and name C4') (resid 15 and name O4')
       (resid 15 and name C1') (resid 15 and name C2')
       1 3 15 2

! c15 nu1
assign (resid 15 and name O4') (resid 15 and name C1')
       (resid 15 and name C2') (resid 15 and name C3')
       1 -25 15 2

! c15 nu2
assign (resid 15 and name C1') (resid 15 and name C2')
       (resid 15 and name C3') (resid 15 and name C4')
       1 37 15 2

! c15 nu3
assign (resid 15 and name C2') (resid 15 and name C3')
       (resid 15 and name C4') (resid 15 and name O4')
       1 -36 15 2

! c15 nu4
assign (resid 15 and name C3') (resid 15 and name C4')
       (resid 15 and name O4') (resid 15 and name C1')
       1 21 15 2

! c16 alpha
assign (resid 15 and name O3') (resid 16 and name P  )
       (resid 16 and name O5') (resid 16 and name C5')
       1 -68 15 2

! c16 beta
assign (resid 16 and name P  ) (resid 16 and name O5')
       (resid 16 and name C5') (resid 16 and name C4')
       1 178 15 2

! c16 gamma
assign (resid 16 and name O5') (resid 16 and name C5')
       (resid 16 and name C4') (resid 16 and name C3')
       1 54 15 2

! c16 epsilon
assign (resid 16 and name C4') (resid 16 and name C3')
       (resid 16 and name O3') (resid 17 and name P  )
       1 -153 15 2

! c16 zeta
assign (resid 16 and name C3') (resid 16 and name O3')
       (resid 17 and name P  ) (resid 17 and name O5')
       1 -71 15 2

! c16 chi
assign (resid 16 and name O4') (resid 16 and name C1')
       (resid 16 and name N1 ) (resid 16 and name C2 )
       1 -158 15 2

! c16 nu0
assign (resid 16 and name C4') (resid 16 and name O4')
       (resid 16 and name C1') (resid 16 and name C2')
       1 3 15 2

! c16 nu1
assign (resid 16 and name O4') (resid 16 and name C1')
       (resid 16 and name C2') (resid 16 and name C3')
       1 -25 15 2

! c16 nu2
assign (resid 16 and name C1') (resid 16 and name C2')
       (resid 16 and name C3') (resid 16 and name C4')
       1 37 15 2

! c16 nu3
assign (resid 16 and name C2') (resid 16 and name C3')
       (resid 16 and name C4') (resid 16 and name O4')
       1 -36 15 2

! c16 nu4
assign (resid 16 and name C3') (resid 16 and name C4')
       (resid 16 and name O4') (resid 16 and name C1')
       1 21 15 2

! c17 alpha
assign (resid 16 and name O3') (resid 17 and name P  )
       (resid 17 and name O5') (resid 17 and name C5')
       1 -68 15 2

! c17 beta
assign (resid 17 and name P  ) (resid 17 and name O5')
       (resid 17 and name C5') (resid 17 and name C4')
       1 178 15 2

! c17 gamma
assign (resid 17 and name O5') (resid 17 and name C5')
       (resid 17 and name C4') (resid 17 and name C3')
       1 54 15 2

! c17 epsilon
assign (resid 17 and name C4') (resid 17 and name C3')
       (resid 17 and name O3') (resid 18 and name P  )
       1 -153 15 2

! c17 zeta
assign (resid 17 and name C3') (resid 17 and name O3')
       (resid 18 and name P  ) (resid 18 and name O5')
       1 -71 15 2

! c17 chi
assign (resid 17 and name O4') (resid 17 and name C1')
       (resid 17 and name N1 ) (resid 17 and name C2 )
       1 -158 15 2

! c17 nu0
assign (resid 17 and name C4') (resid 17 and name O4')
       (resid 17 and name C1') (resid 17 and name C2')
       1 3 15 2

! c17 nu1
assign (resid 17 and name O4') (resid 17 and name C1')
       (resid 17 and name C2') (resid 17 and name C3')
       1 -25 15 2

! c17 nu2
assign (resid 17 and name C1') (resid 17 and name C2')
       (resid 17 and name C3') (resid 17 and name C4')
       1 37 15 2

! c17 nu3
assign (resid 17 and name C2') (resid 17 and name C3')
       (resid 17 and name C4') (resid 17 and name O4')
       1 -36 15 2

! c17 nu4
assign (resid 17 and name C3') (resid 17 and name C4')
       (resid 17 and name O4') (resid 17 and name C1')
       1 21 15 2

! u18 alpha
assign (resid 17 and name O3') (resid 18 and name P  )
       (resid 18 and name O5') (resid 18 and name C5')
       1 -68 15 2

! u18 beta
assign (resid 18 and name P  ) (resid 18 and name O5')
       (resid 18 and name C5') (resid 18 and name C4')
       1 178 15 2

! u18 gamma
assign (resid 18 and name O5') (resid 18 and name C5')
       (resid 18 and name C4') (resid 18 and name C3')
       1 54 15 2

! u18 epsilon
assign (resid 18 and name C4') (resid 18 and name C3')
       (resid 18 and name O3') (resid 19 and name P  )
       1 -153 15 2

! u18 zeta
assign (resid 18 and name C3') (resid 18 and name O3')
       (resid 19 and name P  ) (resid 19 and name O5')
       1 -71 15 2

! u18 chi
assign (resid 18 and name O4') (resid 18 and name C1')
       (resid 18 and name N1 ) (resid 18 and name C2 )
       1 -158 15 2

! u18 nu0
assign (resid 18 and name C4') (resid 18 and name O4')
       (resid 18 and name C1') (resid 18 and name C2')
       1 3 15 2

! u18 nu1
assign (resid 18 and name O4') (resid 18 and name C1')
       (resid 18 and name C2') (resid 18 and name C3')
       1 -25 15 2

! u18 nu2
assign (resid 18 and name C1') (resid 18 and name C2')
       (resid 18 and name C3') (resid 18 and name C4')
       1 37 15 2

! u18 nu3
assign (resid 18 and name C2') (resid 18 and name C3')
       (resid 18 and name C4') (resid 18 and name O4')
       1 -36 15 2

! u18 nu4
assign (resid 18 and name C3') (resid 18 and name C4')
       (resid 18 and name O4') (resid 18 and name C1')
       1 21 15 2

! g19 alpha
assign (resid 18 and name O3') (resid 19 and name P  )
       (resid 19 and name O5') (resid 19 and name C5')
       1 -68 15 2

! g19 beta
assign (resid 19 and name P  ) (resid 19 and name O5')
       (resid 19 and name C5') (resid 19 and name C4')
       1 178 15 2

! g19 gamma
assign (resid 19 and name O5') (resid 19 and name C5')
       (resid 19 and name C4') (resid 19 and name C3')
       1 54 15 2

! g19 epsilon
assign (resid 19 and name C4') (resid 19 and name C3')
       (resid 19 and name O3') (resid 20 and name P  )
       1 -153 15 2

! g19 zeta
assign (resid 19 and name C3') (resid 19 and name O3')
       (resid 20 and name P  ) (resid 20 and name O5')
       1 -71 15 2

! g19 chi
assign (resid 19 and name O4') (resid 19 and name C1')
       (resid 19 and name N9 ) (resid 19 and name C4 )
       1 -158 15 2

! g19 nu0
assign (resid 19 and name C4') (resid 19 and name O4')
       (resid 19 and name C1') (resid 19 and name C2')
       1 3 15 2

! g19 nu1
assign (resid 19 and name O4') (resid 19 and name C1')
       (resid 19 and name C2') (resid 19 and name C3')
       1 -25 15 2

! g19 nu2
assign (resid 19 and name C1') (resid 19 and name C2')
       (resid 19 and name C3') (resid 19 and name C4')
       1 37 15 2

! g19 nu3
assign (resid 19 and name C2') (resid 19 and name C3')
       (resid 19 and name C4') (resid 19 and name O4')
       1 -36 15 2

! g19 nu4
assign (resid 19 and name C3') (resid 19 and name C4')
       (resid 19 and name O4') (resid 19 and name C1')
       1 21 15 2

! c20 alpha
assign (resid 19 and name O3') (resid 20 and name P  )
       (resid 20 and name O5') (resid 20 and name C5')
       1 -68 15 2

! c20 beta
assign (resid 20 and name P  ) (resid 20 and name O5')
       (resid 20 and name C5') (resid 20 and name C4')
       1 178 15 2

! c20 gamma
assign (resid 20 and name O5') (resid 20 and name C5')
       (resid 20 and name C4') (resid 20 and name C3')
       1 54 15 2

! c20 epsilon
assign (resid 20 and name C4') (resid 20 and name C3')
       (resid 20 and name O3') (resid 21 and name P  )
       1 -153 15 2

! c20 zeta
assign (resid 20 and name C3') (resid 20 and name O3')
       (resid 21 and name P  ) (resid 21 and name O5')
       1 -71 15 2

! c20 chi
assign (resid 20 and name O4') (resid 20 and name C1')
       (resid 20 and name N1 ) (resid 20 and name C2 )
       1 -158 15 2

! c20 nu0
assign (resid 20 and name C4') (resid 20 and name O4')
       (resid 20 and name C1') (resid 20 and name C2')
       1 3 15 2

! c20 nu1
assign (resid 20 and name O4') (resid 20 and name C1')
       (resid 20 and name C2') (resid 20 and name C3')
       1 -25 15 2

! c20 nu2
assign (resid 20 and name C1') (resid 20 and name C2')
       (resid 20 and name C3') (resid 20 and name C4')
       1 37 15 2

! c20 nu3
assign (resid 20 and name C2') (resid 20 and name C3')
       (resid 20 and name C4') (resid 20 and name O4')
       1 -36 15 2

! c20 nu4
assign (resid 20 and name C3') (resid 20 and name C4')
       (resid 20 and name O4') (resid 20 and name C1')
       1 21 15 2

! c21 alpha
assign (resid 20 and name O3') (resid 21 and name P  )
       (resid 21 and name O5') (resid 21 and name C5')
       1 -68 15 2

! c21 beta
assign (resid 21 and name P  ) (resid 21 and name O5')
       (resid 21 and name C5') (resid 21 and name C4')
       1 178 15 2

! c21 gamma
assign (resid 21 and name O5') (resid 21 and name C5')
       (resid 21 and name C4') (resid 21 and name C3')
       1 54 15 2

! c21 chi
assign (resid 21 and name O4') (resid 21 and name C1')
       (resid 21 and name N1 ) (resid 21 and name C2 )
       1 -158 15 2

! c21 nu0
assign (resid 21 and name C4') (resid 21 and name O4')
       (resid 21 and name C1') (resid 21 and name C2')
       1 3 15 2

! c21 nu1
assign (resid 21 and name O4') (resid 21 and name C1')
       (resid 21 and name C2') (resid 21 and name C3')
       1 -25 15 2

! c21 nu2
assign (resid 21 and name C1') (resid 21 and name C2')
       (resid 21 and name C3') (resid 21 and name C4')
       1 37 15 2

! c21 nu3
assign (resid 21 and name C2') (resid 21 and name C3')
       (resid 21 and name C4') (resid 21 and name O4')
       1 -36 15 2

! c21 nu4
assign (resid 21 and name C3') (resid 21 and name C4')
       (resid 21 and name O4') (resid 21 and name C1')
       1 21 15 2

! make-rsf.inp -- Build RNA structure file
! Dave Schweisguth , 11 Apr 1996
! Derived from generate/generatedna.inp

set echo=off message=off end  ! Normal use
!set echo=on message=all end  ! Auxiliary file debugging

topology @XPLORLIB:toppar/dna-rna-allatom.top end

set echo=on message=all end

segment
    name=a
    chain
 link nuc head - * tail + * end
 first 5pho tail + * end  ! Patches must precede sequence
 last 3ter head - * end
 sequence
     gua gua cyt ade gua gua gua
     cyt uri cyt ade uri ade ade
     cyt cyt cyt uri gua cyt cyt
 end
    end
end

write structure output=rsf.inp end

stop
! make-template.inp -- Build extended structure for local geometry reference
! Dave Schweisguth , 27 Apr 1996
! Derived from nmr/generate_template.inp

set seed=@xplor.seed end  ! Use xplor -s

set echo=off message=off end  ! Normal use
!set echo=on message=all end  ! Auxiliary file debugging

structure @rsf.inp end
parameter @XPLORLIB:toppar/dna-rna-allatom.par end

set echo=on message=all end

vector ident (x) (all)   ! Set X coordinate to atom number(!)
vector do (x=x/10) (all)
vector do (y=random(0.5)) (all)
vector do (z=random(0.5)) (all)
vector do (fbeta=50) (all)  ! Friction coefficient, in 1/ps
vector do (mass=100) (all)  ! Heavy masses, in amu

parameter
    nbonds
 cutnb=5.5
 rconst=20
 nbxmod=-2
 repel=0.9 ! Repulsive non-bonded energy only
 wmin=0.1
 tolerance=1
 rexp=2  ! default
 irexp=2  ! default
 inhibit=0.25
    end       
end 

! Parameter set may or may not contain dihedral energies

flags exclude * include bond angle dihe vdw end
minimize powell nstep=200 nprint=10 end

flags include impr end
minimize powell nstep=200 nprint=10 end

dynamics verlet
    nstep=200
    timestep=0.001 ! default
    iasvel=maxwell
    firsttemp=300
    tcoupling=true
    tbath=300
    nprint=50
    iprfrq=0  
end

parameter 
    nbonds
 rconst=2
 nbxmod=-3
 repel=0.75 ! Repulsive non-bonded energy only
    end
end

minimize powell nstep=400 nprint=25 end 

dynamics verlet
    nstep=1000
    timestep=0.005
    iasvel=maxwell
    firsttemp=300
    tcoupling=true 
    tbath=300
    nprint=100
    iprfrq=0
end

! H-building won't actually place protons, since we're using a fully protonated
!   topology/parameter set, but it may improve their positions
! We're using "nbonds repel", so the "elec" flag is irrelevant

flags exclude vdw end
vector do (mass=1) (name h*) 
hbuild selection=(name h*) phistep=360 end

flags include vdw end
minimize powell nstep=800 nprint=50 end

! Analyze and write out the final structure.
! Total energy should be no more than about 100. If it is, it is probably
! because one or more purines are trapped in a crumpled conformation.

flags exclude * include bond angle dihe impr vdw end

print threshold=0.05 bonds          
evaluate ($rms_bond=$result)
evaluate ($v_bond=$violations)
print threshold=5 angles
evaluate ($rms_angl=$result)
evaluate ($v_angl=$violations)
print threshold=15 dihedrals
evaluate ($rms_dihe=$result)
evaluate ($v_dihe=$violations)
print threshold=5 impropers
evaluate ($rms_impr=$result)
evaluate ($v_impr=$violations)

set echo=off message=off end

display Energy:      bond $bond, angle $angl, dihedral $dihe,
display              improper $impr, VdW $vdw, total $ener
display RMSD:        bond $rms_bond, angle $rms_angl, dihedral $rms_dihe,
display              improper $rms_impr
display Violations:  bond $v_bond, angle $v_angl, dihedral $v_dihe,
display              improper $v_impr

set echo=on message=all end

write coordinates output=template.pdb end  

stop
#!/bin/csh -f
#$ -cwd -o make-template.run.o -e make-template.run.e -m bae -M dcs@proton.chem.yale.edu

xplor < make-rsf.inp > make-rsf.out

set i=1
while ($i <= 10)
    set ii=`nawk 'BEGIN { printf "%02d", '$i' }'`

    xplor -s < make-template.inp > make-template.$ii.out
    ip 'repdb -ix -om' template.pdb
    mv template.pdb template.$ii.pdb

