# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 13:17:29 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2S,4Z,6E)-2-amino-5-hydroxy-7-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}hepta-4,6-dienoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(/C=C/C(O)=C/C[C@H](N)C(O)=O)c1O
#
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
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PFM  PFM  '(2S,4Z,6E)-2-amino-5-hydroxy-7-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}hepta-4,6-dienoic acid'  ligand  44  25  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PFM
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PFM  N     N  NH2   0  -0.780  -1.1403   1.1863  -4.7866
 PFM  CA    C  CH1   0  -0.205  -0.0234   0.6247  -5.5065
 PFM  C     C  C     0   0.547  -0.4648   0.2413  -6.9034
 PFM  OA    O  O     0  -0.435  -1.6112   0.1119  -7.2495
 PFM  OB    O  OH1   0  -0.593   0.5712   0.0273  -7.7050
 PFM  CB    C  CH2   0  -0.528   0.6478  -0.6007  -4.8314
 PFM  CG    C  C1    0  -0.356   1.1664  -0.2429  -3.4792
 PFM  CD    C  C     0   0.338   0.6699  -0.6273  -2.2910
 PFM  OE    O  OH1   0  -0.626  -0.3923  -1.4412  -2.1143
 PFM  C4B   C  C1    0  -0.294   1.2927  -0.1793  -1.0538
 PFM  C4A   C  C1    0  -0.308   0.8877  -0.5503   0.1694
 PFM  C4    C  CR6   0   0.121   1.4486  -0.1292   1.4543
 PFM  C3    C  CR6   0   0.235   2.7956   0.1960   1.6431
 PFM  O3    O  OH1   0  -0.616   3.6289   0.1286   0.5911
 PFM  C2    C  CR6   0   0.124   3.2565   0.5659   2.9143
 PFM  C2A   C  CH3   0  -0.790   4.7007   0.9091   3.1294
 PFM  N1    N  N     0  -0.407   2.4428   0.6200   3.9548
 PFM  C6    C  CR16  0  -0.135   1.1606   0.3095   3.7984
 PFM  C5    C  CR6   0  -0.074   0.6156  -0.0739   2.5860
 PFM  C5A   C  CH2   0  -0.214  -0.8431  -0.4067   2.4444
 PFM  P     P  P     0   1.458  -3.0665  -0.1089   3.7747
 PFM  OP1   O  O     0  -0.706  -3.8763  -0.9818   2.9061
 PFM  OP2   O  OH1   0  -0.727  -3.2148  -0.2695   5.3514
 PFM  OP3   O  OH1   0  -0.738  -3.3420   1.4204   3.4045
 PFM  OP4   O  O2    0  -0.591  -1.4824  -0.3136   3.7126
 PFM  HN1   H  HNH2  0   0.358  -0.8383   1.4496  -3.8569
 PFM  HN2   H  HNH2  0   0.343  -1.8730   0.4967  -4.6689
 PFM  HA    H  HCH1  0   0.279   0.7424   1.4010  -5.6050
 PFM  HOB   H  HOH1  0   0.483   0.2648  -0.2639  -8.5772
 PFM  HB1   H  HCH2  0   0.271   1.4798  -0.9490  -5.4481
 PFM  HB2   H  HCH2  0   0.243  -0.0717  -1.4261  -4.8036
 PFM  HG    H  H     0   0.261   2.0236   0.4199  -3.4553
 PFM  HOE   H  HOH1  0   0.469  -0.7510  -1.7304  -2.9601
 PFM  H4B   H  H     0   0.271   2.1163   0.5074  -1.1878
 PFM  H4A   H  H     0   0.262   0.0371  -1.2191   0.2362
 PFM  HO3   H  HOH1  0   0.488   4.5344   0.3323   0.8510
 PFM  H2A1  H  HCH3  0   0.258   5.3620   0.0641   2.9192
 PFM  H2A2  H  HCH3  0   0.259   5.0261   1.7449   2.5048
 PFM  H2A3  H  HCH3  0   0.273   4.8585   1.1940   4.1667
 PFM  H6    H  HCR6  0   0.259   0.5467   0.3759   4.6869
 PFM  H5A1  H  HCH2  0   0.257  -1.3024   0.2739   1.7191
 PFM  H5A2  H  HCH2  0   0.266  -0.9732  -1.4216   2.0590
 PFM  HOP2  H  HOH1  0   0.506  -4.1313  -0.3060   5.6576
 PFM  HOP3  H  HOH1  0   0.496  -2.9054   2.0752   3.9658

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
_chem_comp_bond.value_dist_neutron
 PFM  N    CA    single    1.443  0.020  1.443
 PFM  N    HN1   single    0.890  0.020  1.040
