Hello,
I am running phenix version 1.9-1692. I have restrains for a nitric oxide ligand that I have used previously to refine a heme iron-NO linked structure. I have pasted them below. For some reason. The NO always gets moved a little to far from the iron. Here is a coot screen shot:
Can someone please help me resolve this issue? Thank you.
-Yarrow
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metal edits file:
refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = name FE and chain A and resname FE and resseq 499
atom_selection_2 = name N and chain A and resname NMO and resseq 510
distance_ideal = 1.75
sigma = 0.1
}
}
refinement.geometry_restraints.edits {
angle {
action = *add
atom_selection_1 = name FE and chain A and resname FE and resseq 499
atom_selection_2 = name N and chain A and resname NMO and resseq 510
atom_selection_3 = name O and chain A and resname NMO and resseq 510
angle_ideal = 160
sigma = 5
}
}
refinement.geometry_restraints.edits {
bond {
action = *add
atom_selection_1 = name FE and chain B and resname FE and resseq 499
atom_selection_2 = name N and chain B and resname NMO and resseq 510
distance_ideal = 1.75
sigma = 0.1
}
}
refinement.geometry_restraints.edits {
angle {
action = *add
atom_selection_1 = name FE and chain B and resname FE and resseq 499
atom_selection_2 = name N and chain B and resname NMO and resseq 510
atom_selection_3 = name O and chain B and resname NMO and resseq 510
angle_ideal = 160
sigma = 5
}
}
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CIF file
#
data_comp_list
loop_
_chem_comp.three_letter_code
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
NMO NMO "nitric oxide " ligand 2 2 .
#
data_comp_NMO
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
NMO N N N . -0.1324 -0.0924 0.5896
NMO O O O . 0.1324 0.0924 -0.5896
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
NMO N O double 1.223 0.020
#
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
NMO plan-1 N 0.020
NMO plan-1 O 0.020