    @ i++
end

perl -ne 'print if /^Ener/ .. /^ X-PLOR/' make-template.??.out > make-template.summary
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=7:H8 \
/grpat2=8:H6
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=7:H8 \
/grpat2=8:H5
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=7:H1' \
/grpat2=8:H6
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=7:H2' \
/grpat2=8:H6
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=7:H2' \
/grpat2=8:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=7:H2' \
/grpat2=8:H5
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=7:H3' \
/grpat2=8:H6
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=7:H3' \
/grpat2=8:H5
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=8:H6 \
/grpat2=8:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=8:H6 \
/grpat2=8:H5
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=8:H6 \
/grpat2=8:H2'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=8:H6 \
/grpat2=8:H3'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=8:H6 \
/grpat2=8:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=8:H6 \
/grpat2=8:H5'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=8:H1' \
/grpat2=8:H2'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=8:H1' \
/grpat2=8:H3'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=8:H1' \
/grpat2=8:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=8:H1' \
/grpat2=8:H5'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=8:H1' \
/grpat2=9:H6
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=8:H5 \
/grpat2=8:H3'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=8:H5 \
/grpat2=9:H5
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=8:H2' \
/grpat2=9:H6
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=8:H2' \
/grpat2=9:H1'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=8:H2' \
/grpat2=9:H5
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=8:H3' \
/grpat2=9:H6
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=8:H3' \
/grpat2=9:H5
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=8:H5' \
/grpat2=9:H6
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=9:H6 \
/grpat2=9:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=9:H6 \
/grpat2=9:H5
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=9:H6 \
/grpat2=9:H2'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=9:H6 \
/grpat2=9:H3'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=9:H6 \
/grpat2=9:H4'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=9:H1' \
/grpat2=9:H2'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=9:H1' \
/grpat2=9:H3'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=9:H1' \
/grpat2=9:H4'
restraint/ at1=XXX /at2=XXX \
/r1=-0.300 /r2=0.200 /r3=5.800 /r4=6.300 /k2=XXX /k3=XXX \
/grpat1=9:H1' \
/grpat2=9:H5''
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=9:H1' \
/grpat2=10:H2'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=9:H1' \
/grpat2=11:H8
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=9:H2' \
/grpat2=10:H6
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=9:H2' \
/grpat2=11:H8
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=10:H6 \
/grpat2=10:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=10:H6 \
/grpat2=10:H5
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=10:H6 \
/grpat2=10:H2'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=10:H6 \
/grpat2=10:H3'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=10:H6 \
/grpat2=10:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=10:H6 \
/grpat2=10:H5'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=10:H6 \
/grpat2=11:H8
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=10:H1' \
/grpat2=10:H2'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=10:H1' \
/grpat2=10:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=10:H1' \
/grpat2=10:H5'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=10:H1' \
/grpat2=11:H8
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=10:H2' \
/grpat2=11:H8
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=10:H3' \
/grpat2=11:H8
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=10:H4' \
/grpat2=11:H8
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=10:H5' \
/grpat2=11:H8
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=11:H2 \
/grpat2=12:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=11:H8 \
/grpat2=11:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=11:H8 \
/grpat2=11:H2'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=11:H8 \
/grpat2=11:H3'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=11:H8 \
/grpat2=11:H5'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=11:H8 \
/grpat2=12:H6
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=11:H1' \
/grpat2=11:H2'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=11:H1' \
/grpat2=11:H3'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=11:H1' \
/grpat2=11:H4'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=11:H2' \
/grpat2=11:H3'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=11:H2' \
/grpat2=12:H6
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=11:H3' \
/grpat2=11:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=11:H3' \
/grpat2=11:H5'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=11:H3' \
/grpat2=11:H5''
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=11:H3' \
/grpat2=12:H6
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=11:H3' \
/grpat2=12:H5''
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=12:H6 \
/grpat2=12:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=12:H6 \
/grpat2=12:H5
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=12:H6 \
/grpat2=12:H2'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=12:H6 \
/grpat2=12:H3'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=12:H6 \
/grpat2=12:H5'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=12:H6 \
/grpat2=12:H5''
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=12:H1' \
/grpat2=12:H2'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=12:H1' \
/grpat2=12:H3'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=12:H1' \
/grpat2=12:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=12:H1' \
/grpat2=12:H5'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=12:H1' \
/grpat2=12:H5''
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=12:H2' \
/grpat2=13:H8
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=12:H2' \
/grpat2=13:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=12:H3' \
/grpat2=13:H8
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=12:H4' \
/grpat2=13:H8
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=13:H2 \
/grpat2=13:H2'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=13:H2 \
/grpat2=14:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=13:H8 \
/grpat2=13:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=13:H8 \
/grpat2=13:H2'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=13:H8 \
/grpat2=13:H3'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=13:H8 \
/grpat2=13:H4'
restraint/ at1=XXX /at2=XXX \
/r1=-0.500 /r2=0.000 /r3=4.800 /r4=5.300 /k2=XXX /k3=XXX \
/grpat1=13:H8 \
/grpat2=13:H5'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=13:H1' \
/grpat2=13:H2'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=13:H1' \
/grpat2=13:H3'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=13:H1' \
/grpat2=13:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=13:H1' \
/grpat2=13:H5'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=13:H1' \
/grpat2=14:H8
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=13:H1' \
/grpat2=14:H1'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=13:H1' \
/grpat2=14:H5'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=13:H2' \
/grpat2=13:H3'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=13:H2' \
/grpat2=13:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=13:H2' \
/grpat2=13:H5'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=13:H2' \
/grpat2=14:H8
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=13:H2' \
/grpat2=14:H1'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=13:H2' \
/grpat2=14:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=13:H2' \
/grpat2=14:H5'
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=13:H3' \
/grpat2=14:H8
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=14:H2 \
/grpat2=15:H1'
restraint/ at1=XXX /at2=XXX \
/r1=1.500 /r2=2.000 /r3=4.000 /r4=4.500 /k2=XXX /k3=XXX \
/grpat1=14:H8 \
/grpat2=14:H1'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=14:H8 \
/grpat2=14:H3'
restraint/ at1=XXX /at2=XXX \
/r1=-0.300 /r2=0.200 /r3=5.800 /r4=6.300 /k2=XXX /k3=XXX \
/grpat1=14:H8 \
/grpat2=14:H5'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=14:H8 \
/grpat2=15:H6
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=14:H8 \
/grpat2=15:H5
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=14:H1' \
/grpat2=14:H2'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=14:H1' \
/grpat2=14:H3'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=14:H1' \
/grpat2=14:H4'
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=14:H1' \
/grpat2=14:H5'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=14:H1' \
/grpat2=15:H6
restraint/ at1=XXX /at2=XXX \
/r1=0.700 /r2=1.200 /r3=6.800 /r4=7.300 /k2=XXX /k3=XXX \
/grpat1=14:H1' \
/grpat2=15:H5''
restraint/ at1=XXX /at2=XXX \
/r1=1.300 /r2=1.800 /r3=3.000 /r4=3.500 /k2=XXX /k3=XXX \
/grpat1=14:H3' \
/grpat2=15:H6
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=14:H3' \
/grpat2=15:H1'
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=14:H3' \
/grpat2=15:H5
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=14:H4' \
/grpat2=15:H6
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=11:H1' \
/grpat2=12:H6
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=12:H1' \
/grpat2=13:H8
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=8:H6 \
/grpat2=9:H5
restraint/ at1=XXX /at2=XXX \
/r1=2.500 /r2=3.000 /r3=5.000 /r4=5.500 /k2=XXX /k3=XXX \
/grpat1=12:H6 \
/grpat2=13:H8
assign (resid 7 and name h8) (resid 8 and name h6) 4   1   1
assign (resid 7 and name h8) (resid 8 and name h5) 3   1   1
assign (resid 7 and name h1') (resid 8 and name h6) 4   1   1
!assign (resid 7 and name h1') (resid 8 and name h3') 4   1   1     ! secondary
assign (resid 7 and name h2') (resid 8 and name h6) 2.4 0.6 0.6
assign (resid 7 and name h2') (resid 8 and name h1') 4   1   1
assign (resid 7 and name h2') (resid 8 and name h5) 2.4 0.6 0.6
assign (resid 7 and name h3') (resid 8 and name h6) 3   1   1
assign (resid 7 and name h3') (resid 8 and name h5) 2.4 0.6 0.6
!assign (resid 7 and name h5') (resid 8 and name h5) 4   2.8 2.8    ! secondary
assign (resid 8 and name h6) (resid 8 and name h1') 3   1   1
assign (resid 8 and name h6) (resid 8 and name h5) 2.4 0.6 0.6
assign (resid 8 and name h6) (resid 8 and name h2') 3   1   1
assign (resid 8 and name h6) (resid 8 and name h3') 3   1   1     ! reduced
assign (resid 8 and name h6) (resid 8 and name h4') 3   1   1     ! reduced
assign (resid 8 and name h6) (resid 8 and name h5') 4 2.8 2.8
!assign (resid 8 and name h6) (resid 11 and name h8) 2.4 0.6 0.6    ! secondary
!assign (resid 8 and name h1') (resid 8 and name h5) 4   1   1     ! secondary
assign (resid 8 and name h1') (resid 8 and name h2') 2.4 0.6 0.6
assign (resid 8 and name h1') (resid 8 and name h3') 4   1   1
assign (resid 8 and name h1') (resid 8 and name h4') 4   1   1
assign (resid 8 and name h1') (resid 8 and name h5') 4 2.8 2.8
assign (resid 8 and name h1') (resid 9 and name h6) 4   1   1
assign (resid 8 and name h5) (resid 8 and name h3') 4   1   1
!assign (resid 8 and name h5) (resid 8 and name h4') 4   1   1     ! secondary
assign (resid 8 and name h5) (resid 9 and name h5) 4   1   1
assign (resid 8 and name h2') (resid 9 and name h6) 2.4 0.6 0.6
assign (resid 8 and name h2') (resid 9 and name h1') 4   1   1
assign (resid 8 and name h2') (resid 9 and name h5) 4   1   1
assign (resid 8 and name h3') (resid 9 and name h6) 3   1   1
assign (resid 8 and name h3') (resid 9 and name h5) 4   1   1
assign (resid 8 and name h5') (resid 9 and name h6) 4 2.8 2.8
assign (resid 9 and name h6) (resid 9 and name h1') 3   1   1
assign (resid 9 and name h6) (resid 9 and name h5) 2.4 0.6 0.6
assign (resid 9 and name h6) (resid 9 and name h2') 3   1   1
assign (resid 9 and name h6) (resid 9 and name h3') 4   1   1
assign (resid 9 and name h6) (resid 9 and name h4') 4   1   1
assign (resid 9 and name h1') (resid 9 and name h2') 2.4 0.6 0.6
assign (resid 9 and name h1') (resid 9 and name h3') 4   1   1
assign (resid 9 and name h1') (resid 9 and name h4') 3   1   1
assign (resid 9 and name h1') (resid 9 and name h5'') 3 2.8 2.8
assign (resid 9 and name h1') (resid 10 and name h2') 4   1   1
assign (resid 9 and name h1') (resid 11 and name h8) 3   1   1
assign (resid 9 and name h2') (resid 10 and name h6) 4   1   1
assign (resid 9 and name h2') (resid 11 and name h8) 3   1   1     ! reduced
!assign (resid 9 and name h3') (resid 10 and name h1') 4   1   1    ! secondary
assign (resid 10 and name h6) (resid 10 and name h1') 3   1   1
assign (resid 10 and name h6) (resid 10 and name h5) 2.4 0.6 0.6
assign (resid 10 and name h6) (resid 10 and name h2') 3   1   1
assign (resid 10 and name h6) (resid 10 and name h3') 3   1   1
assign (resid 10 and name h6) (resid 10 and name h4') 4   1   1
assign (resid 10 and name h6) (resid 10 and name h5') 4 2.8 2.8
assign (resid 10 and name h6) (resid 11 and name h8) 4   1   1
assign (resid 10 and name h1') (resid 10 and name h2') 2.4 0.6 0.6
assign (resid 10 and name h1') (resid 10 and name h4') 3   1   1
assign (resid 10 and name h1') (resid 10 and name h5') 4 2.8 2.8
assign (resid 10 and name h1') (resid 11 and name h8) 4   1   1
assign (resid 10 and name h2') (resid 11 and name h8) 2.4 0.6 0.6
assign (resid 10 and name h3') (resid 11 and name h8) 2.4 0.6 0.6
assign (resid 10 and name h4') (resid 11 and name h8) 4   1   1     ! reduced
!assign (resid 10 and name h4') (resid 11 and name h3') 4   1   1   ! secondary
assign (resid 10 and name h5') (resid 11 and name h8) 4 2.8 2.8
assign (resid 11 and name h2) (resid 12 and name h1') 4   1   1
assign (resid 11 and name h8) (resid 11 and name h1') 3   1   1
assign (resid 11 and name h8) (resid 11 and name h2') 3   1   1     ! reduced
assign (resid 11 and name h8) (resid 11 and name h3') 2.4 0.6 0.6
assign (resid 11 and name h8) (resid 11 and name h5') 4 2.8 2.8
assign (resid 11 and name h8) (resid 12 and name h6) 4   1   1
assign (resid 11 and name h1') (resid 11 and name h2') 3   1   1    ! increased
assign (resid 11 and name h1') (resid 11 and name h3') 4   1   1
assign (resid 11 and name h1') (resid 11 and name h4') 3   1   1
assign (resid 11 and name h2') (resid 11 and name h3') 3   1   1    ! increased
assign (resid 11 and name h2') (resid 12 and name h6) 3   1   1
assign (resid 11 and name h3') (resid 11 and name h4') 4   1   1
assign (resid 11 and name h3') (resid 11 and name h5') 4 2.8 2.8
assign (resid 11 and name h3') (resid 11 and name h5'') 4 2.8 2.8
assign (resid 11 and name h3') (resid 12 and name h6) 4   1   1
assign (resid 11 and name h3') (resid 12 and name h5'') 4 2.8 2.8
assign (resid 12 and name h6) (resid 12 and name h1') 3   1   1
assign (resid 12 and name h6) (resid 12 and name h5) 2.4 0.6 0.6
assign (resid 12 and name h6) (resid 12 and name h2') 2.4 0.6 0.6
assign (resid 12 and name h6) (resid 12 and name h3') 3   1   1
assign (resid 12 and name h6) (resid 12 and name h5') 4 2.8 2.8
assign (resid 12 and name h6) (resid 12 and name h5'') 4 2.8 2.8
assign (resid 12 and name h1') (resid 12 and name h2') 2.4 0.6 0.6
assign (resid 12 and name h1') (resid 12 and name h3') 4   1   1
assign (resid 12 and name h1') (resid 12 and name h4') 4   1   1
assign (resid 12 and name h1') (resid 12 and name h5') 4 2.8 2.8
assign (resid 12 and name h1') (resid 12 and name h5'') 4 2.8 2.8
assign (resid 12 and name h2') (resid 13 and name h8) 4   1   1
assign (resid 12 and name h2') (resid 13 and name h1') 4   1   1
assign (resid 12 and name h3') (resid 13 and name h8) 2.4 0.6 0.6
assign (resid 12 and name h4') (resid 13 and name h8) 4   1   1
assign (resid 13 and name h2) (resid 13 and name h2') 4   1   1
assign (resid 13 and name h2) (resid 14 and name h1') 2.4 0.6 0.6
assign (resid 13 and name h8) (resid 13 and name h1') 3   1   1
assign (resid 13 and name h8) (resid 13 and name h2') 3   1   1
assign (resid 13 and name h8) (resid 13 and name h3') 2.4 0.6 0.6
assign (resid 13 and name h8) (resid 13 and name h4') 3   1   1
assign (resid 13 and name h8) (resid 13 and name h5') 2.4 2.4 2.4
assign (resid 13 and name h1') (resid 13 and name h2') 2.4 0.6 0.6
assign (resid 13 and name h1') (resid 13 and name h3') 3   1   1    ! reduced
assign (resid 13 and name h1') (resid 13 and name h4') 4   1   1
assign (resid 13 and name h1') (resid 13 and name h5') 4 2.8 2.8
assign (resid 13 and name h1') (resid 14 and name h8) 4   1   1     ! reduced
assign (resid 13 and name h1') (resid 14 and name h1') 3   1   1
assign (resid 13 and name h1') (resid 14 and name h5') 4 2.8 2.8
assign (resid 13 and name h2') (resid 13 and name h3') 3   1   1    ! increased
assign (resid 13 and name h2') (resid 13 and name h4') 4   1   1
assign (resid 13 and name h2') (resid 13 and name h5') 4 2.8 2.8
assign (resid 13 and name h2') (resid 14 and name h8) 2.4 0.6 0.6
assign (resid 13 and name h2') (resid 14 and name h1') 2.4 0.6 0.6
assign (resid 13 and name h2') (resid 14 and name h4') 4   1   1
assign (resid 13 and name h2') (resid 14 and name h5') 4 2.8 2.8
assign (resid 13 and name h3') (resid 14 and name h8) 2.4 0.6 0.6
assign (resid 14 and name h2) (resid 15 and name h1') 2.4 0.6 0.6
assign (resid 14 and name h8) (resid 14 and name h1') 3   1   1
assign (resid 14 and name h8) (resid 14 and name h3') 4   1   1
assign (resid 14 and name h8) (resid 14 and name h5') 3 2.8 2.8
assign (resid 14 and name h8) (resid 15 and name h6) 4   1   1     ! reduced
assign (resid 14 and name h8) (resid 15 and name h5) 4   1   1
assign (resid 14 and name h1') (resid 14 and name h2') 2.4 0.6 0.6
assign (resid 14 and name h1') (resid 14 and name h3') 4   1   1
assign (resid 14 and name h1') (resid 14 and name h4') 4   1   1
assign (resid 14 and name h1') (resid 14 and name h5') 4 2.8 2.8
assign (resid 14 and name h1') (resid 15 and name h6) 4   1   1
assign (resid 14 and name h1') (resid 15 and name h5'') 4 2.8 2.8    ! reduced
assign (resid 14 and name h3') (resid 15 and name h6) 2.4 0.6 0.6
assign (resid 14 and name h3') (resid 15 and name h1') 4   1   1
assign (resid 14 and name h3') (resid 15 and name h5) 4   1   1
assign (resid 14 and name h4') (resid 15 and name h6) 4   1   1
! From kangaroo, added by hand
assign (resid 11 and name h1') (resid 12 and name h6) 4   1   1
assign (resid 12 and name h1') (resid 13 and name h8) 4   1   1
! From rugen, added by hand
assign (resid 8 and name h6) (resid 9 and name h5) 4   1   1
assign (resid 12 and name h6) (resid 13 and name h8) 4   1   1
assign (resid 7 and name h8) (resid 8 and name h6) 4   1   1
assign (resid 7 and name h8) (resid 8 and name h5) 3   1   1
assign (resid 7 and name h1') (resid 8 and name h6) 4   1   1
assign (resid 7 and name h1') (resid 8 and name h3') 4   1   1
assign (resid 7 and name h2') (resid 8 and name h6) 2.4 0.6 0.6
assign (resid 7 and name h2') (resid 8 and name h1') 4   1   1
assign (resid 7 and name h2') (resid 8 and name h5) 2.4 0.6 0.6
assign (resid 7 and name h3') (resid 8 and name h6) 3   1   1
assign (resid 7 and name h3') (resid 8 and name h5) 2.4 0.6 0.6
assign (resid 7 and name h5') (resid 8 and name h5) 4 2.8 2.8
assign (resid 8 and name h6) (resid 8 and name h1') 3   1   1
assign (resid 8 and name h6) (resid 8 and name h5) 2.4 0.6 0.6
assign (resid 8 and name h6) (resid 8 and name h2') 3   1   1
assign (resid 8 and name h6) (resid 8 and name h3') 2.4 0.6 0.6
assign (resid 8 and name h6) (resid 8 and name h4') 2.4 0.6 0.6
assign (resid 8 and name h6) (resid 8 and name h5') 4 2.8 2.8
assign (resid 8 and name h6) (resid 11 and name h8) 2.4 0.6 0.6
assign (resid 8 and name h1') (resid 8 and name h5) 4   1   1
assign (resid 8 and name h1') (resid 8 and name h2') 2.4 0.6 0.6
assign (resid 8 and name h1') (resid 8 and name h3') 4   1   1
assign (resid 8 and name h1') (resid 8 and name h4') 4   1   1
assign (resid 8 and name h1') (resid 8 and name h5') 4 2.8 2.8
assign (resid 8 and name h1') (resid 9 and name h6) 4   1   1
assign (resid 8 and name h5) (resid 8 and name h3') 4   1   1
assign (resid 8 and name h5) (resid 8 and name h4') 4   1   1
assign (resid 8 and name h5) (resid 9 and name h5) 4   1   1
assign (resid 8 and name h2') (resid 9 and name h6) 2.4 0.6 0.6
assign (resid 8 and name h2') (resid 9 and name h1') 4   1   1
assign (resid 8 and name h2') (resid 9 and name h5) 4   1   1
assign (resid 8 and name h3') (resid 9 and name h6) 3   1   1
assign (resid 8 and name h3') (resid 9 and name h5) 4   1   1
assign (resid 8 and name h5') (resid 9 and name h6) 4 2.8 2.8
assign (resid 9 and name h6) (resid 9 and name h1') 3   1   1
assign (resid 9 and name h6) (resid 9 and name h5) 2.4 0.6 0.6
assign (resid 9 and name h6) (resid 9 and name h2') 3   1   1
assign (resid 9 and name h6) (resid 9 and name h3') 4   1   1
assign (resid 9 and name h6) (resid 9 and name h4') 4   1   1
assign (resid 9 and name h1') (resid 9 and name h2') 2.4 0.6 0.6
assign (resid 9 and name h1') (resid 9 and name h3') 4   1   1
assign (resid 9 and name h1') (resid 9 and name h4') 3   1   1
assign (resid 9 and name h1') (resid 9 and name h5'') 3 2.8 2.8
assign (resid 9 and name h1') (resid 10 and name h2') 4   1   1
assign (resid 9 and name h1') (resid 11 and name h8) 3   1   1
assign (resid 9 and name h2') (resid 10 and name h6) 4   1   1
assign (resid 9 and name h2') (resid 11 and name h8) 2.4 0.6 0.6
assign (resid 9 and name h3') (resid 10 and name h1') 4   1   1
assign (resid 10 and name h6) (resid 10 and name h1') 3   1   1
assign (resid 10 and name h6) (resid 10 and name h5) 2.4 0.6 0.6
assign (resid 10 and name h6) (resid 10 and name h2') 3   1   1
assign (resid 10 and name h6) (resid 10 and name h3') 3   1   1
assign (resid 10 and name h6) (resid 10 and name h4') 4   1   1
assign (resid 10 and name h6) (resid 10 and name h5') 4 2.8 2.8
assign (resid 10 and name h6) (resid 11 and name h8) 4   1   1
assign (resid 10 and name h1') (resid 10 and name h2') 2.4 0.6 0.6
assign (resid 10 and name h1') (resid 10 and name h4') 3   1   1
assign (resid 10 and name h1') (resid 10 and name h5') 4 2.8 2.8
assign (resid 10 and name h1') (resid 11 and name h8) 4   1   1
assign (resid 10 and name h2') (resid 11 and name h8) 2.4 0.6 0.6
assign (resid 10 and name h3') (resid 11 and name h8) 2.4 0.6 0.6
assign (resid 10 and name h4') (resid 11 and name h8) 3   1   1
assign (resid 10 and name h4') (resid 11 and name h3') 4   1   1
assign (resid 10 and name h5') (resid 11 and name h8) 4 2.8 2.8
assign (resid 11 and name h2) (resid 12 and name h1') 4   1   1
assign (resid 11 and name h8) (resid 11 and name h1') 3   1   1
assign (resid 11 and name h8) (resid 11 and name h2') 2.4 0.6 0.6
assign (resid 11 and name h8) (resid 11 and name h3') 2.4 0.6 0.6
assign (resid 11 and name h8) (resid 11 and name h5') 4 2.8 2.8
assign (resid 11 and name h8) (resid 12 and name h6) 4   1   1
assign (resid 11 and name h1') (resid 11 and name h2') 4   1   1
assign (resid 11 and name h1') (resid 11 and name h3') 4   1   1
assign (resid 11 and name h1') (resid 11 and name h4') 3   1   1
assign (resid 11 and name h2') (resid 11 and name h3') 4   1   1
assign (resid 11 and name h2') (resid 12 and name h6) 3   1   1
assign (resid 11 and name h3') (resid 11 and name h4') 4   1   1
assign (resid 11 and name h3') (resid 11 and name h5') 4 2.8 2.8
assign (resid 11 and name h3') (resid 11 and name h5'') 4 2.8 2.8
assign (resid 11 and name h3') (resid 12 and name h6) 4   1   1
assign (resid 11 and name h3') (resid 12 and name h5'') 4 2.8 2.8
assign (resid 12 and name h6) (resid 12 and name h1') 3   1   1
assign (resid 12 and name h6) (resid 12 and name h5) 2.4 0.6 0.6
assign (resid 12 and name h6) (resid 12 and name h2') 2.4 0.6 0.6
assign (resid 12 and name h6) (resid 12 and name h3') 3   1   1
assign (resid 12 and name h6) (resid 12 and name h5') 4 2.8 2.8
assign (resid 12 and name h6) (resid 12 and name h5'') 4 2.8 2.8
assign (resid 12 and name h1') (resid 12 and name h2') 2.4 0.6 0.6
assign (resid 12 and name h1') (resid 12 and name h3') 4   1   1
assign (resid 12 and name h1') (resid 12 and name h4') 4   1   1
assign (resid 12 and name h1') (resid 12 and name h5') 4 2.8 2.8
assign (resid 12 and name h1') (resid 12 and name h5'') 4 2.8 2.8
assign (resid 12 and name h2') (resid 13 and name h8) 4   1   1
assign (resid 12 and name h2') (resid 13 and name h1') 4   1   1
assign (resid 12 and name h3') (resid 13 and name h8) 2.4 0.6 0.6
assign (resid 12 and name h4') (resid 13 and name h8) 4   1   1
assign (resid 13 and name h2) (resid 13 and name h2') 4   1   1
assign (resid 13 and name h2) (resid 14 and name h1') 2.4 0.6 0.6
assign (resid 13 and name h8) (resid 13 and name h1') 3   1   1
assign (resid 13 and name h8) (resid 13 and name h2') 3   1   1
assign (resid 13 and name h8) (resid 13 and name h3') 2.4 0.6 0.6
assign (resid 13 and name h8) (resid 13 and name h4') 3   1   1
assign (resid 13 and name h8) (resid 13 and name h5') 2.4 2.4 2.4
assign (resid 13 and name h1') (resid 13 and name h2') 2.4 0.6 0.6
assign (resid 13 and name h1') (resid 13 and name h3') 2.4 0.6 0.6
assign (resid 13 and name h1') (resid 13 and name h4') 4   1   1
assign (resid 13 and name h1') (resid 13 and name h5') 4 2.8 2.8
assign (resid 13 and name h1') (resid 14 and name h8) 3   1   1
assign (resid 13 and name h1') (resid 14 and name h1') 3   1   1
assign (resid 13 and name h1') (resid 14 and name h5') 4 2.8 2.8
assign (resid 13 and name h2') (resid 13 and name h3') 4   1   1
assign (resid 13 and name h2') (resid 13 and name h4') 4   1   1
assign (resid 13 and name h2') (resid 13 and name h5') 4 2.8 2.8
assign (resid 13 and name h2') (resid 14 and name h8) 2.4 0.6 0.6
assign (resid 13 and name h2') (resid 14 and name h1') 2.4 0.6 0.6
assign (resid 13 and name h2') (resid 14 and name h4') 4   1   1
assign (resid 13 and name h2') (resid 14 and name h5') 4 2.8 2.8
assign (resid 13 and name h3') (resid 14 and name h8) 2.4 0.6 0.6
assign (resid 14 and name h2) (resid 15 and name h1') 2.4 0.6 0.6
assign (resid 14 and name h8) (resid 14 and name h1') 3   1   1
assign (resid 14 and name h8) (resid 14 and name h3') 4   1   1
assign (resid 14 and name h8) (resid 14 and name h5') 3 2.8 2.8
assign (resid 14 and name h8) (resid 15 and name h6) 2.4 0.6 0.6
assign (resid 14 and name h8) (resid 15 and name h5) 4   1   1
assign (resid 14 and name h1') (resid 14 and name h2') 2.4 0.6 0.6
assign (resid 14 and name h1') (resid 14 and name h3') 4   1   1
assign (resid 14 and name h1') (resid 14 and name h4') 4   1   1
assign (resid 14 and name h1') (resid 14 and name h5') 4 2.8 2.8
assign (resid 14 and name h1') (resid 15 and name h6) 4   1   1
assign (resid 14 and name h1') (resid 15 and name h5'') 2.4 2.4 2.4
assign (resid 14 and name h3') (resid 15 and name h6) 2.4 0.6 0.6
assign (resid 14 and name h3') (resid 15 and name h1') 4   1   1
assign (resid 14 and name h3') (resid 15 and name h5) 4   1   1
assign (resid 14 and name h4') (resid 15 and name h6) 4   1   1
assign (resid 1 and name H1')
    (resid 1 and name H2') 2.805 0.1 0.1
assign (resid 1 and name H1')
    (resid 1 and name H3') 3.857 0.1 0.1
assign (resid 1 and name H1')
    (resid 1 and name H4') 3.398 0.1 0.1
assign (resid 1 and name H1')
    (resid 1 and name H5') 4.577 0.1 0.1
assign (resid 1 and name H1')
    (resid 1 and name HO2') 2.565 0.1 0.1
assign (resid 1 and name H1')
    (resid 1 and name H21) 4.774 0.1 0.1
assign (resid 1 and name H1')
    (resid 1 and name H8) 3.727 0.1 0.1
assign (resid 1 and name H1')
    (resid 2 and name H5') 4.676 0.1 0.1
assign (resid 1 and name H1')
    (resid 2 and name H8) 4.319 0.1 0.1
assign (resid 1 and name H2')
    (resid 1 and name H3') 2.425 0.1 0.1
assign (resid 1 and name H2')
    (resid 1 and name H4') 3.813 0.1 0.1
assign (resid 1 and name H2')
    (resid 1 and name HO2') 2.946 0.1 0.1
assign (resid 1 and name H2')
    (resid 1 and name H21) 4.702 0.1 0.1
assign (resid 1 and name H2')
    (resid 1 and name H8) 4.149 0.1 0.1
assign (resid 1 and name H2')
    (resid 2 and name H1') 4.193 0.1 0.1
assign (resid 1 and name H2')
    (resid 2 and name H3') 4.263 0.1 0.1
assign (resid 1 and name H2')
    (resid 2 and name H4') 4.442 0.1 0.1
assign (resid 1 and name H2')
    (resid 2 and name H5') 2.890 0.1 0.1
assign (resid 1 and name H2')
    (resid 2 and name H5'') 4.268 0.1 0.1
assign (resid 1 and name H2')
    (resid 2 and name H8) 1.674 0.1 0.1
assign (resid 1 and name H3')
    (resid 1 and name H4') 3.007 0.1 0.1
assign (resid 1 and name H3')
    (resid 1 and name H5') 3.686 0.1 0.1
assign (resid 1 and name H3')
    (resid 1 and name H5'') 3.085 0.1 0.1
assign (resid 1 and name H3')
    (resid 1 and name HO2') 3.596 0.1 0.1
assign (resid 1 and name H3')
    (resid 1 and name H8) 3.196 0.1 0.1
assign (resid 1 and name H3')
    (resid 2 and name H5') 3.959 0.1 0.1
assign (resid 1 and name H3')
    (resid 2 and name H5'') 4.908 0.1 0.1
assign (resid 1 and name H3')
    (resid 2 and name H8) 3.024 0.1 0.1
assign (resid 1 and name H4')
    (resid 1 and name H5') 2.534 0.1 0.1
assign (resid 1 and name H4')
    (resid 1 and name H5'') 2.370 0.1 0.1
assign (resid 1 and name H4')
    (resid 1 and name HO2') 2.043 0.1 0.1
assign (resid 1 and name H4')
    (resid 1 and name H8) 4.410 0.1 0.1
assign (resid 1 and name H4')
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    (resid 17 and name H5') 3.686 0.1 0.1
assign (resid 17 and name H3')
    (resid 17 and name H5'') 3.085 0.1 0.1
assign (resid 17 and name H3')
    (resid 17 and name HO2') 3.993 0.1 0.1
assign (resid 17 and name H3')
    (resid 17 and name H6) 2.989 0.1 0.1
assign (resid 17 and name H3')
    (resid 17 and name H5) 4.769 0.1 0.1
assign (resid 17 and name H3')
    (resid 18 and name H5') 3.958 0.1 0.1
assign (resid 17 and name H3')
    (resid 18 and name H5'') 4.907 0.1 0.1
assign (resid 17 and name H3')
    (resid 18 and name H6) 3.100 0.1 0.1
assign (resid 17 and name H3')
    (resid 18 and name H5) 3.248 0.1 0.1
assign (resid 17 and name H4')
    (resid 17 and name H5') 2.534 0.1 0.1
assign (resid 17 and name H4')
    (resid 17 and name H5'') 2.370 0.1 0.1
assign (resid 17 and name H4')
    (resid 17 and name HO2') 3.778 0.1 0.1
assign (resid 17 and name H4')
    (resid 17 and name H6) 4.053 0.1 0.1
assign (resid 17 and name H4')
    (resid 18 and name H5') 4.167 0.1 0.1
assign (resid 17 and name H5')
    (resid 17 and name H5'') 1.776 0.1 0.1
assign (resid 17 and name H5')
    (resid 17 and name H6) 3.241 0.1 0.1
assign (resid 17 and name H5'')
    (resid 17 and name H6) 4.056 0.1 0.1
assign (resid 17 and name HO2')
    (resid 18 and name H1') 4.151 0.1 0.1
assign (resid 17 and name HO2')
    (resid 18 and name H3') 4.845 0.1 0.1
assign (resid 17 and name HO2')
    (resid 18 and name H4') 3.521 0.1 0.1
assign (resid 17 and name HO2')
    (resid 18 and name H5') 1.994 0.1 0.1
assign (resid 17 and name HO2')
    (resid 18 and name H5'') 3.738 0.1 0.1
assign (resid 17 and name HO2')
    (resid 18 and name H6) 3.200 0.1 0.1
assign (resid 17 and name H41)
    (resid 17 and name H42) 1.784 0.1 0.1
assign (resid 17 and name H41)
    (resid 17 and name H6) 4.650 0.1 0.1
assign (resid 17 and name H41)
    (resid 17 and name H5) 2.425 0.1 0.1
assign (resid 17 and name H41)
    (resid 18 and name H5) 4.531 0.1 0.1
assign (resid 17 and name H42)
    (resid 17 and name H5) 3.708 0.1 0.1
assign (resid 17 and name H42)
    (resid 18 and name H3) 4.568 0.1 0.1
assign (resid 17 and name H42)
    (resid 18 and name H5) 4.454 0.1 0.1
assign (resid 17 and name H6)
    (resid 17 and name H5) 2.456 0.1 0.1
assign (resid 17 and name H6)
    (resid 18 and name H6) 4.950 0.1 0.1
assign (resid 17 and name H6)
    (resid 18 and name H5) 3.980 0.1 0.1
assign (resid 17 and name H5)
    (resid 18 and name H5) 4.017 0.1 0.1
assign (resid 18 and name H1')
    (resid 18 and name H2') 2.805 0.1 0.1
assign (resid 18 and name H1')
    (resid 18 and name H3') 3.857 0.1 0.1
assign (resid 18 and name H1')
    (resid 18 and name H4') 3.397 0.1 0.1
assign (resid 18 and name H1')
    (resid 18 and name H5') 4.576 0.1 0.1
assign (resid 18 and name H1')
    (resid 18 and name HO2') 2.990 0.1 0.1
assign (resid 18 and name H1')
    (resid 18 and name H3) 4.622 0.1 0.1
assign (resid 18 and name H1')
    (resid 18 and name H6) 3.514 0.1 0.1
assign (resid 18 and name H1')
    (resid 19 and name H5') 4.677 0.1 0.1
assign (resid 18 and name H1')
    (resid 19 and name H8) 4.320 0.1 0.1
assign (resid 18 and name H2')
    (resid 18 and name H3') 2.425 0.1 0.1
assign (resid 18 and name H2')
    (resid 18 and name H4') 3.813 0.1 0.1
assign (resid 18 and name H2')
    (resid 18 and name HO2') 2.193 0.1 0.1
assign (resid 18 and name H2')
    (resid 18 and name H3) 4.540 0.1 0.1
assign (resid 18 and name H2')
    (resid 18 and name H6) 4.005 0.1 0.1
assign (resid 18 and name H2')
    (resid 19 and name H1') 4.192 0.1 0.1
assign (resid 18 and name H2')
    (resid 19 and name H3') 4.263 0.1 0.1
assign (resid 18 and name H2')
    (resid 19 and name H4') 4.442 0.1 0.1
assign (resid 18 and name H2')
    (resid 19 and name H5') 2.891 0.1 0.1
assign (resid 18 and name H2')
    (resid 19 and name H5'') 4.268 0.1 0.1
assign (resid 18 and name H2')
    (resid 19 and name H8) 1.673 0.1 0.1
assign (resid 18 and name H3')
    (resid 18 and name H4') 3.007 0.1 0.1
assign (resid 18 and name H3')
    (resid 18 and name H5') 3.686 0.1 0.1
assign (resid 18 and name H3')
    (resid 18 and name H5'') 3.085 0.1 0.1
assign (resid 18 and name H3')
    (resid 18 and name HO2') 3.993 0.1 0.1
assign (resid 18 and name H3')
    (resid 18 and name H6) 2.992 0.1 0.1
assign (resid 18 and name H3')
    (resid 18 and name H5) 4.723 0.1 0.1
assign (resid 18 and name H3')
    (resid 19 and name H5') 3.958 0.1 0.1
assign (resid 18 and name H3')
    (resid 19 and name H5'') 4.908 0.1 0.1
assign (resid 18 and name H3')
    (resid 19 and name H8) 3.024 0.1 0.1
assign (resid 18 and name H4')
    (resid 18 and name H5') 2.533 0.1 0.1
assign (resid 18 and name H4')
    (resid 18 and name H5'') 2.370 0.1 0.1
assign (resid 18 and name H4')
    (resid 18 and name HO2') 3.778 0.1 0.1
assign (resid 18 and name H4')
    (resid 18 and name H6) 4.039 0.1 0.1
assign (resid 18 and name H4')
    (resid 19 and name H5') 4.167 0.1 0.1
assign (resid 18 and name H5')
    (resid 18 and name H5'') 1.776 0.1 0.1
assign (resid 18 and name H5')
    (resid 18 and name H6) 3.223 0.1 0.1
assign (resid 18 and name H5'')
    (resid 18 and name H6) 4.044 0.1 0.1
assign (resid 18 and name HO2')
    (resid 19 and name H1') 4.151 0.1 0.1
assign (resid 18 and name HO2')
    (resid 19 and name H3') 4.845 0.1 0.1
assign (resid 18 and name HO2')
    (resid 19 and name H4') 3.521 0.1 0.1
assign (resid 18 and name HO2')
    (resid 19 and name H5') 1.995 0.1 0.1
assign (resid 18 and name HO2')
    (resid 19 and name H5'') 3.738 0.1 0.1
assign (resid 18 and name HO2')
    (resid 19 and name H8) 3.488 0.1 0.1
assign (resid 18 and name H3)
    (resid 18 and name H6) 4.817 0.1 0.1
assign (resid 18 and name H3)
    (resid 18 and name H5) 4.231 0.1 0.1
assign (resid 18 and name H3)
    (resid 19 and name H8) 4.402 0.1 0.1
assign (resid 18 and name H6)
    (resid 18 and name H5) 2.416 0.1 0.1
assign (resid 18 and name H6)
    (resid 19 and name H8) 4.761 0.1 0.1
assign (resid 19 and name H1')
    (resid 19 and name H2') 2.805 0.1 0.1
assign (resid 19 and name H1')
    (resid 19 and name H3') 3.857 0.1 0.1
assign (resid 19 and name H1')
    (resid 19 and name H4') 3.398 0.1 0.1
assign (resid 19 and name H1')
    (resid 19 and name H5') 4.577 0.1 0.1
assign (resid 19 and name H1')
    (resid 19 and name HO2') 2.990 0.1 0.1
assign (resid 19 and name H1')
    (resid 19 and name H21) 4.775 0.1 0.1
assign (resid 19 and name H1')
    (resid 19 and name H8) 3.727 0.1 0.1
assign (resid 19 and name H1')
    (resid 20 and name H5') 4.678 0.1 0.1
assign (resid 19 and name H1')
    (resid 20 and name H6) 4.297 0.1 0.1
assign (resid 19 and name H1')
    (resid 20 and name H5) 4.979 0.1 0.1
assign (resid 19 and name H2')
    (resid 19 and name H3') 2.425 0.1 0.1
assign (resid 19 and name H2')
    (resid 19 and name H4') 3.813 0.1 0.1
assign (resid 19 and name H2')
    (resid 19 and name HO2') 2.193 0.1 0.1
assign (resid 19 and name H2')
    (resid 19 and name H21) 4.702 0.1 0.1
assign (resid 19 and name H2')
    (resid 19 and name H8) 4.149 0.1 0.1
assign (resid 19 and name H2')
    (resid 20 and name H1') 4.193 0.1 0.1
assign (resid 19 and name H2')
    (resid 20 and name H3') 4.263 0.1 0.1
assign (resid 19 and name H2')
    (resid 20 and name H4') 4.441 0.1 0.1
assign (resid 19 and name H2')
    (resid 20 and name H5') 2.892 0.1 0.1
assign (resid 19 and name H2')
    (resid 20 and name H5'') 4.268 0.1 0.1
assign (resid 19 and name H2')
    (resid 20 and name H6) 1.583 0.1 0.1
assign (resid 19 and name H2')
    (resid 20 and name H5) 3.089 0.1 0.1
assign (resid 19 and name H3')
    (resid 19 and name H4') 3.008 0.1 0.1
assign (resid 19 and name H3')
    (resid 19 and name H5') 3.686 0.1 0.1
assign (resid 19 and name H3')
    (resid 19 and name H5'') 3.085 0.1 0.1
assign (resid 19 and name H3')
    (resid 19 and name HO2') 3.994 0.1 0.1
assign (resid 19 and name H3')
    (resid 19 and name H8) 3.196 0.1 0.1
assign (resid 19 and name H3')
    (resid 20 and name H5') 3.959 0.1 0.1
assign (resid 19 and name H3')
    (resid 20 and name H5'') 4.908 0.1 0.1
assign (resid 19 and name H3')
    (resid 20 and name H6) 3.104 0.1 0.1
assign (resid 19 and name H3')
    (resid 20 and name H5) 3.313 0.1 0.1
assign (resid 19 and name H4')
    (resid 19 and name H5') 2.534 0.1 0.1
assign (resid 19 and name H4')
    (resid 19 and name H5'') 2.370 0.1 0.1
assign (resid 19 and name H4')
    (resid 19 and name HO2') 3.779 0.1 0.1
assign (resid 19 and name H4')
    (resid 19 and name H8) 4.410 0.1 0.1
assign (resid 19 and name H4')
    (resid 20 and name H5') 4.167 0.1 0.1
assign (resid 19 and name H5')
    (resid 19 and name H5'') 1.775 0.1 0.1
assign (resid 19 and name H5')
    (resid 19 and name H8) 3.564 0.1 0.1
assign (resid 19 and name H5'')
    (resid 19 and name H8) 4.368 0.1 0.1
assign (resid 19 and name HO2')
    (resid 19 and name H21) 4.795 0.1 0.1
assign (resid 19 and name HO2')
    (resid 20 and name H1') 4.150 0.1 0.1
assign (resid 19 and name HO2')
    (resid 20 and name H3') 4.844 0.1 0.1
assign (resid 19 and name HO2')
    (resid 20 and name H4') 3.521 0.1 0.1
assign (resid 19 and name HO2')
    (resid 20 and name H5') 1.995 0.1 0.1
assign (resid 19 and name HO2')
    (resid 20 and name H5'') 3.738 0.1 0.1
assign (resid 19 and name HO2')
    (resid 20 and name H6) 3.221 0.1 0.1
assign (resid 19 and name H21)
    (resid 19 and name H22) 1.784 0.1 0.1
assign (resid 19 and name H21)
    (resid 19 and name H1) 3.480 0.1 0.1
assign (resid 19 and name H21)
    (resid 20 and name H1') 3.255 0.1 0.1
assign (resid 19 and name H21)
    (resid 20 and name H6) 4.826 0.1 0.1
assign (resid 19 and name H22)
    (resid 19 and name H1) 2.169 0.1 0.1
assign (resid 19 and name H22)
    (resid 20 and name H1') 4.205 0.1 0.1
assign (resid 19 and name H8)
    (resid 20 and name H5) 3.899 0.1 0.1
assign (resid 19 and name H1)
    (resid 20 and name H41) 4.353 0.1 0.1
assign (resid 19 and name H1)
    (resid 20 and name H42) 3.748 0.1 0.1
assign (resid 19 and name H1)
    (resid 20 and name H5) 4.950 0.1 0.1
assign (resid 20 and name H1')
    (resid 20 and name H2') 2.805 0.1 0.1
assign (resid 20 and name H1')
    (resid 20 and name H3') 3.857 0.1 0.1
assign (resid 20 and name H1')
    (resid 20 and name H4') 3.397 0.1 0.1
assign (resid 20 and name H1')
    (resid 20 and name H5') 4.578 0.1 0.1
assign (resid 20 and name H1')
    (resid 20 and name HO2') 2.989 0.1 0.1
assign (resid 20 and name H1')
    (resid 20 and name H6) 3.521 0.1 0.1
assign (resid 20 and name H1')
    (resid 21 and name H5') 4.677 0.1 0.1
assign (resid 20 and name H1')
    (resid 21 and name H6) 4.298 0.1 0.1
assign (resid 20 and name H1')
    (resid 21 and name H5) 4.980 0.1 0.1
assign (resid 20 and name H2')
    (resid 20 and name H3') 2.425 0.1 0.1
assign (resid 20 and name H2')
    (resid 20 and name H4') 3.813 0.1 0.1
assign (resid 20 and name H2')
    (resid 20 and name HO2') 2.193 0.1 0.1
assign (resid 20 and name H2')
    (resid 20 and name H6) 3.999 0.1 0.1
assign (resid 20 and name H2')
    (resid 21 and name H1') 4.192 0.1 0.1
assign (resid 20 and name H2')
    (resid 21 and name H3') 4.263 0.1 0.1
assign (resid 20 and name H2')
    (resid 21 and name H4') 4.442 0.1 0.1
assign (resid 20 and name H2')
    (resid 21 and name H5') 2.892 0.1 0.1
assign (resid 20 and name H2')
    (resid 21 and name H5'') 4.269 0.1 0.1
assign (resid 20 and name H2')
    (resid 21 and name H6) 1.582 0.1 0.1
assign (resid 20 and name H2')
    (resid 21 and name H5) 3.089 0.1 0.1
assign (resid 20 and name H3')
    (resid 20 and name H4') 3.007 0.1 0.1
assign (resid 20 and name H3')
    (resid 20 and name H5') 3.687 0.1 0.1
assign (resid 20 and name H3')
    (resid 20 and name H5'') 3.085 0.1 0.1
assign (resid 20 and name H3')
    (resid 20 and name HO2') 3.993 0.1 0.1
assign (resid 20 and name H3')
    (resid 20 and name H6) 2.988 0.1 0.1
assign (resid 20 and name H3')
    (resid 20 and name H5) 4.769 0.1 0.1
assign (resid 20 and name H3')
    (resid 21 and name H5') 3.958 0.1 0.1
assign (resid 20 and name H3')
    (resid 21 and name H5'') 4.908 0.1 0.1
assign (resid 20 and name H3')
    (resid 21 and name H6) 3.104 0.1 0.1
assign (resid 20 and name H3')
    (resid 21 and name H5) 3.313 0.1 0.1
assign (resid 20 and name H4')
    (resid 20 and name H5') 2.533 0.1 0.1
assign (resid 20 and name H4')
    (resid 20 and name H5'') 2.370 0.1 0.1
assign (resid 20 and name H4')
    (resid 20 and name HO2') 3.778 0.1 0.1
assign (resid 20 and name H4')
    (resid 20 and name H6) 4.052 0.1 0.1
assign (resid 20 and name H4')
    (resid 21 and name H5') 4.167 0.1 0.1
assign (resid 20 and name H5')
    (resid 20 and name H5'') 1.775 0.1 0.1
assign (resid 20 and name H5')
    (resid 20 and name H6) 3.242 0.1 0.1
assign (resid 20 and name H5'')
    (resid 20 and name H6) 4.055 0.1 0.1
assign (resid 20 and name HO2')
    (resid 21 and name H1') 4.151 0.1 0.1
assign (resid 20 and name HO2')
    (resid 21 and name H3') 4.844 0.1 0.1
assign (resid 20 and name HO2')
    (resid 21 and name H4') 3.521 0.1 0.1
assign (resid 20 and name HO2')
    (resid 21 and name H5') 1.995 0.1 0.1
assign (resid 20 and name HO2')
    (resid 21 and name H5'') 3.738 0.1 0.1
assign (resid 20 and name HO2')
    (resid 21 and name H6) 3.222 0.1 0.1
assign (resid 20 and name H41)
    (resid 20 and name H42) 1.784 0.1 0.1
assign (resid 20 and name H41)
    (resid 20 and name H6) 4.650 0.1 0.1
assign (resid 20 and name H41)
    (resid 20 and name H5) 2.425 0.1 0.1
assign (resid 20 and name H41)
    (resid 21 and name H41) 3.221 0.1 0.1
assign (resid 20 and name H41)
    (resid 21 and name H42) 4.124 0.1 0.1
assign (resid 20 and name H41)
    (resid 21 and name H5) 4.475 0.1 0.1
assign (resid 20 and name H42)
    (resid 20 and name H5) 3.708 0.1 0.1
assign (resid 20 and name H42)
    (resid 21 and name H41) 3.065 0.1 0.1
assign (resid 20 and name H42)
    (resid 21 and name H42) 3.264 0.1 0.1
assign (resid 20 and name H42)
    (resid 21 and name H5) 4.393 0.1 0.1
assign (resid 20 and name H6)
    (resid 20 and name H5) 2.457 0.1 0.1
assign (resid 20 and name H6)
    (resid 21 and name H6) 4.952 0.1 0.1
assign (resid 20 and name H6)
    (resid 21 and name H5) 4.001 0.1 0.1
assign (resid 20 and name H5)
    (resid 21 and name H41) 4.046 0.1 0.1
assign (resid 20 and name H5)
    (resid 21 and name H5) 3.994 0.1 0.1
assign (resid 21 and name H1')
    (resid 21 and name H2') 2.805 0.1 0.1
assign (resid 21 and name H1')
    (resid 21 and name H3') 3.857 0.1 0.1
assign (resid 21 and name H1')
    (resid 21 and name H4') 3.398 0.1 0.1
assign (resid 21 and name H1')
    (resid 21 and name H5') 4.578 0.1 0.1
assign (resid 21 and name H1')
    (resid 21 and name HO2') 2.989 0.1 0.1
assign (resid 21 and name H1')
    (resid 21 and name H6) 3.520 0.1 0.1
assign (resid 21 and name H2')
    (resid 21 and name H3') 2.425 0.1 0.1
assign (resid 21 and name H2')
    (resid 21 and name H4') 3.813 0.1 0.1
assign (resid 21 and name H2')
    (resid 21 and name HO2') 2.193 0.1 0.1
assign (resid 21 and name H2')
    (resid 21 and name H6) 3.999 0.1 0.1
assign (resid 21 and name H3')
    (resid 21 and name H4') 3.007 0.1 0.1
assign (resid 21 and name H3')
    (resid 21 and name H5') 3.686 0.1 0.1
assign (resid 21 and name H3')
    (resid 21 and name H5'') 3.085 0.1 0.1
assign (resid 21 and name H3')
    (resid 21 and name HO2') 3.994 0.1 0.1
assign (resid 21 and name H3')
    (resid 21 and name H6) 2.988 0.1 0.1
assign (resid 21 and name H3')
    (resid 21 and name H5) 4.769 0.1 0.1
assign (resid 21 and name H4')
    (resid 21 and name H5') 2.534 0.1 0.1
assign (resid 21 and name H4')
    (resid 21 and name H5'') 2.370 0.1 0.1
assign (resid 21 and name H4')
    (resid 21 and name HO2') 3.779 0.1 0.1
assign (resid 21 and name H4')
    (resid 21 and name H6) 4.052 0.1 0.1
assign (resid 21 and name H5')
    (resid 21 and name H5'') 1.775 0.1 0.1
assign (resid 21 and name H5')
    (resid 21 and name H6) 3.241 0.1 0.1
assign (resid 21 and name H5'')
    (resid 21 and name H6) 4.055 0.1 0.1
assign (resid 21 and name H41)
    (resid 21 and name H42) 1.784 0.1 0.1
assign (resid 21 and name H41)
    (resid 21 and name H6) 4.650 0.1 0.1
assign (resid 21 and name H41)
    (resid 21 and name H5) 2.425 0.1 0.1
assign (resid 21 and name H42)
    (resid 21 and name H5) 3.708 0.1 0.1
assign (resid 21 and name H6)
    (resid 21 and name H5) 2.457 0.1 0.1
group
    selection=(
 (resid 1 and name N1) or
 (resid 1 and name N3) or
 (resid 1 and name C5) or
 (resid 21 and name N1) or
 (resid 21 and name N3) or
 (resid 21 and name C5)
    )
    weight=$planarweight
end

