HEADER    RNA                                     10-APR-00   1ESH              
TITLE     THE SOLUTION STRUCTURE OF THE STEM LOOP C 5'AUA3' TRILOOP             
TITLE    2 OF BROME MOSAIC VIRUS (+) STRAND RNA                                 
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: RNA (5'-R(*GP*GP*UP*GP*CP*AP*UP*AP*GP*CP*AP*CP*C)          
COMPND   3 -3');                                                                
COMPND   4 CHAIN: A;                                                            
COMPND   5 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 OTHER_DETAILS: SEQUENCE OCCURS NATURALLY IN BROME MOSAIC             
SOURCE   4 VIRUS EXCEPT FOR THE TERMINAL TWO GC BPS                             
KEYWDS    RNA, TRILOOP, STEM-LOOP, BROME MOSAIC VIRUS                           
EXPDTA    NMR                                                                   
AUTHOR    C.-H.KIM, C.C.KAO, I.TINOCO JR.                                       
REVDAT   1   24-APR-00 1ESH    0                                                


slc13.noe{slc13.noe for refinement and minimization}

{BASE PAIRING - based on standard H-bond distances}

 {base pair G1-C13}
assign (residue 13 and name h41)(residue 1 and name o6) 1.7 .1 .1
assign (residue 13 and name n3)(residue 1 and name h21) 3.0 .1 .1
assign (residue 13 and name o2)(residue 1 and name h21) 2.0 .1 .1
assign (residue 13 and name n3)(residue 1 and name h1) 1.9 .1 .1

 {base pair G2-C12}
assign (residue 12 and name h41)(residue 2 and name o6) 1.7 .1 .1
assign (residue 12 and name n3)(residue 2 and name h21) 3.0 .1 .1
assign (residue 12 and name o2)(residue 2 and name h21) 2.0 .1 .1
assign (residue 12 and name n3)(residue 2 and name h1) 1.9 .1 .1
 
      {base pairing U3-A11}
assign (residue 11 and name h2)(residue 3 and name o2) 3.2 .1 .1  
assign (residue 11 and name n1)(residue 3 and name h3) 1.9 .1 .1  
assign (residue 11 and name h61)(residue 3 and name o4) 1.8 .1 .1 
assign (residue 11 and name h2)(residue 3 and name h3) 2.9 .1 .1  
 
        {base pair G4-C10}
assign (residue 10 and name h41)(residue 4 and name o6) 1.7 .1 .1
assign (residue 10 and name n3)(residue 4 and name h21) 3.0 .1 .1
assign (residue 10 and name o2)(residue 4 and name h21) 2.0 .1 .1
assign (residue 10 and name n3)(residue 4 and name h1) 1.9 .1 .1 

  {base pair C5-G9}
assign (residue 5 and name h41)(residue 9 and name o6) 1.7 .1 .1
assign (residue 5 and name n3)(residue 9 and name h21) 3.0 .1 .1
assign (residue 5 and name o2)(residue 9 and name h21) 2.0 .1 .1
assign (residue 5 and name n3)(residue 9 and name h1) 1.9 .1 .1 

        
{DISTANCE RESTRICTIONS FOR EXCHANGEABLE PROTONS FROM THE H2O NOESY}

{from 200ms H2O NOESY at 20c and 300ms H2O NOESY at 10c}
  
{imino proton to imino proton}
assign (residue 2 and name h1)(residue 3 and name h3) 1.8 0 3.2
assign (residue 3 and name h3)(residue 4 and name h1) 1.8 0 3.2
assign (residue 4 and name h1)(residue 9 and name h1) 1.8 0 3.2


  {imino proton to amino proton A h2 proton aromatic proton, or}
assign (residue 2 and name h1)(residue 12 and name h41) 1.8 0 3.2
assign (residue 2 and name h1)(residue 12 and name h42) 1.8 0 3.2
assign (residue 3 and name h3)(residue 11 and name h2) 1.8 0 3.2
assign (residue 4 and name h1)(residue 10 and name h41) 1.8 0 3.2
assign (residue 4 and name h1)(residue 10 and name h42) 1.8 0 3.2
assign (residue 9 and name h1)(residue 5 and name h41) 1.8 0 3.2 
assign (residue 9 and name h1)(residue 5 and name h42) 1.8 0 3.2
assign (residue 9 and name h1)(residue 6 and name h1') 1.8 0 3.2
assign (residue 9 and name h1)(residue 8 and name h2) 1.8 0 3.2


{Distance restriction for nonexchangeable protons from D2O NOESY}
 
{G1}
assign (residue 1 and name h1')(residue 1 and name h2'') 1.8 0 1.4
assign (residue 1 and name h8)(residue 1 and name h1') 2.5 0 2.5
assign (residue 1 and name h8)(residue 1 and name h2'') 2.0 0 2.0
assign (residue 1 and name h8)(residue 1 and name h3') 2.5 0 2.5
assign (residue 1 and name h8)(residue 2 and name h8) 3.0 0 4.0
assign (residue 1 and name h8)(residue 1 and name h4') 2.5 0 2.5

{G2}
assign (residue 2 and name h1')(residue 2 and name h2'') 1.8 0 1.4
assign (residue 2 and name h1')(residue 3 and name h5) 3.0 0 4.0
assign (residue 2 and name h8)(residue 1 and name h1') 2.5 0 2.5
assign (residue 2 and name h8)(residue 2 and name h1') 2.5 0 2.5
assign (residue 2 and name h8)(residue 1 and name h2'') 1.8 0 1.4
assign (residue 2 and name h8)(residue 1 and name h3') 3.0 0 4.0
assign (residue 2 and name h8)(residue 2 and name h3') 2.0 0 2.0
assign (residue 2 and name h8)(residue 3 and name h6) 3.0 0 4.0
assign (residue 2 and name h8)(residue 3 and name h5) 3.0 0 4.0
assign (residue 2 and name h8)(residue 2 and name h4') 3.0 0 4.0


