# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:08:38 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (1S)-1-carboxy-5-[(3-carboxypropanoyl)amino]-8,9-dihydroxy-1,2,3,4-tetrahydropyrimido[1,2-a]quinolin-11-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)Nc1cc2cc(O)c(O)cc2[n+]3[C@@H](CCNc13)C(O)=O
#
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
 PVE  PVE  (1S)-1-carboxy-5-[(3-carboxypropanoyl)amino]-8,9-dihydroxy-1,2,3,4-tetrahydropyrimido[1,2-a]quinolin-11-ium  ligand  43  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PVE
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
 PVE  O23   O  O      0  -0.693  -70.7411  -28.2466  21.7573
 PVE  C22   C  C      0   0.438  -70.6349  -27.1810  22.4176
 PVE  O24   O  OC    -1  -0.620  -71.5632  -26.5866  22.9849
 PVE  C21   C  CH2    0  -0.552  -69.2372  -26.5601  22.5374
 PVE  C20   C  CH2    0  -0.544  -68.1977  -27.1615  21.6040
 PVE  C18   C  C      0   0.533  -67.9601  -28.6173  21.9042
 PVE  O19   O  O      0  -0.570  -67.6975  -29.0279  23.0202
 PVE  N17   N  NH1    0  -0.710  -68.0256  -29.4555  20.8347
 PVE  C3    C  CR6    0   0.227  -67.9304  -30.8485  20.9878
 PVE  C4    C  CR16   0  -0.217  -66.8199  -31.5288  20.6380
 PVE  C10   C  CR6    0   0.104  -66.7573  -32.9383  20.7633
 PVE  C5    C  C1     0  -0.374  -65.6201  -33.6574  20.3582
 PVE  C6    C  C      0   0.246  -65.5769  -35.0209  20.4629
 PVE  O25   O  OH1    0  -0.651  -64.5361  -35.7988  20.1052
 PVE  C7    C  C      0   0.299  -66.7019  -35.7049  20.9766
 PVE  O26   O  OH1    0  -0.628  -66.7084  -37.0390  21.0751
 PVE  C8    C  C1     0  -0.424  -67.8230  -35.0111  21.3837
 PVE  C9    C  CR6    0   0.417  -67.8654  -33.6156  21.2918
 PVE  N1    N  NR6    1  -0.548  -68.9730  -32.8901  21.7104
 PVE  C14   C  CH1    0  -0.263  -70.1261  -33.6255  22.2393
 PVE  C15   C  C      0   0.418  -70.9800  -34.2162  21.0814
 PVE  O16   O  O      0  -0.674  -70.8015  -33.7329  19.9542
 PVE  C2    C  CR6    0   0.639  -69.0670  -31.5591  21.5163
 PVE  N11   N  NH1    0  -0.698  -70.1628  -30.8913  21.8098
 PVE  C12   C  CH2    0  -0.234  -71.3509  -31.4751  22.3898
 PVE  C13   C  CH2    0  -0.485  -70.9621  -32.7272  23.1354
 PVE  OXT   O  OC    -1  -0.518  -71.7808  -35.0970  21.4356
 PVE  H211  H  HCH2   0   0.234  -69.3071  -25.4852  22.3545
 PVE  H212  H  HCH2   0   0.262  -68.9039  -26.6593  23.5748
 PVE  H201  H  HCH2   0   0.271  -68.4859  -27.0131  20.5620
 PVE  H202  H  HCH2   0   0.270  -67.2442  -26.6434  21.7414
 PVE  H17   H  HNH1   0   0.435  -68.3283  -29.0916  19.9440
 PVE  H4    H  HCR6   0   0.276  -65.9684  -30.9905  20.2407
 PVE  H5    H  H      0   0.284  -64.7734  -33.1129  19.9566
 PVE  H25   H  HOH1   0   0.469  -63.8301  -35.2777  19.7063
 PVE  H26   H  HOH1   0   0.484  -65.8846  -37.4138  20.7388