group
    selection=(
 (resid 2 and name N1) or
 (resid 2 and name N3) or
 (resid 2 and name C5) or
 (resid 20 and name N1) or
 (resid 20 and name N3) or
 (resid 20 and name C5)
    )
    weight=$planarweight
end

group
    selection=(
 (resid 3 and name N1) or
 (resid 3 and name N3) or
 (resid 3 and name C5) or
 (resid 19 and name N1) or
 (resid 19 and name N3) or
 (resid 19 and name C5)
    )
    weight=$planarweight
end

group
    selection=(
 (resid 4 and name N1) or
 (resid 4 and name N3) or
 (resid 4 and name C5) or
 (resid 18 and name N1) or
 (resid 18 and name N3) or
 (resid 18 and name C5)
    )
    weight=$planarweight
end

group
    selection=(
 (resid 5 and name N1) or
 (resid 5 and name N3) or
 (resid 5 and name C5) or
 (resid 17 and name N1) or
 (resid 17 and name N3) or
 (resid 17 and name C5)
    )
    weight=$planarweight
end

group
    selection=(
 (resid 6 and name N1) or
 (resid 6 and name N3) or
 (resid 6 and name C5) or
 (resid 16 and name N1) or
 (resid 16 and name N3) or
 (resid 16 and name C5)
    )
    weight=$planarweight
end

group
    selection=(
 (resid 7 and name N1) or
 (resid 7 and name N3) or
 (resid 7 and name C5) or
 (resid 15 and name N1) or
 (resid 15 and name N3) or
 (resid 15 and name C5)
    )
    weight=$planarweight
end
Distances:
    A-form NOEs for stem:
 cp ../stem/noes.inp noes.stem.inp
 Hand-edited noes.stem.inp to change segid b resid 1-7 to segid b resid
     15-21, then removed segids
    Real NOES for loop:
 I'm artificially constraining the stem to A-form and there are no
     exchangeable NOEs in the loop (or between stem and loop) so I need
     concern myself only with nonexchangeable NOEs involving at least
     one loop proton.
 egrep 'resid ([8-9]|1[0-4])' ~/nmr/italy2-30c.int/noes.d2o.inp >
     noes.loop.inp.old
 cp noes.loop.inp.old noes.loop.inp
 Hand-edited

Dihedrals:
    Hand-created dihedrals.d2x using values from
 - inspection of 31P-1H COSY (alpha-zeta)
 - inspection of aromatic-sugar region of NOESY (chi)
 - ~/nmr/italy2-30c.j/j2nu.out (nu0-nu4); left intermediate Js
   unconstrained and constrained U12 (75% C2'-endo) to C2'-endo
        - used A-form angles for G1 and C21, since I'm using A-form NOEs there
    dihedrals2xplor dihedrals.d2x > dihedrals.inp

Template:
    Ran run.make-template.
    Moved make-template.??.out, template.??.pdb and make-template.summary to
 template/.
    Examined templates; template/template.07.pdb has the lowest energy
 (out of a not very large range)
    Linked template/template.07.pdb to template.pdb.

Miscellaneous:
    Increased dgsa.inp's weighting of cdih term by 4x relative to the manual.
 Doing so eliminated almost all dihedral angle violations (although
 violations were usually only 5 degrees or so anyway) and did not
 increase (in fact may have reduced) NOE violations.
    Ran series of calculations varying times and timesteps in template.inp and
 dgsa.inp; see ../italy2.results/{template,dgsa}.
    Ran calculations including interesting NOEs predicted by 4tna; see
 ../italy2.results/33-36.
    Ran calculations omitting scary (not A-like, nonsequential) NOEs and then
 reincluding them; see ../italy2.results/scary.
    Ran calculations on each set of dihedral angles. The cheating sets always
        result in more tRNAPhe-like structures than the corresponding honest
 sets. The free and fixed sets come out about the same.
    Ran calculations with and without tcoupling=true in refine.inp (it was
 only omitted due to an error in the first place) and with an extra
 cooling step to get down to 0K. Neither made much difference; I'm now
 using the former (which I'd have used without thinking in the first
 place if I hadn't left it out by accident) but not the latter.
 See ../italy2.results/tcoup,cool
    Ran calculations with U12 ribose free; didn't make much difference.
    Increased NOE weighting by twofold relative to the manual. See
 ../italy2.results/noe-weighting

Averaging:
    Determined that 3, 5, 8, 11, 14, 17, 18, 20, 22, 23, 24, 27 had converged.
    Ran average-dihedrals on those structures. Observed that A11 alpha, beta
 and gamma are in one distinct range in 8, 18, 27 and another in the
 rest.
    Ran average-dihedrals on 3, 5, 8, 11, 14, 17, 18, 20, 22, 23, 24, 27 and
 on 8, 18, 27.
    Will report average across all converged structures for all angles except
 A11 alpha, beta, gamma, for which I'll report averages for each subset.
    Ran average.inp once on all 12 and once on all but 8, 18, 27. The
 averaged structure is the same. Threw away the former.
! refine.inp -- Clean up the output of dgsa.inp using simulated annealing,
!     including Van der Waals and electrostatic forces
! Dave Schweisguth , 21 Jul 1996
! Derived from nmr/refine_gentle.inp

evaluate ($t=300)  ! Temperature for constant-temperature MD
evaluate ($steps=40000)     ! Number of steps of constant-temperature MD
evaluate ($timestep=0.0005) ! Time of each MD step

set seed=@xplor.seed end ! Use 'xplor -s'

set echo=off message=off end ! Normal use
!set echo=on message=all end ! Auxiliary file debugging

structure @rsf.inp end
parameter @XPLORLIB:toppar/dna-rna-allatom.par end

noe nres=1000 @noes.stem.inp @noes.loop.inp @base-pairs.inp end
restraints dihedral nassign=300 @dihedrals.inp end
evaluate($planarweight=50) ! AAFS' choice
restraints planar @planars.inp end

set echo=on message=all end

noe    ! Parameters for NOE effective energy term.
    ceiling=1000                      
    averaging  * cent
    potential  * square
    sqconstant * 1
    sqexponent * 2
    scale      * 100  ! Constant NOE scale throughout the protocol.
end

parameter
    nbonds
 ctonnb=9.5
 ctofnb=10.5
 cutnb=11.5
 tolerance=0.5
 rdie
 switch
 vswitch
    end
end

restraints dihedral scale=800 end

coordinates @dgsa.pdb  ! END in PDB file

flags exclude * include bond angl dihe impr vdw elec noe cdih plan end

! Intial minimization.

minimize powell nstep=200 nprint=25 end

! Constant temperature SA

vector do (fbeta=100) (all) ! Coupling to heat bath.
dynamics verlet
    iasvel=maxwell
    firsttemperature=$t
    tbath=$t
    tcoup=true
    nstep=$steps
    timestep=$timestep
    nprint=250
    iprfrq=2500
    trajectory=refine.tra
    nsavc=200   ! Save trajectory to file.
end
close refine.tra end

! Compute dynamics average over second half of trajectory.

evaluate ($steps2=$steps/2)
dynamics analysis average
    input=refine.tra
    begin=$steps2
    skip=200
    stop=$steps
end
close refine.tra end  ! disposition=delete doesn't work

! Final minimization.

minimize powell nstep=200 nprint=25 end

! Analyze and write out the final structure.

print threshold=0.05 bonds          
evaluate ($rms_bond=$result)
evaluate ($v_bond=$violations)
print threshold=5 angles
evaluate ($rms_angl=$result)
evaluate ($v_angl=$violations)
print threshold=15 dihedrals
evaluate ($rms_dihe=$result)
evaluate ($v_dihe=$violations)
print threshold=5 impropers
evaluate ($rms_impr=$result)
evaluate ($v_impr=$violations)
print threshold=0.2 noe 
evaluate ($rms_noe=$result)
evaluate ($v_noe=$violations)
print threshold=5 cdih
evaluate ($rms_cdih=$result)
evaluate ($v_cdih=$violations)

set echo=off message=off end

display Energy:      bond $bond, angle $angl, dihedral $dihe,
display              improper $impr, NOE $noe, c-dihedral $cdih,
display              planar $plan, VdW $vdw, elec $elec, total $ener
display RMSD:        bond $rms_bond, angle $rms_angl, dihedral $rms_dihe,
display              improper $rms_impr, NOE $rms_noe, c-dihedral $rms_cdih
display Violations:  bond $v_bond, angle $v_angl, dihedral $v_dihe,
display              improper $v_impr, NOE $v_noe, c-dihedral $v_cdih

set echo=on message=all end

write coordinates output=refine.pdb end
    
stop
#!/bin/csh -f
#$ -cwd -o refine.run.o -e refine.run.e -m bae -M dcs@proton.chem.yale.edu

set i=21
while ($i <= 30)
    set ii=`nawk 'BEGIN { printf "%02d", '$i' }'`

    ln -s dgsa.$ii.pdb dgsa.pdb
    xplor -s < refine.inp > refine.$ii.out
    ip 'repdb -ix -om' refine.pdb
    mv refine.pdb refine.$ii.pdb
    rm -f dgsa.pdb refine.tra

    @ i++
end

perl -ne 'print if /^Ener/ .. /^ X-PLOR/' refine.??.out > refine.summary
perl -ne 'print if /0.2 noe/ .. /NOEPRI/' refine.??.out > refine.summary.noes
perl -ne 'print if /5 cdih/ .. /RMS deviation/' refine.??.out > refine.summary.cdih
Energy:      bond 6.82185, angle 75.9282, dihedral 0,
             improper 12.9596, NOE 30.7869, c-dihedral 0.377104,
             planar 11.2312, VdW -272.878, elec -156.266, total -291.039
RMSD:        bond 2.128274E-03, angle 0.63725, dihedral 0,
             improper 0.362077, NOE 1.821415E-02, c-dihedral 8.730925E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 1, c-dihedral 0
 X-PLOR> 
Energy:      bond 13.4799, angle 156.74, dihedral 0,
             improper 16.1502, NOE 73.7451, c-dihedral 7.72301,
             planar 14.2996, VdW -217.112, elec -151.646, total -86.6203
RMSD:        bond 2.923283E-03, angle 0.856688, dihedral 0,
             improper 0.402924, NOE 2.818983E-02, c-dihedral 0.395114
Violations:  bond 0, angle 5, dihedral 0,
             improper 0, NOE 7, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.49434, angle 80.8167, dihedral 0,
             improper 11.5539, NOE 11.0032, c-dihedral 0.168536,
             planar 10.971, VdW -295.59, elec -150.824, total -326.407
RMSD:        bond 1.885609E-03, angle 0.643418, dihedral 0,
             improper 0.335364, NOE 1.088895E-02, c-dihedral 5.836815E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 17.4186, angle 138.517, dihedral 0,
             improper 16.9854, NOE 214.993, c-dihedral 5.2163,
             planar 11.3582, VdW -249.783, elec -155.397, total -0.691197
RMSD:        bond 3.314792E-03, angle 0.798054, dihedral 0,
             improper 0.395005, NOE 4.813252E-02, c-dihedral 0.324722
Violations:  bond 0, angle 4, dihedral 0,
             improper 0, NOE 5, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.56008, angle 79.9851, dihedral 0,
             improper 11.3117, NOE 9.74306, c-dihedral 8.297671E-02,
             planar 10.8271, VdW -294.217, elec -150.812, total -327.519
RMSD:        bond 1.88621E-03, angle 0.636034, dihedral 0,
             improper 0.327116, NOE 1.024646E-02, c-dihedral 4.095508E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 7.3353, angle 77.8862, dihedral 0,
             improper 11.2836, NOE 38.8648, c-dihedral 0.536194,
             planar 10.8003, VdW -285.768, elec -160.194, total -299.256
RMSD:        bond 2.186013E-03, angle 0.643811, dihedral 0,
             improper 0.332809, NOE 2.046466E-02, c-dihedral 0.10411
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 2, c-dihedral 0
 X-PLOR> 
Energy:      bond 47.9089, angle 302.448, dihedral 0,
             improper 53.7644, NOE 335.551, c-dihedral 20.0301,
             planar 12.2942, VdW -76.8289, elec -151.636, total 543.531
RMSD:        bond 5.595598E-03, angle 1.12278, dihedral 0,
             improper 0.666547, NOE 6.013195E-02, c-dihedral 0.636313
Violations:  bond 2, angle 9, dihedral 0,
             improper 1, NOE 12, c-dihedral 1
 X-PLOR> 
Energy:      bond 5.38235, angle 81.2672, dihedral 0,
             improper 11.4693, NOE 10.38, c-dihedral 0.224272,
             planar 11.1517, VdW -297.755, elec -156.622, total -334.502
RMSD:        bond 1.871638E-03, angle 0.641118, dihedral 0,
             improper 0.329779, NOE 1.057607E-02, c-dihedral 6.733133E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 12.9795, angle 145.228, dihedral 0,
             improper 18.4764, NOE 104.509, c-dihedral 14.7462,
             planar 12.1111, VdW -230.48, elec -145.001, total -67.4298
RMSD:        bond 2.948581E-03, angle 0.817938, dihedral 0,
             improper 0.45324, NOE 3.355854E-02, c-dihedral 0.545972
Violations:  bond 0, angle 3, dihedral 0,
             improper 0, NOE 5, c-dihedral 1
 X-PLOR> 
Energy:      bond 14.1555, angle 146.412, dihedral 0,
             improper 16.6931, NOE 93.2807, c-dihedral 3.74333,
             planar 11.7385, VdW -199.13, elec -163.401, total -76.5086
RMSD:        bond 2.968463E-03, angle 0.83363, dihedral 0,
             improper 0.41344, NOE 3.170457E-02, c-dihedral 0.27508
Violations:  bond 0, angle 6, dihedral 0,
             improper 0, NOE 5, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.3733, angle 80.3415, dihedral 0,
             improper 11.1568, NOE 10.4632, c-dihedral 0.201885,
             planar 11.2012, VdW -298.683, elec -159.944, total -339.888
RMSD:        bond 1.857353E-03, angle 0.638548, dihedral 0,
             improper 0.325363, NOE 1.06184E-02, c-dihedral 6.388247E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 6.86849, angle 76.5621, dihedral 0,
             improper 12.9839, NOE 30.7148, c-dihedral 0.301037,
             planar 11.5348, VdW -273.004, elec -158.195, total -292.234
RMSD:        bond 2.135129E-03, angle 0.637426, dihedral 0,
             improper 0.363439, NOE 1.819282E-02, c-dihedral 7.800802E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 1, c-dihedral 0
 X-PLOR> 
Energy:      bond 15.6069, angle 136.799, dihedral 0,
             improper 16.993, NOE 121.925, c-dihedral 1.01242,
             planar 11.1758, VdW -204.524, elec -141.84, total -42.8518
RMSD:        bond 3.118086E-03, angle 0.823723, dihedral 0,
             improper 0.448135, NOE 3.624701E-02, c-dihedral 0.143057
Violations:  bond 0, angle 2, dihedral 0,
             improper 0, NOE 8, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.44256, angle 81.2518, dihedral 0,
             improper 11.2316, NOE 10.3389, c-dihedral 0.158032,
             planar 11.3796, VdW -299.278, elec -156.166, total -335.641
RMSD:        bond 1.867033E-03, angle 0.64166, dihedral 0,
             improper 0.32578, NOE 1.055513E-02, c-dihedral 5.652006E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 7.83963, angle 103.102, dihedral 0,
             improper 16.5605, NOE 42.9527, c-dihedral 1.21144,
             planar 14.4401, VdW -264.943, elec -144.214, total -223.051
RMSD:        bond 2.250803E-03, angle 0.717568, dihedral 0,
             improper 0.438425, NOE 2.151401E-02, c-dihedral 0.156488
Violations:  bond 0, angle 2, dihedral 0,
             improper 0, NOE 3, c-dihedral 0
 X-PLOR> 
Energy:      bond 14.7665, angle 114.55, dihedral 0,
             improper 15.5392, NOE 102.098, c-dihedral 12.817,
             planar 11.244, VdW -221.362, elec -156.881, total -107.228
RMSD:        bond 2.99944E-03, angle 0.744821, dihedral 0,
             improper 0.380885, NOE 3.316923E-02, c-dihedral 0.509005
Violations:  bond 0, angle 1, dihedral 0,
             improper 0, NOE 5, c-dihedral 1
 X-PLOR> 
Energy:      bond 6.04426, angle 82.3145, dihedral 0,
             improper 11.3813, NOE 12.2905, c-dihedral 0.121711,
             planar 11.2325, VdW -301.139, elec -154.956, total -332.71
RMSD:        bond 1.976642E-03, angle 0.647884, dihedral 0,
             improper 0.331282, NOE 1.15083E-02, c-dihedral 4.96014E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.55146, angle 81.9342, dihedral 0,
             improper 11.3297, NOE 9.79527, c-dihedral 0.28896,
             planar 10.8065, VdW -297.008, elec -158.362, total -335.664
RMSD:        bond 1.896888E-03, angle 0.641563, dihedral 0,
             improper 0.325173, NOE 1.027387E-02, c-dihedral 7.642728E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 6.46286, angle 88.0539, dihedral 0,
             improper 11.9755, NOE 16.4402, c-dihedral 0.298963,
             planar 11.5966, VdW -284.158, elec -156.251, total -305.581
RMSD:        bond 2.061992E-03, angle 0.676729, dihedral 0,
             improper 0.352732, NOE 1.331004E-02, c-dihedral 7.773894E-02
Violations:  bond 0, angle 1, dihedral 0,
             improper 0, NOE 1, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.34347, angle 80.531, dihedral 0,
             improper 11.2726, NOE 10.4319, c-dihedral 0.129335,
             planar 11.1576, VdW -297.78, elec -159.751, total -338.664
RMSD:        bond 1.8552E-03, angle 0.640319, dihedral 0,
             improper 0.32678, NOE 1.060251E-02, c-dihedral 5.113147E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 8.05805, angle 87.5132, dihedral 0,
             improper 15.6142, NOE 33.9665, c-dihedral 1.77375,
             planar 11.7193, VdW -268.5, elec -140.585, total -250.44
RMSD:        bond 2.28512E-03, angle 0.676461, dihedral 0,
             improper 0.402375, NOE 1.913161E-02, c-dihedral 0.189355
Violations:  bond 0, angle 1, dihedral 0,
             improper 0, NOE 2, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.38552, angle 79.8292, dihedral 0,
             improper 10.9971, NOE 10.6675, c-dihedral 0.195734,
             planar 11.2265, VdW -298.203, elec -162.185, total -342.086
RMSD:        bond 1.863103E-03, angle 0.638561, dihedral 0,
             improper 0.321073, NOE 1.072153E-02, c-dihedral 6.290168E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.26856, angle 78.4088, dihedral 0,
             improper 10.8304, NOE 10.6594, c-dihedral 0.126883,
             planar 11.1955, VdW -296.969, elec -160.947, total -341.427
RMSD:        bond 1.840111E-03, angle 0.635118, dihedral 0,
             improper 0.317483, NOE 1.071745E-02, c-dihedral 5.064444E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.62076, angle 81.751, dihedral 0,
             improper 11.3325, NOE 10.726, c-dihedral 9.574263E-02,
             planar 11.2148, VdW -296.91, elec -156.322, total -332.491
RMSD:        bond 1.903787E-03, angle 0.644033, dihedral 0,
             improper 0.32811, NOE 1.07509E-02, c-dihedral 4.399287E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 6.02136, angle 79.8281, dihedral 0,
             improper 13.4188, NOE 21.3356, c-dihedral 0.969462,
             planar 11.5337, VdW -286.637, elec -162.914, total -316.444
RMSD:        bond 1.991372E-03, angle 0.641434, dihedral 0,
             improper 0.39248, NOE 1.516277E-02, c-dihedral 0.139989
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 1, c-dihedral 0
 X-PLOR> 
Energy:      bond 7.081, angle 80.5539, dihedral 0,
             improper 19.1881, NOE 42.6479, c-dihedral 1.6066,
             planar 13.5833, VdW -267.533, elec -158.45, total -261.323
RMSD:        bond 2.186578E-03, angle 0.640659, dihedral 0,
             improper 0.503011, NOE 2.143754E-02, c-dihedral 0.180212
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 3, c-dihedral 0
 X-PLOR> 
Energy:      bond 5.16548, angle 78.8711, dihedral 0,
             improper 11.0963, NOE 10.4088, c-dihedral 0.174039,
             planar 11.1508, VdW -295.94, elec -158.751, total -337.824
RMSD:        bond 1.835891E-03, angle 0.633608, dihedral 0,
             improper 0.321732, NOE 1.059076E-02, c-dihedral 5.931346E-02
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 0, c-dihedral 0
 X-PLOR> 
Energy:      bond 6.30609, angle 79.3936, dihedral 0,
             improper 13.4801, NOE 23.1387, c-dihedral 1.03891,
             planar 11.4371, VdW -292.613, elec -164.211, total -322.029
RMSD:        bond 2.008711E-03, angle 0.638578, dihedral 0,
             improper 0.383185, NOE 1.57905E-02, c-dihedral 0.144917
Violations:  bond 0, angle 0, dihedral 0,
             improper 0, NOE 1, c-dihedral 0
 X-PLOR> 
Energy:      bond 3375.12, angle 1077.59, dihedral 0,
             improper 1351.19, NOE 5140.31, c-dihedral 190.518,
             planar 408.112, VdW 3321.4, elec -145.675, total 14718.6
RMSD:        bond 5.118243E-02, angle 3.00728, dihedral 0,
             improper 4.65881, NOE 0.235354, c-dihedral 1.96244
Violations:  bond 36, angle 50, dihedral 0,
             improper 53, NOE 108, c-dihedral 6
 X-PLOR> 
Energy:      bond 14.1521, angle 120.576, dihedral 0,
             improper 21.5735, NOE 74.0342, c-dihedral 8.24043,
             planar 11.2254, VdW -253.816, elec -155.755, total -159.77
RMSD:        bond 2.976148E-03, angle 0.781102, dihedral 0,
             improper 0.519056, NOE 2.824505E-02, c-dihedral 0.408136
Violations:  bond 0, angle 1, dihedral 0,
             improper 0, NOE 5, c-dihedral 0
 X-PLOR> 
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.087
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.395
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.058
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.325
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.041
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.104
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 ========================================
 A    11   ADE  O4' 
 A    11   ADE  C1' 
 A    11   ADE  N9  
 A    11   ADE  C4  
 Dihedral= -121.332  Energy=    0.014 C=    1.000 Equil= -158.000 Delta=   -6.668
 Range=  30.000 Exponent=  2
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     1
 RMS deviation=   0.636
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.067
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 ========================================
 A    13   ADE  P   
 A    13   ADE  O5' 
 A    13   ADE  C5' 
 A    13   ADE  C4' 
 Dihedral=  142.714  Energy=    0.009 C=    1.000 Equil=  178.000 Delta=    5.286
 Range=  30.000 Exponent=  2
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     1
 RMS deviation=   0.546
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.275
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.064
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.078
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.143
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.057
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.156
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 ========================================
 A    10   CYT  O5' 
 A    10   CYT  C5' 
 A    10   CYT  C4' 
 A    10   CYT  C3' 
 Dihedral=   89.808  Energy=    0.010 C=    1.000 Equil=   54.000 Delta=   -5.808
 Range=  30.000 Exponent=  2
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     1
 RMS deviation=   0.509
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.050
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.076
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.078
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.051
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.189
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.063
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.051
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.044
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.140
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.180
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.059
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.145
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 ========================================
 A    1    GUA  O4' 
 A    1    GUA  C1' 
 A    1    GUA  N9  
 A    1    GUA  C4  
 Dihedral=  165.941  Energy=    0.135 C=    1.000 Equil= -158.000 Delta=   21.059
 Range=  15.000 Exponent=  2
 ========================================
 A    2    GUA  C4' 
 A    2    GUA  C3' 
 A    2    GUA  O3' 
 A    3    CYT  P   
 Dihedral= -179.213  Energy=    0.038 C=    1.000 Equil= -153.000 Delta=   11.213
 Range=  15.000 Exponent=  2
 ========================================
 A    2    GUA  O4' 
 A    2    GUA  C1' 
 A    2    GUA  N9  
 A    2    GUA  C4  
 Dihedral=  179.816  Energy=    0.016 C=    1.000 Equil= -158.000 Delta=    7.184
 Range=  15.000 Exponent=  2
 ========================================
 A    3    CYT  P   
 A    3    CYT  O5' 
 A    3    CYT  C5' 
 A    3    CYT  C4' 
 Dihedral=  157.096  Energy=    0.011 C=    1.000 Equil=  178.000 Delta=    5.904
 Range=  15.000 Exponent=  2
 ========================================
 A    3    CYT  C4' 
 A    3    CYT  C3' 
 A    3    CYT  O3' 
 A    4    ADE  P   
 Dihedral= -173.658  Energy=    0.010 C=    1.000 Equil= -153.000 Delta=    5.658
 Range=  15.000 Exponent=  2
 ========================================
 A    21   CYT  O4' 
 A    21   CYT  C1' 
 A    21   CYT  N1  
 A    21   CYT  C2  
 Dihedral= -137.247  Energy=    0.010 C=    1.000 Equil= -158.000 Delta=   -5.753
 Range=  15.000 Exponent=  2
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     6
 RMS deviation=   1.962
 X-PLOR>print threshold=5 cdih 
 Total number of dihedral angle restraints=   203
  overall scale =  800.0000
 Number of dihedral angle restraints=  203
 Number of violations greater than    5.000:     0
 RMS deviation=   0.408
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H1' 
 set-j-atoms
          A    13   ADE  H8  
 R=   5.288 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.288  E(NOE)=   8.276

