# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 16:14:28 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H](CO)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
 1W9  1W9  (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-serine  ligand  37  22  .  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_1W9
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
 1W9  C    C  C     0   0.561  -3.9797  -1.7189   0.8280
 1W9  N    N  N     0  -0.444  -2.3604  -0.2997  -0.2355
 1W9  O    O  O     0  -0.424  -4.0277  -0.9654   1.7627
 1W9  P    P  P     0   1.464   4.2438  -1.3177  -0.0155
 1W9  N1   N  N     0  -0.397   1.0453   3.3190   0.1203
 1W9  C2   C  CR6   0   0.132  -0.2707   3.3438   0.1040
 1W9  C3   C  CR6   0   0.301  -1.0174   2.1526  -0.0035
 1W9  O3   O  OH1   0  -0.624  -2.3406   2.2403  -0.0123
 1W9  C4   C  CR6   0  -0.022  -0.3368   0.9321  -0.0982
 1W9  C5   C  CR6   0  -0.069   1.0690   0.9404  -0.0785
 1W9  C6   C  CR16  0  -0.146   1.7033   2.1602   0.0330
 1W9  CA   C  CH1   0  -0.275  -3.0822  -1.5332  -0.3845
 1W9  CB   C  CH2   0  -0.145  -3.9115  -1.4972  -1.6644
 1W9  OG   O  OH1   0  -0.662  -4.9040  -0.5169  -1.5073
 1W9  O1P  O  OH1   0  -0.740   4.0672  -1.9168   1.4552
 1W9  O2P  O  OH1   0  -0.728   5.5757  -0.4472  -0.0405
 1W9  O3P  O  O     0  -0.706   4.0973  -2.3948  -1.0107
 1W9  C4A  C  C1    0   0.069  -1.0910  -0.3126  -0.2150
 1W9  O4P  O  O2    0  -0.591   3.2216  -0.0927  -0.1380
 1W9  C5A  C  CH2   0  -0.217   1.8259  -0.3536  -0.1945
 1W9  OXT  O  OH1   0  -0.590  -4.6874  -2.8341   0.7332
 1W9  H1   H  HOH1  0   0.475  -2.7027   1.3115  -0.1023
 1W9  H2   H  HCR6  0   0.261   2.7825   2.2300   0.0532
 1W9  H3   H  HCH1  0   0.292  -2.4069  -2.3988  -0.4445
 1W9  H4   H  HCH2  0   0.228  -3.2361  -1.2792  -2.5002
 1W9  H5   H  HCH2  0   0.224  -4.3303  -2.4933  -1.8411
 1W9  H6   H  HOH1  0   0.464  -5.4451  -0.5013  -2.3021
 1W9  H7   H  HOH1  0   0.498   4.2115  -1.2978   2.1839
 1W9  H8   H  HCH3  0   0.249  -1.6279   4.8336  -0.6515
 1W9  H9   H  HCH3  0   0.249  -1.5977   4.7144   1.0976
 1W9  H10  H  HCH3  0   0.249  -0.2443   5.4681   0.2475
 1W9  H11  H  HOH1  0   0.506   6.3861  -0.9702  -0.1098
 1W9  H12  H  H     0   0.265  -0.5363  -1.2501  -0.2875
 1W9  H13  H  HCH2  0   0.261   1.5337  -1.0300   0.6153
 1W9  H14  H  HCH2  0   0.267   1.5792  -0.8462  -1.1396
 1W9  H15  H  HOH1  0   0.487  -5.2496  -2.9403   1.5154
 1W9  C2A  C  CH3   0  -0.720  -0.9726   4.6615   0.2041

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
 1W9  O    C    double    1.202  0.020  1.202
 1W9  OXT  C    single    1.324  0.020  1.324
 1W9  C    CA   single    1.520  0.020  1.520
