# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 02:39:11 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 4-{[(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)carbamoyl]amino}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=C(NC(=O)Nc2ccc(cc2)C(O)=O)C(=O)N1)N
#
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
 9LO  9LO  '4-{[(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)carbamoyl]amino}benzoic acid'  ligand  34  22  .  2022-07-24  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9LO
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
 9LO  N2A   N  NH2   0  -0.825   6.5479  -1.2346  -0.3509
 9LO  N1    N  N     0  -0.531   4.9775   0.3047  -0.9738
 9LO  C2    C  CR6   0   0.696   5.3523  -0.6631  -0.1764
 9LO  N3    N  NR16  0  -0.720   4.5687  -1.1399   0.8177
 9LO  C4    C  CR6   0   0.527   3.2891  -0.6475   1.0901
 9LO  O4A   O  O     0  -0.507   2.6375  -1.1392   2.0063
 9LO  C5    C  CR6   0  -0.064   2.8907   0.4035   0.2298
 9LO  C6    C  CR6   0   0.492   3.7482   0.8316  -0.7813
 9LO  N7    N  NH2   0  -0.821   3.4025   1.8170  -1.6172
 9LO  O8A   O  O     0  -0.494   0.5266  -0.6872  -0.6853
 9LO  N9    N  NH1   0  -0.787  -0.6613   0.9365   0.4102
 9LO  C1B   C  CR6   0   0.395  -1.9724   0.5673   0.1692
 9LO  C2B   C  CR16  0  -0.346  -2.9660   1.4250   0.6631
 9LO  C3B   C  CR16  0  -0.243  -4.3012   1.1427   0.4802
 9LO  C4B   C  CR6   0  -0.102  -4.6998  -0.0066  -0.2030
 9LO  C5B   C  CR16  0  -0.249  -3.7123  -0.8593  -0.6922
 9LO  C6B   C  CR16  0  -0.306  -2.3669  -0.5884  -0.5142
 9LO  C7B   C  C     0   0.525  -6.1415  -0.2686  -0.3740
 9LO  O7B   O  O     0  -0.448  -7.0151   0.4543   0.0482
 9LO  CAW   C  C     0   0.724   0.4980   0.3234  -0.0088
 9LO  H2A1  H  HNH2  0   0.412   7.1836  -0.8213  -1.0110
 9LO  H2A2  H  HNH2  0   0.416   6.9329  -1.8741   0.3224
 9LO  H71N  H  HNH2  0   0.398   4.0153   2.0725  -2.3710
 9LO  H72N  H  HNH2  0   0.403   2.4884   2.2314  -1.5810
 9LO  H9    H  HNH1  0   0.414  -0.5567   1.7912   0.9372
 9LO  H2B   H  HCR6  0   0.275  -2.6806   2.3246   1.1951
 9LO  H6B   H  HCR6  0   0.286  -1.6368  -1.2766  -0.9046
 9LO  H3B   H  HCR6  0   0.266  -5.0421   1.8257   0.8736
 9LO  H5B   H  HCR6  0   0.267  -3.9794  -1.7620  -1.2244
 9LO  H5A   H  HNH1  0   0.397   1.5262   1.7337   1.0638
 9LO  HN3   H  HNR6  0   0.418   4.9000  -1.8992   1.3977
 9LO  OXT   O  OH1   0  -0.597  -6.3939  -1.3874  -1.0437
 9LO  HXT   H  HOH1  0   0.485  -7.3508  -1.5147  -1.1213
 9LO  N5A   N  NH1   0  -0.756   1.6212   0.9843   0.3942

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
 9LO  N2A  C2    single    1.337  0.020  1.337
 9LO  N1   C2    double    1.309  0.020  1.309
 9LO  N1   C6    single    1.351  0.020  1.351
 9LO  C2   N3    single    1.353  0.020  1.353
 9LO  N3   C4    single    1.398  0.020  1.398
 9LO  C4   O4A   double    1.227  0.020  1.227
 9LO  C4   C5    single    1.415  0.020  1.415
 9LO  N5A  C5    single    1.406  0.020  1.406
 9LO  N5A  CAW   single    1.364  0.020  1.364
 9LO  C5   C6    double    1.393  0.020  1.393
 9LO  C6   N7    single    1.338  0.020  1.338
 9LO  O8A  CAW   double    1.216  0.020  1.216
 9LO  N9   C1B   single    1.383  0.020  1.383