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     1 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.320 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.320  E(NOE)=  10.267
 ========================================
 set-i-atoms
          A    10   CYT  H6  
 set-j-atoms
          A    11   ADE  H8  
 R=   2.782 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.218  E(NOE)=   4.755
 ========================================
 set-i-atoms
          A    10   CYT  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.261 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.261  E(NOE)=   6.799
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.370 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.370  E(NOE)=  13.656
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.787 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.213  E(NOE)=   4.519
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.317 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.317  E(NOE)=  10.039
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.234 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.234  E(NOE)=   5.490

 NOEPRI: RMS diff. =   0.028,  #(violat.> 0.2)=     7 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.011,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.415 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.415  E(NOE)=  17.246
 ========================================
 set-i-atoms
          A    10   CYT  H1' 
 set-j-atoms
          A    11   ADE  H8  
 R=   2.328 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.672  E(NOE)=  45.151
 ========================================
 set-i-atoms
          A    10   CYT  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.354 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.354  E(NOE)=  12.539
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.891 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.891  E(NOE)=  79.392
 ========================================
 set-i-atoms
          A    10   CYT  H4' 
 set-j-atoms
          A    11   ADE  H8  
 R=   2.340 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.660  E(NOE)=  43.547

 NOEPRI: RMS diff. =   0.048,  #(violat.> 0.2)=     5 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.010,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.690 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.310  E(NOE)=   9.626
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.305 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.305  E(NOE)=   9.305

 NOEPRI: RMS diff. =   0.020,  #(violat.> 0.2)=     2 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    10   CYT  H6  
 R=   5.444 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.444  E(NOE)=  19.733
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.504 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.504  E(NOE)=  25.401
 ========================================
 set-i-atoms
          A    10   CYT  H1' 
 set-j-atoms
          A    11   ADE  H8  
 R=   5.912 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.912  E(NOE)=  83.138
 ========================================
 set-i-atoms
          A    10   CYT  H4' 
 set-j-atoms
          A    11   ADE  H8  
 R=   5.646 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.646  E(NOE)=  41.775
 ========================================
 set-i-atoms
          A    11   ADE  H2  
 set-j-atoms
          A    12   URI  H1' 
 R=   5.362 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.362  E(NOE)=  13.074
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   2.779 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.221  E(NOE)=   4.898
 ========================================
 set-i-atoms
          A    11   ADE  H2' 
 set-j-atoms
          A    12   URI  H6  
 R=   4.769 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.769  E(NOE)=  59.196
 ========================================
 set-i-atoms
          A    11   ADE  H3' 
 set-j-atoms
          A    12   URI  H6  
 R=   2.763 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.237  E(NOE)=   5.627
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    12   URI  H3' 
 R=   4.355 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.355  E(NOE)=  12.625
 ========================================
 set-i-atoms
          A    12   URI  H1' 
 set-j-atoms
          A    12   URI  H4' 
 R=   2.724 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.276  E(NOE)=   7.617
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.699 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.301  E(NOE)=   9.076
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.569 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.569  E(NOE)=  32.324

 NOEPRI: RMS diff. =   0.060,  #(violat.> 0.2)=    12 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.011,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.585 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.585  E(NOE)=  34.212
 ========================================
 set-i-atoms
          A    10   CYT  H1' 
 set-j-atoms
          A    11   ADE  H8  
 R=   5.297 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.297  E(NOE)=   8.823
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.209 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.209  E(NOE)=   4.348
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.344 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.344  E(NOE)=  11.834
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.407 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.407  E(NOE)=  16.588

 NOEPRI: RMS diff. =   0.034,  #(violat.> 0.2)=     5 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.348 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.348  E(NOE)=  12.100
 ========================================
 set-i-atoms
          A    10   CYT  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.218 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.218  E(NOE)=   4.735
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.534 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.534  E(NOE)=  28.473
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    11   ADE  H3' 
 R=   3.253 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.253  E(NOE)=   6.419
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    12   URI  H3' 
 R=   4.248 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.248  E(NOE)=   6.167

 NOEPRI: RMS diff. =   0.032,  #(violat.> 0.2)=     5 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.011,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H1' 
 set-j-atoms
          A    13   ADE  H8  
 R=   5.285 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.285  E(NOE)=   8.139

 NOEPRI: RMS diff. =   0.018,  #(violat.> 0.2)=     1 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H1' 
 set-j-atoms
          A    10   CYT  H2' 
 R=   5.333 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.333  E(NOE)=  11.079
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.394 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.394  E(NOE)=  15.535
 ========================================
 set-i-atoms
          A    11   ADE  H2  
 set-j-atoms
          A    12   URI  H1' 
 R=   5.413 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.413  E(NOE)=  17.039
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.477 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.477  E(NOE)=  22.766
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.762 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.238  E(NOE)=   5.667
 ========================================
 set-i-atoms
          A    12   URI  H3' 
 set-j-atoms
          A    13   ADE  H8  
 R=   3.346 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.346  E(NOE)=  11.982
 ========================================
 set-i-atoms
          A    13   ADE  H8  
 set-j-atoms
          A    13   ADE  H4' 
 R=   4.203 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.203  E(NOE)=   4.128
 ========================================
 set-i-atoms
          A    11   ADE  H1' 
 set-j-atoms
          A    12   URI  H6  
 R=   2.667 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.333  E(NOE)=  11.059

 NOEPRI: RMS diff. =   0.036,  #(violat.> 0.2)=     8 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.011,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.323 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.323  E(NOE)=  10.449
 ========================================
 set-i-atoms
          A    12   URI  H4' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.773 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.227  E(NOE)=   5.170
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.251 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.251  E(NOE)=   6.325

 NOEPRI: RMS diff. =   0.022,  #(violat.> 0.2)=     3 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H1' 
 set-j-atoms
          A    10   CYT  H2' 
 R=   5.540 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.540  E(NOE)=  29.125
 ========================================
 set-i-atoms
          A    9    URI  H1' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.245 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.245  E(NOE)=   5.999
 ========================================
 set-i-atoms
          A    9    URI  H2' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.239 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.239  E(NOE)=   5.718
 ========================================
 set-i-atoms
          A    10   CYT  H3' 
 set-j-atoms
          A    11   ADE  H8  
 R=   3.470 NOE= 2.40 (- 0.60/+ 0.60) Delta=  -0.470  E(NOE)=  22.132
 ========================================
 set-i-atoms
          A    10   CYT  H4' 
 set-j-atoms
          A    11   ADE  H8  
 R=   2.516 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.484  E(NOE)=  23.458

 NOEPRI: RMS diff. =   0.033,  #(violat.> 0.2)=     5 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.012,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.010,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    9    URI  H6  
 set-j-atoms
          A    9    URI  H2' 
 R=   4.226 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.226  E(NOE)=   5.104

 NOEPRI: RMS diff. =   0.013,  #(violat.> 0.2)=     1 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.011,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.315 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.315  E(NOE)=   9.949
 ========================================
 set-i-atoms
          A    13   ADE  H1' 
 set-j-atoms
          A    14   ADE  H1' 
 R=   4.218 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.218  E(NOE)=   4.761

 NOEPRI: RMS diff. =   0.019,  #(violat.> 0.2)=     2 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.011,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.011,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.011,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.259 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.259  E(NOE)=   6.692

 NOEPRI: RMS diff. =   0.015,  #(violat.> 0.2)=     1 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.333 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.333  E(NOE)=  11.113
 ========================================
 set-i-atoms
          A    12   URI  H4' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.771 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.229  E(NOE)=   5.243
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.292 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.292  E(NOE)=   8.536

 NOEPRI: RMS diff. =   0.021,  #(violat.> 0.2)=     3 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 NOEPRI: RMS diff. =   0.011,  #(violat.> 0.2)=     0 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.288 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.288  E(NOE)=   8.315

 NOEPRI: RMS diff. =   0.016,  #(violat.> 0.2)=     1 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    1    GUA  H1' 
 set-j-atoms
          A    1    GUA  H3' 
 R=   3.548 NOE= 3.86 (- 0.10/+ 0.10) Delta=   0.209  E(NOE)=   4.386
 ========================================
 set-i-atoms
          A    1    GUA  H1' 
 set-j-atoms
          A    1    GUA  H21 
 R=   6.092 NOE= 4.77 (- 0.10/+ 0.10) Delta=  -1.218  E(NOE)= 148.414
 ========================================
 set-i-atoms
          A    1    GUA  H1' 
 set-j-atoms
          A    1    GUA  H8  
 R=   3.294 NOE= 3.73 (- 0.10/+ 0.10) Delta=   0.333  E(NOE)=  11.096
 ========================================
 set-i-atoms
          A    1    GUA  H1' 
 set-j-atoms
          A    2    GUA  H8  
 R=   2.935 NOE= 4.32 (- 0.10/+ 0.10) Delta=   1.284  E(NOE)= 164.902
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    1    GUA  H21 
 R=   4.001 NOE= 4.70 (- 0.10/+ 0.10) Delta=   0.601  E(NOE)=  36.092
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    1    GUA  H8  
 R=   4.480 NOE= 4.15 (- 0.10/+ 0.10) Delta=  -0.231  E(NOE)=   5.352
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    2    GUA  H1' 
 R=   4.578 NOE= 4.19 (- 0.10/+ 0.10) Delta=  -0.285  E(NOE)=   8.138
 ========================================
 set-i-atoms
          A    1    GUA  H2' 
 set-j-atoms
          A    2    GUA  H5''
 R=   3.822 NOE= 4.27 (- 0.10/+ 0.10) Delta=   0.346  E(NOE)=  11.988
 ========================================
 set-i-atoms
          A    1    GUA  H3' 
 set-j-atoms
          A    1    GUA  H8  
 R=   3.562 NOE= 3.20 (- 0.10/+ 0.10) Delta=  -0.266  E(NOE)=   7.075
 ========================================
 set-i-atoms
          A    1    GUA  H3' 
 set-j-atoms
          A    2    GUA  H8  
 R=   3.831 NOE= 3.02 (- 0.10/+ 0.10) Delta=  -0.707  E(NOE)=  50.055
 ========================================
 set-i-atoms
          A    1    GUA  H21 
 set-j-atoms
          A    2    GUA  H1' 
 R=   4.136 NOE= 3.25 (- 0.10/+ 0.10) Delta=  -0.781  E(NOE)=  60.955
 ========================================
 set-i-atoms
          A    1    GUA  H21 
 set-j-atoms
          A    2    GUA  H8  
 R=   3.300 NOE= 4.88 (- 0.10/+ 0.10) Delta=   1.476  E(NOE)= 217.784
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    2    GUA  H1' 
 R=   4.731 NOE= 4.21 (- 0.10/+ 0.10) Delta=  -0.426  E(NOE)=  18.168
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    2    GUA  H21 
 R=   4.080 NOE= 4.77 (- 0.10/+ 0.10) Delta=   0.593  E(NOE)=  35.167
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    2    GUA  H1  
 R=   5.321 NOE= 4.79 (- 0.10/+ 0.10) Delta=  -0.431  E(NOE)=  18.536
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    21   CYT  H1' 
 R=   3.191 NOE= 4.32 (- 0.10/+ 0.10) Delta=   1.026  E(NOE)= 105.168
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    21   CYT  H2' 
 R=   5.463 NOE= 4.67 (- 0.10/+ 0.10) Delta=  -0.696  E(NOE)=  48.504
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    21   CYT  H42 
 R=   4.246 NOE= 4.57 (- 0.10/+ 0.10) Delta=   0.220  E(NOE)=   4.826
 ========================================
 set-i-atoms
          A    1    GUA  H1  
 set-j-atoms
          A    21   CYT  H41 
 R=   4.424 NOE= 4.02 (- 0.10/+ 0.10) Delta=  -0.301  E(NOE)=   9.087
 ========================================
 set-i-atoms
          A    1    GUA  H1  
 set-j-atoms
          A    21   CYT  H42 
 R=   2.945 NOE= 2.48 (- 0.10/+ 0.10) Delta=  -0.366  E(NOE)=  13.368
 ========================================
 set-i-atoms
          A    2    GUA  H1' 
 set-j-atoms
          A    2    GUA  H21 
 R=   5.587 NOE= 4.78 (- 0.10/+ 0.10) Delta=  -0.712  E(NOE)=  50.716
 ========================================
 set-i-atoms
          A    2    GUA  H1' 
 set-j-atoms
          A    2    GUA  H8  
 R=   3.229 NOE= 3.73 (- 0.10/+ 0.10) Delta=   0.398  E(NOE)=  15.808
 ========================================
 set-i-atoms
          A    2    GUA  H1' 
 set-j-atoms
          A    3    CYT  H6  
 R=   3.650 NOE= 4.30 (- 0.10/+ 0.10) Delta=   0.548  E(NOE)=  30.019
 ========================================
 set-i-atoms
          A    2    GUA  H2' 
 set-j-atoms
          A    3    CYT  H1' 
 R=   3.544 NOE= 4.19 (- 0.10/+ 0.10) Delta=   0.548  E(NOE)=  30.070
 ========================================
 set-i-atoms
          A    2    GUA  H2' 
 set-j-atoms
          A    3    CYT  H3' 
 R=   3.855 NOE= 4.26 (- 0.10/+ 0.10) Delta=   0.308  E(NOE)=   9.493
 ========================================
 set-i-atoms
          A    2    GUA  H2' 
 set-j-atoms
          A    3    CYT  H4' 
 R=   3.998 NOE= 4.44 (- 0.10/+ 0.10) Delta=   0.344  E(NOE)=  11.808
 ========================================
 set-i-atoms
          A    2    GUA  H2' 
 set-j-atoms
          A    3    CYT  H5''
 R=   3.715 NOE= 4.27 (- 0.10/+ 0.10) Delta=   0.453  E(NOE)=  20.541
 ========================================
 set-i-atoms
          A    2    GUA  H3' 
 set-j-atoms
          A    2    GUA  H8  
 R=   3.624 NOE= 3.20 (- 0.10/+ 0.10) Delta=  -0.328  E(NOE)=  10.770
 ========================================
 set-i-atoms
          A    2    GUA  H3' 
 set-j-atoms
          A    3    CYT  H5' 
 R=   4.402 NOE= 3.96 (- 0.10/+ 0.10) Delta=  -0.344  E(NOE)=  11.827
 ========================================
 set-i-atoms
          A    2    GUA  H3' 
 set-j-atoms
          A    3    CYT  H5''
 R=   5.334 NOE= 4.91 (- 0.10/+ 0.10) Delta=  -0.326  E(NOE)=  10.618
 ========================================
 set-i-atoms
          A    2    GUA  H3' 
 set-j-atoms
          A    3    CYT  H5  
 R=   3.617 NOE= 3.31 (- 0.10/+ 0.10) Delta=  -0.203  E(NOE)=   4.141
 ========================================
 set-i-atoms
          A    2    GUA  H5''
 set-j-atoms
          A    2    GUA  H8  
 R=   4.670 NOE= 4.37 (- 0.10/+ 0.10) Delta=  -0.202  E(NOE)=   4.076
 ========================================
 set-i-atoms
          A    2    GUA  H21 
 set-j-atoms
          A    3    CYT  H1' 
 R=   4.713 NOE= 3.25 (- 0.10/+ 0.10) Delta=  -1.358  E(NOE)= 184.306
 ========================================
 set-i-atoms
          A    2    GUA  H21 
 set-j-atoms
          A    3    CYT  H6  
 R=   3.344 NOE= 4.83 (- 0.10/+ 0.10) Delta=   1.382  E(NOE)= 191.068
 ========================================
 set-i-atoms
          A    2    GUA  H21 
 set-j-atoms
          A    21   CYT  H1' 
 R=   5.438 NOE= 4.49 (- 0.10/+ 0.10) Delta=  -0.845  E(NOE)=  71.346
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    3    CYT  H1' 
 R=   5.782 NOE= 4.21 (- 0.10/+ 0.10) Delta=  -1.477  E(NOE)= 218.028
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    19   GUA  H21 
 R=   5.457 NOE= 4.57 (- 0.10/+ 0.10) Delta=  -0.786  E(NOE)=  61.802
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    19   GUA  H22 
 R=   4.351 NOE= 3.56 (- 0.10/+ 0.10) Delta=  -0.686  E(NOE)=  47.000
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    20   CYT  H1' 
 R=   5.317 NOE= 4.32 (- 0.10/+ 0.10) Delta=  -0.900  E(NOE)=  80.951
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    20   CYT  H2' 
 R=   5.642 NOE= 4.67 (- 0.10/+ 0.10) Delta=  -0.876  E(NOE)=  76.737
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    20   CYT  H42 
 R=   4.164 NOE= 4.57 (- 0.10/+ 0.10) Delta=   0.302  E(NOE)=   9.140
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    21   CYT  H1' 
 R=   4.980 NOE= 4.37 (- 0.10/+ 0.10) Delta=  -0.506  E(NOE)=  25.568
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    21   CYT  H6  
 R=   5.651 NOE= 4.96 (- 0.10/+ 0.10) Delta=  -0.590  E(NOE)=  34.808
 ========================================
 set-i-atoms
          A    2    GUA  H8  
 set-j-atoms
          A    3    CYT  H5  
 R=   4.792 NOE= 3.90 (- 0.10/+ 0.10) Delta=  -0.793  E(NOE)=  62.916
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    3    CYT  H41 
 R=   3.338 NOE= 4.35 (- 0.10/+ 0.10) Delta=   0.915  E(NOE)=  83.778
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    3    CYT  H42 
 R=   2.302 NOE= 3.75 (- 0.10/+ 0.10) Delta=   1.346  E(NOE)= 181.198
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    19   GUA  H1  
 R=   2.658 NOE= 3.52 (- 0.10/+ 0.10) Delta=   0.762  E(NOE)=  58.061
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    21   CYT  H42 
 R=   2.643 NOE= 3.89 (- 0.10/+ 0.10) Delta=   1.145  E(NOE)= 131.159
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    21   CYT  H5  
 R=   5.575 NOE= 4.40 (- 0.10/+ 0.10) Delta=  -1.077  E(NOE)= 116.041
 ========================================
 set-i-atoms
          A    3    CYT  H1' 
 set-j-atoms
          A    4    ADE  H5' 
 R=   4.309 NOE= 4.68 (- 0.10/+ 0.10) Delta=   0.267  E(NOE)=   7.153
 ========================================
 set-i-atoms
          A    3    CYT  H2' 
 set-j-atoms
          A    4    ADE  H1' 
 R=   3.767 NOE= 4.19 (- 0.10/+ 0.10) Delta=   0.325  E(NOE)=  10.577
 ========================================
 set-i-atoms
          A    3    CYT  H2' 
 set-j-atoms
          A    4    ADE  H4' 
 R=   4.055 NOE= 4.44 (- 0.10/+ 0.10) Delta=   0.287  E(NOE)=   8.250
 ========================================
 set-i-atoms
          A    3    CYT  H2' 
 set-j-atoms
          A    19   GUA  H22 
 R=   5.199 NOE= 4.67 (- 0.10/+ 0.10) Delta=  -0.433  E(NOE)=  18.736
 ========================================
 set-i-atoms
          A    3    CYT  H3' 
 set-j-atoms
          A    3    CYT  H5' 
 R=   4.020 NOE= 3.69 (- 0.10/+ 0.10) Delta=  -0.234  E(NOE)=   5.489
 ========================================
 set-i-atoms
          A    3    CYT  H3' 
 set-j-atoms
          A    4    ADE  H5''
 R=   5.228 NOE= 4.91 (- 0.10/+ 0.10) Delta=  -0.220  E(NOE)=   4.829
 ========================================
 set-i-atoms
          A    3    CYT  H3' 
 set-j-atoms
          A    4    ADE  H8  
 R=   3.462 NOE= 3.03 (- 0.10/+ 0.10) Delta=  -0.329  E(NOE)=  10.799
 ========================================
 set-i-atoms
          A    3    CYT  H5''
 set-j-atoms
          A    3    CYT  H6  
 R=   3.531 NOE= 4.06 (- 0.10/+ 0.10) Delta=   0.425  E(NOE)=  18.060
 ========================================
 set-i-atoms
          A    3    CYT  HO2'
 set-j-atoms
          A    4    ADE  H5' 
 R=   2.618 NOE= 2.94 (- 0.10/+ 0.10) Delta=   0.223  E(NOE)=   4.972
 ========================================
 set-i-atoms
          A    3    CYT  H41 
 set-j-atoms
          A    4    ADE  H62 
 R=   5.064 NOE= 4.59 (- 0.10/+ 0.10) Delta=  -0.371  E(NOE)=  13.751
 ========================================
 set-i-atoms
          A    3    CYT  H41 
 set-j-atoms
          A    4    ADE  H61 
 R=   4.117 NOE= 3.57 (- 0.10/+ 0.10) Delta=  -0.451  E(NOE)=  20.349
 ========================================
 set-i-atoms
          A    3    CYT  H41 
 set-j-atoms
          A    19   GUA  H1  
 R=   4.798 NOE= 4.02 (- 0.10/+ 0.10) Delta=  -0.675  E(NOE)=  45.496
 ========================================
 set-i-atoms
          A    3    CYT  H41 
 set-j-atoms
          A    20   CYT  H41 
 R=   5.181 NOE= 4.82 (- 0.10/+ 0.10) Delta=  -0.264  E(NOE)=   6.970
 ========================================
 set-i-atoms
          A    3    CYT  H41 
 set-j-atoms
          A    20   CYT  H42 
 R=   4.059 NOE= 3.71 (- 0.10/+ 0.10) Delta=  -0.254  E(NOE)=   6.467
 ========================================
 set-i-atoms
          A    3    CYT  H42 
 set-j-atoms
          A    4    ADE  H61 
 R=   3.336 NOE= 3.02 (- 0.10/+ 0.10) Delta=  -0.211  E(NOE)=   4.451
 ========================================
 set-i-atoms
          A    3    CYT  H42 
 set-j-atoms
          A    19   GUA  H22 
 R=   3.770 NOE= 4.57 (- 0.10/+ 0.10) Delta=   0.697  E(NOE)=  48.626
 ========================================
 set-i-atoms
          A    3    CYT  H42 
 set-j-atoms
          A    19   GUA  H1  
 R=   3.360 NOE= 2.48 (- 0.10/+ 0.10) Delta=  -0.781  E(NOE)=  61.037
 ========================================
 set-i-atoms
          A    3    CYT  H5  
 set-j-atoms
          A    4    ADE  H61 
 R=   5.939 NOE= 4.82 (- 0.10/+ 0.10) Delta=  -1.018  E(NOE)= 103.598
 ========================================
 set-i-atoms
          A    4    ADE  H1' 
 set-j-atoms
          A    19   GUA  H21 
 R=   5.417 NOE= 4.49 (- 0.10/+ 0.10) Delta=  -0.823  E(NOE)=  67.783
 ========================================
 set-i-atoms
          A    4    ADE  H1' 
 set-j-atoms
          A    19   GUA  H22 
 R=   3.993 NOE= 4.37 (- 0.10/+ 0.10) Delta=   0.281  E(NOE)=   7.920
 ========================================
 set-i-atoms
          A    4    ADE  H62 
 set-j-atoms
          A    18   URI  H3  
 R=   2.743 NOE= 2.40 (- 0.10/+ 0.10) Delta=  -0.247  E(NOE)=   6.114
 ========================================
 set-i-atoms
          A    4    ADE  H62 
 set-j-atoms
          A    19   GUA  H1  
 R=   3.945 NOE= 4.42 (- 0.10/+ 0.10) Delta=   0.373  E(NOE)=  13.909
 ========================================
 set-i-atoms
          A    4    ADE  H61 
 set-j-atoms
          A    18   URI  H3  
 R=   4.272 NOE= 3.96 (- 0.10/+ 0.10) Delta=  -0.213  E(NOE)=   4.547
 ========================================
 set-i-atoms
          A    4    ADE  H2  
 set-j-atoms
          A    19   GUA  H1' 
 R=   5.852 NOE= 4.66 (- 0.10/+ 0.10) Delta=  -1.094  E(NOE)= 119.630
 ========================================
 set-i-atoms
          A    18   URI  H1' 
 set-j-atoms
          A    19   GUA  H5' 
 R=   5.101 NOE= 4.68 (- 0.10/+ 0.10) Delta=  -0.324  E(NOE)=  10.480
 ========================================
 set-i-atoms
          A    18   URI  HO2'
 set-j-atoms
          A    19   GUA  H4' 
 R=   4.077 NOE= 3.52 (- 0.10/+ 0.10) Delta=  -0.456  E(NOE)=  20.826
 ========================================
 set-i-atoms
          A    18   URI  H6  
 set-j-atoms
          A    19   GUA  H8  
 R=   4.432 NOE= 4.76 (- 0.10/+ 0.10) Delta=   0.229  E(NOE)=   5.263
 ========================================
 set-i-atoms
          A    19   GUA  H1' 
 set-j-atoms
          A    19   GUA  H21 
 R=   4.460 NOE= 4.78 (- 0.10/+ 0.10) Delta=   0.215  E(NOE)=   4.606
 ========================================
 set-i-atoms
          A    19   GUA  H1' 
 set-j-atoms
          A    20   CYT  H5' 
 R=   5.027 NOE= 4.68 (- 0.10/+ 0.10) Delta=  -0.249  E(NOE)=   6.218
 ========================================
 set-i-atoms
          A    19   GUA  H2' 
 set-j-atoms
          A    19   GUA  H8  
 R=   3.760 NOE= 4.15 (- 0.10/+ 0.10) Delta=   0.289  E(NOE)=   8.324
 ========================================
 set-i-atoms
          A    19   GUA  H3' 
 set-j-atoms
          A    19   GUA  H8  
 R=   2.783 NOE= 3.20 (- 0.10/+ 0.10) Delta=   0.313  E(NOE)=   9.807
 ========================================
 set-i-atoms
          A    19   GUA  H4' 
 set-j-atoms
          A    20   CYT  H5' 
 R=   4.516 NOE= 4.17 (- 0.10/+ 0.10) Delta=  -0.249  E(NOE)=   6.201
 ========================================
 set-i-atoms
          A    19   GUA  HO2'
 set-j-atoms
          A    20   CYT  H4' 
 R=   3.848 NOE= 3.52 (- 0.10/+ 0.10) Delta=  -0.227  E(NOE)=   5.168
 ========================================
 set-i-atoms
          A    19   GUA  H21 
 set-j-atoms
          A    19   GUA  H1  
 R=   3.152 NOE= 3.48 (- 0.10/+ 0.10) Delta=   0.228  E(NOE)=   5.212
 ========================================
 set-i-atoms
          A    19   GUA  H21 
 set-j-atoms
          A    20   CYT  H1' 
 R=   4.353 NOE= 3.25 (- 0.10/+ 0.10) Delta=  -0.998  E(NOE)=  99.604
 ========================================
 set-i-atoms
          A    19   GUA  H21 
 set-j-atoms
          A    20   CYT  H6  
 R=   5.625 NOE= 4.83 (- 0.10/+ 0.10) Delta=  -0.699  E(NOE)=  48.820
 ========================================
 set-i-atoms
          A    19   GUA  H22 
 set-j-atoms
          A    20   CYT  H1' 
 R=   5.109 NOE= 4.21 (- 0.10/+ 0.10) Delta=  -0.804  E(NOE)=  64.721
 ========================================
 set-i-atoms
          A    19   GUA  H8  
 set-j-atoms
          A    20   CYT  H5  
 R=   3.185 NOE= 3.90 (- 0.10/+ 0.10) Delta=   0.614  E(NOE)=  37.734
 ========================================
 set-i-atoms
          A    19   GUA  H1  
 set-j-atoms
          A    20   CYT  H41 
 R=   4.682 NOE= 4.35 (- 0.10/+ 0.10) Delta=  -0.229  E(NOE)=   5.245
 ========================================
 set-i-atoms
          A    19   GUA  H1  
 set-j-atoms
          A    20   CYT  H5  
 R=   5.722 NOE= 4.95 (- 0.10/+ 0.10) Delta=  -0.672  E(NOE)=  45.190
 ========================================
 set-i-atoms
          A    20   CYT  H3' 
 set-j-atoms
          A    20   CYT  H5''
 R=   3.400 NOE= 3.08 (- 0.10/+ 0.10) Delta=  -0.215  E(NOE)=   4.613
 ========================================
 set-i-atoms
          A    20   CYT  H3' 
 set-j-atoms
          A    20   CYT  H5  
 R=   4.432 NOE= 4.77 (- 0.10/+ 0.10) Delta=   0.237  E(NOE)=   5.618
 ========================================
 set-i-atoms
          A    20   CYT  H42 
 set-j-atoms
          A    21   CYT  H42 
 R=   2.710 NOE= 3.26 (- 0.10/+ 0.10) Delta=   0.454  E(NOE)=  20.609
 ========================================
 set-i-atoms
          A    20   CYT  H6  
 set-j-atoms
          A    21   CYT  H5  
 R=   4.383 NOE= 4.00 (- 0.10/+ 0.10) Delta=  -0.282  E(NOE)=   7.943
 ========================================
 set-i-atoms
          A    21   CYT  H2' 
 set-j-atoms
          A    21   CYT  H6  
 R=   3.620 NOE= 4.00 (- 0.10/+ 0.10) Delta=   0.279  E(NOE)=   7.772
 ========================================
 set-i-atoms
          A    21   CYT  H41 
 set-j-atoms
          A    21   CYT  H6  
 R=   4.333 NOE= 4.65 (- 0.10/+ 0.10) Delta=   0.217  E(NOE)=   4.710
 ========================================
 set-i-atoms
          A    21   CYT  H42 
 set-j-atoms
          A    21   CYT  H5  
 R=   3.000 NOE= 3.71 (- 0.10/+ 0.10) Delta=   0.608  E(NOE)=  36.945
 ========================================
 set-i-atoms
          A    12   URI  H4' 
 set-j-atoms
          A    13   ADE  H8  
 R=   2.790 NOE= 4.00 (- 1.00/+ 1.00) Delta=   0.210  E(NOE)=   4.396
 ========================================
 set-i-atoms
          A    12   URI  H1' 
 set-j-atoms
          A    13   ADE  H8  
 R=   5.282 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.282  E(NOE)=   7.944
 ========================================
 set-i-atoms
          A    1    GUA  O6  
 set-j-atoms
          A    21   CYT  H42 
 R=   3.724 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -1.724  E(NOE)= 297.350
 ========================================
 set-i-atoms
          A    1    GUA  H1  
 set-j-atoms
          A    21   CYT  N3  
 R=   3.028 NOE= 1.94 (- 0.10/+ 0.10) Delta=  -0.988  E(NOE)=  97.652
 ========================================
 set-i-atoms
          A    1    GUA  H22 
 set-j-atoms
          A    21   CYT  O2  
 R=   2.550 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -0.550  E(NOE)=  30.274
 ========================================
 set-i-atoms
          A    2    GUA  O6  
 set-j-atoms
          A    20   CYT  H42 
 R=   2.650 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -0.650  E(NOE)=  42.272
 ========================================
 set-i-atoms
          A    2    GUA  H1  
 set-j-atoms
          A    20   CYT  N3  
 R=   3.201 NOE= 1.94 (- 0.10/+ 0.10) Delta=  -1.161  E(NOE)= 134.774
 ========================================
 set-i-atoms
          A    2    GUA  H22 
 set-j-atoms
          A    20   CYT  O2  
 R=   3.313 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -1.313  E(NOE)= 172.303
 ========================================
 set-i-atoms
          A    3    CYT  H42 
 set-j-atoms
          A    19   GUA  O6  
 R=   3.269 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -1.269  E(NOE)= 161.034
 ========================================
 set-i-atoms
          A    3    CYT  N3  
 set-j-atoms
          A    19   GUA  H1  
 R=   2.494 NOE= 1.94 (- 0.10/+ 0.10) Delta=  -0.454  E(NOE)=  20.640
 ========================================
 set-i-atoms
          A    3    CYT  O2  
 set-j-atoms
          A    19   GUA  H22 
 R=   2.669 NOE= 1.90 (- 0.10/+ 0.10) Delta=  -0.669  E(NOE)=  44.810
 ========================================
 set-i-atoms
          A    4    ADE  N1  
 set-j-atoms
          A    18   URI  H3  
 R=   2.198 NOE= 1.81 (- 0.10/+ 0.10) Delta=  -0.288  E(NOE)=   8.275