{U3}
assign (residue 3 and name h1')(residue 3 and name h2'') 1.8 0 1.4
assign (residue 3 and name h6)(residue 2 and name h1') 2.5 0 2.5
assign (residue 3 and name h6)(residue 3 and name h1') 2.5 0 2.5
assign (residue 3 and name h6)(residue 2 and name h2'') 1.8 0 1.4
assign (residue 3 and name h6)(residue 3 and name h2'') 2.0 0 2.0
assign (residue 3 and name h6)(residue 3 and name h5) 1.8 0 1.4
assign (residue 3 and name h6)(residue 4 and name h8) 3.0 0 4.0
assign (residue 3 and name h6)(residue 3 and name h3') 2.0 0 2.0





{G4}
assign (residue 4 and name h1')(residue 4 and name h2'') 1.8 0 1.4
assign (residue 4 and name h8)(residue 4 and name h1') 2.5 0 2.5
assign (residue 4 and name h8)(residue 3 and name h1') 2.5 0 2.5
assign (residue 4 and name h8)(residue 3 and name h2'') 1.8 0 1.4
assign (residue 4 and name h8)(residue 3 and name h3') 2.5 0 2.5
assign (residue 4 and name h8)(residue 4 and name h2'') 2.5 0 2.5
assign (residue 4 and name h8)(residue 4 and name h3') 2.0 0 2.0
assign (residue 4 and name h8)(residue 5 and name h6) 3.0 0 4.0


{C5}
assign (residue 5 and name h1')(residue 5 and name h2'') 1.8 0 1.4
assign (residue 5 and name h1')(residue 4 and name h2'') 3.0 0 4.0
assign (residue 5 and name h1')(residue 5 and name h5) 3.0 0 4.0
assign (residue 5 and name h5)(residue 4 and name h2'') 2.5 0 2.5
assign (residue 5 and name h5)(residue 4 and name h3') 2.5 0 2.5
assign (residue 5 and name h5)(residue 5 and name h6) 1.8 0 1.4
assign (residue 5 and name h6)(residue 4 and name h2'') 1.8 0 1.4
assign (residue 5 and name h6)(residue 5 and name h2'') 2.0 0 2.0
assign (residue 5 and name h6)(residue 4 and name h1') 2.5 0 2.5
assign (residue 5 and name h6)(residue 4 and name h3') 2.5 0 2.5
assign (residue 5 and name h6)(residue 5 and name h3') 2.0 0 2.0
assign (residue 5 and name h6)(residue 5 and name h1') 2.5 0 2.5
assign (residue 5 and name h6)(residue 6 and name h8) 3.0 0 4.0
assign (residue 5 and name h6)(residue 5 and name h4') 3.0 0 4.0
assign (residue 5 and name h6)(residue 5 and name h5') 3.0 0 4.0


{A6}
assign (residue 6 and name h1')(residue 5 and name h5') 3.0 0 4.0
assign (residue 6 and name h1')(residue 6 and name h2'') 1.8 0 1.4
assign (residue 6 and name h1')(residue 6 and name h5') 3.0 0 4.0
assign (residue 6 and name h1')(residue 7 and name h4') 3.0 0 4.0
assign (residue 6 and name h1')(residue 7 and name h2'') 3.0 0 4.0
assign (residue 6 and name h8)(residue 5 and name h2'') 2.5 0 2.5
assign (residue 6 and name h8)(residue 6 and name h2'') 2.5 0 2.5
assign (residue 6 and name h8)(residue 6 and name h1') 2.5 0 2.5
assign (residue 6 and name h8)(residue 5 and name h1') 2.5 0 2.5
assign (residue 6 and name h8)(residue 5 and name h4') 3.0 0 4.0
assign (residue 6 and name h8)(residue 5 and name h3') 2.0 0 2.0
assign (residue 6 and name h8)(residue 6 and name h3') 2.5 0 2.5
assign (residue 6 and name h8)(residue 6 and name h4') 2.5 0 2.5
assign (residue 6 and name h8)(residue 6 and name h5') 3.0 0 4.0
assign (residue 6 and name h8)(residue 5 and name h5') 3.0 0 4.0
assign (residue 6 and name h2)(residue 6 and name h1') 3.0 0 4.0
assign (residue 6 and name h2)(residue 6 and name h2'') 3.0 0 4.0


{U7}
assign (residue 7 and name h1')(residue 7 and name h2'') 1.8 0 1.4
assign (residue 7 and name h1')(residue 7 and name h3') 2.5 0 2.5
assign (residue 7 and name h1')(residue 7 and name h4') 2.5 0 2.5
assign (residue 7 and name h6)(residue 7 and name h5) 1.8 0 1.4
assign (residue 7 and name h6)(residue 7 and name h2'') 1.8 0 1.4
assign (residue 7 and name h6)(residue 7 and name h1') 2.5 0 2.5
assign (residue 7 and name h6)(residue 6 and name h1') 2.5 0 2.5
assign (residue 7 and name h5)(residue 6 and name h1') 2.5 0 2.5
assign (residue 7 and name h5)(residue 6 and name h4') 2.5 0 2.5
assign (residue 7 and name h5)(residue 7 and name h2'') 2.5 0 2.5
assign (residue 7 and name h6)(residue 7 and name h3') 2.0 0 2.0
assign (residue 7 and name h6)(residue 6 and name h2'') 3.0 0 4.0
assign (residue 7 and name h6)(residue 6 and name h3') 3.0 0 4.0
assign (residue 7 and name h6)(residue 6 and name h4') 3.0 0 4.0
assign (residue 7 and name h6)(residue 7 and name h4') 2.5 0 2.5
assign (residue 7 and name h6)(residue 7 and name h5') 3.0 0 4.0



