[phenixbb] Nitric Oxide ligand keeps getting pushed far away from specified links in CIF
Dale Tronrud
det102 at uoxray.uoregon.edu
Mon Nov 28 14:28:01 PST 2011
I'm not sure this is your problem but I noticed that you have
a space in the middle of "NO -HEM" where ever it occurs. I don't
think it is supposed to.
Dale Tronrud
On 11/28/11 14:19, Yarrow Madrona wrote:
> 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
>
>
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