Result table
| image | mrblock_id | pdb_id | bmrb_id | cing | stage | position | program | type | subtype |
|
|
15610 | 1ymo RC | 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