 NOEPRI: RMS diff. =   0.235,  #(violat.> 0.2)=   108 of    928 NOEs
 X-PLOR>print threshold=0.2 noe 

 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 +++++++++++++++++++++++++++++++ CLASS NIL  +++++++++++++++++++++++++++++++++++
 for this class: SCALe= 100.000 AVERage=center POTEntial=square-well
                 SQCOnstant=   1.000 SQEXponent=    2 SQOFfset=   0.000
 
 ========================================
 set-i-atoms
          A    7    GUA  H8  
 set-j-atoms
          A    8    CYT  H6  
 R=   5.257 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.257  E(NOE)=   6.584
 ========================================
 set-i-atoms
          A    9    URI  H1' 
 set-j-atoms
          A    11   ADE  H8  
 R=   4.272 NOE= 3.00 (- 1.00/+ 1.00) Delta=  -0.272  E(NOE)=   7.404
 ========================================
 set-i-atoms
          A    11   ADE  H8  
 set-j-atoms
          A    12   URI  H6  
 R=   5.280 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.280  E(NOE)=   7.859
 ========================================
 set-i-atoms
          A    12   URI  H2' 
 set-j-atoms
          A    13   ADE  H1' 
 R=   5.307 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.307  E(NOE)=   9.442
 ========================================
 set-i-atoms
          A    12   URI  H6  
 set-j-atoms
          A    13   ADE  H8  
 R=   5.367 NOE= 4.00 (- 1.00/+ 1.00) Delta=  -0.367  E(NOE)=  13.490

 NOEPRI: RMS diff. =   0.028,  #(violat.> 0.2)=     5 of    928 NOEs
PSF 

       2 !NTITLE
 REMARKS FILENAME="/sgi/people/dcs/ws/xplor/italy2.4x/rsf.inp"                                                                      
 REMARKS DATE:27-Apr-96  13:37:21       created by user:                                                                            

