# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 20:17:59 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNc2cccc(c2)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
 PXG  PXG  '3-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]benzoic acid'  ligand  42  25  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PXG
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
 PXG  N1    N  N     0  -0.404   2.2068   0.4392   3.8098
 PXG  C2    C  CR6   0   0.127   3.1762   0.4554   2.9076
 PXG  C2A   C  CH3   0  -0.787   4.4896   1.0685   3.2908
 PXG  C3    C  CR6   0   0.266   2.9879  -0.0876   1.6289
 PXG  O3    O  OH1   0  -0.619   3.9627  -0.0707   0.7016
 PXG  C5    C  CR6   0  -0.039   0.7580  -0.6593   2.2593
 PXG  C6    C  CR16  0  -0.116   1.0381  -0.1008   3.4984
 PXG  C5A   C  CH2   0  -0.270  -0.6068  -1.2513   2.0250
 PXG  OP4   O  O2    0  -0.579  -1.6412  -0.3191   2.3661
 PXG  P     P  P     0   1.455  -2.1185   0.8021   1.3314
 PXG  OP1   O  OH1   0  -0.731  -3.1711   1.5007   2.3053
 PXG  OP2   O  OH1   0  -0.740  -0.8972   1.8195   1.1375
 PXG  OP3   O  O     0  -0.691  -2.6025   0.3484   0.0166
 PXG  C4    C  CR6   0   0.053   1.7640  -0.6634   1.2920
 PXG  C4A   C  CH2   0  -0.371   1.5319  -1.2347  -0.0828
 PXG  C8    C  CR6   0  -0.078  -1.0367  -0.0021  -4.0531
 PXG  O2    O  OH1   0  -0.595  -2.2341   0.7074  -5.9434
 PXG  C9    C  CR16  0  -0.341  -0.5861   0.2590  -2.7687
 PXG  C10   C  CR6   0   0.421   0.1841  -0.6794  -2.0694
 PXG  C11   C  CR16  0  -0.348   0.4777  -1.8941  -2.7019
 PXG  C12   C  CR16  0  -0.233   0.0104  -2.1500  -3.9837
 PXG  C13   C  CR16  0  -0.304  -0.7434  -1.2183  -4.6759
 PXG  O8    O  O     0  -0.441  -2.1018   2.1218  -4.2284
 PXG  N9    N  NH1   0  -0.698   0.6050  -0.3935  -0.8005
 PXG  H2A1  H  HCH3  0   0.260   5.3142   0.3556   3.2099
 PXG  H2A2  H  HCH3  0   0.260   4.7401   1.9320   2.6691
 PXG  H2A3  H  HCH3  0   0.273   4.4499   1.4095   4.3224
 PXG  HO3   H  HOH1  0   0.490   4.7585   0.3578   1.0358
 PXG  H6    H  HCR6  0   0.263   0.2834  -0.0911   4.2776
 PXG  H5A1  H  HCH2  0   0.267  -0.7364  -1.6003   1.0013
 PXG  H5A2  H  HCH2  0   0.280  -0.7611  -2.1034   2.6866
 PXG  HOP1  H  HOH1  0   0.503  -3.7992   2.0770   1.8497
 PXG  HOP2  H  HOH1  0   0.493  -0.5274   2.1977   1.9465
 PXG  H4A1  H  HCH2  0   0.266   2.4782  -1.3545  -0.6178
 PXG  H4A2  H  HCH2  0   0.255   1.1142  -2.2420   0.0167
 PXG  HO2   H  HOH1  0   0.486  -2.7454   1.4287  -6.3393
 PXG  H9    H  HCR6  0   0.257  -0.8390   1.1966  -2.2910
 PXG  H11   H  HCR6  0   0.275   1.0715  -2.6465  -2.2002
 PXG  H12   H  HCR6  0   0.259   0.2502  -3.0977  -4.4485
 PXG  H13   H  HCR6  0   0.256  -1.0891  -1.4384  -5.6750
 PXG  HN9   H  HNH1  0   0.388   0.5785   0.5753  -0.5282
 PXG  C7    C  C     0   0.533  -1.8364   1.0533  -4.7261

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
 PXG  N1   C2    aromatic  1.324  0.020  1.324
 PXG  N1   C6    aromatic  1.325  0.020  1.325
 PXG  C2   C2A   single    1.499  0.020  1.499
 PXG  C2   C3    aromatic  1.402  0.020  1.402
 PXG  C2A  H2A1  single    0.970  0.020  1.090
 PXG  C2A  H2A2  single    0.970  0.020  1.090
 PXG  C2A  H2A3  single    0.970  0.020  1.090
 PXG  C3   O3    single    1.346  0.020  1.346
 PXG  C3   C4    aromatic  1.394  0.020  1.394
 PXG  O3   HO3   single    0.850  0.020  0.980
 PXG  C5   C6    aromatic  1.388  0.020  1.388
 PXG  C5   C5A   single    1.506  0.020  1.506
 PXG  C5   C4    aromatic  1.396  0.020  1.396