{A8}
assign (residue 8 and name h1')(residue 8 and name h2'') 1.8 0 1.4
assign (residue 8 and name h1')(residue 7 and name h4') 3.0 0 4.0
assign (residue 8 and name h8)(residue 7 and name h1') 3.0 0 4.0
assign (residue 8 and name h8)(residue 7 and name h2'') 3.0 0 4.0
assign (residue 8 and name h8)(residue 8 and name h1') 2.0 0 2.0
assign (residue 8 and name h8)(residue 8 and name h2'') 2.0 0 2.0
assign (residue 8 and name h8)(residue 8 and name h3') 2.5 0 2.5
assign (residue 8 and name h8)(residue 7 and name h4') 2.5 0 2.5
assign (residue 8 and name h8)(residue 9 and name h1') 3.0 0 4.0
assign (residue 8 and name h8)(residue 8 and name h4') 3.0 0 4.0
assign (residue 8 and name h8)(residue 8 and name h5') 3.0 0 4.0
assign (residue 8 and name h2)(residue 6 and name h1') 3.0 0 4.0
assign (residue 8 and name h2)(residue 8 and name h1') 2.5 0 2.5
assign (residue 8 and name h2)(residue 8 and name h3') 3.0 0 4.0
assign (residue 8 and name h2)(residue 5 and name h2'') 2.5 0 2.5
assign (residue 8 and name h2)(residue 5 and name h1') 2.5 0 2.5
assign (residue 8 and name h2)(residue 7 and name h1') 2.5 0 2.5
assign (residue 8 and name h2)(residue 7 and name h4') 2.5 0 2.5
assign (residue 8 and name h2)(residue 7 and name h5') 2.5 0 2.5
assign (residue 8 and name h2)(residue 6 and name h2'') 3.0 0 4.0




{G9}
assign (residue 9 and name h1')(residue 9 and name h2'') 1.8 0 1.4
assign (residue 9 and name h1')(residue 8 and name h2'') 3.0 0 4.0
assign (residue 9 and name h8)(residue 9 and name h1') 2.5 0 2.5
assign (residue 9 and name h8)(residue 9 and name h2'') 1.8 0 1.4
assign (residue 9 and name h8)(residue 9 and name h3') 2.5 0 2.5
assign (residue 9 and name h8)(residue 9 and name h4') 3.0 0 4.0
assign (residue 9 and name h8)(residue 10 and name h5) 3.0 0 4.0
assign (residue 9 and name h8)(residue 10 and name h6) 3.0 0 4.0
assign (residue 9 and name h8)(residue 8 and name h5') 3.0 0 4.0
assign (residue 9 and name h8)(residue 8 and name h5'') 3.0 0 4.0
assign (residue 9 and name h8)(residue 9 and name h5') 3.0 0 4.0



{C10}
assign (residue 10 and name h1')(residue 10 and name h2'') 1.8 0 1.4
assign (residue 10 and name h1')(residue 10 and name h5) 3.0 0 4.0
assign (residue 10 and name h5)(residue 9 and name h2'') 3.0 0 4.0
assign (residue 10 and name h5)(residue 11 and name h2'') 3.0 0 4.0
assign (residue 10 and name h6)(residue 10 and name h5) 1.8 0 1.4
assign (residue 10 and name h6)(residue 9 and name h1') 1.8 0 1.4
assign (residue 10 and name h6)(residue 9 and name h2'') 3.0 0 4.0
assign (residue 10 and name h6)(residue 9 and name h4') 3.0 0 4.0
assign (residue 10 and name h6)(residue 10 and name h1') 2.5 0 2.5
assign (residue 10 and name h6)(residue 10 and name h2'') 2.5 0 2.5


{A11}
assign (residue 11 and name h1')(residue 11 and name h2'') 1.8 0 1.4
assign (residue 11 and name h1')(residue 12 and name h5) 3.0 0 4.0
assign (residue 11 and name h8)(residue 11 and name h1') 2.5 0 2.5
assign (residue 11 and name h8)(residue 11 and name h2'') 2.5 0 2.5
assign (residue 11 and name h8)(residue 11 and name h3') 2.5 0 2.5
assign (residue 11 and name h8)(residue 11 and name h4') 3.0 0 4.0
assign (residue 11 and name h8)(residue 10 and name h1') 2.5 0 2.5
assign (residue 11 and name h8)(residue 10 and name h2'') 1.8 0 1.4
assign (residue 11 and name h8)(residue 10 and name h6) 3.0 0 4.0
assign (residue 11 and name h2)(residue 4 and name h1') 2.5 0 2.5
assign (residue 11 and name h2)(residue 12 and name h1') 2.5 0 2.5
assign (residue 11 and name h2)(residue 11 and name h1') 3.0 0 4.0


{C12}
assign (residue 12 and name h1')(residue 12 and name h2'') 1.8 0 1.4
assign (residue 12 and name h6)(residue 12 and name h5) 1.8 0 1.4
assign (residue 12 and name h6)(residue 11 and name h8) 3.0 0 4.0
assign (residue 12 and name h6)(residue 11 and name h1') 2.5 0 2.5
assign (residue 12 and name h6)(residue 11 and name h2'') 1.8 0 1.4
assign (residue 12 and name h6)(residue 12 and name h1') 2.5 0 2.5
assign (residue 12 and name h6)(residue 12 and name h2') 2.5 0 2.5
assign (residue 12 and name h6)(residue 12 and name h3') 2.0 0 2.0
assign (residue 12 and name h6)(residue 12 and name h4') 3.0 0 4.0