 PVE  H8    H  H      0   0.280  -68.6523  -35.5961  21.7519
 PVE  H14   H  HCH1   0   0.302  -69.7397  -34.4269  22.8661
 PVE  H131  H  HCH2   0   0.248  -71.8440  -33.2794  23.4546
 PVE  H132  H  HCH2   0   0.306  -70.3976  -32.4649  24.0329
 PVE  H11   H  HNH1   0   0.423  -70.1894  -29.8658  21.6883
 PVE  H121  H  HCH2   0   0.298  -71.7905  -30.7361  23.0579
 PVE  H122  H  HCH2   0   0.243  -72.0863  -31.6841  21.6089

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
 PVE  O23  C22   deloc     1.258  0.020  1.258
 PVE  C22  O24   deloc     1.240  0.020  1.240
 PVE  C22  C21   single    1.534  0.020  1.534
 PVE  C21  C20   single    1.521  0.020  1.521
 PVE  C20  C18   single    1.505  0.020  1.505
 PVE  C18  O19   double    1.218  0.020  1.218
 PVE  C18  N17   single    1.360  0.020  1.360
 PVE  N17  C3    single    1.405  0.020  1.405
 PVE  C3   C4    aromatic  1.348  0.020  1.348
 PVE  C3   C2    aromatic  1.441  0.020  1.441
 PVE  C4   C10   aromatic  1.417  0.020  1.417
 PVE  C10  C5    aromatic  1.405  0.020  1.405
 PVE  C10  C9    aromatic  1.402  0.020  1.402
 PVE  C5   C6    aromatic  1.368  0.020  1.368
 PVE  C6   O25   single    1.348  0.020  1.348
 PVE  C6   C7    aromatic  1.413  0.020  1.413
 PVE  C7   O26   single    1.338  0.020  1.338
 PVE  C7   C8    aromatic  1.380  0.020  1.380
 PVE  C8   C9    aromatic  1.399  0.020  1.399
 PVE  C9   N1    aromatic  1.389  0.020  1.389
 PVE  N1   C14   single    1.466  0.020  1.466
 PVE  N1   C2    aromatic  1.348  0.020  1.348
 PVE  C14  C15   single    1.555  0.020  1.555
 PVE  C14  C13   single    1.519  0.020  1.519
 PVE  C15  O16   deloc     1.239  0.020  1.239
 PVE  C15  OXT   deloc     1.242  0.020  1.242
 PVE  C2   N11   single    1.316  0.020  1.316
 PVE  N11  C12   single    1.445  0.020  1.445
 PVE  C12  C13   single    1.508  0.020  1.508
 PVE  C21  H211  single    0.970  0.020  1.090
 PVE  C21  H212  single    0.970  0.020  1.090
 PVE  C20  H201  single    0.970  0.020  1.090
 PVE  C20  H202  single    0.970  0.020  1.090
 PVE  N17  H17   single    0.860  0.020  1.020
 PVE  C4   H4    single    0.930  0.020  1.080
 PVE  C5   H5    single    0.930  0.020  1.080
 PVE  O25  H25   single    0.850  0.020  0.980
 PVE  O26  H26   single    0.850  0.020  0.980
 PVE  C8   H8    single    0.930  0.020  1.080
 PVE  C14  H14   single    0.970  0.020  1.090
 PVE  C13  H131  single    0.970  0.020  1.090
 PVE  C13  H132  single    0.970  0.020  1.090
 PVE  N11  H11   single    0.860  0.020  1.020
 PVE  C12  H121  single    0.970  0.020  1.090
 PVE  C12  H122  single    0.970  0.020  1.090

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
 PVE  C21   C22  O24   116.90  3.000
 PVE  C21   C22  O23   117.44  3.000
 PVE  O24   C22  O23   125.66  3.000
 PVE  H212  C21  H211  105.51  3.000
