# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 00:46:11 2021
#   Inital geometry file: a 96 line input string
#   Ligand name: (2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[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
 O3Z  O3Z  '(2~{R})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]-3-oxidanyl-propanoic acid'  ligand  39  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_O3Z
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
 O3Z  C3   C  CR6   0   0.266  -10.7050  -39.4278   1.1348
 O3Z  C4   C  CR6   0   0.026  -10.3083  -40.7304   1.4441
 O3Z  C6   C  CR16  0  -0.146  -11.1855  -41.3771  -0.6840
 O3Z  C2   C  CR6   0   0.127  -11.3310  -39.1667  -0.0943
 O3Z  C    C  C     0   0.562   -9.1906  -39.5695   5.6101
 O3Z  OXT  O  OH1   0  -0.580  -10.3225  -39.0670   5.1471
 O3Z  CA   C  CH1   0  -0.246   -8.2167  -39.9936   4.5220
 O3Z  CB   C  CH2   0  -0.165   -7.5192  -41.2894   4.9243
 O3Z  OG   O  OH1   0  -0.665   -8.4869  -42.2606   5.2403
 O3Z  N    N  NH1   0  -0.661   -8.7832  -39.9553   3.1838
 O3Z  C4A  C  CH2   0  -0.333   -9.6799  -41.0394   2.7825
 O3Z  O3   O  OH1   0  -0.646  -10.5224  -38.4008   1.9745
 O3Z  C2A  C  CH3   0  -0.720  -11.7622  -37.7745  -0.4388
 O3Z  N1   N  N     0  -0.408  -11.5601  -40.1332  -0.9666
 O3Z  C5   C  CR6   0  -0.073  -10.5560  -41.7313   0.4986
 O3Z  C5A  C  CH2   0  -0.223  -10.1570  -43.1523   0.7900
 O3Z  O4P  O  O2    0  -0.590  -10.3826  -43.9642  -0.3558
 O3Z  P    P  P     0   1.468  -10.6873  -45.5325  -0.2561
 O3Z  O3P  O  O     0  -0.695  -10.7274  -46.1077  -1.6120
 O3Z  O1P  O  OH1   0  -0.742   -9.6483  -46.1400   0.7893
 O3Z  O2P  O  OH1   0  -0.741  -11.9834  -45.6964   0.6565
 O3Z  H1   H  HCR6  0   0.253  -11.3998  -42.1188  -1.4421
 O3Z  H2   H  HOH1  0   0.485  -10.8873  -38.7900   5.8852
 O3Z  H3   H  HCH1  0   0.321   -7.4412  -39.2187   4.5298
 O3Z  H4   H  HCH2  0   0.228   -6.8798  -41.6004   4.0893
 O3Z  H5   H  HCH2  0   0.224   -6.8556  -41.0866   5.7726
 O3Z  H6   H  HOH1  0   0.462   -8.0482  -43.1118   5.3266
 O3Z  H7   H  HNH1  0   0.388   -8.0170  -39.9051   2.5222
 O3Z  H9   H  HCH2  0   0.275  -10.4728  -41.1386   3.5281
 O3Z  H10  H  HCH2  0   0.253   -9.1695  -42.0039   2.7534
 O3Z  H11  H  HOH1  0   0.481   -9.8668  -38.7044   2.6582
 O3Z  H12  H  HCH3  0   0.244  -12.1662  -37.7496  -1.4488
 O3Z  H13  H  HCH3  0   0.245  -12.5326  -37.4094   0.2437
 O3Z  H14  H  HCH3  0   0.244  -10.9308  -37.0702  -0.3816
 O3Z  H15  H  HCH2  0   0.255  -10.7200  -43.5219   1.6531
 O3Z  H16  H  HCH2  0   0.260   -9.0960  -43.2040   1.0494
 O3Z  H17  H  HOH1  0   0.504   -8.7444  -46.2142   0.4545
 O3Z  H18  H  HOH1  0   0.504  -12.8152  -45.5455   0.1882
 O3Z  O    O  O     0  -0.442   -8.9257  -39.6464   6.7828

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
 O3Z  N1   C6   aromatic  1.330  0.020  1.330