{C13}
assign (residue 13 and name h6)(residue 13 and name h5) 1.8 0 1.4
assign (residue 13 and name h6)(residue 12 and name h6) 3.0 0 4.0
assign (residue 13 and name h1')(residue 13 and name h2'') 1.8 0 1.4
assign (residue 13 and name h6)(residue 12 and name h2'') 1.8 0 1.4
assign (residue 13 and name h6)(residue 12 and name h1') 2.5 0 2.5
assign (residue 13 and name h6)(residue 13 and name h1') 2.5 0 2.5
assign (residue 13 and name h6)(residue 13 and name h2'') 2.0 0 2.0
assign (residue 13 and name h6)(residue 13 and name h3') 2.0 0 2.0
assign (residue 13 and name h6)(residue 12 and name h3') 2.5 0 2.5
assign (residue 13 and name h6)(residue 13 and name h4') 3.0 0 4.0

slc13.dihed {Torsion angle constraints of slc-13 RNA}

{used for refinement and minimization }

constraints
dihedral
reset

{Keep G amino groups in the plane of the base}
assign (residue 1 and name h22)(residue 1 and name n2)
    (residue 1 and name c2)(residue 1 and name n3) 10 0 5 2
assign (residue 2 and name h22)(residue 2 and name n2)
    (residue 2 and name c2)(residue 2 and name n3) 10 0 5 2
assign (residue 4 and name h22)(residue 4 and name n2)
    (residue 4 and name c2)(residue 4 and name n3) 10 0 5 2
assign (residue 9 and name h22)(residue 9 and name n2)
    (residue 9 and name c2)(residue 9 and name n3) 10 0 5 2


{Keep C amino groups in the plane of the base}

assign (residue 5 and name h42)(residue 5 and name n4)
    (residue 5 and name c4)(residue 5 and name c5) 10 0 5 2
assign (residue 10 and name h42)(residue 10 and name n4)
    (residue 10 and name c4)(residue 10 and name c5) 10 0 5 2
assign (residue 12 and name h42)(residue 12 and name n4)
    (residue 12 and name c4)(residue 12 and name c5) 10 0 5 2
assign (residue 13 and name h42)(residue 13 and name n4)
    (residue 13 and name c4)(residue 13 and name c5) 10 0 5 2

{Keep A amino groups in the plane of the base}
assign (residue 6 and name h62)(residue 6 and name n6)
    (residue 6 and name c6)(residue 6 and name c5) 10 0 5 2
assign (residue 8 and name h62)(residue 8 and name n6)
    (residue 8 and name c6)(residue 8 and name c5) 10 0 5 2
assign (residue 11 and name h62)(residue 11 and name n6)
    (residue 11 and name c6)(residue 11 and name c5) 10 0 5 2

{Make some nucleotides c3'-endo, restrain v0, v1,v2, and v3 instead of delta}

assign (residue 2 and name c4')(residue 2 and name o4')
    (residue 2 and name c1')(residue 2 and name c2') 2 0 5 2
assign (residue 2 and name o4')(residue 2 and name c1')
    (residue 2 and name c2')(residue 2 and name c3') 2 -22 5 2
assign (residue 2 and name c1')(residue 2 and name c2')
    (residue 2 and name c3')(residue 2 and name c4') 2 36 5 2 
assign (residue 2 and name c2')(residue 2 and name c3')
    (residue 2 and name c4')(residue 2 and name o4') 2 -36 5 2 

assign (residue 3 and name c4')(residue 3 and name o4')
    (residue 3 and name c1')(residue 3 and name c2') 2 0 5 2
assign (residue 3 and name o4')(residue 3 and name c1')
    (residue 3 and name c2')(residue 3 and name c3') 2 -22 5 2
assign (residue 3 and name c1')(residue 3 and name c2')
    (residue 3 and name c3')(residue 3 and name c4') 2 36 5 2 
assign (residue 3 and name c2')(residue 3 and name c3')
    (residue 3 and name c4')(residue 3 and name o4') 2 -36 5 2 

assign (residue 4 and name c4')(residue 4 and name o4')
    (residue 4 and name c1')(residue 4 and name c2') 2 0 5 2
assign (residue 4 and name o4')(residue 4 and name c1')
    (residue 4 and name c2')(residue 4 and name c3') 2 -22 5 2
assign (residue 4 and name c1')(residue 4 and name c2')
    (residue 4 and name c3')(residue 4 and name c4') 2 36 5 2 
assign (residue 4 and name c2')(residue 4 and name c3')
    (residue 4 and name c4')(residue 4 and name o4') 2 -36 5 2 


assign (residue 10 and name c4')(residue 10 and name o4')
    (residue 10 and name c1')(residue 10 and name c2') 2 0 5 2
assign (residue 10 and name o4')(residue 10 and name c1')
    (residue 10 and name c2')(residue 10 and name c3') 2 -22 5 2
assign (residue 10 and name c1')(residue 10 and name c2')
    (residue 10 and name c3')(residue 10 and name c4') 2 36 5 2 
assign (residue 10 and name c2')(residue 10 and name c3')
    (residue 10 and name c4')(residue 10 and name o4') 2 -36 5 2

assign (residue 11 and name c4')(residue 11 and name o4')
    (residue 11 and name c1')(residue 11 and name c2') 2 0 5 2
assign (residue 11 and name o4')(residue 11 and name c1')
    (residue 11 and name c2')(residue 11 and name c3') 2 -22 5 2
assign (residue 11 and name c1')(residue 11 and name c2')
    (residue 11 and name c3')(residue 11 and name c4') 2 36 5 2 
assign (residue 11 and name c2')(residue 11 and name c3')
    (residue 11 and name c4')(residue 11 and name o4') 2 -36 5 2

assign (residue 12 and name c4')(residue 12 and name o4')
    (residue 12 and name c1')(residue 12 and name c2') 2 0 5 2
assign (residue 12 and name o4')(residue 12 and name c1')
    (residue 12 and name c2')(residue 12 and name c3') 2 -22 5 2
assign (residue 12 and name c1')(residue 12 and name c2')
    (residue 12 and name c3')(residue 12 and name c4') 2 36 5 2 
assign (residue 12 and name c2')(residue 12 and name c3')
    (residue 12 and name c4')(residue 12 and name o4') 2 -36 5 2