 PXG  C6   H6    single    0.930  0.020  1.080
 PXG  C5A  OP4   single    1.434  0.020  1.434
 PXG  C5A  H5A1  single    0.970  0.020  1.090
 PXG  C5A  H5A2  single    0.970  0.020  1.090
 PXG  OP4  P     single    1.599  0.020  1.599
 PXG  P    OP1   single    1.595  0.020  1.595
 PXG  P    OP2   single    1.601  0.020  1.601
 PXG  P    OP3   double    1.473  0.020  1.473
 PXG  OP1  HOP1  single    0.850  0.020  0.980
 PXG  OP2  HOP2  single    0.850  0.020  0.980
 PXG  C4   C4A   single    1.507  0.020  1.507
 PXG  C4A  N9    single    1.443  0.020  1.443
 PXG  C4A  H4A1  single    0.970  0.020  1.090
 PXG  C4A  H4A2  single    0.970  0.020  1.090
 PXG  C7   C8    single    1.485  0.020  1.485
 PXG  C7   O2    single    1.326  0.020  1.326
 PXG  C7   O8    double    1.208  0.020  1.208
 PXG  C8   C9    aromatic  1.386  0.020  1.386
 PXG  C8   C13   aromatic  1.397  0.020  1.397
 PXG  O2   HO2   single    0.850  0.020  0.980
 PXG  C9   C10   aromatic  1.401  0.020  1.401
 PXG  C9   H9    single    0.930  0.020  1.080
 PXG  C10  C11   aromatic  1.401  0.020  1.401
 PXG  C10  N9    single    1.367  0.020  1.367
 PXG  C11  C12   aromatic  1.388  0.020  1.388
 PXG  C11  H11   single    0.930  0.020  1.080
 PXG  C12  C13   aromatic  1.384  0.020  1.384
 PXG  C12  H12   single    0.930  0.020  1.080
 PXG  C13  H13   single    0.930  0.020  1.080
 PXG  N9   HN9   single    0.890  0.020  1.040

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
 PXG  C6    N1   C2    119.39  3.000
 PXG  C3    C2   C2A   120.61  3.000
 PXG  C3    C2   N1    121.22  3.000
 PXG  C2A   C2   N1    118.18  3.000
 PXG  H2A3  C2A  H2A2  107.47  3.000
 PXG  H2A3  C2A  H2A1  107.60  3.000
 PXG  H2A2  C2A  H2A1  107.47  3.000
 PXG  H2A3  C2A  C2    109.80  3.000
 PXG  H2A2  C2A  C2    112.24  3.000
 PXG  H2A1  C2A  C2    112.04  3.000
 PXG  C4    C3   O3    118.34  3.000
 PXG  C4    C3   C2    119.89  3.000
 PXG  O3    C3   C2    121.76  3.000
 PXG  HO3   O3   C3    111.39  3.000
 PXG  C4    C5   C5A   122.97  3.000
 PXG  C4    C5   C6    118.33  3.000
 PXG  C5A   C5   C6    118.69  3.000
 PXG  H6    C6   C5    120.30  3.000
 PXG  H6    C6   N1    116.19  3.000
 PXG  C5    C6   N1    123.51  3.000
 PXG  H5A2  C5A  H5A1  107.65  3.000
 PXG  H5A2  C5A  OP4   105.18  3.000
 PXG  H5A1  C5A  OP4   110.26  3.000
 PXG  H5A2  C5A  C5    109.94  3.000
 PXG  H5A1  C5A  C5    112.33  3.000
 PXG  OP4   C5A  C5    111.18  3.000
 PXG  P     OP4  C5A   121.16  3.000
 PXG  OP3   P    OP2   109.77  3.000
 PXG  OP3   P    OP1   117.59  3.000
 PXG  OP2   P    OP1   107.39  3.000
 PXG  OP3   P    OP4   117.38  3.000
 PXG  OP2   P    OP4   107.23  3.000
 PXG  OP1   P    OP4    96.26  3.000
 PXG  HOP1  OP1  P     113.71  3.000
 PXG  HOP2  OP2  P     116.04  3.000
 PXG  C4A   C4   C5    121.50  3.000
 PXG  C4A   C4   C3    120.82  3.000
 PXG  C5    C4   C3    117.66  3.000
 PXG  H4A2  C4A  H4A1  105.88  3.000
 PXG  H4A2  C4A  N9    109.67  3.000
 PXG  H4A1  C4A  N9    112.11  3.000
 PXG  H4A2  C4A  C4    108.94  3.000
 PXG  H4A1  C4A  C4    110.77  3.000
 PXG  N9    C4A  C4    109.38  3.000
 PXG  C13   C8   C9    120.58  3.000
 PXG  C13   C8   C7    121.97  3.000
 PXG  C9    C8   C7    117.45  3.000
 PXG  HO2   O2   C7    109.82  3.000
 PXG  H9    C9   C10   119.24  3.000
 PXG  H9    C9   C8    119.76  3.000
 PXG  C10   C9   C8    121.00  3.000
 PXG  N9    C10  C11   122.41  3.000
 PXG  N9    C10  C9    119.50  3.000
 PXG  C11   C10  C9    118.08  3.000
 PXG  H11   C11  C12   119.00  3.000