 1W9  O3   C3   single    1.326  0.020  1.326
 1W9  CA   N    single    1.437  0.020  1.437
 1W9  CA   CB   single    1.526  0.020  1.526
 1W9  C2A  C2   single    1.496  0.020  1.496
 1W9  N    C4A  double    1.270  0.020  1.270
 1W9  C3   C2   aromatic  1.410  0.020  1.410
 1W9  C3   C4   aromatic  1.401  0.020  1.401
 1W9  CB   OG   single    1.404  0.020  1.404
 1W9  C2   N1   aromatic  1.316  0.020  1.316
 1W9  C4A  C4   single    1.460  0.020  1.460
 1W9  C4   C5   aromatic  1.406  0.020  1.406
 1W9  N1   C6   aromatic  1.335  0.020  1.335
 1W9  C5   C6   aromatic  1.379  0.020  1.379
 1W9  C5   C5A  single    1.504  0.020  1.504
 1W9  C5A  O4P  single    1.421  0.020  1.421
 1W9  O4P  P    single    1.600  0.020  1.600
 1W9  O3P  P    double    1.474  0.020  1.474
 1W9  P    O2P  single    1.591  0.020  1.591
 1W9  P    O1P  single    1.598  0.020  1.598
 1W9  O3   H1   single    0.850  0.020  0.980
 1W9  C6   H2   single    0.930  0.020  1.080
 1W9  CA   H3   single    0.970  0.020  1.090
 1W9  CB   H4   single    0.970  0.020  1.090
 1W9  CB   H5   single    0.970  0.020  1.090
 1W9  OG   H6   single    0.850  0.020  0.980
 1W9  O1P  H7   single    0.850  0.020  0.980
 1W9  C2A  H8   single    0.970  0.020  1.090
 1W9  C2A  H9   single    0.970  0.020  1.090
 1W9  C2A  H10  single    0.970  0.020  1.090
 1W9  O2P  H11  single    0.850  0.020  0.980
 1W9  C4A  H12  single    0.930  0.020  1.080
 1W9  C5A  H13  single    0.970  0.020  1.090
 1W9  C5A  H14  single    0.970  0.020  1.090
 1W9  OXT  H15  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
 1W9  OXT  C    CA   111.18  3.000
 1W9  CA   C    O    124.58  3.000
 1W9  OXT  C    O    124.23  3.000
 1W9  C4A  N    CA   119.68  3.000
 1W9  O4P  P    O3P  116.37  3.000
 1W9  O3P  P    O2P  118.19  3.000
 1W9  O4P  P    O2P   96.59  3.000
 1W9  O2P  P    O1P  108.18  3.000
 1W9  O3P  P    O1P  109.66  3.000
 1W9  O4P  P    O1P  106.68  3.000
 1W9  C6   N1   C2   120.54  3.000
 1W9  C2A  C2   C3   120.04  3.000
 1W9  C3   C2   N1   120.96  3.000
 1W9  C2A  C2   N1   118.99  3.000
 1W9  C4   C3   O3   122.82  3.000
 1W9  C4   C3   C2   118.95  3.000
 1W9  O3   C3   C2   118.23  3.000
 1W9  H1   O3   C3   107.47  3.000
 1W9  C4A  C4   C5   121.51  3.000
 1W9  C5   C4   C3   118.67  3.000
 1W9  C4A  C4   C3   119.82  3.000
 1W9  C5A  C5   C6   122.40  3.000
 1W9  C5A  C5   C4   119.81  3.000
 1W9  C6   C5   C4   117.79  3.000
 1W9  H2   C6   C5   121.16  3.000
 1W9  H2   C6   N1   115.75  3.000
 1W9  C5   C6   N1   123.10  3.000
 1W9  H3   CA   CB   107.86  3.000
 1W9  H3   CA   N    111.90  3.000
 1W9  CB   CA   N    109.87  3.000
 1W9  H3   CA   C    108.06  3.000
 1W9  CB   CA   C    110.56  3.000