     677 !NATOM
       1 A    1    GUA  P    P       1.20000       30.9740           0
       2 A    1    GUA  O1P  O1P   -0.400000       15.9994           0
       3 A    1    GUA  O2P  O2P   -0.400000       15.9994           0
       4 A    1    GUA  O5'  O5R   -0.360000       15.9994           0
       5 A    1    GUA  H5T  HO     0.150000       1.00800           0
       6 A    1    GUA  O5T  OH    -0.150000       15.9994           0
       7 A    1    GUA  C5'  C5R   -0.700000E-01   12.0110           0
       8 A    1    GUA  H5'  H      0.350000E-01   1.00800           0
       9 A    1    GUA  H5'' H      0.350000E-01   1.00800           0
      10 A    1    GUA  C4'  C4R    0.650000E-01   12.0110           0
      11 A    1    GUA  H4'  H      0.350000E-01   1.00800           0
      12 A    1    GUA  O4'  O4R   -0.300000       15.9994           0
      13 A    1    GUA  C1'  C1R    0.165000       12.0110           0
      14 A    1    GUA  H1'  H      0.350000E-01   1.00800           0
      15 A    1    GUA  N9   N9G   -0.190000       14.0067           0
      16 A    1    GUA  C4   C4G    0.190000       12.0110           0
      17 A    1    GUA  N3   N3G   -0.350000       14.0067           0
      18 A    1    GUA  C2   C2G    0.350000       12.0110           0
      19 A    1    GUA  N2   N2G   -0.420000       14.0067           0
      20 A    1    GUA  H21  H2     0.210000       1.00800           0
      21 A    1    GUA  H22  H2     0.210000       1.00800           0
      22 A    1    GUA  N1   NNA   -0.260000       14.0067           0
      23 A    1    GUA  H1   HN     0.260000       1.00800           0
      24 A    1    GUA  C6   C6G    0.300000       12.0110           0
      25 A    1    GUA  O6   O6G   -0.300000       15.9994           0
      26 A    1    GUA  C5   C5G    0.200000E-01   12.0110           0
      27 A    1    GUA  N7   N7G   -0.250000       14.0067           0
      28 A    1    GUA  C8   C8G    0.145000       12.0110           0
      29 A    1    GUA  H8   H      0.350000E-01   1.00800           0
      30 A    1    GUA  C2'  C2R    0.115000       12.0110           0
      31 A    1    GUA  H2'  H      0.350000E-01   1.00800           0
      32 A    1    GUA  O2'  O2R   -0.400000       15.9994           0
      33 A    1    GUA  HO2' HO     0.250000       1.00800           0
      34 A    1    GUA  C3'  C3R   -0.350000E-01   12.0110           0
      35 A    1    GUA  H3'  H      0.350000E-01   1.00800           0
      36 A    1    GUA  O3'  O3R   -0.360000       15.9994           0
      37 A    2    GUA  P    P       1.20000       30.9740           0
      38 A    2    GUA  O1P  O1P   -0.400000       15.9994           0
      39 A    2    GUA  O2P  O2P   -0.400000       15.9994           0
      40 A    2    GUA  O5'  O5R   -0.360000       15.9994           0
      41 A    2    GUA  C5'  C5R   -0.700000E-01   12.0110           0
      42 A    2    GUA  H5'  H      0.350000E-01   1.00800           0
      43 A    2    GUA  H5'' H      0.350000E-01   1.00800           0
      44 A    2    GUA  C4'  C4R    0.650000E-01   12.0110           0
      45 A    2    GUA  H4'  H      0.350000E-01   1.00800           0
      46 A    2    GUA  O4'  O4R   -0.300000       15.9994           0
      47 A    2    GUA  C1'  C1R    0.165000       12.0110           0
      48 A    2    GUA  H1'  H      0.350000E-01   1.00800           0
      49 A    2    GUA  N9   N9G   -0.190000       14.0067           0
      50 A    2    GUA  C4   C4G    0.190000       12.0110           0
      51 A    2    GUA  N3   N3G   -0.350000       14.0067           0
      52 A    2    GUA  C2   C2G    0.350000       12.0110           0
      53 A    2    GUA  N2   N2G   -0.420000       14.0067           0
      54 A    2    GUA  H21  H2     0.210000       1.00800           0
      55 A    2    GUA  H22  H2     0.210000       1.00800           0
      56 A    2    GUA  N1   NNA   -0.260000       14.0067           0
      57 A    2    GUA  H1   HN     0.260000       1.00800           0
      58 A    2    GUA  C6   C6G    0.300000       12.0110           0
      59 A    2    GUA  O6   O6G   -0.300000       15.9994           0
      60 A    2    GUA  C5   C5G    0.200000E-01   12.0110           0
      61 A    2    GUA  N7   N7G   -0.250000       14.0067           0
      62 A    2    GUA  C8   C8G    0.145000       12.0110           0
      63 A    2    GUA  H8   H      0.350000E-01   1.00800           0
      64 A    2    GUA  C2'  C2R    0.115000       12.0110           0
      65 A    2    GUA  H2'  H      0.350000E-01   1.00800           0
      66 A    2    GUA  O2'  O2R   -0.400000       15.9994           0
      67 A    2    GUA  HO2' HO     0.250000       1.00800           0
      68 A    2    GUA  C3'  C3R   -0.350000E-01   12.0110           0
      69 A    2    GUA  H3'  H      0.350000E-01   1.00800           0
      70 A    2    GUA  O3'  O3R   -0.360000       15.9994           0
      71 A    3    CYT  P    P       1.20000       30.9740           0
      72 A    3    CYT  O1P  O1P   -0.400000       15.9994           0
      73 A    3    CYT  O2P  O2P   -0.400000       15.9994           0
      74 A    3    CYT  O5'  O5R   -0.360000       15.9994           0
      75 A    3    CYT  C5'  C5R   -0.700000E-01   12.0110           0
      76 A    3    CYT  H5'  H      0.350000E-01   1.00800           0
      77 A    3    CYT  H5'' H      0.350000E-01   1.00800           0
      78 A    3    CYT  C4'  C4R    0.650000E-01   12.0110           0
      79 A    3    CYT  H4'  H      0.350000E-01   1.00800           0
      80 A    3    CYT  O4'  O4R   -0.300000       15.9994           0
      81 A    3    CYT  C1'  C1R    0.165000       12.0110           0
      82 A    3    CYT  H1'  H      0.350000E-01   1.00800           0
      83 A    3    CYT  N1   N1C   -0.190000       14.0067           0
      84 A    3    CYT  C6   C6C    0.155000       12.0110           0
      85 A    3    CYT  H6   H      0.350000E-01   1.00800           0
      86 A    3    CYT  C2   C2C    0.300000       12.0110           0
      87 A    3    CYT  O2   ON    -0.300000       15.9994           0
      88 A    3    CYT  N3   NC    -0.280000       14.0067           0
      89 A    3    CYT  C4   C4C    0.280000       12.0110           0
      90 A    3    CYT  N4   N4C   -0.420000       14.0067           0
      91 A    3    CYT  H41  H2     0.210000       1.00800           0
      92 A    3    CYT  H42  H2     0.210000       1.00800           0
      93 A    3    CYT  C5   C5C   -0.350000E-01   12.0110           0
      94 A    3    CYT  H5   H      0.350000E-01   1.00800           0
      95 A    3    CYT  C2'  C2R    0.115000       12.0110           0
      96 A    3    CYT  H2'  H      0.350000E-01   1.00800           0
      97 A    3    CYT  O2'  O2R   -0.400000       15.9994           0
      98 A    3    CYT  HO2' HO     0.250000       1.00800           0
      99 A    3    CYT  C3'  C3R   -0.350000E-01   12.0110           0
     100 A    3    CYT  H3'  H      0.350000E-01   1.00800           0
     101 A    3    CYT  O3'  O3R   -0.360000       15.9994           0
     102 A    4    ADE  P    P       1.20000       30.9740           0
     103 A    4    ADE  O1P  O1P   -0.400000       15.9994           0
     104 A    4    ADE  O2P  O2P   -0.400000       15.9994           0
     105 A    4    ADE  O5'  O5R   -0.360000       15.9994           0
     106 A    4    ADE  C5'  C5R   -0.700000E-01   12.0110           0
     107 A    4    ADE  H5'  H      0.350000E-01   1.00800           0
     108 A    4    ADE  H5'' H      0.350000E-01   1.00800           0
     109 A    4    ADE  C4'  C4R    0.650000E-01   12.0110           0
     110 A    4    ADE  H4'  H      0.350000E-01   1.00800           0
     111 A    4    ADE  O4'  O4R   -0.300000       15.9994           0
     112 A    4    ADE  C1'  C1R    0.165000       12.0110           0
     113 A    4    ADE  H1'  H      0.350000E-01   1.00800           0
     114 A    4    ADE  N9   N9A   -0.190000       14.0067           0
     115 A    4    ADE  C4   C4A    0.190000       12.0110           0
     116 A    4    ADE  N3   N3A   -0.260000       14.0067           0
     117 A    4    ADE  C2   C2A    0.225000       12.0110           0
     118 A    4    ADE  H2   H      0.350000E-01   1.00800           0
     119 A    4    ADE  N1   NC    -0.280000       14.0067           0
     120 A    4    ADE  C6   C6A    0.280000       12.0110           0
     121 A    4    ADE  N6   N6A   -0.420000       14.0067           0
     122 A    4    ADE  H61  H2     0.210000       1.00800           0
     123 A    4    ADE  H62  H2     0.210000       1.00800           0
     124 A    4    ADE  C5   C5A    0.200000E-01   12.0110           0
     125 A    4    ADE  N7   N7A   -0.250000       14.0067           0
     126 A    4    ADE  C8   C8A    0.195000       12.0110           0
     127 A    4    ADE  H8   H      0.350000E-01   1.00800           0
     128 A    4    ADE  C2'  C2R    0.115000       12.0110           0
     129 A    4    ADE  H2'  H      0.350000E-01   1.00800           0
     130 A    4    ADE  O2'  O2R   -0.400000       15.9994           0
     131 A    4    ADE  HO2' HO     0.250000       1.00800           0
     132 A    4    ADE  C3'  C3R   -0.350000E-01   12.0110           0
     133 A    4    ADE  H3'  H      0.350000E-01   1.00800           0
     134 A    4    ADE  O3'  O3R   -0.360000       15.9994           0
     135 A    5    GUA  P    P       1.20000       30.9740           0
     136 A    5    GUA  O1P  O1P   -0.400000       15.9994           0
     137 A    5    GUA  O2P  O2P   -0.400000       15.9994           0
     138 A    5    GUA  O5'  O5R   -0.360000       15.9994           0
     139 A    5    GUA  C5'  C5R   -0.700000E-01   12.0110           0
     140 A    5    GUA  H5'  H      0.350000E-01   1.00800           0
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     192 A    6    GUA  C5   C5G    0.200000E-01   12.0110           0
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     201 A    6    GUA  H3'  H      0.350000E-01   1.00800           0
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     294 A    9    URI  HO2' HO     0.250000       1.00800           0
     295 A    9    URI  C3'  C3R   -0.350000E-01   12.0110           0
     296 A    9    URI  H3'  H      0.350000E-01   1.00800           0
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     300 A    10   CYT  O2P  O2P   -0.400000       15.9994           0
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     303 A    10   CYT  H5'  H      0.350000E-01   1.00800           0
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     321 A    10   CYT  H5   H      0.350000E-01   1.00800           0
     322 A    10   CYT  C2'  C2R    0.115000       12.0110           0
     323 A    10   CYT  H2'  H      0.350000E-01   1.00800           0
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     325 A    10   CYT  HO2' HO     0.250000       1.00800           0
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     327 A    10   CYT  H3'  H      0.350000E-01   1.00800           0
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     331 A    11   ADE  O2P  O2P   -0.400000       15.9994           0
     332 A    11   ADE  O5'  O5R   -0.360000       15.9994           0
     333 A    11   ADE  C5'  C5R   -0.700000E-01   12.0110           0
     334 A    11   ADE  H5'  H      0.350000E-01   1.00800           0
     335 A    11   ADE  H5'' H      0.350000E-01   1.00800           0
     336 A    11   ADE  C4'  C4R    0.650000E-01   12.0110           0
     337 A    11   ADE  H4'  H      0.350000E-01   1.00800           0
     338 A    11   ADE  O4'  O4R   -0.300000       15.9994           0
     339 A    11   ADE  C1'  C1R    0.165000       12.0110           0
     340 A    11   ADE  H1'  H      0.350000E-01   1.00800           0
     341 A    11   ADE  N9   N9A   -0.190000       14.0067           0
     342 A    11   ADE  C4   C4A    0.190000       12.0110           0
     343 A    11   ADE  N3   N3A   -0.260000       14.0067           0
     344 A    11   ADE  C2   C2A    0.225000       12.0110           0
     345 A    11   ADE  H2   H      0.350000E-01   1.00800           0
     346 A    11   ADE  N1   NC    -0.280000       14.0067           0
     347 A    11   ADE  C6   C6A    0.280000       12.0110           0
     348 A    11   ADE  N6   N6A   -0.420000       14.0067           0
     349 A    11   ADE  H61  H2     0.210000       1.00800           0
     350 A    11   ADE  H62  H2     0.210000       1.00800           0
     351 A    11   ADE  C5   C5A    0.200000E-01   12.0110           0
     352 A    11   ADE  N7   N7A   -0.250000       14.0067           0
     353 A    11   ADE  C8   C8A    0.195000       12.0110           0
     354 A    11   ADE  H8   H      0.350000E-01   1.00800           0
     355 A    11   ADE  C2'  C2R    0.115000       12.0110           0
     356 A    11   ADE  H2'  H      0.350000E-01   1.00800           0
     357 A    11   ADE  O2'  O2R   -0.400000       15.9994           0
     358 A    11   ADE  HO2' HO     0.250000       1.00800           0
     359 A    11   ADE  C3'  C3R   -0.350000E-01   12.0110           0
     360 A    11   ADE  H3'  H      0.350000E-01   1.00800           0
     361 A    11   ADE  O3'  O3R   -0.360000       15.9994           0
     362 A    12   URI  P    P       1.20000       30.9740           0
     363 A    12   URI  O1P  O1P   -0.400000       15.9994           0
     364 A    12   URI  O2P  O2P   -0.400000       15.9994           0
     365 A    12   URI  O5'  O5R   -0.360000       15.9994           0
     366 A    12   URI  C5'  C5R   -0.700000E-01   12.0110           0
     367 A    12   URI  H5'  H      0.350000E-01   1.00800           0
     368 A    12   URI  H5'' H      0.350000E-01   1.00800           0
     369 A    12   URI  C4'  C4R    0.650000E-01   12.0110           0
     370 A    12   URI  H4'  H      0.350000E-01   1.00800           0
     371 A    12   URI  O4'  O4R   -0.300000       15.9994           0
     372 A    12   URI  C1'  C1R    0.165000       12.0110           0
     373 A    12   URI  H1'  H      0.350000E-01   1.00800           0
     374 A    12   URI  N1   N1U   -0.190000       14.0067           0
     375 A    12   URI  C6   C6U    0.155000       12.0110           0
     376 A    12   URI  H6   H      0.350000E-01   1.00800           0
     377 A    12   URI  C2   C2U    0.300000       12.0110           0
     378 A    12   URI  O2   ON    -0.300000       15.9994           0
     379 A    12   URI  N3   N3U   -0.280000       14.0067           0
     380 A    12   URI  H3   HN     0.260000       1.00800           0
     381 A    12   URI  C4   C4U    0.280000       12.0110           0
     382 A    12   URI  O4   ON    -0.300000       15.9994           0
     383 A    12   URI  C5   C5U   -0.350000E-01   12.0110           0
     384 A    12   URI  H5   H      0.350000E-01   1.00800           0
     385 A    12   URI  C2'  C2R    0.115000       12.0110           0
     386 A    12   URI  H2'  H      0.350000E-01   1.00800           0
     387 A    12   URI  O2'  O2R   -0.400000       15.9994           0
     388 A    12   URI  HO2' HO     0.250000       1.00800           0
     389 A    12   URI  C3'  C3R   -0.350000E-01   12.0110           0
     390 A    12   URI  H3'  H      0.350000E-01   1.00800           0
     391 A    12   URI  O3'  O3R   -0.360000       15.9994           0
     392 A    13   ADE  P    P       1.20000       30.9740           0
     393 A    13   ADE  O1P  O1P   -0.400000       15.9994           0
     394 A    13   ADE  O2P  O2P   -0.400000       15.9994           0
     395 A    13   ADE  O5'  O5R   -0.360000       15.9994           0
     396 A    13   ADE  C5'  C5R   -0.700000E-01   12.0110           0
     397 A    13   ADE  H5'  H      0.350000E-01   1.00800           0
     398 A    13   ADE  H5'' H      0.350000E-01   1.00800           0
     399 A    13   ADE  C4'  C4R    0.650000E-01   12.0110           0
     400 A    13   ADE  H4'  H      0.350000E-01   1.00800           0
     401 A    13   ADE  O4'  O4R   -0.300000       15.9994           0
     402 A    13   ADE  C1'  C1R    0.165000       12.0110           0
     403 A    13   ADE  H1'  H      0.350000E-01   1.00800           0
     404 A    13   ADE  N9   N9A   -0.190000       14.0067           0
     405 A    13   ADE  C4   C4A    0.190000       12.0110           0
     406 A    13   ADE  N3   N3A   -0.260000       14.0067           0
     407 A    13   ADE  C2   C2A    0.225000       12.0110           0
     408 A    13   ADE  H2   H      0.350000E-01   1.00800           0
     409 A    13   ADE  N1   NC    -0.280000       14.0067           0
     410 A    13   ADE  C6   C6A    0.280000       12.0110           0
     411 A    13   ADE  N6   N6A   -0.420000       14.0067           0
     412 A    13   ADE  H61  H2     0.210000       1.00800           0
     413 A    13   ADE  H62  H2     0.210000       1.00800           0
     414 A    13   ADE  C5   C5A    0.200000E-01   12.0110           0
     415 A    13   ADE  N7   N7A   -0.250000       14.0067           0
     416 A    13   ADE  C8   C8A    0.195000       12.0110           0
     417 A    13   ADE  H8   H      0.350000E-01   1.00800           0
     418 A    13   ADE  C2'  C2R    0.115000       12.0110           0
     419 A    13   ADE  H2'  H      0.350000E-01   1.00800           0
     420 A    13   ADE  O2'  O2R   -0.400000       15.9994           0
     421 A    13   ADE  HO2' HO     0.250000       1.00800           0
     422 A    13   ADE  C3'  C3R   -0.350000E-01   12.0110           0
     423 A    13   ADE  H3'  H      0.350000E-01   1.00800           0
     424 A    13   ADE  O3'  O3R   -0.360000       15.9994           0
     425 A    14   ADE  P    P       1.20000       30.9740           0
     426 A    14   ADE  O1P  O1P   -0.400000       15.9994           0
     427 A    14   ADE  O2P  O2P   -0.400000       15.9994           0
     428 A    14   ADE  O5'  O5R   -0.360000       15.9994           0
     429 A    14   ADE  C5'  C5R   -0.700000E-01   12.0110           0
     430 A    14   ADE  H5'  H      0.350000E-01   1.00800           0
     431 A    14   ADE  H5'' H      0.350000E-01   1.00800           0
     432 A    14   ADE  C4'  C4R    0.650000E-01   12.0110           0
     433 A    14   ADE  H4'  H      0.350000E-01   1.00800           0
     434 A    14   ADE  O4'  O4R   -0.300000       15.9994           0
     435 A    14   ADE  C1'  C1R    0.165000       12.0110           0
     436 A    14   ADE  H1'  H      0.350000E-01   1.00800           0
     437 A    14   ADE  N9   N9A   -0.190000       14.0067           0
     438 A    14   ADE  C4   C4A    0.190000       12.0110           0
     439 A    14   ADE  N3   N3A   -0.260000       14.0067           0
     440 A    14   ADE  C2   C2A    0.225000       12.0110           0
     441 A    14   ADE  H2   H      0.350000E-01   1.00800           0
     442 A    14   ADE  N1   NC    -0.280000       14.0067           0
     443 A    14   ADE  C6   C6A    0.280000       12.0110           0
     444 A    14   ADE  N6   N6A   -0.420000       14.0067           0
     445 A    14   ADE  H61  H2     0.210000       1.00800           0
     446 A    14   ADE  H62  H2     0.210000       1.00800           0
     447 A    14   ADE  C5   C5A    0.200000E-01   12.0110           0
     448 A    14   ADE  N7   N7A   -0.250000       14.0067           0
     449 A    14   ADE  C8   C8A    0.195000       12.0110           0
     450 A    14   ADE  H8   H      0.350000E-01   1.00800           0
     451 A    14   ADE  C2'  C2R    0.115000       12.0110           0
     452 A    14   ADE  H2'  H      0.350000E-01   1.00800           0
     453 A    14   ADE  O2'  O2R   -0.400000       15.9994           0
     454 A    14   ADE  HO2' HO     0.250000       1.00800           0
     455 A    14   ADE  C3'  C3R   -0.350000E-01   12.0110           0
     456 A    14   ADE  H3'  H      0.350000E-01   1.00800           0
     457 A    14   ADE  O3'  O3R   -0.360000       15.9994           0
     458 A    15   CYT  P    P       1.20000       30.9740           0
     459 A    15   CYT  O1P  O1P   -0.400000       15.9994           0
     460 A    15   CYT  O2P  O2P   -0.400000       15.9994           0
     461 A    15   CYT  O5'  O5R   -0.360000       15.9994           0
     462 A    15   CYT  C5'  C5R   -0.700000E-01   12.0110           0
     463 A    15   CYT  H5'  H      0.350000E-01   1.00800           0
     464 A    15   CYT  H5'' H      0.350000E-01   1.00800           0
     465 A    15   CYT  C4'  C4R    0.650000E-01   12.0110           0
     466 A    15   CYT  H4'  H      0.350000E-01   1.00800           0
     467 A    15   CYT  O4'  O4R   -0.300000       15.9994           0
     468 A    15   CYT  C1'  C1R    0.165000       12.0110           0
     469 A    15   CYT  H1'  H      0.350000E-01   1.00800           0
     470 A    15   CYT  N1   N1C   -0.190000       14.0067           0
     471 A    15   CYT  C6   C6C    0.155000       12.0110           0
     472 A    15   CYT  H6   H      0.350000E-01   1.00800           0
     473 A    15   CYT  C2   C2C    0.300000       12.0110           0
     474 A    15   CYT  O2   ON    -0.300000       15.9994           0
     475 A    15   CYT  N3   NC    -0.280000       14.0067           0
     476 A    15   CYT  C4   C4C    0.280000       12.0110           0
     477 A    15   CYT  N4   N4C   -0.420000       14.0067           0
     478 A    15   CYT  H41  H2     0.210000       1.00800           0
     479 A    15   CYT  H42  H2     0.210000       1.00800           0
     480 A    15   CYT  C5   C5C   -0.350000E-01   12.0110           0
     481 A    15   CYT  H5   H      0.350000E-01   1.00800           0
     482 A    15   CYT  C2'  C2R    0.115000       12.0110           0
     483 A    15   CYT  H2'  H      0.350000E-01   1.00800           0
     484 A    15   CYT  O2'  O2R   -0.400000       15.9994           0
     485 A    15   CYT  HO2' HO     0.250000       1.00800           0
     486 A    15   CYT  C3'  C3R   -0.350000E-01   12.0110           0
     487 A    15   CYT  H3'  H      0.350000E-01   1.00800           0
     488 A    15   CYT  O3'  O3R   -0.360000       15.9994           0
     489 A    16   CYT  P    P       1.20000       30.9740           0
     490 A    16   CYT  O1P  O1P   -0.400000       15.9994           0
     491 A    16   CYT  O2P  O2P   -0.400000       15.9994           0
     492 A    16   CYT  O5'  O5R   -0.360000       15.9994           0
     493 A    16   CYT  C5'  C5R   -0.700000E-01   12.0110           0
     494 A    16   CYT  H5'  H      0.350000E-01   1.00800           0
     495 A    16   CYT  H5'' H      0.350000E-01   1.00800           0
     496 A    16   CYT  C4'  C4R    0.650000E-01   12.0110           0
     497 A    16   CYT  H4'  H      0.350000E-01   1.00800           0
     498 A    16   CYT  O4'  O4R   -0.300000       15.9994           0
     499 A    16   CYT  C1'  C1R    0.165000       12.0110           0
     500 A    16   CYT  H1'  H      0.350000E-01   1.00800           0
     501 A    16   CYT  N1   N1C   -0.190000       14.0067           0
     502 A    16   CYT  C6   C6C    0.155000       12.0110           0
     503 A    16   CYT  H6   H      0.350000E-01   1.00800           0
     504 A    16   CYT  C2   C2C    0.300000       12.0110           0
     505 A    16   CYT  O2   ON    -0.300000       15.9994           0
     506 A    16   CYT  N3   NC    -0.280000       14.0067           0
     507 A    16   CYT  C4   C4C    0.280000       12.0110           0
     508 A    16   CYT  N4   N4C   -0.420000       14.0067           0
     509 A    16   CYT  H41  H2     0.210000       1.00800           0
     510 A    16   CYT  H42  H2     0.210000       1.00800           0
     511 A    16   CYT  C5   C5C   -0.350000E-01   12.0110           0
     512 A    16   CYT  H5   H      0.350000E-01   1.00800           0
     513 A    16   CYT  C2'  C2R    0.115000       12.0110           0
     514 A    16   CYT  H2'  H      0.350000E-01   1.00800           0
     515 A    16   CYT  O2'  O2R   -0.400000       15.9994           0
     516 A    16   CYT  HO2' HO     0.250000       1.00800           0
     517 A    16   CYT  C3'  C3R   -0.350000E-01   12.0110           0
     518 A    16   CYT  H3'  H      0.350000E-01   1.00800           0
     519 A    16   CYT  O3'  O3R   -0.360000       15.9994           0
     520 A    17   CYT  P    P       1.20000       30.9740           0
     521 A    17   CYT  O1P  O1P   -0.400000       15.9994           0
     522 A    17   CYT  O2P  O2P   -0.400000       15.9994           0
     523 A    17   CYT  O5'  O5R   -0.360000       15.9994           0
     524 A    17   CYT  C5'  C5R   -0.700000E-01   12.0110           0
     525 A    17   CYT  H5'  H      0.350000E-01   1.00800           0
     526 A    17   CYT  H5'' H      0.350000E-01   1.00800           0
     527 A    17   CYT  C4'  C4R    0.650000E-01   12.0110           0
     528 A    17   CYT  H4'  H      0.350000E-01   1.00800           0
     529 A    17   CYT  O4'  O4R   -0.300000       15.9994           0
     530 A    17   CYT  C1'  C1R    0.165000       12.0110           0
     531 A    17   CYT  H1'  H      0.350000E-01   1.00800           0
     532 A    17   CYT  N1   N1C   -0.190000       14.0067           0
     533 A    17   CYT  C6   C6C    0.155000       12.0110           0
     534 A    17   CYT  H6   H      0.350000E-01   1.00800           0
     535 A    17   CYT  C2   C2C    0.300000       12.0110           0
     536 A    17   CYT  O2   ON    -0.300000       15.9994           0
     537 A    17   CYT  N3   NC    -0.280000       14.0067           0
     538 A    17   CYT  C4   C4C    0.280000       12.0110           0
     539 A    17   CYT  N4   N4C   -0.420000       14.0067           0
     540 A    17   CYT  H41  H2     0.210000       1.00800           0
     541 A    17   CYT  H42  H2     0.210000       1.00800           0
     542 A    17   CYT  C5   C5C   -0.350000E-01   12.0110           0
     543 A    17   CYT  H5   H      0.350000E-01   1.00800           0
     544 A    17   CYT  C2'  C2R    0.115000       12.0110           0
     545 A    17   CYT  H2'  H      0.350000E-01   1.00800           0
     546 A    17   CYT  O2'  O2R   -0.400000       15.9994           0
     547 A    17   CYT  HO2' HO     0.250000       1.00800           0
     548 A    17   CYT  C3'  C3R   -0.350000E-01   12.0110           0
     549 A    17   CYT  H3'  H      0.350000E-01   1.00800           0
     550 A    17   CYT  O3'  O3R   -0.360000       15.9994           0
     551 A    18   URI  P    P       1.20000       30.9740           0
     552 A    18   URI  O1P  O1P   -0.400000       15.9994           0
     553 A    18   URI  O2P  O2P   -0.400000       15.9994           0
     554 A    18   URI  O5'  O5R   -0.360000       15.9994           0
     555 A    18   URI  C5'  C5R   -0.700000E-01   12.0110           0
     556 A    18   URI  H5'  H      0.350000E-01   1.00800           0
     557 A    18   URI  H5'' H      0.350000E-01   1.00800           0
     558 A    18   URI  C4'  C4R    0.650000E-01   12.0110           0
     559 A    18   URI  H4'  H      0.350000E-01   1.00800           0
     560 A    18   URI  O4'  O4R   -0.300000       15.9994           0
     561 A    18   URI  C1'  C1R    0.165000       12.0110           0
     562 A    18   URI  H1'  H      0.350000E-01   1.00800           0
     563 A    18   URI  N1   N1U   -0.190000       14.0067           0
     564 A    18   URI  C6   C6U    0.155000       12.0110           0
     565 A    18   URI  H6   H      0.350000E-01   1.00800           0
     566 A    18   URI  C2   C2U    0.300000       12.0110           0
     567 A    18   URI  O2   ON    -0.300000       15.9994           0
     568 A    18   URI  N3   N3U   -0.280000       14.0067           0
     569 A    18   URI  H3   HN     0.260000       1.00800           0
     570 A    18   URI  C4   C4U    0.280000       12.0110           0
     571 A    18   URI  O4   ON    -0.300000       15.9994           0
     572 A    18   URI  C5   C5U   -0.350000E-01   12.0110           0
     573 A    18   URI  H5   H      0.350000E-01   1.00800           0
     574 A    18   URI  C2'  C2R    0.115000       12.0110           0
     575 A    18   URI  H2'  H      0.350000E-01   1.00800           0
     576 A    18   URI  O2'  O2R   -0.400000       15.9994           0
     577 A    18   URI  HO2' HO     0.250000       1.00800           0
     578 A    18   URI  C3'  C3R   -0.350000E-01   12.0110           0
     579 A    18   URI  H3'  H      0.350000E-01   1.00800           0
     580 A    18   URI  O3'  O3R   -0.360000       15.9994           0
     581 A    19   GUA  P    P       1.20000       30.9740           0
     582 A    19   GUA  O1P  O1P   -0.400000       15.9994           0
     583 A    19   GUA  O2P  O2P   -0.400000       15.9994           0
     584 A    19   GUA  O5'  O5R   -0.360000       15.9994           0
     585 A    19   GUA  C5'  C5R   -0.700000E-01   12.0110           0
     586 A    19   GUA  H5'  H      0.350000E-01   1.00800           0
     587 A    19   GUA  H5'' H      0.350000E-01   1.00800           0
     588 A    19   GUA  C4'  C4R    0.650000E-01   12.0110           0
     589 A    19   GUA  H4'  H      0.350000E-01   1.00800           0
     590 A    19   GUA  O4'  O4R   -0.300000       15.9994           0
     591 A    19   GUA  C1'  C1R    0.165000       12.0110           0
     592 A    19   GUA  H1'  H      0.350000E-01   1.00800           0
     593 A    19   GUA  N9   N9G   -0.190000       14.0067           0
     594 A    19   GUA  C4   C4G    0.190000       12.0110           0
     595 A    19   GUA  N3   N3G   -0.350000       14.0067           0
     596 A    19   GUA  C2   C2G    0.350000       12.0110           0
     597 A    19   GUA  N2   N2G   -0.420000       14.0067           0
     598 A    19   GUA  H21  H2     0.210000       1.00800           0
     599 A    19   GUA  H22  H2     0.210000       1.00800           0
     600 A    19   GUA  N1   NNA   -0.260000       14.0067           0
     601 A    19   GUA  H1   HN     0.260000       1.00800           0
     602 A    19   GUA  C6   C6G    0.300000       12.0110           0
     603 A    19   GUA  O6   O6G   -0.300000       15.9994           0
     604 A    19   GUA  C5   C5G    0.200000E-01   12.0110           0
     605 A    19   GUA  N7   N7G   -0.250000       14.0067           0
     606 A    19   GUA  C8   C8G    0.145000       12.0110           0
     607 A    19   GUA  H8   H      0.350000E-01   1.00800           0
     608 A    19   GUA  C2'  C2R    0.115000       12.0110           0
     609 A    19   GUA  H2'  H      0.350000E-01   1.00800           0
     610 A    19   GUA  O2'  O2R   -0.400000       15.9994           0
     611 A    19   GUA  HO2' HO     0.250000       1.00800           0
     612 A    19   GUA  C3'  C3R   -0.350000E-01   12.0110           0
     613 A    19   GUA  H3'  H      0.350000E-01   1.00800           0
     614 A    19   GUA  O3'  O3R   -0.360000       15.9994           0
     615 A    20   CYT  P    P       1.20000       30.9740           0
     616 A    20   CYT  O1P  O1P   -0.400000       15.9994           0
     617 A    20   CYT  O2P  O2P   -0.400000       15.9994           0
     618 A    20   CYT  O5'  O5R   -0.360000       15.9994           0
     619 A    20   CYT  C5'  C5R   -0.700000E-01   12.0110           0
     620 A    20   CYT  H5'  H      0.350000E-01   1.00800           0
     621 A    20   CYT  H5'' H      0.350000E-01   1.00800           0
     622 A    20   CYT  C4'  C4R    0.650000E-01   12.0110           0
     623 A    20   CYT  H4'  H      0.350000E-01   1.00800           0
     624 A    20   CYT  O4'  O4R   -0.300000       15.9994           0
     625 A    20   CYT  C1'  C1R    0.165000       12.0110           0
     626 A    20   CYT  H1'  H      0.350000E-01   1.00800           0
     627 A    20   CYT  N1   N1C   -0.190000       14.0067           0
     628 A    20   CYT  C6   C6C    0.155000       12.0110           0
     629 A    20   CYT  H6   H      0.350000E-01   1.00800           0
     630 A    20   CYT  C2   C2C    0.300000       12.0110           0
     631 A    20   CYT  O2   ON    -0.300000       15.9994           0
     632 A    20   CYT  N3   NC    -0.280000       14.0067           0
     633 A    20   CYT  C4   C4C    0.280000       12.0110           0
     634 A    20   CYT  N4   N4C   -0.420000       14.0067           0
     635 A    20   CYT  H41  H2     0.210000       1.00800           0
     636 A    20   CYT  H42  H2     0.210000       1.00800           0
     637 A    20   CYT  C5   C5C   -0.350000E-01   12.0110           0
     638 A    20   CYT  H5   H      0.350000E-01   1.00800           0
     639 A    20   CYT  C2'  C2R    0.115000       12.0110           0
     640 A    20   CYT  H2'  H      0.350000E-01   1.00800           0
     641 A    20   CYT  O2'  O2R   -0.400000       15.9994           0
     642 A    20   CYT  HO2' HO     0.250000       1.00800           0
     643 A    20   CYT  C3'  C3R   -0.350000E-01   12.0110           0
     644 A    20   CYT  H3'  H      0.350000E-01   1.00800           0
     645 A    20   CYT  O3'  O3R   -0.360000       15.9994           0
     646 A    21   CYT  P    P       1.20000       30.9740           0
     647 A    21   CYT  O1P  O1P   -0.400000       15.9994           0
     648 A    21   CYT  O2P  O2P   -0.400000       15.9994           0
     649 A    21   CYT  O5'  O5R   -0.360000       15.9994           0
     650 A    21   CYT  C5'  C5R   -0.700000E-01   12.0110           0
     651 A    21   CYT  H5'  H      0.350000E-01   1.00800           0
     652 A    21   CYT  H5'' H      0.350000E-01   1.00800           0
     653 A    21   CYT  C4'  C4R    0.650000E-01   12.0110           0
     654 A    21   CYT  H4'  H      0.350000E-01   1.00800           0
     655 A    21   CYT  O4'  O4R   -0.300000       15.9994           0
     656 A    21   CYT  C1'  C1R    0.165000       12.0110           0
     657 A    21   CYT  H1'  H      0.350000E-01   1.00800           0
     658 A    21   CYT  N1   N1C   -0.190000       14.0067           0
     659 A    21   CYT  C6   C6C    0.155000       12.0110           0
     660 A    21   CYT  H6   H      0.350000E-01   1.00800           0
     661 A    21   CYT  C2   C2C    0.300000       12.0110           0
     662 A    21   CYT  O2   ON    -0.300000       15.9994           0
     663 A    21   CYT  N3   NC    -0.280000       14.0067           0
     664 A    21   CYT  C4   C4C    0.280000       12.0110           0
     665 A    21   CYT  N4   N4C   -0.420000       14.0067           0
     666 A    21   CYT  H41  H2     0.210000       1.00800           0
     667 A    21   CYT  H42  H2     0.210000       1.00800           0
     668 A    21   CYT  C5   C5C   -0.350000E-01   12.0110           0
     669 A    21   CYT  H5   H      0.350000E-01   1.00800           0
     670 A    21   CYT  C2'  C2R    0.115000       12.0110           0
     671 A    21   CYT  H2'  H      0.350000E-01   1.00800           0
     672 A    21   CYT  O2'  O2R   -0.400000       15.9994           0
     673 A    21   CYT  HO2' HO     0.250000       1.00800           0
     674 A    21   CYT  H3'  H      0.350000E-01   1.00800           0
     675 A    21   CYT  C3'  C3R    0.150000       12.0110           0
     676 A    21   CYT  O3'  OH    -0.400000       15.9994           0
     677 A    21   CYT  H3T  HO     0.250000       1.00800           0

     728 !NBOND: bonds
       1       2       1       3       1       4       4       7
       7      10      10      12      10      34      12      13
      13      15      13      30      15      16      15      28
      16      17      16      26      17      18      18      19
      18      22      19      20      19      21      22      23
      22      24      24      25      24      26      26      27
      27      28      30      34      34      36      30      32
      28      29      32      33       7       8       7       9
      10      11      34      35      30      31      13      14
       5       6       6       1      37      38      37      39
      37      40      40      41      41      44      44      46
      44      68      46      47      47      49      47      64
      49      50      49      62      50      51      50      60
      51      52      52      53      52      56      53      54
      53      55      56      57      56      58      58      59
      58      60      60      61      61      62      64      68
      68      70      64      66      62      63      66      67
      41      42      41      43      44      45      68      69
      64      65      47      48      36      37      71      72
      71      73      71      74      74      75      75      78
      78      80      78      99      80      81      81      83
      81      95      83      86      83      84      86      88
      88      89      89      90      90      91      90      92
      86      87      89      93      93      84      95      99
      99     101      95      97      84      85      93      94
      97      98      75      76      75      77      78      79
      99     100      95      96      81      82      70      71
     102     103     102     104     102     105     105     106
     106     109     109     111     109     132     111     112
     112     114     112     128     114     115     114     126
     115     116     115     124     116     117     117     119
     119     120     120     121     121     122     121     123
     120     124     124     125     125     126     128     132
     128     130     132     134     126     127     117     118
     130     131     106     107     106     108     109     110
     132     133     128     129     112     113     101     102
     135     136     135     137     135     138     138     139
     139     142     142     144     142     166     144     145
     145     147     145     162     147     148     147     160
     148     149     148     158     149     150     150     151
     150     154     151     152     151     153     154     155
     154     156     156     157     156     158     158     159
     159     160     162     166     166     168     162     164
     160     161     164     165     139     140     139     141
     142     143     166     167     162     163     145     146
     134     135     169     170     169     171     169     172
     172     173     173     176     176     178     176     200
     178     179     179     181     179     196     181     182
     181     194     182     183     182     192     183     184
     184     185     184     188     185     186     185     187
     188     189     188     190     190     191     190     192
     192     193     193     194     196     200     200     202
     196     198     194     195     198     199     173     174
     173     175     176     177     200     201     196     197
     179     180     168     169     203     204     203     205
     203     206     206     207     207     210     210     212
     210     234     212     213     213     215     213     230
     215     216     215     228     216     217     216     226
     217     218     218     219     218     222     219     220
     219     221     222     223     222     224     224     225
     224     226     226     227     227     228     230     234
     234     236     230     232     228     229     232     233
     207     208     207     209     210     211     234     235
     230     231     213     214     202     203     237     238
     237     239     237     240     240     241     241     244
     244     246     244     265     246     247     247     249
     247     261     249     252     249     250     252     254
     254     255     255     256     256     257     256     258
     252     253     255     259     259     250     261     265
     265     267     261     263     250     251     259     260
     263     264     241     242     241     243     244     245
     265     266     261     262     247     248     236     237
     268     269     268     270     268     271     271     272
     272     275     275     277     275     295     277     278
     278     280     278     291     280     283     280     281
     283     284     283     285     285     286     285     287
     287     288     287     289     289     281     291     295
     295     297     291     293     289     290     281     282
     293     294     272     273     272     274     275     276
     295     296     291     292     278     279     267     268
     298     299     298     300     298     301     301     302
     302     305     305     307     305     326     307     308
     308     310     308     322     310     313     310     311
     313     315     315     316     316     317     317     318
     317     319     313     314     316     320     320     311
     322     326     326     328     322     324     311     312
     320     321     324     325     302     303     302     304
     305     306     326     327     322     323     308     309
     297     298     329     330     329     331     329     332
     332     333     333     336     336     338     336     359
     338     339     339     341     339     355     341     342
     341     353     342     343     342     351     343     344
     344     346     346     347     347     348     348     349
     348     350     347     351     351     352     352     353
     355     359     355     357     359     361     353     354
     344     345     357     358     333     334     333     335
     336     337     359     360     355     356     339     340
     328     329     362     363     362     364     362     365
     365     366     366     369     369     371     369     389
     371     372     372     374     372     385     374     377
     374     375     377     378     377     379     379     380
     379     381     381     382     381     383     383     375
     385     389     389     391     385     387     383     384
     375     376     387     388     366     367     366     368
     369     370     389     390     385     386     372     373
     361     362     392     393     392     394     392     395
     395     396     396     399     399     401     399     422
     401     402     402     404     402     418     404     405
     404     416     405     406     405     414     406     407
     407     409     409     410     410     411     411     412
     411     413     410     414     414     415     415     416
     418     422     418     420     422     424     416     417
     407     408     420     421     396     397     396     398
     399     400     422     423     418     419     402     403
     391     392     425     426     425     427     425     428
     428     429     429     432     432     434     432     455
     434     435     435     437     435     451     437     438
     437     449     438     439     438     447     439     440
     440     442     442     443     443     444     444     445
     444     446     443     447     447     448     448     449
     451     455     451     453     455     457     449     450
     440     441     453     454     429     430     429     431
     432     433     455     456     451     452     435     436
     424     425     458     459     458     460     458     461
     461     462     462     465     465     467     465     486
     467     468     468     470     468     482     470     473
     470     471     473     475     475     476     476     477
     477     478     477     479     473     474     476     480
     480     471     482     486     486     488     482     484
     471     472     480     481     484     485     462     463
     462     464     465     466     486     487     482     483
     468     469     457     458     489     490     489     491
     489     492     492     493     493     496     496     498
     496     517     498     499     499     501     499     513
     501     504     501     502     504     506     506     507
     507     508     508     509     508     510     504     505
     507     511     511     502     513     517     517     519
     513     515     502     503     511     512     515     516
     493     494     493     495     496     497     517     518
     513     514     499     500     488     489     520     521
     520     522     520     523     523     524     524     527
     527     529     527     548     529     530     530     532
     530     544     532     535     532     533     535     537
     537     538     538     539     539     540     539     541
     535     536     538     542     542     533     544     548
     548     550     544     546     533     534     542     543
     546     547     524     525     524     526     527     528
     548     549     544     545     530     531     519     520
     551     552     551     553     551     554     554     555
     555     558     558     560     558     578     560     561
     561     563     561     574     563     566     563     564
     566     567     566     568     568     569     568     570
     570     571     570     572     572     564     574     578
     578     580     574     576     572     573     564     565
     576     577     555     556     555     557     558     559
     578     579     574     575     561     562     550     551
     581     582     581     583     581     584     584     585
     585     588     588     590     588     612     590     591
     591     593     591     608     593     594     593     606
     594     595     594     604     595     596     596     597
     596     600     597     598     597     599     600     601
     600     602     602     603     602     604     604     605
     605     606     608     612     612     614     608     610
     606     607     610     611     585     586     585     587
     588     589     612     613     608     609     591     592
     580     581     615     616     615     617     615     618
     618     619     619     622     622     624     622     643
     624     625     625     627     625     639     627     630
     627     628     630     632     632     633     633     634
     634     635     634     636     630     631     633     637
     637     628     639     643     643     645     639     641
     628     629     637     638     641     642     619     620
     619     621     622     623     643     644     639     640
     625     626     614     615     646     647     646     648
     646     649     649     650     650     653     653     655
     653     675     655     656     656     658     656     670
     658     661     658     659     661     663     663     664
     664     665     665     666     665     667     661     662
     664     668     668     659     670     675     675     676
     670     672     659     660     668     669     672     673
     650     651     650     652     653     654     675     674
     670     671     656     657     645     646     676     677

