NMR Restraints Grid

Result table
 (Save to zip file containing files for each block)

image mrblock_id pdb_id bmrb_id cing stage position program type subtype
15610 1ymo 6477 cing 1-original 5 XPLOR/CNS protocol structure calculation


{* The following dihedral constraints enforce the correct chirality on
   deoxyribose ring atoms. The four ligand atoms in each case are selected
   in a way that the improper dihedral angle is always around +70 deg for
   the correct configuration. The target values get loose bounds of +/- 50 deg.
   Violations are sanctioned with the very high force constant of 500.0
*}

set message=on echo=on end

for $nchir in (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24) loop chiral

restraints dihedral

 scale= 1.0

assign 
   (resid $nchir and name O4' )
   (resid $nchir and  ((resname CYT and name N1) 
                   or (resname URI and name N1)
                   or (resname GUA and name N9)
                   or (resname ADE and name N9)
   ) )
   (resid $nchir and name C2' )
   (resid $nchir and name H1' )      3.0  70.0  20.0  2

assign 
   (resid $nchir and name C1' )
   (resid $nchir and name C3' )
   (resid $nchir and name O2' )      {changed from H2'' for use on ribose--jem}
   (resid $nchir and name H2' )      3.0  70.0  20.0  2

assign 
   (resid $nchir and name C2' )
   (resid $nchir and name C4' )
   (resid $nchir and name O3' )
   (resid $nchir and name H3' )      3.0  70.0  20.0  2

assign 
   (resid $nchir and name C3' )
   (resid $nchir and name C5' )
   (resid $nchir and name O4' )
   (resid $nchir and name H4' )      3.0  70.0  20.0  2

assign 
   (resid $nchir and name C4' )
   (resid $nchir and name O5' )
   (resid $nchir and name H5'' )
   (resid $nchir and name H5' )      3.0  70.0  20.0  2

end

end loop chiral

for $nchir in (25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47) loop chiral

restraints dihedral

 scale= 1.0

assign 
   (resid $nchir and name O4' )
   (resid $nchir and  ((resname CYT and name N1) 
                   or (resname URI and name N1)
                   or (resname GUA and name N9)
                   or (resname ADE and name N9)
   ) )
   (resid $nchir and name C2' )
   (resid $nchir and name H1' )      3.0  70.0  20.0  2

assign 
   (resid $nchir and name C1' )
   (resid $nchir and name C3' )
   (resid $nchir and name O2' )      {changed from H2'' for use on ribose--jem}
   (resid $nchir and name H2' )      3.0  70.0  20.0  2

assign 
   (resid $nchir and name C2' )
   (resid $nchir and name C4' )
   (resid $nchir and name O3' )
   (resid $nchir and name H3' )      3.0  70.0  20.0  2

assign 
   (resid $nchir and name C3' )
   (resid $nchir and name C5' )
   (resid $nchir and name O4' )
   (resid $nchir and name H4' )      3.0  70.0  20.0  2

assign 
   (resid $nchir and name C4' )
   (resid $nchir and name O5' )
   (resid $nchir and name H5'' )
   (resid $nchir and name H5' )      3.0  70.0  20.0  2

end

end loop chiral

 
!{* keep Gua amino groups flat *}
for $namin in (1 2 3 6 15 18 26 41 45) loop amino 

restraints  dihedral

 scale= 1.0

assign 
   (resid $namin and name H21 )
   (resid $namin and name N2  )
   (resid $namin and name C2  )
   (resid $namin and name N1  )        3.0  0.0  3.0  2
assign 
   (resid $namin and name H22 )
   (resid $namin and name N2  )
   (resid $namin and name C2  )
   (resid $namin and name N3  )        3.0  0.0  3.0  2
end

end loop amino

!{* keep cytosine amino flat *}
for $namin2 in (4 12 14 16 20 24 27 28 29 30 34 43 46) loop amino2

 restraints dihedral

 scale= 1.0

assign 
    (resid $namin2 and name H41)
    (resid $namin2 and name N4 )
    (resid $namin2 and name C4 )
    (resid $namin2 and name N3 )       3.0  0.0  3.0  2

assign
    (resid $namin2 and name H42)
    (resid $namin2 and name N4 )
    (resid $namin2 and name C4 )
    (resid $namin2 and name C5 )       3.0  0.0  3.0  2  
end 

end loop amino2

!{* keep adenine amino flat *}
for $namin3 in (19 25 31 32 33 35 36 37 38 39 40 44 47) loop amino3

 restraints dihedral

 scale= 1.0

assign 
    (resid $namin3 and name H61)
    (resid $namin3 and name N6 )
    (resid $namin3 and name C6 )
    (resid $namin3 and name N1 )       3.0  0.0  3.0  2

assign
    (resid $namin3 and name H62)
    (resid $namin3 and name N6 )
    (resid $namin3 and name C6 )
    (resid $namin3 and name C5 )       3.0  0.0  3.0  2  
end 

end loop amino3

set message=on echo=on end



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