 1W9  N    CA   C    108.59  3.000
 1W9  H5   CB   H4   107.06  3.000
 1W9  H5   CB   OG   112.52  3.000
 1W9  H4   CB   OG   112.45  3.000
 1W9  H5   CB   CA   108.78  3.000
 1W9  H4   CB   CA   108.02  3.000
 1W9  OG   CB   CA   107.88  3.000
 1W9  H6   OG   CB   108.46  3.000
 1W9  H7   O1P  P    115.91  3.000
 1W9  H11  O2P  P    114.00  3.000
 1W9  H12  C4A  C4   118.35  3.000
 1W9  H12  C4A  N    121.05  3.000
 1W9  C4   C4A  N    120.60  3.000
 1W9  C5A  O4P  P    119.34  3.000
 1W9  H14  C5A  H13  107.50  3.000
 1W9  H14  C5A  O4P  109.78  3.000
 1W9  H13  C5A  O4P  110.25  3.000
 1W9  H14  C5A  C5   109.92  3.000
 1W9  H13  C5A  C5   109.89  3.000
 1W9  O4P  C5A  C5   109.47  3.000
 1W9  H15  OXT  C    110.15  3.000
 1W9  H10  C2A  H9   108.35  3.000
 1W9  H10  C2A  H8   108.45  3.000
 1W9  H9   C2A  H8   106.87  3.000
 1W9  H10  C2A  C2   109.97  3.000
 1W9  H9   C2A  C2   111.47  3.000
 1W9  H8   C2A  C2   111.60  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
 1W9  CONST_01  C4   C3   C2   N1     0.00   0.0  0
 1W9  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 1W9  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 1W9  CONST_04  C5   C6   N1   C2     0.00   0.0  0
 1W9  CONST_05  C6   N1   C2   C3     0.00   0.0  0
 1W9  CONST_06  C6   C5   C4   C3     0.00   0.0  0
 1W9  CONST_07  O3   C3   C2   N1   180.00   0.0  0
 1W9  CONST_08  C5A  C5   C6   N1   180.00   0.0  0
 1W9  CONST_09  C4A  C4   C3   C2   180.00   0.0  0
 1W9  CONST_10  C5A  C5   C4   C3   180.00   0.0  0
 1W9  CONST_11  C5   C4   C3   O3   180.00   0.0  0
 1W9  CONST_12  C2A  C2   C3   C4   180.00   0.0  0
 1W9  CONST_13  C2A  C2   N1   C6   180.00   0.0  0
 1W9  CONST_14  C4A  C4   C5   C6   180.00   0.0  0
 1W9  CONST_15  H2   C6   N1   C2   180.00   0.0  0
 1W9  CONST_16  H15  OXT  C    O      0.00   0.0  0
 1W9  Var_01    C3   C4   C4A  N      0.20  30.0  2
 1W9  Var_02    O4P  C5A  C5   C4  -179.48  30.0  2
 1W9  Var_03    H8   C2A  C2   N1   122.29  30.0  2
 1W9  Var_04    C5   C5A  O4P  P    170.73  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
 1W9  chir_01  CA  C  N  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
 1W9  plan-1  N1   0.020
 1W9  plan-1  C2   0.020
 1W9  plan-1  C3   0.020
 1W9  plan-1  O3   0.020
 1W9  plan-1  C4   0.020
 1W9  plan-1  C5   0.020
 1W9  plan-1  C6   0.020
 1W9  plan-1  C4A  0.020
 1W9  plan-1  C5A  0.020
 1W9  plan-1  H2   0.020
 1W9  plan-1  C2A  0.020
 1W9  plan-2  C    0.020
 1W9  plan-2  O    0.020
 1W9  plan-2  CA   0.020
 1W9  plan-2  OXT  0.020
 1W9  plan-2  H15  0.020
 1W9  plan-3  N    0.020
 1W9  plan-3  C4   0.020
 1W9  plan-3  CA   0.020
 1W9  plan-3  C4A  0.020
 1W9  plan-3  H12  0.020