    1299 !NTHETA: angles
       2       1       3       2       1       4       3       1       4
       1       4       7       4       7      10       4       7       8
       4       7       9       7      10      12       7      10      34
      10       7       8      10       7       9       7      10      11
      12      10      34      10      12      13      12      10      11
      10      34      30      10      34      36      34      10      11
      10      34      35      12      13      15      12      13      30
      12      13      14      15      13      30      13      15      16
      13      15      28      15      13      14      13      30      34
      13      30      32      13      30      31      30      13      14
      16      15      28      15      16      17      15      16      26
      15      28      27      15      28      29      17      16      26
      16      17      18      16      26      24      16      26      27
      17      18      19      17      18      22      19      18      22
      18      19      20      18      19      21      18      22      23
      18      22      24      20      19      21      23      22      24
      22      24      25      22      24      26      25      24      26
      24      26      27      26      27      28      27      28      29
      30      34      36      34      30      32      30      34      35
      34      30      31      36      34      35      30      32      33
      32      30      31       8       7       9       5       6       1
       4       1       6       6       1       2       6       1       3
      38      37      39      38      37      40      39      37      40
      37      40      41      40      41      44      40      41      42
      40      41      43      41      44      46      41      44      68
      44      41      42      44      41      43      41      44      45
      46      44      68      44      46      47      46      44      45
      44      68      64      44      68      70      68      44      45
      44      68      69      46      47      49      46      47      64
      46      47      48      49      47      64      47      49      50
      47      49      62      49      47      48      47      64      68
      47      64      66      47      64      65      64      47      48
      50      49      62      49      50      51      49      50      60
      49      62      61      49      62      63      51      50      60
      50      51      52      50      60      58      50      60      61
      51      52      53      51      52      56      53      52      56
      52      53      54      52      53      55      52      56      57
      52      56      58      54      53      55      57      56      58
      56      58      59      56      58      60      59      58      60
      58      60      61      60      61      62      61      62      63
      64      68      70      68      64      66      64      68      69
      68      64      65      70      68      69      64      66      67
      66      64      65      42      41      43      34      36      37
      36      37      38      36      37      39      36      37      40
      72      71      73      72      71      74      73      71      74
      71      74      75      74      75      78      74      75      76
      74      75      77      75      78      80      75      78      99
      78      75      76      78      75      77      75      78      79
      80      78      99      78      80      81      80      78      79
      78      99      95      78      99     101      99      78      79
      78      99     100      80      81      83      80      81      95
      80      81      82      83      81      95      81      83      86
      81      83      84      83      81      82      81      95      99
      81      95      97      81      95      96      95      81      82
      86      83      84      83      86      88      83      86      87
      83      84      93      83      84      85      86      88      89
      88      86      87      88      89      90      88      89      93
      89      90      91      89      90      92      90      89      93
      91      90      92      89      93      84      89      93      94
      93      84      85      84      93      94      95      99     101
      99      95      97      95      99     100      99      95      96
     101      99     100      95      97      98      97      95      96
      76      75      77      68      70      71      70      71      72
      70      71      73      70      71      74     103     102     104
     103     102     105     104     102     105     102     105     106
     105     106     109     105     106     107     105     106     108
     106     109     111     106     109     132     109     106     107
     109     106     108     106     109     110     111     109     132
     109     111     112     111     109     110     109     132     128
     109     132     134     132     109     110     109     132     133
     111     112     114     111     112     128     111     112     113
     114     112     128     112     114     115     112     114     126
     114     112     113     112     128     132     112     128     130
     112     128     129     128     112     113     115     114     126
     114     115     116     114     115     124     114     126     125
     114     126     127     116     115     124     115     116     117
     115     124     120     115     124     125     116     117     119
     116     117     118     117     119     120     119     117     118
     119     120     121     119     120     124     120     121     122
     120     121     123     121     120     124     122     121     123
     120     124     125     124     125     126     125     126     127
     132     128     130     128     132     134     128     132     133
     132     128     129     128     130     131     130     128     129
     134     132     133     107     106     108      99     101     102
     101     102     103     101     102     104     101     102     105
     136     135     137     136     135     138     137     135     138
     135     138     139     138     139     142     138     139     140
     138     139     141     139     142     144     139     142     166
     142     139     140     142     139     141     139     142     143
     144     142     166     142     144     145     144     142     143
     142     166     162     142     166     168     166     142     143
     142     166     167     144     145     147     144     145     162
     144     145     146     147     145     162     145     147     148
     145     147     160     147     145     146     145     162     166
     145     162     164     145     162     163     162     145     146
     148     147     160     147     148     149     147     148     158
     147     160     159     147     160     161     149     148     158
     148     149     150     148     158     156     148     158     159
     149     150     151     149     150     154     151     150     154
     150     151     152     150     151     153     150     154     155
     150     154     156     152     151     153     155     154     156
     154     156     157     154     156     158     157     156     158
     156     158     159     158     159     160     159     160     161
     162     166     168     166     162     164     162     166     167
     166     162     163     168     166     167     162     164     165
     164     162     163     140     139     141     132     134     135
     134     135     136     134     135     137     134     135     138
     170     169     171     170     169     172     171     169     172
     169     172     173     172     173     176     172     173     174
     172     173     175     173     176     178     173     176     200
     176     173     174     176     173     175     173     176     177
     178     176     200     176     178     179     178     176     177
     176     200     196     176     200     202     200     176     177
     176     200     201     178     179     181     178     179     196
     178     179     180     181     179     196     179     181     182
     179     181     194     181     179     180     179     196     200
     179     196     198     179     196     197     196     179     180
     182     181     194     181     182     183     181     182     192
     181     194     193     181     194     195     183     182     192
     182     183     184     182     192     190     182     192     193
     183     184     185     183     184     188     185     184     188
     184     185     186     184     185     187     184     188     189
     184     188     190     186     185     187     189     188     190
     188     190     191     188     190     192     191     190     192
     190     192     193     192     193     194     193     194     195
     196     200     202     200     196     198     196     200     201
     200     196     197     202     200     201     196     198     199
     198     196     197     174     173     175     166     168     169
     168     169     170     168     169     171     168     169     172
     204     203     205     204     203     206     205     203     206
     203     206     207     206     207     210     206     207     208
     206     207     209     207     210     212     207     210     234
     210     207     208     210     207     209     207     210     211
     212     210     234     210     212     213     212     210     211
     210     234     230     210     234     236     234     210     211
     210     234     235     212     213     215     212     213     230
     212     213     214     215     213     230     213     215     216
     213     215     228     215     213     214     213     230     234
     213     230     232     213     230     231     230     213     214
     216     215     228     215     216     217     215     216     226
     215     228     227     215     228     229     217     216     226
     216     217     218     216     226     224     216     226     227
     217     218     219     217     218     222     219     218     222
     218     219     220     218     219     221     218     222     223
     218     222     224     220     219     221     223     222     224
     222     224     225     222     224     226     225     224     226
     224     226     227     226     227     228     227     228     229
     230     234     236     234     230     232     230     234     235
     234     230     231     236     234     235     230     232     233
     232     230     231     208     207     209     200     202     203
     202     203     204     202     203     205     202     203     206
     238     237     239     238     237     240     239     237     240
     237     240     241     240     241     244     240     241     242
     240     241     243     241     244     246     241     244     265
     244     241     242     244     241     243     241     244     245
     246     244     265     244     246     247     246     244     245
     244     265     261     244     265     267     265     244     245
     244     265     266     246     247     249     246     247     261
     246     247     248     249     247     261     247     249     252
     247     249     250     249     247     248     247     261     265
     247     261     263     247     261     262     261     247     248
     252     249     250     249     252     254     249     252     253
     249     250     259     249     250     251     252     254     255
     254     252     253     254     255     256     254     255     259
     255     256     257     255     256     258     256     255     259
     257     256     258     255     259     250     255     259     260
     259     250     251     250     259     260     261     265     267
     265     261     263     261     265     266     265     261     262
     267     265     266     261     263     264     263     261     262
     242     241     243     234     236     237     236     237     238
     236     237     239     236     237     240     269     268     270
     269     268     271     270     268     271     268     271     272
     271     272     275     271     272     273     271     272     274
     272     275     277     272     275     295     275     272     273
     275     272     274     272     275     276     277     275     295
     275     277     278     277     275     276     275     295     291
     275     295     297     295     275     276     275     295     296
     277     278     280     277     278     291     277     278     279
     280     278     291     278     280     283     278     280     281
     280     278     279     278     291     295     278     291     293
     278     291     292     291     278     279     283     280     281
     280     283     284     280     283     285     280     281     289
     280     281     282     284     283     285     283     285     286
     283     285     287     286     285     287     285     287     288
     285     287     289     288     287     289     287     289     281
     287     289     290     281     289     290     289     281     282
     291     295     297     295     291     293     291     295     296
     295     291     292     297     295     296     291     293     294
     293     291     292     273     272     274     265     267     268
     267     268     269     267     268     270     267     268     271
     299     298     300     299     298     301     300     298     301
     298     301     302     301     302     305     301     302     303
     301     302     304     302     305     307     302     305     326
     305     302     303     305     302     304     302     305     306
     307     305     326     305     307     308     307     305     306
     305     326     322     305     326     328     326     305     306
     305     326     327     307     308     310     307     308     322
     307     308     309     310     308     322     308     310     313
     308     310     311     310     308     309     308     322     326
     308     322     324     308     322     323     322     308     309
     313     310     311     310     313     315     310     313     314
     310     311     320     310     311     312     313     315     316
     315     313     314     315     316     317     315     316     320
     316     317     318     316     317     319     317     316     320
     318     317     319     316     320     311     316     320     321
     320     311     312     311     320     321     322     326     328
     326     322     324     322     326     327     326     322     323
     328     326     327     322     324     325     324     322     323
     303     302     304     295     297     298     297     298     299
     297     298     300     297     298     301     330     329     331
     330     329     332     331     329     332     329     332     333
     332     333     336     332     333     334     332     333     335
     333     336     338     333     336     359     336     333     334
     336     333     335     333     336     337     338     336     359
     336     338     339     338     336     337     336     359     355
     336     359     361     359     336     337     336     359     360
     338     339     341     338     339     355     338     339     340
     341     339     355     339     341     342     339     341     353
     341     339     340     339     355     359     339     355     357
     339     355     356     355     339     340     342     341     353
     341     342     343     341     342     351     341     353     352
     341     353     354     343     342     351     342     343     344
     342     351     347     342     351     352     343     344     346
     343     344     345     344     346     347     346     344     345
     346     347     348     346     347     351     347     348     349
     347     348     350     348     347     351     349     348     350
     347     351     352     351     352     353     352     353     354
     359     355     357     355     359     361     355     359     360
     359     355     356     355     357     358     357     355     356
     361     359     360     334     333     335     326     328     329
     328     329     330     328     329     331     328     329     332
     363     362     364     363     362     365     364     362     365
     362     365     366     365     366     369     365     366     367
     365     366     368     366     369     371     366     369     389
     369     366     367     369     366     368     366     369     370
     371     369     389     369     371     372     371     369     370
     369     389     385     369     389     391     389     369     370
     369     389     390     371     372     374     371     372     385
     371     372     373     374     372     385     372     374     377
     372     374     375     374     372     373     372     385     389
     372     385     387     372     385     386     385     372     373
     377     374     375     374     377     378     374     377     379
     374     375     383     374     375     376     378     377     379
     377     379     380     377     379     381     380     379     381
     379     381     382     379     381     383     382     381     383
     381     383     375     381     383     384     375     383     384
     383     375     376     385     389     391     389     385     387
     385     389     390     389     385     386     391     389     390
     385     387     388     387     385     386     367     366     368
     359     361     362     361     362     363     361     362     364
     361     362     365     393     392     394     393     392     395
     394     392     395     392     395     396     395     396     399
     395     396     397     395     396     398     396     399     401
     396     399     422     399     396     397     399     396     398
     396     399     400     401     399     422     399     401     402
     401     399     400     399     422     418     399     422     424
     422     399     400     399     422     423     401     402     404
     401     402     418     401     402     403     404     402     418
     402     404     405     402     404     416     404     402     403
     402     418     422     402     418     420     402     418     419
     418     402     403     405     404     416     404     405     406
     404     405     414     404     416     415     404     416     417
     406     405     414     405     406     407     405     414     410
     405     414     415     406     407     409     406     407     408
     407     409     410     409     407     408     409     410     411
     409     410     414     410     411     412     410     411     413
     411     410     414     412     411     413     410     414     415
     414     415     416     415     416     417     422     418     420
     418     422     424     418     422     423     422     418     419
     418     420     421     420     418     419     424     422     423
     397     396     398     389     391     392     391     392     393
     391     392     394     391     392     395     426     425     427
     426     425     428     427     425     428     425     428     429
     428     429     432     428     429     430     428     429     431
     429     432     434     429     432     455     432     429     430
     432     429     431     429     432     433     434     432     455
     432     434     435     434     432     433     432     455     451
     432     455     457     455     432     433     432     455     456
     434     435     437     434     435     451     434     435     436
     437     435     451     435     437     438     435     437     449
     437     435     436     435     451     455     435     451     453
     435     451     452     451     435     436     438     437     449
     437     438     439     437     438     447     437     449     448
     437     449     450     439     438     447     438     439     440
     438     447     443     438     447     448     439     440     442
     439     440     441     440     442     443     442     440     441
     442     443     444     442     443     447     443     444     445
     443     444     446     444     443     447     445     444     446
     443     447     448     447     448     449     448     449     450
     455     451     453     451     455     457     451     455     456
     455     451     452     451     453     454     453     451     452
     457     455     456     430     429     431     422     424     425
     424     425     426     424     425     427     424     425     428
     459     458     460     459     458     461     460     458     461
     458     461     462     461     462     465     461     462     463
     461     462     464     462     465     467     462     465     486
     465     462     463     465     462     464     462     465     466
     467     465     486     465     467     468     467     465     466
     465     486     482     465     486     488     486     465     466
     465     486     487     467     468     470     467     468     482
     467     468     469     470     468     482     468     470     473
     468     470     471     470     468     469     468     482     486
     468     482     484     468     482     483     482     468     469
     473     470     471     470     473     475     470     473     474
     470     471     480     470     471     472     473     475     476
     475     473     474     475     476     477     475     476     480
     476     477     478     476     477     479     477     476     480
     478     477     479     476     480     471     476     480     481
     480     471     472     471     480     481     482     486     488
     486     482     484     482     486     487     486     482     483
     488     486     487     482     484     485     484     482     483
     463     462     464     455     457     458     457     458     459
     457     458     460     457     458     461     490     489     491
     490     489     492     491     489     492     489     492     493
     492     493     496     492     493     494     492     493     495
     493     496     498     493     496     517     496     493     494
     496     493     495     493     496     497     498     496     517
     496     498     499     498     496     497     496     517     513
     496     517     519     517     496     497     496     517     518
     498     499     501     498     499     513     498     499     500
     501     499     513     499     501     504     499     501     502
     501     499     500     499     513     517     499     513     515
     499     513     514     513     499     500     504     501     502
     501     504     506     501     504     505     501     502     511
     501     502     503     504     506     507     506     504     505
     506     507     508     506     507     511     507     508     509
     507     508     510     508     507     511     509     508     510
     507     511     502     507     511     512     511     502     503
     502     511     512     513     517     519     517     513     515
     513     517     518     517     513     514     519     517     518
     513     515     516     515     513     514     494     493     495
     486     488     489     488     489     490     488     489     491
     488     489     492     521     520     522     521     520     523
     522     520     523     520     523     524     523     524     527
     523     524     525     523     524     526     524     527     529
     524     527     548     527     524     525     527     524     526
     524     527     528     529     527     548     527     529     530
     529     527     528     527     548     544     527     548     550
     548     527     528     527     548     549     529     530     532
     529     530     544     529     530     531     532     530     544
     530     532     535     530     532     533     532     530     531
     530     544     548     530     544     546     530     544     545
     544     530     531     535     532     533     532     535     537
     532     535     536     532     533     542     532     533     534
     535     537     538     537     535     536     537     538     539
     537     538     542     538     539     540     538     539     541
     539     538     542     540     539     541     538     542     533
     538     542     543     542     533     534     533     542     543
     544     548     550     548     544     546     544     548     549
     548     544     545     550     548     549     544     546     547
     546     544     545     525     524     526     517     519     520
     519     520     521     519     520     522     519     520     523
     552     551     553     552     551     554     553     551     554
     551     554     555     554     555     558     554     555     556
     554     555     557     555     558     560     555     558     578
     558     555     556     558     555     557     555     558     559
     560     558     578     558     560     561     560     558     559
     558     578     574     558     578     580     578     558     559
     558     578     579     560     561     563     560     561     574
     560     561     562     563     561     574     561     563     566
     561     563     564     563     561     562     561     574     578
     561     574     576     561     574     575     574     561     562
     566     563     564     563     566     567     563     566     568
     563     564     572     563     564     565     567     566     568
     566     568     569     566     568     570     569     568     570
     568     570     571     568     570     572     571     570     572
     570     572     564     570     572     573     564     572     573
     572     564     565     574     578     580     578     574     576
     574     578     579     578     574     575     580     578     579
     574     576     577     576     574     575     556     555     557
     548     550     551     550     551     552     550     551     553
     550     551     554     582     581     583     582     581     584
     583     581     584     581     584     585     584     585     588
     584     585     586     584     585     587     585     588     590
     585     588     612     588     585     586     588     585     587
     585     588     589     590     588     612     588     590     591
     590     588     589     588     612     608     588     612     614
     612     588     589     588     612     613     590     591     593
     590     591     608     590     591     592     593     591     608
     591     593     594     591     593     606     593     591     592
     591     608     612     591     608     610     591     608     609
     608     591     592     594     593     606     593     594     595
     593     594     604     593     606     605     593     606     607
     595     594     604     594     595     596     594     604     602
     594     604     605     595     596     597     595     596     600
     597     596     600     596     597     598     596     597     599
     596     600     601     596     600     602     598     597     599
     601     600     602     600     602     603     600     602     604
     603     602     604     602     604     605     604     605     606
     605     606     607     608     612     614     612     608     610
     608     612     613     612     608     609     614     612     613
     608     610     611     610     608     609     586     585     587
     578     580     581     580     581     582     580     581     583
     580     581     584     616     615     617     616     615     618
     617     615     618     615     618     619     618     619     622
     618     619     620     618     619     621     619     622     624
     619     622     643     622     619     620     622     619     621
     619     622     623     624     622     643     622     624     625
     624     622     623     622     643     639     622     643     645
     643     622     623     622     643     644     624     625     627
     624     625     639     624     625     626     627     625     639
     625     627     630     625     627     628     627     625     626
     625     639     643     625     639     641     625     639     640
     639     625     626     630     627     628     627     630     632
     627     630     631     627     628     637     627     628     629
     630     632     633     632     630     631     632     633     634
     632     633     637     633     634     635     633     634     636
     634     633     637     635     634     636     633     637     628
     633     637     638     637     628     629     628     637     638
     639     643     645     643     639     641     639     643     644
     643     639     640     645     643     644     639     641     642
     641     639     640     620     619     621     612     614     615
     614     615     616     614     615     617     614     615     618
     647     646     648     647     646     649     648     646     649
     646     649     650     649     650     653     649     650     651
     649     650     652     650     653     655     650     653     675
     653     650     651     653     650     652     650     653     654
     655     653     675     653     655     656     655     653     654
     653     675     670     653     675     676     675     653     654
     653     675     674     655     656     658     655     656     670
     655     656     657     658     656     670     656     658     661
     656     658     659     658     656     657     656     670     675
     656     670     672     656     670     671     670     656     657
     661     658     659     658     661     663     658     661     662
     658     659     668     658     659     660     661     663     664
     663     661     662     663     664     665     663     664     668
     664     665     666     664     665     667     665     664     668
     666     665     667     664     668     659     664     668     669
     668     659     660     659     668     669     670     675     676
     675     670     672     670     675     674     675     670     671
     676     675     674     670     672     673     672     670     671
     651     650     652     643     645     646     645     646     647
     645     646     648     645     646     649     675     676     677

       0 !NPHI: dihedrals


     461 !NIMPHI: impropers
      17      18      19      20      13      16      28      15
      15      16      26      27      16      26      27      28
      26      27      28      15      27      28      15      16
      28      15      16      26      19      17      22      18
      23      18      24      22      25      22      26      24
      16      17      18      22      17      18      22      24
      18      22      24      26      22      24      26      16
      24      26      16      17      26      16      17      18
      21      20      18      19      29      27      15      28
      28      16      26      22      28      26      16      18
      17      16      26      27      24      26      16      15
      14      30      12      15      31      34      13      32
      35      10      30      36      11       7      34      12
       8       4       9      10      51      52      53      54
      47      50      62      49      49      50      60      61
      50      60      61      62      60      61      62      49
      61      62      49      50      62      49      50      60
      53      51      56      52      57      52      58      56
      59      56      60      58      50      51      52      56
      51      52      56      58      52      56      58      60
      56      58      60      50      58      60      50      51
      60      50      51      52      55      54      52      53
      63      61      49      62      62      50      60      56
      62      60      50      52      51      50      60      61
      58      60      50      49      48      64      46      49
      65      68      47      66      69      44      64      70
      45      41      68      46      42      40      43      44
      93      89      90      91      81      86      84      83
      87      83      88      86      90      88      93      89
      83      86      88      89      86      88      89      93
      88      89      93      84      89      93      84      83
      93      84      83      86      84      83      86      88
      92      89      91      90      94      89      84      93
      85      83      93      84      82      95      80      83
      96      99      81      97     100      78      95     101
      79      75      99      80      76      74      77      78
     124     120     121     122     112     115     126     114
     114     115     124     125     115     124     125     126
     124     125     126     114     125     126     114     115
     126     114     115     124     121     119     124     120
     123     120     122     121     115     116     117     119
     116     117     119     120     117     119     120     124
     119     120     124     115     120     124     115     116
     124     115     116     117     118     119     116     117
     127     125     114     126     126     115     124     119
     126     124     115     117     116     115     124     125
     120     124     115     114     113     128     111     114
     129     132     112     130     133     109     128     134
     110     106     132     111     107     105     108     109
     149     150     151     152     145     148     160     147
     147     148     158     159     148     158     159     160
     158     159     160     147     159     160     147     148
     160     147     148     158     151     149     154     150
     155     150     156     154     157     154     158     156
     148     149     150     154     149     150     154     156
     150     154     156     158     154     156     158     148
     156     158     148     149     158     148     149     150
     153     152     150     151     161     159     147     160
     160     148     158     154     160     158     148     150
     149     148     158     159     156     158     148     147
     146     162     144     147     163     166     145     164
     167     142     162     168     143     139     166     144
     140     138     141     142     183     184     185     186
     179     182     194     181     181     182     192     193
     182     192     193     194     192     193     194     181
     193     194     181     182     194     181     182     192
     185     183     188     184     189     184     190     188
     191     188     192     190     182     183     184     188
     183     184     188     190     184     188     190     192
     188     190     192     182     190     192     182     183
     192     182     183     184     187     186     184     185
     195     193     181     194     194     182     192     188
     194     192     182     184     183     182     192     193
     190     192     182     181     180     196     178     181
     197     200     179     198     201     176     196     202
     177     173     200     178     174     172     175     176
     217     218     219     220     213     216     228     215
     215     216     226     227     216     226     227     228
     226     227     228     215     227     228     215     216
     228     215     216     226     219     217     222     218
     223     218     224     222     225     222     226     224
     216     217     218     222     217     218     222     224
     218     222     224     226     222     224     226     216
     224     226     216     217     226     216     217     218
     221     220     218     219     229     227     215     228
     228     216     226     222     228     226     216     218
     217     216     226     227     224     226     216     215
     214     230     212     215     231     234     213     232
     235     210     230     236     211     207     234     212
     208     206     209     210     259     255     256     257
     247     252     250     249     253     249     254     252
     256     254     259     255     249     252     254     255
     252     254     255     259     254     255     259     250
     255     259     250     249     259     250     249     252
     250     249     252     254     258     255     257     256
     260     255     250     259     251     249     259     250
     248     261     246     249     262     265     247     263
     266     244     261     267     245     241     265     246
     242     240     243     244     278     283     281     280
     284     280     285     283     286     283     287     285
     288     285     289     287     280     283     285     287
     283     285     287     289     285     287     289     281
     287     289     281     280     289     281     280     283
     281     280     283     285     290     287     281     289
     282     280     289     281     279     291     277     280
     292     295     278     293     296     275     291     297
     276     272     295     277     273     271     274     275
     320     316     317     318     308     313     311     310
     314     310     315     313     317     315     320     316
     310     313     315     316     313     315     316     320
     315     316     320     311     316     320     311     310
     320     311     310     313     311     310     313     315
     319     316     318     317     321     316     311     320
     312     310     320     311     309     322     307     310
     323     326     308     324     327     305     322     328
     306     302     326     307     303     301     304     305
     351     347     348     349     339     342     353     341
     341     342     351     352     342     351     352     353
     351     352     353     341     352     353     341     342
     353     341     342     351     348     346     351     347
     350     347     349     348     342     343     344     346
     343     344     346     347     344     346     347     351
     346     347     351     342     347     351     342     343
     351     342     343     344     345     346     343     344
     354     352     341     353     353     342     351     346
     353     351     342     344     343     342     351     352
     347     351     342     341     340     355     338     341
     356     359     339     357     360     336     355     361
     337     333     359     338     334     332     335     336
     372     377     375     374     378     374     379     377
     380     377     381     379     382     379     383     381
     374     377     379     381     377     379     381     383
     379     381     383     375     381     383     375     374
     383     375     374     377     375     374     377     379
     384     381     375     383     376     374     383     375
     373     385     371     374     386     389     372     387
     390     369     385     391     370     366     389     371
     367     365     368     369     414     410     411     412
     402     405     416     404     404     405     414     415
     405     414     415     416     414     415     416     404
     415     416     404     405     416     404     405     414
     411     409     414     410     413     410     412     411
     405     406     407     409     406     407     409     410
     407     409     410     414     409     410     414     405
     410     414     405     406     414     405     406     407
     408     409     406     407     417     415     404     416
     416     405     414     409     416     414     405     407
     406     405     414     415     410     414     405     404
     403     418     401     404     419     422     402     420
     423     399     418     424     400     396     422     401
     397     395     398     399     447     443     444     445
     435     438     449     437     437     438     447     448
     438     447     448     449     447     448     449     437
     448     449     437     438     449     437     438     447
     444     442     447     443     446     443     445     444
     438     439     440     442     439     440     442     443
     440     442     443     447     442     443     447     438
     443     447     438     439     447     438     439     440
     441     442     439     440     450     448     437     449
     449     438     447     442     449     447     438     440
     439     438     447     448     443     447     438     437
     436     451     434     437     452     455     435     453
     456     432     451     457     433     429     455     434
     430     428     431     432     480     476     477     478
     468     473     471     470     474     470     475     473
     477     475     480     476     470     473     475     476
     473     475     476     480     475     476     480     471
     476     480     471     470     480     471     470     473
     471     470     473     475     479     476     478     477
     481     476     471     480     472     470     480     471
     469     482     467     470     483     486     468     484
     487     465     482     488     466     462     486     467
     463     461     464     465     511     507     508     509
     499     504     502     501     505     501     506     504
     508     506     511     507     501     504     506     507
     504     506     507     511     506     507     511     502
     507     511     502     501     511     502     501     504
     502     501     504     506     510     507     509     508
     512     507     502     511     503     501     511     502
     500     513     498     501     514     517     499     515
     518     496     513     519     497     493     517     498
     494     492     495     496     542     538     539     540
     530     535     533     532     536     532     537     535
     539     537     542     538     532     535     537     538
     535     537     538     542     537     538     542     533
     538     542     533     532     542     533     532     535
     533     532     535     537     541     538     540     539
     543     538     533     542     534     532     542     533
     531     544     529     532     545     548     530     546
     549     527     544     550     528     524     548     529
     525     523     526     527     561     566     564     563
     567     563     568     566     569     566     570     568
     571     568     572     570     563     566     568     570
     566     568     570     572     568     570     572     564
     570     572     564     563     572     564     563     566
     564     563     566     568     573     570     564     572
     565     563     572     564     562     574     560     563
     575     578     561     576     579     558     574     580
     559     555     578     560     556     554     557     558
     595     596     597     598     591     594     606     593
     593     594     604     605     594     604     605     606
     604     605     606     593     605     606     593     594
     606     593     594     604     597     595     600     596
     601     596     602     600     603     600     604     602
     594     595     596     600     595     596     600     602
     596     600     602     604     600     602     604     594
     602     604     594     595     604     594     595     596
     599     598     596     597     607     605     593     606
     606     594     604     600     606     604     594     596
     595     594     604     605     602     604     594     593
     592     608     590     593     609     612     591     610
     613     588     608     614     589     585     612     590
     586     584     587     588     637     633     634     635
     625     630     628     627     631     627     632     630
     634     632     637     633     627     630     632     633
     630     632     633     637     632     633     637     628
     633     637     628     627     637     628     627     630
     628     627     630     632     636     633     635     634
     638     633     628     637     629     627     637     628
     626     639     624     627     640     643     625     641
     644     622     639     645     623     619     643     624
     620     618     621     622     668     664     665     666
     656     661     659     658     662     658     663     661
     665     663     668     664     658     661     663     664
     661     663     664     668     663     664     668     659
     664     668     659     658     668     659     658     661
     659     658     661     663     667     664     666     665
     669     664     659     668     660     658     668     659
     657     670     655     658     671     675     656     672
     674     653     670     676     654     650     675     655
     651     649     652     653