{Sugar puckering between  2'-endo and 3'-endo}

assign (residue 1 and name c4')(residue 1 and name o4')
    (residue 1 and name c1')(residue 1 and name c2') 2 -20 20 2
assign (residue 1 and name o4')(residue 1 and name c1')
    (residue 1 and name c2')(residue 1 and name c3') 2 15 25 2
assign (residue 1 and name c1')(residue 1 and name c2')
    (residue 1 and name c3')(residue 1 and name c4') 2 0 35 2 
assign (residue 1 and name c2')(residue 1 and name c3')
    (residue 1 and name c4')(residue 1 and name o4') 2 0 40 2 

assign (residue 5 and name c4')(residue 5 and name o4')
    (residue 5 and name c1')(residue 5 and name c2') 2 -20 20 2
assign (residue 5 and name o4')(residue 5 and name c1')
    (residue 5 and name c2')(residue 5 and name c3') 2 15 25 2
assign (residue 5 and name c1')(residue 5 and name c2')
    (residue 5 and name c3')(residue 5 and name c4') 2 0 35 2 
assign (residue 5 and name c2')(residue 5 and name c3')
    (residue 5 and name c4')(residue 5 and name o4') 2 0 40 2

assign (residue 8 and name c4')(residue 8 and name o4')
    (residue 8 and name c1')(residue 8 and name c2') 2 -20 20 2
assign (residue 8 and name o4')(residue 8 and name c1')
    (residue 8 and name c2')(residue 8 and name c3') 2 15 25 2
assign (residue 8 and name c1')(residue 8 and name c2')
    (residue 8 and name c3')(residue 8 and name c4') 2 0 35 2 
assign (residue 8 and name c2')(residue 8 and name c3')
    (residue 8 and name c4')(residue 8 and name o4') 2 0 40 2

assign (residue 13 and name c4')(residue 13 and name o4')
    (residue 13 and name c1')(residue 13 and name c2') 2 -20 20 2
assign (residue 13 and name o4')(residue 13 and name c1')
    (residue 13 and name c2')(residue 13 and name c3') 2 15 25 2
assign (residue 13 and name c1')(residue 13 and name c2')
    (residue 13 and name c3')(residue 13 and name c4') 2 0 35 2 
assign (residue 13 and name c2')(residue 13 and name c3')
    (residue 13 and name c4')(residue 13 and name o4') 2 0 40 2

 
{sugar puckering of 2'-endo}


assign (residue 6 and name c4')(residue 6 and name o4')
    (residue 6 and name c1')(residue 6 and name c2') 2 -18 5 2
assign (residue 6 and name o4')(residue 6 and name c1')
    (residue 6 and name c2')(residue 6 and name c3') 2 34 5 2
assign (residue 6 and name c1')(residue 6 and name c2')
    (residue 6 and name c3')(residue 6 and name c4') 2 -37 5 2 
assign (residue 6 and name c2')(residue 6 and name c3')
    (residue 6 and name c4')(residue 6 and name o4') 2 26 5 2 

assign (residue 7 and name c4')(residue 7 and name o4')
    (residue 7 and name c1')(residue 7 and name c2') 2 -18 5 2
assign (residue 7 and name o4')(residue 7 and name c1')
    (residue 7 and name c2')(residue 7 and name c3') 2 34 5 2
assign (residue 7 and name c1')(residue 7 and name c2')
    (residue 7 and name c3')(residue 7 and name c4') 2 -37 5 2 
assign (residue 7 and name c2')(residue 7 and name c3')
    (residue 7 and name c4')(residue 7 and name o4') 2 26 5 2 

assign (residue 9 and name c4')(residue 9 and name o4')
    (residue 9 and name c1')(residue 9 and name c2') 2 -18 5 2
assign (residue 9 and name o4')(residue 9 and name c1')
    (residue 9 and name c2')(residue 9 and name c3') 2 34 5 2
assign (residue 9 and name c1')(residue 9 and name c2')
    (residue 9 and name c3')(residue 9 and name c4') 2 -37 5 2 
assign (residue 9 and name c2')(residue 9 and name c3')
    (residue 9 and name c4')(residue 9 and name o4') 2 26 5 2 


{Restriction of nucleotides to anti}

assign (residue 1 and name o4') (residue 1 and name c1')
        (residue 1 and name n9) (residue 1 and name c4) 2 -160 50 2
assign (residue 2 and name o4') (residue 2 and name c1')
        (residue 2 and name n9) (residue 2 and name c4) 2 -160 50 2
assign (residue 3 and name o4') (residue 3 and name c1')
        (residue 3 and name n1) (residue 3 and name c2) 2 -160 50 2
assign (residue 4 and name o4') (residue 4 and name c1')
        (residue 4 and name n9) (residue 4 and name c4) 2 -160 50 2
assign (residue 5 and name o4') (residue 5 and name c1')
        (residue 5 and name n1) (residue 5 and name c2) 2 -160 50 2
assign (residue 6 and name o4') (residue 6 and name c1')
        (residue 6 and name n9) (residue 6 and name c4) 2 -160 50 2
assign (residue 7 and name o4') (residue 7 and name c1')
        (residue 7 and name n1) (residue 7 and name c2) 2 -160 50 2
assign (residue 9 and name o4') (residue 9 and name c1')
        (residue 9 and name n9) (residue 9 and name c4) 2 -160 50 2
assign (residue 10 and name o4') (residue 10 and name c1')
        (residue 10 and name n1) (residue 10 and name c2) 2 -160 50 2
assign (residue 11 and name o4') (residue 11 and name c1')
        (residue 11 and name n9) (residue 11 and name c4) 2 -160 50 2
assign (residue 12 and name o4') (residue 12 and name c1')
        (residue 12 and name n1) (residue 12 and name c2) 2 -160 50 2
assign (residue 13 and name o4') (residue 13 and name c1')
        (residue 13 and name n1) (residue 13 and name c2) 2 -160 50 2


{Restriction of nucleotides to syn}

assign (residue 8 and name o4') (residue 8 and name c1')
        (residue 8 and name n9) (residue 8 and name c4) 2 30 40 2

