NMR Restraints Grid
| |
NMR Restraints Grid |
|
Result table
| image | mrblock_id | pdb_id | cing | stage | position | program | type |
|
|
12445 |
1szy   |
cing | 1-original | 2 | XPLOR/CNS | molecular system |
!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
Contact the webmaster for help, if required. Thursday, April 18, 2024 1:34:21 PM GMT (wattos1)