 PFM  N    HN2   single    0.890  0.020  1.040
 PFM  CA   C     single    1.514  0.020  1.514
 PFM  CA   CB    single    1.552  0.020  1.552
 PFM  CA   HA    single    0.970  0.020  1.090
 PFM  C    OA    double    1.205  0.020  1.205
 PFM  C    OB    single    1.327  0.020  1.327
 PFM  OB   HOB   single    0.850  0.020  0.980
 PFM  CB   CG    single    1.492  0.020  1.492
 PFM  CB   HB1   single    0.970  0.020  1.090
 PFM  CB   HB2   single    0.970  0.020  1.090
 PFM  CG   CD    double    1.344  0.020  1.344
 PFM  CG   HG    single    0.930  0.020  1.080
 PFM  CD   OE    single    1.350  0.020  1.350
 PFM  CD   C4B   single    1.456  0.020  1.456
 PFM  OE   HOE   single    0.850  0.020  0.980
 PFM  C4B  C4A   double    1.341  0.020  1.341
 PFM  C4B  H4B   single    0.930  0.020  1.080
 PFM  C4A  C4    single    1.464  0.020  1.464
 PFM  C4A  H4A   single    0.930  0.020  1.080
 PFM  C4   C3    aromatic  1.398  0.020  1.398
 PFM  C4   C5    aromatic  1.406  0.020  1.406
 PFM  C3   O3    single    1.344  0.020  1.344
 PFM  C3   C2    aromatic  1.402  0.020  1.402
 PFM  O3   HO3   single    0.850  0.020  0.980
 PFM  C2   C2A   single    1.500  0.020  1.500
 PFM  C2   N1    aromatic  1.322  0.020  1.322
 PFM  C2A  H2A1  single    0.970  0.020  1.090
 PFM  C2A  H2A2  single    0.970  0.020  1.090
 PFM  C2A  H2A3  single    0.970  0.020  1.090
 PFM  N1   C6    aromatic  1.329  0.020  1.329
 PFM  C6   C5    aromatic  1.383  0.020  1.383
 PFM  C6   H6    single    0.930  0.020  1.080
 PFM  C5   C5A   single    1.503  0.020  1.503
 PFM  C5A  OP4   single    1.423  0.020  1.423
 PFM  C5A  H5A1  single    0.970  0.020  1.090
 PFM  C5A  H5A2  single    0.970  0.020  1.090
 PFM  P    OP1   double    1.474  0.020  1.474
 PFM  P    OP2   single    1.592  0.020  1.592
 PFM  P    OP3   single    1.597  0.020  1.597
 PFM  P    OP4   single    1.598  0.020  1.598
 PFM  OP2  HOP2  single    0.850  0.020  0.980
 PFM  OP3  HOP3  single    0.850  0.020  0.980

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
 PFM  HN2   N    HN1   106.63  3.000
 PFM  HN2   N    CA    110.66  3.000
 PFM  HN1   N    CA    109.18  3.000
 PFM  HA    CA   CB    107.25  3.000
 PFM  HA    CA   C     107.48  3.000
 PFM  CB    CA   C     109.11  3.000
 PFM  HA    CA   N     108.08  3.000
 PFM  CB    CA   N     115.16  3.000
 PFM  C     CA   N     109.47  3.000
 PFM  OB    C    OA    123.51  3.000
 PFM  OB    C    CA    111.74  3.000
 PFM  OA    C    CA    124.73  3.000
 PFM  HOB   OB   C     110.19  3.000
 PFM  HB2   CB   HB1   105.92  3.000
 PFM  HB2   CB   CG    112.71  3.000
 PFM  HB1   CB   CG    108.87  3.000
 PFM  HB2   CB   CA    108.78  3.000
 PFM  HB1   CB   CA    109.61  3.000
 PFM  CG    CB   CA    110.81  3.000
 PFM  HG    CG   CD    116.59  3.000
 PFM  HG    CG   CB    116.20  3.000
 PFM  CD    CG   CB    127.19  3.000
 PFM  C4B   CD   OE    114.27  3.000
 PFM  C4B   CD   CG    120.36  3.000
 PFM  OE    CD   CG    125.37  3.000
 PFM  HOE   OE   CD    111.05  3.000
 PFM  H4B   C4B  C4A   121.28  3.000
 PFM  H4B   C4B  CD    114.59  3.000
 PFM  C4A   C4B  CD    124.12  3.000
 PFM  H4A   C4A  C4    115.09  3.000
 PFM  H4A   C4A  C4B   117.64  3.000
 PFM  C4    C4A  C4B   127.26  3.000
 PFM  C5    C4   C3    116.92  3.000
 PFM  C5    C4   C4A   119.39  3.000
 PFM  C3    C4   C4A   123.67  3.000
 PFM  C2    C3   O3    121.28  3.000
 PFM  C2    C3   C4    120.03  3.000