 PXG  H11   C11  C10   120.58  3.000
 PXG  C12   C11  C10   120.42  3.000
 PXG  H12   C12  C13   119.69  3.000
 PXG  H12   C12  C11   118.90  3.000
 PXG  C13   C12  C11   121.40  3.000
 PXG  H13   C13  C12   119.99  3.000
 PXG  H13   C13  C8    121.50  3.000
 PXG  C12   C13  C8    118.51  3.000
 PXG  HN9   N9   C10   116.37  3.000
 PXG  HN9   N9   C4A   116.33  3.000
 PXG  C10   N9   C4A   122.52  3.000
 PXG  O8    C7   O2    122.87  3.000
 PXG  O8    C7   C8    124.05  3.000
 PXG  O2    C7   C8    113.07  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
 PXG  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 PXG  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PXG  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 PXG  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 PXG  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 PXG  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 PXG  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 PXG  CONST_08  C11   C12  C13  C8      0.00   0.0  0
 PXG  CONST_09  C12   C13  C8   C9      0.00   0.0  0
 PXG  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 PXG  CONST_11  C13   C8   C9   C10     0.00   0.0  0
 PXG  CONST_12  C13   C12  C11  C10     0.00   0.0  0
 PXG  CONST_13  O3    C3   C2   N1    180.00   0.0  0
 PXG  CONST_14  C5A   C5   C6   N1    180.00   0.0  0
 PXG  CONST_15  C4A   C4   C3   C2    180.00   0.0  0
 PXG  CONST_16  C6    N1   C2   C2A   180.00   0.0  0
 PXG  CONST_17  C4    C3   C2   C2A   180.00   0.0  0
 PXG  CONST_18  C5A   C5   C4   C3    180.00   0.0  0
 PXG  CONST_19  C5    C4   C3   O3    180.00   0.0  0
 PXG  CONST_20  C4A   C4   C5   C6    180.00   0.0  0
 PXG  CONST_21  C10   C9   C8   C7    180.00   0.0  0
 PXG  CONST_22  C12   C13  C8   C7    180.00   0.0  0
 PXG  CONST_23  N9    C10  C9   C8    180.00   0.0  0
 PXG  CONST_24  N9    C10  C11  C12   180.00   0.0  0
 PXG  CONST_25  H6    C6   N1   C2    180.00   0.0  0
 PXG  CONST_26  H12   C12  C13  C8    180.00   0.0  0
 PXG  CONST_27  H13   C13  C8   C9    180.00   0.0  0
 PXG  CONST_28  H11   C11  C10  C9    180.00   0.0  0
 PXG  CONST_29  H9    C9   C10  C11   180.00   0.0  0
 PXG  CONST_30  C9    C10  N9   C4A   180.00   0.0  0
 PXG  CONST_31  C11   C10  N9   C4A     0.00   0.0  0
 PXG  CONST_33  HO2   O2   C7   C8    180.00   0.0  0
 PXG  Var_01    N9    C4A  C4   C3   -109.72  30.0  2
 PXG  Var_02    OP4   C5A  C5   C6     52.14  30.0  2
 PXG  Var_03    C10   N9   C4A  C4   -178.63  30.0  3
 PXG  Var_04    C9    C8   C7   O2   -179.32  30.0  2
 PXG  Var_05    H2A1  C2A  C2   N1    120.73  30.0  2
 PXG  Var_06    OP1   P    OP4  C5A  -177.43  30.0  3

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
 PXG  plan-1  N1   0.020
 PXG  plan-1  C2   0.020
 PXG  plan-1  C2A  0.020
 PXG  plan-1  C3   0.020
 PXG  plan-1  O3   0.020
 PXG  plan-1  C5   0.020
 PXG  plan-1  C6   0.020
 PXG  plan-1  C5A  0.020
 PXG  plan-1  C4   0.020
 PXG  plan-1  C4A  0.020
 PXG  plan-1  H6   0.020
 PXG  plan-2  C8   0.020
 PXG  plan-2  C9   0.020
 PXG  plan-2  C10  0.020
 PXG  plan-2  C11  0.020
 PXG  plan-2  C12  0.020
 PXG  plan-2  C13  0.020
 PXG  plan-2  N9   0.020
 PXG  plan-2  H9   0.020
 PXG  plan-2  H11  0.020
 PXG  plan-2  H12  0.020
 PXG  plan-2  H13  0.020
 PXG  plan-2  C7   0.020
 PXG  plan-3  C4A  0.020
 PXG  plan-3  C10  0.020
 PXG  plan-3  N9   0.020
 PXG  plan-3  HN9  0.020
 PXG  plan-4  C8   0.020
 PXG  plan-4  O2   0.020
 PXG  plan-4  O8   0.020
 PXG  plan-4  HO2  0.020
 PXG  plan-4  C7   0.020