{backbone torsion angle beta - standard A form from Kieft}
{used in refinement only}
{Restrain all the residues to standard A form except for loop and closing bp}

assign (residue 2 and name p)(residue 2 and name o5')
    (residue 2 and name c5')(residue 2 and name c4') 2 180 20 2
assign (residue 3 and name p)(residue 3 and name o5')
    (residue 3 and name c5')(residue 3 and name c4') 2 180 20 2
assign (residue 4 and name p)(residue 4 and name o5')
    (residue 4 and name c5')(residue 4 and name c4') 2 180 20 2
assign (residue 10 and name p)(residue 10 and name o5')
    (residue 10 and name c5')(residue 10 and name c4') 2 180 20 2
assign (residue 11 and name p)(residue 11 and name o5')
    (residue 11 and name c5')(residue 11 and name c4') 2 180 20 2
assign (residue 12 and name p)(residue 12 and name o5')
    (residue 12 and name c5')(residue 12 and name c4') 2 180 20 2
assign (residue 13 and name p)(residue 13 and name o5')
    (residue 13 and name c5')(residue 13 and name c4') 2 180 20 2



{backbone torsion angle gamma - standard A form from Kieft}
{used in refinement only}
{Restrain all the residues to standard A form except for loop and closing bp}

assign (residue 1 and name o5')(residue 1 and name c5')
    (residue 1 and name c4')(residue 1 and name c3') 2 55 30 2
assign (residue 2 and name o5')(residue 2 and name c5')
    (residue 2 and name c4')(residue 2 and name c3') 2 55 30 2
assign (residue 3 and name o5')(residue 3 and name c5')
    (residue 3 and name c4')(residue 3 and name c3') 2 55 30 2
assign (residue 4 and name o5')(residue 4 and name c5')
    (residue 4 and name c4')(residue 4 and name c3') 2 55 30 2
assign (residue 10 and name o5')(residue 10 and name c5')
    (residue 10 and name c4')(residue 10 and name c3') 2 55 30 2
assign (residue 11 and name o5')(residue 11 and name c5')
    (residue 11 and name c4')(residue 11 and name c3') 2 55 30 2
assign (residue 12 and name o5')(residue 12 and name c5')
    (residue 12 and name c4')(residue 12 and name c3') 2 55 30 2
assign (residue 13 and name o5')(residue 13 and name c5')
    (residue 13 and name c4')(residue 13 and name c3') 2 55 30 2


{backbone torsion angle epsilon- standard A form from Kieft}
{used in refinement only}
{Restrain all the residues to standard A form except for loop and closing bp}

assign (residue 1 and name c4')(residue 1 and name c3')
    (residue 1 and name o3')(residue 2 and name p) 2 -155 20 2
assign (residue 2 and name c4')(residue 2 and name c3')
    (residue 2 and name o3')(residue 3 and name p) 2 -155 20 2
assign (residue 3 and name c4')(residue 3 and name c3')
    (residue 3 and name o3')(residue 4 and name p) 2 -155 20 2
assign (residue 4 and name c4')(residue 4 and name c3')
    (residue 4 and name o3')(residue 5 and name p) 2 -155 20 2
assign (residue 10 and name c4')(residue 10 and name c3')
    (residue 10 and name o3')(residue 11 and name p) 2 -155 20 2
assign (residue 11 and name c4')(residue 11 and name c3')
    (residue 11 and name o3')(residue 12 and name p) 2 -155 20 2
assign (residue 12 and name c4')(residue 12 and name c3')
    (residue 12 and name o3')(residue 13 and name p) 2 -155 20 2


{backbone torsion angle alpha- standard A form from Kieft}
{used in refinement only}
{Restrain all the stem to standard A form except for loop and closing bp}

assign (residue 1 and name o3')(residue 2 and name p)
    (residue 2 and name o5')(residue 2 and name c5') 2 -70 30 2
assign (residue 2 and name o3')(residue 3 and name p)
    (residue 3 and name o5')(residue 3 and name c5') 2 -70 30 2
assign (residue 3 and name o3')(residue 4 and name p)
    (residue 4 and name o5')(residue 4 and name c5') 2 -70 30 2
assign (residue 4 and name o3')(residue 5 and name p)
    (residue 5 and name o5')(residue 5 and name c5') 2 -70 30 2
assign (residue 10 and name o3')(residue 11 and name p)
    (residue 11 and name o5')(residue 11 and name c5') 2 -70 30 2
assign (residue 11 and name o3')(residue 12 and name p)
    (residue 12 and name o5')(residue 12 and name c5') 2 -70 30 2
assign (residue 12 and name o3')(residue 13 and name p)
    (residue 13 and name o5')(residue 13 and name c5') 2 -70 30 2

 

{backbone torsion angle zeta -standard A form from Michael}
{used in refinement only}
{Restrain all the stem to standard A form except for loop and closing bp}

assign (residue 1 and name c3')(residue 1 and name o3')
    (residue 2 and name p)(residue 2 and name o5') 2 -70 30 2
assign (residue 2 and name c3')(residue 2 and name o3')
    (residue 3 and name p)(residue 3 and name o5') 2 -70 30 2
assign (residue 3 and name c3')(residue 3 and name o3')
    (residue 4 and name p)(residue 4 and name o5') 2 -70 30 2
assign (residue 4 and name c3')(residue 4 and name o3')
    (residue 5 and name p)(residue 5 and name o5') 2 -70 30 2
assign (residue 10 and name c3')(residue 10 and name o3')
    (residue 11 and name p)(residue 11 and name o5') 2 -70 30 2
assign (residue 11 and name c3')(residue 11 and name o3')
    (residue 12 and name p)(residue 12 and name o5') 2 -70 30 2
assign (residue 12 and name c3')(residue 12 and name o3')
    (residue 13 and name p)(residue 13 and name o5') 2 -70 30 2