 O3Z  N1   C2   aromatic  1.322  0.020  1.322
 O3Z  O3P  P    double    1.473  0.020  1.473
 O3Z  C6   C5   aromatic  1.386  0.020  1.386
 O3Z  O4P  P    single    1.601  0.020  1.601
 O3Z  O4P  C5A  single    1.422  0.020  1.422
 O3Z  C2A  C2   single    1.498  0.020  1.498
 O3Z  C2   C3   aromatic  1.404  0.020  1.404
 O3Z  P    O2P  single    1.594  0.020  1.594
 O3Z  P    O1P  single    1.594  0.020  1.594
 O3Z  C5   C5A  single    1.504  0.020  1.504
 O3Z  C5   C4   aromatic  1.399  0.020  1.399
 O3Z  C3   C4   aromatic  1.396  0.020  1.396
 O3Z  C3   O3   single    1.339  0.020  1.339
 O3Z  C4   C4A  single    1.511  0.020  1.511
 O3Z  C4A  N    single    1.463  0.020  1.463
 O3Z  N    CA   single    1.454  0.020  1.454
 O3Z  CA   CB   single    1.526  0.020  1.526
 O3Z  CA   C    single    1.521  0.020  1.521
 O3Z  CB   OG   single    1.407  0.020  1.407
 O3Z  C    O    double    1.205  0.020  1.205
 O3Z  C    OXT  single    1.322  0.020  1.322
 O3Z  C6   H1   single    0.930  0.020  1.080
 O3Z  OXT  H2   single    0.850  0.020  0.980
 O3Z  CA   H3   single    0.970  0.020  1.090
 O3Z  CB   H4   single    0.970  0.020  1.090
 O3Z  CB   H5   single    0.970  0.020  1.090
 O3Z  OG   H6   single    0.850  0.020  0.980
 O3Z  N    H7   single    0.890  0.020  1.040
 O3Z  C4A  H9   single    0.970  0.020  1.090
 O3Z  C4A  H10  single    0.970  0.020  1.090
 O3Z  O3   H11  single    0.850  0.020  0.980
 O3Z  C2A  H12  single    0.970  0.020  1.090
 O3Z  C2A  H13  single    0.970  0.020  1.090
 O3Z  C2A  H14  single    0.970  0.020  1.090
 O3Z  C5A  H15  single    0.970  0.020  1.090
 O3Z  C5A  H16  single    0.970  0.020  1.090
 O3Z  O1P  H17  single    0.850  0.020  0.980
 O3Z  O2P  H18  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
 O3Z  O3   C3   C2   117.86  3.000
 O3Z  O3   C3   C4   122.53  3.000
 O3Z  C2   C3   C4   119.61  3.000
 O3Z  C5   C4   C4A  121.74  3.000
 O3Z  C4A  C4   C3   120.36  3.000
 O3Z  C5   C4   C3   117.87  3.000
 O3Z  H1   C6   C5   120.85  3.000
 O3Z  H1   C6   N1   115.89  3.000
 O3Z  C5   C6   N1   123.27  3.000
 O3Z  N1   C2   C2A  118.55  3.000
 O3Z  C2A  C2   C3   120.18  3.000
 O3Z  N1   C2   C3   121.27  3.000
 O3Z  CA   C    OXT  113.82  3.000
 O3Z  OXT  C    O    123.60  3.000
 O3Z  CA   C    O    122.53  3.000
 O3Z  H2   OXT  C    109.91  3.000
 O3Z  H3   CA   N    105.28  3.000
 O3Z  H3   CA   CB   105.97  3.000
 O3Z  N    CA   CB   116.31  3.000
 O3Z  H3   CA   C    104.53  3.000
 O3Z  CB   CA   C    109.94  3.000
 O3Z  N    CA   C    113.69  3.000
 O3Z  H5   CB   H4   106.79  3.000
 O3Z  H5   CB   OG   111.74  3.000
 O3Z  H4   CB   OG   112.11  3.000
 O3Z  H5   CB   CA   108.89  3.000
 O3Z  H4   CB   CA   107.86  3.000
 O3Z  OG   CB   CA   109.33  3.000
 O3Z  H6   OG   CB   108.51  3.000
 O3Z  H7   N    C4A  108.72  3.000
 O3Z  H7   N    CA   107.92  3.000
