[phenixbb] Nitric Oxide ligand keeps getting pushed far away from specified links in CIF
Yarrow Madrona
amadrona at uci.edu
Mon Nov 28 14:19:34 PST 2011
Hello,
I am having some trouble refining a structure with Nitric Oxide
coordinated to the Heme Fe. I attempted to merge two Cif files. One for
another ligand (CNL) and one for NO (NO.cif). I have saved the merged file
as CinNO2.cif. In the defualt refinement I type the following into the
command line:
Mymodel.mtz mymodel.pdb CinNO2.cif
Phenix refine runs fine without any errors but pushes the NO much further
than the 1.9 angstrom specified by the links in the cif file. I have
pasted the contents of the cif file below. The NO, Fe links are at the end
of the file. Thank you for any help you can provide.
-Yarrow
# Files merged : Tue Oct 4 10:11:22 2011
#
# CNL.cif
# NO.cif
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
CNL CNL Unknown ligand 29 11 .
NO NO Unknown ligand 2 2 .
#
data_comp_CNL
#
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
CNL C1 C CT . 55.3085 -9.1280 -43.0216
CNL C2 C CH2 . 55.6432 -10.5699 -43.1750
CNL C3 C CH2 . 54.6509 -11.3139 -43.9725
CNL C4 C CH1 . 53.4902 -10.4784 -44.3504
CNL C5 C CH2 . 53.9278 -9.3349 -45.0693
CNL C6 C CH2 . 54.8932 -8.4964 -44.3064
CNL C7 C CH3 . 56.3801 -8.3679 -42.3275
CNL C8 C CT . 52.9353 -9.9244 -43.0573
CNL C9 C CH3 . 52.3495 -11.0301 -42.2453
CNL C10 C CH3 . 51.8314 -8.9341 -43.2982
CNL O O O2 . 54.1049 -9.2461 -42.2221
#
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
CNL C1 C2 single 1.488 0.020
CNL C1 C6 single 1.491 0.020
CNL C1 C7 single 1.486 0.020
CNL C1 O single 1.450 0.020
CNL C2 C3 single 1.475 0.020
CNL C3 C4 single 1.479 0.020
CNL C4 C5 single 1.420 0.020
CNL C4 C8 single 1.512 0.020
CNL C5 C6 single 1.489 0.020
CNL C8 C9 single 1.492 0.020
CNL C8 C10 single 1.502 0.020
CNL C8 O single 1.589 0.020
#
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
CNL C3 C2 C1 113.16 3.000
CNL C5 C6 C1 112.56 3.000
CNL C8 O C1 110.85 3.000
CNL C6 C1 C2 112.60 3.000
CNL C7 C1 C2 112.43 3.000
CNL O C1 C2 99.48 3.000
CNL C4 C3 C2 112.41 3.000
CNL C5 C4 C3 110.02 3.000
CNL C8 C4 C3 106.05 3.000
CNL C6 C5 C4 113.20 3.000
CNL C9 C8 C4 109.75 3.000
CNL C10 C8 C4 111.96 3.000
CNL O C8 C4 109.61 3.000
CNL C8 C4 C5 104.53 3.000
CNL C7 C1 C6 112.76 3.000
CNL O C1 C6 106.18 3.000
CNL O C1 C7 112.51 3.000
CNL C10 C8 C9 106.70 3.000
CNL O C8 C9 108.62 3.000
CNL O C8 C10 110.10 3.000
#
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
CNL Var_01 C4 C8 O C1 10.40 30.0 3
CNL Var_02 C9 C8 O C1 130.31 30.0 3
CNL Var_03 C10 C8 O C1 -113.19 30.0 3
#
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
CNL chir_01 C1 C6 C7 O both
CNL chir_02 C4 C3 C5 C8 both
#
data_comp__NO
#
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
NO N N N . -5.7690 4.3760 32.3600
NO O O O . -4.8990 5.2460 32.3600
#
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
NO N O double 1.150 0.02
#
data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
HEM-CYS HEM . . CYS . .
bond_CYS-SG_=_HEM-FE
NO -HEM HEM . . NO . .
bond_HEM-FE_=_NO-N
#
data_link_HEM-CYS
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
HEM-CYS 1 FE 2 SG . 2.300000 0.020
#
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
HEM-CYS 2 SG 1 FE 1 NC 109.471221 3.000
HEM-CYS 1 FE 2 SG 2 CB 109.471221 3.000
#
data_link_NO -HEM
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
NO -HEM 1 N 2 FE . 1.900000 0.020
#
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
NO -HEM 2 FE 1 N 1 O 140 3.000
NO -HEM 1 N 2 FE 2 NC 103 3.000
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
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