      68 !NDON: donors
      19      20      19      21      22      23      32      31
       6       5      53      54      53      55      56      57
      66      65      90      92      97      96      90      91
     121     122     121     123     130     129     151     152
     151     153     154     155     164     163     185     186
     185     187     188     189     198     197     219     220
     219     221     222     223     232     231     256     258
     263     262     256     257     285     286     293     292
     317     319     324     323     317     318     348     349
     348     350     357     356     379     380     387     386
     411     412     411     413     420     419     444     445
     444     446     453     452     477     479     484     483
     477     478     508     510     515     514     508     509
     539     541     546     545     539     540     568     569
     576     575     597     598     597     599     600     601
     610     609     634     636     641     640     634     635
     665     667     672     671     665     666     676     677

     105 !NACC: acceptors
      25      24      17       0       2       1       3       1
      32       0      59      58      51       0      38      37
      39      37      66       0      87      86      88       0
      72      71      73      71      97       0     116       0
     119       0     103     102     104     102     130       0
     157     156     149       0     136     135     137     135
     164       0     191     190     183       0     170     169
     171     169     198       0     225     224     217       0
     204     203     205     203     232       0     253     252
     254       0     238     237     239     237     263       0
     284     283     288     287     269     268     270     268
     293       0     314     313     315       0     299     298
     300     298     324       0     343       0     346       0
     330     329     331     329     357       0     378     377
     382     381     363     362     364     362     387       0
     406       0     409       0     393     392     394     392
     420       0     439       0     442       0     426     425
     427     425     453       0     474     473     475       0
     459     458     460     458     484       0     505     504
     506       0     490     489     491     489     515       0
     536     535     537       0     521     520     522     520
     546       0     567     566     571     570     552     551
     553     551     576       0     603     602     595       0
     582     581     583     581     610       0     631     630
     632       0     616     615     617     615     641       0
     662     661     663       0     647     646     648     646
     672       0

      63 !NNB
      22      24      26      56      58      60      89      88
      93     119     120     124     154     156     158     188
     190     192     222     224     226     255     254     259
     287     285     289     316     315     320     346     347
     351     381     379     383     409     410     414     442
     443     447     476     475     480     507     506     511
     538     537     542     570     568     572     600     602
     604     633     632     637     664     663     668
       0       0       0       0       0       0       0       0
       0       0       0       0       0       0       0       1
       2       3       3       3       3       3       3       3
       3       3       3       3       3       3       3       3
       3       3       3       3       3       3       3       3
       3       3       3       3       3       3       3       3
       3       4       5       6       6       6       6       6
       6       6       6       6       6       6       6       6
       6       6       6       6       6       6       6       6
       6       6       6       6       6       6       6       6
       6       6       7       8       8       9       9       9
       9       9       9       9       9       9       9       9
       9       9       9       9       9       9       9       9
       9       9       9       9       9       9       9       9
       9       9      10      11      12      12      12      12
      12      12      12      12      12      12      12      12
      12      12      12      12      12      12      12      12
      12      12      12      12      12      12      12      12
      12      12      12      13      14      15      15      15
      15      15      15      15      15      15      15      15
      15      15      15      15      15      15      15      15
      15      15      15      15      15      15      15      15
      15      15      15      15      15      16      17      18
      18      18      18      18      18      18      18      18
      18      18      18      18      18      18      18      18
      18      18      18      18      18      18      18      18
      18      18      18      18      18      18      18      19
      20      21      21      21      21      21      21      21
      21      21      21      21      21      21      21      21
      21      21      21      21      21      21      21      21
      21      21      21      21      21      21      21      21
      22      23      23      24      24      24      24      24
      24      24      24      24      24      24      24      24
      24      24      24      24      24      24      24      24
      24      24      24      24      24      24      24      25
      26      26      27      27      27      27      27      27
      27      27      27      27      27      27      27      27
      27      27      27      27      27      27      27      27
      27      27      27      27      27      28      29      29
      30      30      30      30      30      30      30      30
      30      30      30      30      30      30      30      30
      30      30      30      30      30      30      30      30
      30      30      30      30      30      31      32      33
      33      33      33      33      33      33      33      33
      33      33      33      33      33      33      33      33
      33      33      33      33      33      33      33      33
      33      33      33      33      33      34      35      35
      36      36      36      36      36      36      36      36
      36      36      36      36      36      36      36      36
      36      36      36      36      36      36      36      36
      36      36      36      36      37      38      39      39
      39      39      39      39      39      39      39      39
      39      39      39      39      39      39      39      39
      39      39      39      39      39      39      39      39
      39      39      39      39      39      40      41      42
      42      42      42      42      42      42      42      42
      42      42      42      42      42      42      42      42
      42      42      42      42      42      42      42      42
      42      42      42      42      42      43      44      44
      45      45      45      45      45      45      45      45
      45      45      45      45      45      45      45      45
      45      45      45      45      45      45      45      45
      45      45      45      45      46      47      47      48
      48      48      48      48      48      48      48      48
      48      48      48      48      48      48      48      48
      48      48      48      48      48      48      48      48
      48      48      48      49      50      50      51      51
      51      51      51      51      51      51      51      51
      51      51      51      51      51      51      51      51
      51      51      51      51      51      51      51      51
      51      51      52      53      53      54      54      54
      54      54      54      54      54      54      54      54
      54      54      54      54      54      54      54      54
      54      54      54      54      54      54      54      54
      54      55      56      57      57      57      57      57
      57      57      57      57      57      57      57      57
      57      57      57      57      57      57      57      57
      57      57      57      57      57      57      57      57
      57      57      58      59      59      60      60      60
      60      60      60      60      60      60      60      60
      60      60      60      60      60      60      60      60
      60      60      60      60      60      60      60      60
      60      61      62      62      63      63      63      63
      63      63      63      63      63      63      63      63
      63      63      63      63      63

     218       0 !NGRP
       0       0       0       4       0       0       6       0       0
       9       0       0      14       0       0      16       0       0
      18       0       0      21       0       0      23       0       0
      25       0       0      29       0       0      33       0       0
      35       0       0      40       0       0      43       0       0
      48       0       0      50       0       0      52       0       0
      55       0       0      57       0       0      59       0       0
      63       0       0      67       0       0      69       0       0
      74       0       0      77       0       0      82       0       0
      85       0       0      87       0       0      89       0       0
      92       0       0      94       0       0      98       0       0
     100       0       0     105       0       0     108       0       0
     113       0       0     115       0       0     118       0       0
     120       0       0     123       0       0     127       0       0
     131       0       0     133       0       0     138       0       0
     141       0       0     146       0       0     148       0       0
     150       0       0     153       0       0     155       0       0
     157       0       0     161       0       0     165       0       0
     167       0       0     172       0       0     175       0       0
     180       0       0     182       0       0     184       0       0
     187       0       0     189       0       0     191       0       0
     195       0       0     199       0       0     201       0       0
     206       0       0     209       0       0     214       0       0
     216       0       0     218       0       0     221       0       0
     223       0       0     225       0       0     229       0       0
     233       0       0     235       0       0     240       0       0
     243       0       0     248       0       0     251       0       0
     253       0       0     255       0       0     258       0       0
     260       0       0     264       0       0     266       0       0
     271       0       0     274       0       0     279       0       0
     282       0       0     284       0       0     286       0       0
     288       0       0     290       0       0     294       0       0
     296       0       0     301       0       0     304       0       0
     309       0       0     312       0       0     314       0       0
     316       0       0     319       0       0     321       0       0
     325       0       0     327       0       0     332       0       0
     335       0       0     340       0       0     342       0       0
     345       0       0     347       0       0     350       0       0
     354       0       0     358       0       0     360       0       0
     365       0       0     368       0       0     373       0       0
     376       0       0     378       0       0     380       0       0
     382       0       0     384       0       0     388       0       0
     390       0       0     395       0       0     398       0       0
     403       0       0     405       0       0     408       0       0
     410       0       0     413       0       0     417       0       0
     421       0       0     423       0       0     428       0       0
     431       0       0     436       0       0     438       0       0
     441       0       0     443       0       0     446       0       0
     450       0       0     454       0       0     456       0       0
     461       0       0     464       0       0     469       0       0
     472       0       0     474       0       0     476       0       0
     479       0       0     481       0       0     485       0       0
     487       0       0     492       0       0     495       0       0
     500       0       0     503       0       0     505       0       0
     507       0       0     510       0       0     512       0       0
     516       0       0     518       0       0     523       0       0
     526       0       0     531       0       0     534       0       0
     536       0       0     538       0       0     541       0       0
     543       0       0     547       0       0     549       0       0
     554       0       0     557       0       0     562       0       0
     565       0       0     567       0       0     569       0       0
     571       0       0     573       0       0     577       0       0
     579       0       0     584       0       0     587       0       0
     592       0       0     594       0       0     596       0       0
     599       0       0     601       0       0     603       0       0
     607       0       0     611       0       0     613       0       0
     618       0       0     621       0       0     626       0       0
     629       0       0     631       0       0     633       0       0
     636       0       0     638       0       0     642       0       0
     644       0       0     649       0       0     652       0       0
     657       0       0     660       0       0     662       0       0
     664       0       0     667       0       0     669       0       0
     673       0       0     674       0       0
# 0.2 NOE quality
1 1 31 b
2 7 74 b
3  11 g
4 5 215 b
5  10 g
6 2 39 b
7 12 336 b
8  10 g
9 5 105 b
10 5 93 b
11  10 g
12 1 31 b
13 8 122 b
14  10 g
15 3 43 b
16 5 102 b
17  12 g
18  10 g
19 1 16 b
20  10 g
21 2 34 b
22  11 g
23  11 g
24  11 g
25 1 21 b
26 3 43 b
27  10 g
28 1 23 b
29 108 5140 b
30 5 74 b

  Entry H atom name         Submitted Coord H atom name
    1   1H5*    G   1          H5'       GUA   1   8.435  12.599  -2.468
    2   2H5*    G   1          H5''      GUA   1   7.186  12.095  -3.622
    3    H4*    G   1           H4'      GUA   1   9.159  11.630  -4.731
    4    H3*    G   1           H3'      GUA   1   8.160   9.101  -3.438
    5    H2*    G   1           H2'      GUA   1  10.070   7.952  -4.361
    6   2HO*    G   1          HO2'      GUA   1  10.335  10.357  -5.864
    7    H1*    G   1           H1'      GUA   1  11.907   9.984  -3.728
    8    H8     G   1           H8       GUA   1   9.693   9.864  -0.791
    9    H1     G   1           H1       GUA   1  13.812   4.951  -0.992
   10   1H2     G   1          H21       GUA   1  14.305   5.894  -4.276
   11   2H2     G   1          H22       GUA   1  14.686   4.784  -2.974
   12    H5T    G   1           H5T      GUA   1   5.500   9.725  -2.464
   13   1H5*    G   2          H5'       GUA   2   9.150   8.065  -7.088
   14   2H5*    G   2          H5''      GUA   2   7.869   7.259  -8.014
   15    H4*    G   2           H4'      GUA   2   9.713   5.870  -8.235
   16    H3*    G   2           H3'      GUA   2   7.940   4.729  -6.076
   17    H2*    G   2           H2'      GUA   2   9.492   2.885  -5.951
   18   2HO*    G   2          HO2'      GUA   2  10.558   4.055  -8.325
   19    H1*    G   2           H1'      GUA   2  11.775   4.523  -6.040
   20    H8     G   2           H8       GUA   2   9.388   6.352  -3.891
   21    H1     G   2           H1       GUA   2  12.128   1.363  -0.928
   22   1H2     G   2          H21       GUA   2  13.111   0.435  -4.118
   23   2H2     G   2          H22       GUA   2  13.109   0.065  -2.406
   24   1H5*    C   3          H5'       CYT   3   8.968   1.724  -8.611
   25   2H5*    C   3          H5''      CYT   3   7.555   0.819  -9.188
   26    H4*    C   3           H4'      CYT   3   9.118  -0.779  -8.479
   27    H3*    C   3           H3'      CYT   3   6.915  -0.463  -6.450
   28    H2*    C   3           H2'      CYT   3   7.972  -2.202  -5.153
   29   2HO*    C   3          HO2'      CYT   3   9.561  -2.520  -7.501
   30    H1*    C   3           H1'      CYT   3  10.573  -1.197  -5.491
   31   1H4     C   3          H41       CYT   3   7.948   2.640  -0.802
   32   2H4     C   3          H42       CYT   3   8.565   1.234   0.025
   33    H5     C   3           H5       CYT   3   7.903   2.791  -3.241
   34    H6     C   3           H6       CYT   3   8.479   1.651  -5.315
   35   1H5*    A   4          H5'       ADE   4   7.453  -4.360  -7.049
   36   2H5*    A   4          H5''      ADE   4   5.984  -5.245  -7.505
   37    H4*    A   4           H4'      ADE   4   6.958  -6.502  -5.800
   38    H3*    A   4           H3'      ADE   4   4.670  -4.887  -4.690
   39    H2*    A   4           H2'      ADE   4   5.089  -5.923  -2.555
   40   2HO*    A   4          HO2'      ADE   4   6.955  -7.557  -3.979
   41    H1*    A   4           H1'      ADE   4   7.887  -5.668  -2.713
   42    H8     A   4           H8       ADE   4   6.563  -2.494  -4.084
   43   1H6     A   4          H61       ADE   4   5.836  -0.082   0.066
   44   2H6     A   4          H62       ADE   4   5.825  -0.559   1.749
   45    H2     A   4           H2       ADE   4   6.644  -4.967   1.840
   46   1H5*    G   5          H5'       GUA   5   4.371  -8.515  -3.324
   47   2H5*    G   5          H5''      GUA   5   2.831  -9.347  -3.605
   48    H4*    G   5           H4'      GUA   5   3.283  -9.670  -1.346
   49    H3*    G   5           H3'      GUA   5   1.283  -7.433  -1.634
   50    H2*    G   5           H2'      GUA   5   1.196  -7.348   0.777
   51   2HO*    G   5          HO2'      GUA   5   2.659  -9.786   0.570
   52    H1*    G   5           H1'      GUA   5   3.984  -7.576   1.103
   53    H8     G   5           H8       GUA   5   3.573  -5.323  -1.784
   54    H1     G   5           H1       GUA   5   2.367  -2.427   3.812
   55   1H2     G   5          H21       GUA   5   2.305  -5.644   5.088
   56   2H2     G   5          H22       GUA   5   2.143  -3.927   5.409
   57   1H5*    G   6          H5'       GUA   6  -0.111  -9.949   1.135
   58   2H5*    G   6          H5''      GUA   6  -1.787 -10.470   0.877
   59    H4*    G   6           H4'      GUA   6  -1.669  -9.754   3.102
   60    H3*    G   6           H3'      GUA   6  -2.972  -7.616   1.417
   61    H2*    G   6           H2'      GUA   6  -3.317  -6.387   3.471
   62   2HO*    G   6          HO2'      GUA   6  -2.333  -8.752   4.741
   63    H1*    G   6           H1'      GUA   6  -0.728  -6.879   4.445
   64    H8     G   6           H8       GUA   6  -0.249  -6.301   0.836
   65    H1     G   6           H1       GUA   6  -1.333  -0.880   4.083
   66   1H2     G   6          H21       GUA   6  -2.292  -2.986   6.653
   67   2H2     G   6          H22       GUA   6  -2.076  -1.340   6.087
   68   1H5*    G   7          H5'       GUA   7  -5.111  -8.212   4.770
   69   2H5*    G   7          H5''      GUA   7  -6.834  -8.502   4.462
   70    H4*    G   7           H4'      GUA   7  -6.659  -6.882   6.185
   71    H3*    G   7           H3'      GUA   7  -7.594  -5.757   3.560
   72    H2*    G   7           H2'      GUA   7  -7.698  -3.575   4.553
   73   2HO*    G   7          HO2'      GUA   7  -7.511  -5.069   6.968
   74    H1*    G   7           H1'      GUA   7  -5.329  -3.832   6.073
   75    H8     G   7           H8       GUA   7  -4.481  -5.226   2.770
   76    H1     G   7           H1       GUA   7  -4.699   1.182   2.798
   77   1H2     G   7          H21       GUA   7  -6.336   0.790   5.821
   78   2H2     G   7          H22       GUA   7  -5.740   1.888   4.592
   79   1H5*    C   8          H5'       CYT   8  -9.763  -3.579   5.903
   80   2H5*    C   8          H5''      CYT   8 -11.419  -4.211   5.836
   81    H4*    C   8           H4'      CYT   8 -11.683  -1.918   5.689
   82    H3*    C   8           H3'      CYT   8 -11.993  -3.244   3.046
   83    H2*    C   8           H2'      CYT   8 -12.049  -1.160   1.869
   84   2HO*    C   8          HO2'      CYT   8 -12.996  -0.315   4.244
   85    H1*    C   8           H1'      CYT   8  -9.986   0.099   3.230
   86   1H4     C   8          H41       CYT   8  -6.804  -4.185  -0.628
   87   2H4     C   8          H42       CYT   8  -7.119  -2.797  -1.649
   88    H5     C   8           H5       CYT   8  -7.692  -4.382   1.621
   89    H6     C   8           H6       CYT   8  -9.081  -3.315   3.310
   90   1H5*    U   9          H5'       URI   9 -14.556  -0.988   2.581
   91   2H5*    U   9          H5''      URI   9 -16.291  -1.363   2.589
   92    H4*    U   9           H4'      URI   9 -16.014  -0.313   0.562
   93    H3*    U   9           H3'      URI   9 -15.911  -3.282   0.128
   94    H2*    U   9           H2'      URI   9 -15.458  -2.931  -2.196
   95   2HO*    U   9          HO2'      URI   9 -16.986  -0.847  -1.831
   96    H1*    U   9           H1'      URI   9 -13.757  -0.691  -1.837
   97    H3     U   9           H3       URI   9 -11.288  -4.092  -3.636
   98    H5     U   9           H5       URI   9 -11.216  -4.681   0.517
   99    H6     U   9           H6       URI   9 -12.916  -2.989   0.712
  100   1H5*    C  10          H5'       CYT  10 -18.085  -6.069  -1.112
  101   2H5*    C  10          H5''      CYT  10 -16.424  -5.446  -1.126
  102    H4*    C  10           H4'      CYT  10 -16.901  -7.037  -2.935
  103    H3*    C  10           H3'      CYT  10 -15.389  -4.772  -3.201
  104    H2*    C  10           H2'      CYT  10 -16.822  -3.402  -4.482
  105   2HO*    C  10          HO2'      CYT  10 -15.537  -5.216  -6.100
  106    H1*    C  10           H1'      CYT  10 -18.264  -5.726  -5.788
  107   1H4     C  10          H41       CYT  10 -22.406  -0.699  -4.708
  108   2H4     C  10          H42       CYT  10 -22.709  -1.282  -6.330
  109    H5     C  10           H5       CYT  10 -20.684  -1.594  -3.283
  110    H6     C  10           H6       CYT  10 -18.922  -3.266  -3.099
  111   1H5*    A  11          H5'       ADE  11 -12.915  -6.328  -6.707
  112   2H5*    A  11          H5''      ADE  11 -11.340  -5.949  -5.980
  113    H4*    A  11           H4'      ADE  11 -11.626  -4.540  -7.862
  114    H3*    A  11           H3'      ADE  11 -11.972  -3.031  -5.274
  115    H2*    A  11           H2'      ADE  11 -12.273  -1.037  -6.576
  116   2HO*    A  11          HO2'      ADE  11 -11.219  -0.850  -8.401
  117    H1*    A  11           H1'      ADE  11 -13.765  -2.324  -8.636
  118    H8     A  11           H8       ADE  11 -14.689  -2.965  -4.960
  119   1H6     A  11          H61       ADE  11 -18.295   0.281  -4.687
  120   2H6     A  11          H62       ADE  11 -18.905   1.495  -5.793
  121    H2     A  11           H2       ADE  11 -16.373   1.271  -9.481
  122   1H5*    U  12          H5'       URI  12  -9.383  -1.337  -8.140
  123   2H5*    U  12          H5''      URI  12  -7.994  -0.462  -7.467
  124    H4*    U  12           H4'      URI  12  -9.301   0.812  -9.139
  125    H3*    U  12           H3'      URI  12  -8.433   1.836  -6.588
  126    H2*    U  12           H2'      URI  12 -10.421   2.920  -5.981
  127   2HO*    U  12          HO2'      URI  12  -9.329   4.296  -7.962
  128    H1*    U  12           H1'      URI  12 -11.690   2.555  -8.715
  129    H3     U  12           H3       URI  12 -15.678   3.317  -6.872
  130    H5     U  12           H5       URI  12 -13.757   0.966  -3.972
  131    H6     U  12           H6       URI  12 -11.799   0.974  -5.377
  132   1H5*    A  13          H5'       ADE  13  -6.414   5.265  -8.810
  133   2H5*    A  13          H5''      ADE  13  -4.760   5.061  -8.202
  134    H4*    A  13           H4'      ADE  13  -5.612   7.106  -7.366
  135    H3*    A  13           H3'      ADE  13  -5.398   4.990  -5.242
  136    H2*    A  13           H2'      ADE  13  -6.151   6.666  -3.644
  137   2HO*    A  13          HO2'      ADE  13  -5.399   8.599  -4.285
  138    H1*    A  13           H1'      ADE  13  -8.349   7.369  -5.138
  139    H8     A  13           H8       ADE  13  -7.651   3.828  -6.050
  140   1H6     A  13          H61       ADE  13 -10.015   1.591  -2.431
  141   2H6     A  13          H62       ADE  13 -10.718   2.157  -0.930
  142    H2     A  13           H2       ADE  13 -10.019   6.584  -0.763
  143   1H5*    A  14          H5'       ADE  14  -3.456   8.517  -3.979
  144   2H5*    A  14          H5''      ADE  14  -2.449   8.324  -2.532
  145    H4*    A  14           H4'      ADE  14  -4.649   9.678  -2.409
  146    H3*    A  14           H3'      ADE  14  -3.755   7.708  -0.313
  147    H2*    A  14           H2'      ADE  14  -5.748   8.248   0.928
  148   2HO*    A  14          HO2'      ADE  14  -5.515  10.551  -0.337
  149    H1*    A  14           H1'      ADE  14  -7.444   8.078  -1.287
  150    H8     A  14           H8       ADE  14  -5.493   5.342  -2.342
  151   1H6     A  14          H61       ADE  14  -6.825   1.845   0.752
  152   2H6     A  14          H62       ADE  14  -7.661   1.857   2.289
  153    H2     A  14           H2       ADE  14  -8.545   6.146   3.248
  154   1H5*    C  15          H5'       CYT  15  -4.158   9.824   2.148
  155   2H5*    C  15          H5''      CYT  15  -2.815  10.256   3.222
  156    H4*    C  15           H4'      CYT  15  -4.282   9.038   4.553
  157    H3*    C  15           H3'      CYT  15  -2.049   7.217   3.658
  158    H2*    C  15           H2'      CYT  15  -3.059   5.511   5.034
  159   2HO*    C  15          HO2'      CYT  15  -4.183   6.092   6.737
  160    H1*    C  15           H1'      CYT  15  -5.667   6.069   4.147
  161   1H4     C  15          H41       CYT  15  -3.014   2.491  -0.696
  162   2H4     C  15          H42       CYT  15  -3.586   1.320   0.475
  163    H5     C  15           H5       CYT  15  -3.030   4.869  -0.279
  164    H6     C  15           H6       CYT  15  -3.614   6.613   1.332
  165   1H5*    C  16          H5'       CYT  16  -2.536   6.835   7.553
  166   2H5*    C  16          H5''      CYT  16  -1.103   7.176   8.542
  167    H4*    C  16           H4'      CYT  16  -1.942   5.227   9.452
  168    H3*    C  16           H3'      CYT  16   0.294   4.542   7.561
  169    H2*    C  16           H2'      CYT  16  -0.046   2.217   8.082
  170   2HO*    C  16          HO2'      CYT  16  -0.760   1.720  10.018
  171    H1*    C  16           H1'      CYT  16  -2.835   2.330   7.935
  172   1H4     C  16          H41       CYT  16  -0.899   2.199   1.641
  173   2H4     C  16          H42       CYT  16  -0.943   0.520   2.127
  174    H5     C  16           H5       CYT  16  -1.231   4.027   3.180
  175    H6     C  16           H6       CYT  16  -1.682   4.622   5.499
  176   1H5*    C  17          H5'       CYT  17   0.947   2.447  10.861
  177   2H5*    C  17          H5''      CYT  17   2.569   2.615  11.560
  178    H4*    C  17           H4'      CYT  17   2.200   0.319  11.408
  179    H3*    C  17           H3'      CYT  17   3.946   1.193   9.110
  180    H2*    C  17           H2'      CYT  17   4.073  -1.128   8.469
  181   2HO*    C  17          HO2'      CYT  17   3.844  -2.642   9.942
  182    H1*    C  17           H1'      CYT  17   1.336  -1.603   8.817
  183   1H4     C  17          H41       CYT  17   1.840   1.550   3.041
  184   2H4     C  17          H42       CYT  17   2.170  -0.133   2.680
  185    H5     C  17           H5       CYT  17   1.543   2.358   5.310
  186    H6     C  17           H6       CYT  17   1.545   1.729   7.663
  187   1H5*    U  18          H5'       URI  18   5.454  -2.020  10.766
  188   2H5*    U  18          H5''      URI  18   7.115  -1.873  11.373
  189    H4*    U  18           H4'      URI  18   7.105  -3.899  10.256
  190    H3*    U  18           H3'      URI  18   8.281  -1.794   8.458
  191    H2*    U  18           H2'      URI  18   8.600  -3.495   6.781
  192   2HO*    U  18          HO2'      URI  18   8.926  -5.493   7.419
  193    H1*    U  18           H1'      URI  18   6.071  -4.650   7.111
  194    H3     U  18           H3       URI  18   6.080  -2.410   3.124
  195    H5     U  18           H5       URI  18   5.035   0.435   6.034
  196    H6     U  18           H6       URI  18   5.595  -1.188   7.712
  197   1H5*    G  19          H5'       GUA  19  10.569  -4.899   8.253
  198   2H5*    G  19          H5''      GUA  19  12.287  -4.679   8.639
  199    H4*    G  19           H4'      GUA  19  12.300  -5.838   6.633
  200    H3*    G  19           H3'      GUA  19  12.718  -2.912   6.043
  201    H2*    G  19           H2'      GUA  19  12.961  -3.530   3.721
  202   2HO*    G  19          HO2'      GUA  19  13.700  -5.464   3.250
  203    H1*    G  19           H1'      GUA  19  10.769  -5.280   3.736
  204    H8     G  19           H8       GUA  19   9.683  -2.439   5.825
  205    H1     G  19           H1       GUA  19   9.613  -1.079  -0.441
  206   1H2     G  19          H21       GUA  19  11.498  -3.962  -0.762
  207   2H2     G  19          H22       GUA  19  10.743  -2.592  -1.553
  208   1H5*    C  20          H5'       CYT  20  15.419  -4.952   3.953
  209   2H5*    C  20          H5''      CYT  20  17.087  -4.416   4.236
  210    H4*    C  20           H4'      CYT  20  16.861  -4.528   1.918
  211    H3*    C  20           H3'      CYT  20  16.643  -1.667   2.832
  212    H2*    C  20           H2'      CYT  20  16.427  -1.030   0.520
  213   2HO*    C  20          HO2'      CYT  20  17.337  -2.231  -0.971
  214    H1*    C  20           H1'      CYT  20  14.627  -3.080  -0.122
  215   1H4     C  20          H41       CYT  20  10.939   1.447   2.958
  216   2H4     C  20          H42       CYT  20  11.024   1.973   1.297
  217    H5     C  20           H5       CYT  20  12.253  -0.420   3.798
  218    H6     C  20           H6       CYT  20  13.850  -2.160   3.202
  219   1H5*    C  21          H5'       CYT  21  19.195  -1.812  -0.326
  220   2H5*    C  21          H5''      CYT  21  20.743  -1.014   0.015
  221    H4*    C  21           H4'      CYT  21  20.003  -0.215  -2.074
  222    H3*    C  21           H3'      CYT  21  19.660   1.822   0.109
  223    H2*    C  21           H2'      CYT  21  18.748   3.350  -1.503
  224   2HO*    C  21          HO2'      CYT  21  19.314   3.209  -3.562
  225    H1*    C  21           H1'      CYT  21  17.171   1.428  -2.828
  226   1H4     C  21          H41       CYT  21  13.699   3.055   2.540
  227   2H4     C  21          H42       CYT  21  13.285   4.263   1.346
  228    H5     C  21           H5       CYT  21  15.409   1.385   2.168
  229    H6     C  21           H6       CYT  21  17.082   0.555   0.601
  230    H3T    C  21           H3T      CYT  21  21.297   1.922  -2.139