 PFM  O3    C3   C4    118.68  3.000
 PFM  HO3   O3   C3    111.16  3.000
 PFM  N1    C2   C2A   118.06  3.000
 PFM  N1    C2   C3    121.48  3.000
 PFM  C2A   C2   C3    120.46  3.000
 PFM  H2A3  C2A  H2A2  107.56  3.000
 PFM  H2A3  C2A  H2A1  107.34  3.000
 PFM  H2A2  C2A  H2A1  107.52  3.000
 PFM  H2A3  C2A  C2    109.66  3.000
 PFM  H2A2  C2A  C2    112.32  3.000
 PFM  H2A1  C2A  C2    112.21  3.000
 PFM  C6    N1   C2    119.46  3.000
 PFM  H6    C6   C5    120.87  3.000
 PFM  H6    C6   N1    115.89  3.000
 PFM  C5    C6   N1    123.24  3.000
 PFM  C5A   C5   C6    121.76  3.000
 PFM  C5A   C5   C4    119.36  3.000
 PFM  C6    C5   C4    118.87  3.000
 PFM  H5A2  C5A  H5A1  107.06  3.000
 PFM  H5A2  C5A  OP4   108.75  3.000
 PFM  H5A1  C5A  OP4   111.16  3.000
 PFM  H5A2  C5A  C5    110.75  3.000
 PFM  H5A1  C5A  C5    109.37  3.000
 PFM  OP4   C5A  C5    109.73  3.000
 PFM  OP4   P    OP3   106.53  3.000
 PFM  OP4   P    OP2    96.77  3.000
 PFM  OP3   P    OP2   108.06  3.000
 PFM  OP4   P    OP1   116.47  3.000
 PFM  OP3   P    OP1   109.62  3.000
 PFM  OP2   P    OP1   118.22  3.000
 PFM  HOP2  OP2  P     113.94  3.000
 PFM  HOP3  OP3  P     115.86  3.000
 PFM  P     OP4  C5A   119.22  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
 PFM  CONST_01  N1    C2   C3   C4      0.00   0.0  0
 PFM  CONST_02  N1    C6   C5   C4      0.00   0.0  0
 PFM  CONST_03  C6    C5   C4   C3      0.00   0.0  0
 PFM  CONST_04  C6    N1   C2   C3      0.00   0.0  0
 PFM  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 PFM  CONST_06  C5    C6   N1   C2      0.00   0.0  0
 PFM  CONST_07  C2    C3   C4   C4A   180.00   0.0  0
 PFM  CONST_08  C6    C5   C4   C4A   180.00   0.0  0
 PFM  CONST_09  C2A   C2   C3   C4    180.00   0.0  0
 PFM  CONST_10  C5A   C5   C4   C3    180.00   0.0  0
 PFM  CONST_11  C5    C4   C3   O3    180.00   0.0  0
 PFM  CONST_12  N1    C2   C3   O3    180.00   0.0  0
 PFM  CONST_13  C6    N1   C2   C2A   180.00   0.0  0
 PFM  CONST_14  C5A   C5   C6   N1    180.00   0.0  0
 PFM  CONST_15  H6    C6   C5   C4    180.00   0.0  0
 PFM  CONST_16  HOB   OB   C    CA    180.00   0.0  0
 PFM  Var_01    C3    C4   C4A  C4B   -31.00  30.0  2
 PFM  Var_02    OP4   C5A  C5   C4    178.76  30.0  2
 PFM  Var_03    H2A1  C2A  C2   C3    -62.30  30.0  2
 PFM  Var_04    C4    C4A  C4B  CD   -179.07   0.0  2
 PFM  Var_05    OE    CD   CG   CB      1.32   0.0  2
 PFM  Var_06    CD    CG   CB   CA    108.47  30.0  3
 PFM  Var_07    C4A   C4B  CD   CG   -177.75  30.0  2
 PFM  Var_08    OP1   P    OP4  C5A    46.81  30.0  1

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
 PFM  chir_01  CA  N  C  CB  positiv

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
 PFM  plan-1  C4A  0.020
 PFM  plan-1  C4   0.020
 PFM  plan-1  C3   0.020
 PFM  plan-1  O3   0.020
 PFM  plan-1  C2   0.020
 PFM  plan-1  C2A  0.020
 PFM  plan-1  N1   0.020
 PFM  plan-1  C6   0.020
 PFM  plan-1  C5   0.020
 PFM  plan-1  C5A  0.020
 PFM  plan-1  H6   0.020
 PFM  plan-2  CA   0.020
 PFM  plan-2  C    0.020
 PFM  plan-2  OA   0.020
 PFM  plan-2  OB   0.020
 PFM  plan-2  HOB  0.020
 PFM  plan-3  CB   0.020
 PFM  plan-3  CG   0.020
 PFM  plan-3  CD   0.020
 PFM  plan-3  OE   0.020
 PFM  plan-3  C4B  0.020
 PFM  plan-3  HG   0.020
 PFM  plan-4  CD   0.020
 PFM  plan-4  C4B  0.020
 PFM  plan-4  C4A  0.020
 PFM  plan-4  C4   0.020
 PFM  plan-4  H4B  0.020
 PFM  plan-4  H4A  0.020