 
end
end



  Entry H atom name         Submitted Coord H atom name
    1   1H5*    G   1          1H5*        G   1  -9.194 -10.994  -1.011
    2   2H5*    G   1          2H5*        G   1  -9.499 -10.222  -2.580
    3    H4*    G   1           H4*        G   1 -10.200  -8.712  -0.824
    4    H3*    G   1           H3*        G   1  -7.617  -7.880  -2.226
    5    H2*    G   1           H2*        G   1  -7.409  -6.052  -0.723
    6   2HO*    G   1          2HO*        G   1  -9.193  -4.917  -0.649
    7    H1*    G   1           H1*        G   1  -8.788  -7.214   1.499
    8    H8     G   1           H8         G   1  -6.038  -9.538   0.709
    9    H1     G   1           H1         G   1  -3.873  -4.117   3.379
   10   1H2     G   1          1H2         G   1  -5.467  -2.572   3.359
   11   2H2     G   1          2H2         G   1  -7.061  -2.891   2.712
   12    H5T    G   1           H5T        G   1  -7.006 -10.290  -1.218
   13   1H5*    G   2          1H5*        G   2 -11.027  -4.436  -1.823
   14   2H5*    G   2          2H5*        G   2 -10.776  -3.602  -3.369
   15    H4*    G   2           H4*        G   2 -10.953  -2.106  -1.328
   16    H3*    G   2           H3*        G   2  -8.471  -1.999  -3.117
   17    H2*    G   2           H2*        G   2  -7.618  -0.259  -1.675
   18   2HO*    G   2          2HO*        G   2  -8.960   1.054  -0.674
   19    H1*    G   2           H1*        G   2  -8.375  -1.409   0.726
   20    H8     G   2           H8         G   2  -7.154  -4.003  -1.817
   21    H1     G   2           H1         G   2  -2.482  -1.175   1.560
   22   1H2     G   2          1H2         G   2  -3.299   0.575   2.666
   23   2H2     G   2          2H2         G   2  -5.016   0.903   2.727
   24   1H5*    U   3          1H5*        U   3  -9.591   2.377  -2.754
   25   2H5*    U   3          2H5*        U   3  -8.699   3.066  -4.126
   26    H4*    U   3           H4*        U   3  -7.946   3.503  -1.592
   27    H3*    U   3           H3*        U   3  -6.080   3.017  -3.976
   28    H2*    U   3           H2*        U   3  -4.251   3.266  -2.426
   29   2HO*    U   3          2HO*        U   3  -4.763   5.039  -1.265
   30    H1*    U   3           H1*        U   3  -5.462   1.946  -0.281
   31    H3     U   3           H3         U   3  -1.880  -0.617  -1.531
   32    H5     U   3           H5         U   3  -4.866  -1.481  -4.380
   33    H6     U   3           H6         U   3  -6.193   0.319  -3.427
   34   1H5*    G   4          1H5*        G   4  -4.782   7.058  -2.111
   35   2H5*    G   4          2H5*        G   4  -4.443   8.043  -3.549
   36    H4*    G   4           H4*        G   4  -2.565   7.969  -1.888
   37    H3*    G   4           H3*        G   4  -2.093   6.921  -4.720
   38    H2*    G   4           H2*        G   4   0.174   6.405  -4.085
   39   2HO*    G   4          2HO*        G   4   0.036   8.566  -2.758
   40    H1*    G   4           H1*        G   4  -0.374   5.443  -1.539
   41    H8     G   4           H8         G   4  -3.006   4.289  -4.050
   42    H1     G   4           H1         G   4   2.313   0.701  -3.958
   43   1H2     G   4          1H2         G   4   3.917   1.751  -2.818
   44   2H2     G   4          2H2         G   4   3.591   3.214  -1.915
   45   1H5*    C   5          1H5*        C   5   1.429   9.078  -4.615
   46   2H5*    C   5          2H5*        C   5   1.678   9.559  -6.306
   47    H4*    C   5           H4*        C   5   3.109   7.600  -5.223
   48    H3*    C   5           H3*        C   5   1.899   7.583  -8.032
   49    H2*    C   5           H2*        C   5   2.682   5.359  -8.297
   50   2HO*    C   5          2HO*        C   5   4.849   6.285  -7.525
   51    H1*    C   5           H1*        C   5   2.751   4.711  -5.480
   52   1H4     C   5          1H4         C   5  -1.293   0.687  -8.303
   53   2H4     C   5          2H4         C   5  -2.612   1.782  -7.951
   54    H5     C   5           H5         C   5  -2.248   3.967  -6.875
   55    H6     C   5           H6         C   5  -0.554   5.555  -6.129
   56   1H5*    A   6          1H5*        A   6   3.094   8.478 -11.491
   57   2H5*    A   6          2H5*        A   6   1.364   8.454 -11.094
   58    H4*    A   6           H4*        A   6   3.426   6.368 -10.308
   59    H3*    A   6           H3*        A   6   2.138   6.436 -12.753
   60    H2*    A   6           H2*        A   6  -0.120   6.418 -11.842
   61   2HO*    A   6          2HO*        A   6   0.079   3.681 -11.621
   62    H1*    A   6           H1*        A   6   0.792   4.313  -9.833
   63    H8     A   6           H8         A   6  -0.367   7.501  -8.398
   64   1H6     A   6          1H6         A   6  -6.096   5.138  -8.188
   65   2H6     A   6          2H6         A   6  -5.071   6.456  -7.666
   66    H2     A   6           H2         A   6  -3.572   2.439 -10.695
   67   1H5*    U   7          1H5*        U   7   4.467   2.246 -10.851
   68   2H5*    U   7          2H5*        U   7   5.830   1.805 -11.899
   69    H4*    U   7           H4*        U   7   4.070   0.000 -11.511
   70    H3*    U   7           H3*        U   7   5.522   0.429 -13.866
   71    H2*    U   7           H2*        U   7   3.755   1.529 -15.084