 PVE  H212  C21  C20   109.74  3.000
 PVE  H211  C21  C20   109.26  3.000
 PVE  H212  C21  C22   108.36  3.000
 PVE  H211  C21  C22   109.08  3.000
 PVE  C20   C21  C22   114.50  3.000
 PVE  H202  C20  H201  106.60  3.000
 PVE  H202  C20  C18   107.18  3.000
 PVE  H201  C20  C18   111.33  3.000
 PVE  H202  C20  C21   109.35  3.000
 PVE  H201  C20  C21   110.60  3.000
 PVE  C18   C20  C21   111.58  3.000
 PVE  N17   C18  O19   121.54  3.000
 PVE  N17   C18  C20   115.56  3.000
 PVE  O19   C18  C20   122.88  3.000
 PVE  H17   N17  C3    118.32  3.000
 PVE  H17   N17  C18   119.10  3.000
 PVE  C3    N17  C18   121.47  3.000
 PVE  C2    C3   C4    119.73  3.000
 PVE  C2    C3   N17   118.40  3.000
 PVE  C4    C3   N17   121.86  3.000
 PVE  H4    C4   C10   119.49  3.000
 PVE  H4    C4   C3    119.47  3.000
 PVE  C10   C4   C3    121.03  3.000
 PVE  C9    C10  C5    120.07  3.000
 PVE  C9    C10  C4    118.63  3.000
 PVE  C5    C10  C4    121.30  3.000
 PVE  H5    C5   C6    120.29  3.000
 PVE  H5    C5   C10   118.82  3.000
 PVE  C6    C5   C10   120.89  3.000
 PVE  C7    C6   O25   115.59  3.000
 PVE  C7    C6   C5    119.01  3.000
 PVE  O25   C6   C5    125.40  3.000
 PVE  H25   O25  C6    111.31  3.000
 PVE  C8    C7   O26   118.41  3.000
 PVE  C8    C7   C6    120.71  3.000
 PVE  O26   C7   C6    120.88  3.000
 PVE  H26   O26  C7    110.94  3.000
 PVE  H8    C8   C9    122.65  3.000
 PVE  H8    C8   C7    116.89  3.000
 PVE  C9    C8   C7    120.45  3.000
 PVE  N1    C9   C8    121.70  3.000
 PVE  N1    C9   C10   119.44  3.000
 PVE  C8    C9   C10   118.85  3.000
 PVE  C2    N1   C14   119.48  3.000
 PVE  C2    N1   C9    121.87  3.000
 PVE  C14   N1   C9    118.29  3.000
 PVE  H14   C14  C13   106.92  3.000
 PVE  H14   C14  C15   110.12  3.000
 PVE  C13   C14  C15   111.20  3.000
 PVE  H14   C14  N1    107.33  3.000
 PVE  C13   C14  N1    110.42  3.000
 PVE  C15   C14  N1    110.71  3.000
 PVE  OXT   C15  O16   128.96  3.000
 PVE  OXT   C15  C14   114.27  3.000
 PVE  O16   C15  C14   116.74  3.000
 PVE  N11   C2   N1    121.78  3.000
 PVE  N11   C2   C3    119.22  3.000
 PVE  N1    C2   C3    118.99  3.000
 PVE  H11   N11  C12   115.28  3.000
 PVE  H11   N11  C2    119.92  3.000
 PVE  C12   N11  C2    124.67  3.000
 PVE  H122  C12  H121  107.25  3.000
 PVE  H122  C12  C13   111.59  3.000
 PVE  H121  C12  C13   111.35  3.000
 PVE  H122  C12  N11   110.10  3.000
 PVE  H121  C12  N11   107.70  3.000
 PVE  C13   C12  N11   108.77  3.000
 PVE  H132  C13  H131  107.44  3.000
 PVE  H132  C13  C12   109.88  3.000
 PVE  H131  C13  C12   110.93  3.000
 PVE  H132  C13  C14   110.01  3.000
 PVE  H131  C13  C14   108.59  3.000
 PVE  C12   C13  C14   109.94  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
 PVE  CONST_01  C5   C10  C4   C3    180.00   0.0  0