 O3Z  C4A  N    CA   118.15  3.000
 O3Z  H10  C4A  H9   106.10  3.000
 O3Z  H10  C4A  N    112.05  3.000
 O3Z  H9   C4A  N    108.96  3.000
 O3Z  H10  C4A  C4   110.59  3.000
 O3Z  H9   C4A  C4   108.74  3.000
 O3Z  N    C4A  C4   110.27  3.000
 O3Z  H11  O3   C3   106.67  3.000
 O3Z  H14  C2A  H13  106.80  3.000
 O3Z  H14  C2A  H12  108.47  3.000
 O3Z  H13  C2A  H12  108.10  3.000
 O3Z  H14  C2A  C2   111.62  3.000
 O3Z  H13  C2A  C2   111.72  3.000
 O3Z  H12  C2A  C2   109.98  3.000
 O3Z  C2   N1   C6   119.67  3.000
 O3Z  C5A  C5   C6   121.82  3.000
 O3Z  C5A  C5   C4   119.86  3.000
 O3Z  C6   C5   C4   118.31  3.000
 O3Z  H16  C5A  H15  107.21  3.000
 O3Z  H16  C5A  O4P  108.55  3.000
 O3Z  H15  C5A  O4P  111.15  3.000
 O3Z  H16  C5A  C5   110.36  3.000
 O3Z  H15  C5A  C5   109.58  3.000
 O3Z  O4P  C5A  C5   109.94  3.000
 O3Z  P    O4P  C5A  122.63  3.000
 O3Z  O2P  P    O1P   96.62  3.000
 O3Z  O1P  P    O3P  118.19  3.000
 O3Z  O2P  P    O3P  117.69  3.000
 O3Z  O1P  P    O4P  106.87  3.000
 O3Z  O2P  P    O4P  106.93  3.000
 O3Z  O3P  P    O4P  109.29  3.000
 O3Z  H17  O1P  P    114.30  3.000
 O3Z  H18  O2P  P    113.98  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
 O3Z  CONST_01  C6   N1   C2   C3      0.00   0.0  0
 O3Z  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 O3Z  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 O3Z  CONST_04  N1   C2   C3   C4      0.00   0.0  0
 O3Z  CONST_05  C5   C6   N1   C2      0.00   0.0  0
 O3Z  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 O3Z  CONST_07  C5A  C5   C4   C3    180.00   0.0  0
 O3Z  CONST_08  C2A  C2   C3   C4    180.00   0.0  0
 O3Z  CONST_09  C2A  C2   N1   C6    180.00   0.0  0
 O3Z  CONST_10  C4A  C4   C5   C6    180.00   0.0  0
 O3Z  CONST_11  C4A  C4   C3   C2    180.00   0.0  0
 O3Z  CONST_12  N1   C2   C3   O3    180.00   0.0  0
 O3Z  CONST_13  C5   C4   C3   O3    180.00   0.0  0
 O3Z  CONST_14  C5A  C5   C6   N1    180.00   0.0  0
 O3Z  CONST_15  H1   C6   C5   C4    180.00   0.0  0
 O3Z  CONST_16  H2   OXT  C    O       0.00   0.0  0
 O3Z  Var_01    N    C4A  C4   C3    -38.74  30.0  2
 O3Z  Var_02    O4P  C5A  C5   C4   -174.26  30.0  2
 O3Z  Var_03    H12  C2A  C2   C3    176.32  30.0  2
 O3Z  Var_04    CA   N    C4A  C4    172.34  30.0  3
 O3Z  Var_05    O3P  P    O4P  C5A  -173.91  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
 O3Z  chir_01  CA  N  CB  C  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
 O3Z  plan-1  C3   0.020
 O3Z  plan-1  C4   0.020
 O3Z  plan-1  C6   0.020
 O3Z  plan-1  C2   0.020
 O3Z  plan-1  C4A  0.020
 O3Z  plan-1  O3   0.020
 O3Z  plan-1  C2A  0.020
 O3Z  plan-1  N1   0.020
 O3Z  plan-1  C5   0.020
 O3Z  plan-1  C5A  0.020
 O3Z  plan-1  H1   0.020
 O3Z  plan-2  C    0.020
 O3Z  plan-2  OXT  0.020
 O3Z  plan-2  CA   0.020
 O3Z  plan-2  H2   0.020
 O3Z  plan-2  O    0.020