   72   2HO*    U   7          2HO*        U   7   3.180  -1.270 -15.224
   73    H1*    U   7           H1*        U   7   1.695  -0.286 -13.760
   74    H3     U   7           H3         U   7  -1.593   2.125 -15.765
   75    H5     U   7           H5         U   7   1.217   5.076 -14.657
   76    H6     U   7           H6         U   7   2.654   3.292 -13.846
   77   1H5*    A   8          1H5*        A   8   5.797  -1.492 -11.598
   78   2H5*    A   8          2H5*        A   8   6.952  -2.726 -11.073
   79    H4*    A   8           H4*        A   8   5.228  -3.865 -10.169
   80    H3*    A   8           H3*        A   8   4.918  -4.546 -12.939
   81    H2*    A   8           H2*        A   8   2.926  -3.233 -13.255
   82   2HO*    A   8          2HO*        A   8   2.386  -5.744 -12.128
   83    H1*    A   8           H1*        A   8   2.289  -3.777 -10.328
   84    H8     A   8           H8         A   8   0.099  -3.069 -12.557
   85   1H6     A   8          1H6         A   8  -0.737   2.830 -10.811
   86   2H6     A   8          2H6         A   8  -1.358   1.554 -11.834
   87    H2     A   8           H2         A   8   3.141   1.319  -9.152
   88   1H5*    G   9          1H5*        G   9   4.205  -8.712  -8.930
   89   2H5*    G   9          2H5*        G   9   3.207  -7.448  -9.671
   90    H4*    G   9           H4*        G   9   5.912  -6.586  -8.814
   91    H3*    G   9           H3*        G   9   4.633  -8.028  -6.778
   92    H2*    G   9           H2*        G   9   2.643  -6.612  -6.735
   93   2HO*    G   9          2HO*        G   9   3.961  -6.526  -4.705
   94    H1*    G   9           H1*        G   9   4.488  -4.207  -7.096
   95    H8     G   9           H8         G   9   1.140  -5.736  -8.424
   96    H1     G   9           H1         G   9   1.034   0.522  -7.045
   97   1H2     G   9          1H2         G   9   3.029   1.173  -6.305
   98   2H2     G   9          2H2         G   9   4.398   0.086  -6.264
   99   1H5*    C  10          1H5*        C  10   8.544  -5.128  -5.259
  100   2H5*    C  10          2H5*        C  10   8.729  -5.707  -3.592
  101    H4*    C  10           H4*        C  10   9.322  -3.321  -3.805
  102    H3*    C  10           H3*        C  10   6.833  -3.965  -2.146
  103    H2*    C  10           H2*        C  10   6.634  -1.598  -1.702
  104   2HO*    C  10          2HO*        C  10   9.242  -1.693  -1.802
  105    H1*    C  10           H1*        C  10   7.231  -0.734  -4.271
  106   1H4     C  10          1H4         C  10   0.871  -1.134  -4.261
  107   2H4     C  10          2H4         C  10   0.912  -2.881  -4.177
  108    H5     C  10           H5         C  10   3.027  -4.140  -4.107
  109    H6     C  10           H6         C  10   5.455  -3.944  -4.026
  110   1H5*    A  11          1H5*        A  11   8.714  -1.381   0.000
  111   2H5*    A  11          2H5*        A  11   8.616  -1.597   1.759
  112    H4*    A  11           H4*        A  11   7.419   0.427   0.988
  113    H3*    A  11           H3*        A  11   5.693  -1.802   2.184
  114    H2*    A  11           H2*        A  11   3.798  -0.382   1.841
  115   2HO*    A  11          2HO*        A  11   4.345   1.544   2.658
  116    H1*    A  11           H1*        A  11   4.698   0.841  -0.536
  117    H8     A  11           H8         A  11   4.966  -2.938  -0.756
  118   1H6     A  11          1H6         A  11  -1.049  -2.858  -2.285
  119   2H6     A  11          2H6         A  11   0.352  -3.880  -2.050
  120    H2     A  11           H2         A  11   0.078   1.228  -0.872
  121   1H5*    C  12          1H5*        C  12   5.072   2.390   4.802
  122   2H5*    C  12          2H5*        C  12   4.607   1.579   6.311
  123    H4*    C  12           H4*        C  12   3.033   3.403   5.374
  124    H3*    C  12           H3*        C  12   2.050   0.622   6.186
  125    H2*    C  12           H2*        C  12  -0.173   1.316   5.565
  126   2HO*    C  12          2HO*        C  12   0.800   3.704   6.328
  127    H1*    C  12           H1*        C  12   0.539   2.741   3.277
  128   1H4     C  12          1H4         C  12  -1.154  -3.047   1.197
  129   2H4     C  12          2H4         C  12   0.386  -3.722   1.681
  130    H5     C  12           H5         C  12   2.087  -2.400   2.876
  131    H6     C  12           H6         C  12   2.589  -0.216   3.840
  132   1H5*    C  13          1H5*        C  13  -0.655   3.138   7.845
  133   2H5*    C  13          2H5*        C  13  -1.319   2.531   9.375
  134    H4*    C  13           H4*        C  13  -2.938   2.639   7.410
  135    H3*    C  13           H3*        C  13  -2.417  -0.051   8.765
  136    H2*    C  13           H2*        C  13  -4.077  -0.968   7.342
  137   2HO*    C  13          2HO*        C  13  -5.389   1.123   7.871
  138    H1*    C  13           H1*        C  13  -3.523   0.789   5.143
  139   1H4     C  13          1H4         C  13  -1.523  -5.017   3.429
  140   2H4     C  13          2H4         C  13  -0.064  -4.834   4.375
  141    H5     C  13           H5         C  13   0.352  -2.860   5.789
  142    H6     C  13           H6         C  13  -0.589  -0.753   6.585
  143    H3T    C  13           H3T        C  13  -3.854   2.206   9.274