 PVE  CONST_02  C9   C10  C4   C3      0.00   0.0  0
 PVE  CONST_03  C9   N1   C2   C3      0.00   0.0  0
 PVE  CONST_04  N1   C2   C3   C4      0.00   0.0  0
 PVE  CONST_05  C6   C5   C10  C4    180.00   0.0  0
 PVE  CONST_06  C8   C9   C10  C4    180.00   0.0  0
 PVE  CONST_07  N1   C9   C10  C4      0.00   0.0  0
 PVE  CONST_08  C2   C3   C4   C10     0.00   0.0  0
 PVE  CONST_09  C7   C6   C5   C10     0.00   0.0  0
 PVE  CONST_10  C7   C8   C9   C10     0.00   0.0  0
 PVE  CONST_11  C2   N1   C9   C10     0.00   0.0  0
 PVE  CONST_12  C8   C9   C10  C5      0.00   0.0  0
 PVE  CONST_13  N1   C9   C10  C5    180.00   0.0  0
 PVE  CONST_14  C8   C7   C6   C5      0.00   0.0  0
 PVE  CONST_15  C9   C10  C5   C6      0.00   0.0  0
 PVE  CONST_16  C9   C8   C7   C6      0.00   0.0  0
 PVE  CONST_17  N1   C9   C8   C7    180.00   0.0  0
 PVE  CONST_18  C2   N1   C9   C8    180.00   0.0  0
 PVE  CONST_19  C10  C4   C3   N17   180.00   0.0  0
 PVE  CONST_20  N1   C2   C3   N17   180.00   0.0  0
 PVE  CONST_21  N11  C2   C3   N17     0.00   0.0  0
 PVE  CONST_22  O25  C6   C5   C10   180.00   0.0  0
 PVE  CONST_23  O26  C7   C6   C5    180.00   0.0  0
 PVE  CONST_24  C8   C7   C6   O25   180.00   0.0  0
 PVE  CONST_25  C9   C8   C7   O26   180.00   0.0  0
 PVE  CONST_26  H5   C5   C10  C4      0.00   0.0  0
 PVE  CONST_27  H8   C8   C9   C10   180.00   0.0  0
 PVE  CONST_28  H4   C4   C10  C5      0.00   0.0  0
 PVE  CONST_32  C3   N17  C18  C20   180.00   0.0  0
 PVE  CONST_33  C3   N17  C18  O19     0.00   0.0  0
 PVE  Var_01    C12  N11  C2   C3   -177.63  30.0  1
 PVE  Var_02    N11  C12  C13  C14   -51.02  30.0  1
 PVE  Var_03    C13  C12  N11  C2     24.50  30.0  1
 PVE  Var_04    C20  C21  C22  O23    11.87  30.0  3
 PVE  Var_05    C18  C20  C21  C22   -62.97  30.0  3
 PVE  Var_06    O19  C18  C20  C21   -51.94  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
 PVE  chir_01  C14  N1  C15  C13  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
 PVE  plan-1  C20  0.020
 PVE  plan-1  C18  0.020
 PVE  plan-1  O19  0.020
 PVE  plan-1  N17  0.020
 PVE  plan-1  C3   0.020
 PVE  plan-1  H17  0.020
 PVE  plan-2  N17  0.020
 PVE  plan-2  C3   0.020
 PVE  plan-2  C4   0.020
 PVE  plan-2  C10  0.020
 PVE  plan-2  C5   0.020
 PVE  plan-2  C6   0.020
 PVE  plan-2  O25  0.020
 PVE  plan-2  C7   0.020
 PVE  plan-2  O26  0.020
 PVE  plan-2  C8   0.020
 PVE  plan-2  C9   0.020
 PVE  plan-2  N1   0.020
 PVE  plan-2  C14  0.020
 PVE  plan-2  C2   0.020
 PVE  plan-2  N11  0.020
 PVE  plan-2  H4   0.020
 PVE  plan-2  H5   0.020
 PVE  plan-2  H8   0.020
 PVE  plan-3  O23  0.020
 PVE  plan-3  C22  0.020
 PVE  plan-3  O24  0.020
 PVE  plan-3  C21  0.020
 PVE  plan-4  C14  0.020
 PVE  plan-4  C15  0.020
 PVE  plan-4  O16  0.020
 PVE  plan-4  OXT  0.020