 9LO  N9   CAW   single    1.377  0.020  1.377
 9LO  C1B  C2B   aromatic  1.402  0.020  1.402
 9LO  C1B  C6B   aromatic  1.399  0.020  1.399
 9LO  C2B  C3B   aromatic  1.377  0.020  1.377
 9LO  C3B  C4B   aromatic  1.395  0.020  1.395
 9LO  C4B  C5B   aromatic  1.393  0.020  1.393
 9LO  C4B  C7B   single    1.475  0.020  1.475
 9LO  C5B  C6B   aromatic  1.384  0.020  1.384
 9LO  C7B  O7B   double    1.210  0.020  1.210
 9LO  N2A  H2A1  single    0.860  0.020  1.020
 9LO  N2A  H2A2  single    0.860  0.020  1.020
 9LO  N7   H71N  single    0.860  0.020  1.020
 9LO  N7   H72N  single    0.860  0.020  1.020
 9LO  N9   H9    single    0.860  0.020  1.020
 9LO  C2B  H2B   single    0.930  0.020  1.080
 9LO  C6B  H6B   single    0.930  0.020  1.080
 9LO  C3B  H3B   single    0.930  0.020  1.080
 9LO  C5B  H5B   single    0.930  0.020  1.080
 9LO  N5A  H5A   single    0.860  0.020  1.020
 9LO  N3   HN3   single    0.860  0.020  1.020
 9LO  C7B  OXT   single    1.328  0.020  1.328
 9LO  OXT  HXT   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
 9LO  H2A2  N2A  H2A1  117.34  3.000
 9LO  H2A2  N2A  C2    121.81  3.000
 9LO  H2A1  N2A  C2    118.40  3.000
 9LO  C6    N1   C2    117.52  3.000
 9LO  N3    C2   N1    122.85  3.000
 9LO  N3    C2   N2A   117.61  3.000
 9LO  N1    C2   N2A   119.52  3.000
 9LO  HN3   N3   C4    116.91  3.000
 9LO  HN3   N3   C2    119.76  3.000
 9LO  C4    N3   C2    123.32  3.000
 9LO  C5    C4   O4A   127.01  3.000
 9LO  C5    C4   N3    113.63  3.000
 9LO  O4A   C4   N3    119.36  3.000
 9LO  C6    C5   N5A   120.91  3.000
 9LO  C6    C5   C4    119.74  3.000
 9LO  N5A   C5   C4    119.34  3.000
 9LO  N7    C6   C5    121.39  3.000
 9LO  N7    C6   N1    115.68  3.000
 9LO  C5    C6   N1    122.92  3.000
 9LO  H72N  N7   H71N  118.51  3.000
 9LO  H72N  N7   C6    121.11  3.000
 9LO  H71N  N7   C6    119.91  3.000
 9LO  H9    N9   CAW   116.66  3.000
 9LO  H9    N9   C1B   114.53  3.000
 9LO  CAW   N9   C1B   128.77  3.000
 9LO  C6B   C1B  C2B   118.51  3.000
 9LO  C6B   C1B  N9    124.94  3.000
 9LO  C2B   C1B  N9    116.55  3.000
 9LO  H2B   C2B  C3B   119.40  3.000
 9LO  H2B   C2B  C1B   119.61  3.000
 9LO  C3B   C2B  C1B   120.99  3.000
 9LO  H3B   C3B  C4B   120.17  3.000
 9LO  H3B   C3B  C2B   119.10  3.000
 9LO  C4B   C3B  C2B   120.73  3.000
 9LO  C7B   C4B  C5B   122.90  3.000
 9LO  C7B   C4B  C3B   118.83  3.000
 9LO  C5B   C4B  C3B   118.26  3.000
 9LO  H5B   C5B  C6B   117.83  3.000
 9LO  H5B   C5B  C4B   120.56  3.000
 9LO  C6B   C5B  C4B   121.60  3.000
 9LO  H6B   C6B  C5B   119.18  3.000
 9LO  H6B   C6B  C1B   120.92  3.000
 9LO  C5B   C6B  C1B   119.90  3.000
 9LO  OXT   C7B  O7B   122.83  3.000
 9LO  OXT   C7B  C4B   113.19  3.000
 9LO  O7B   C7B  C4B   123.99  3.000
 9LO  N9    CAW  O8A   123.99  3.000
 9LO  N9    CAW  N5A   112.81  3.000
 9LO  O8A   CAW  N5A   123.19  3.000
 9LO  HXT   OXT  C7B   109.81  3.000
 9LO  H5A   N5A  CAW   118.56  3.000
 9LO  H5A   N5A  C5    117.99  3.000
 9LO  CAW   N5A  C5    120.59  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
 9LO  CONST_01  C4B   C3B  C2B  C1B    0.00   0.0  0
 9LO  CONST_02  C4B   C5B  C6B  C1B    0.00   0.0  0
 9LO  CONST_03  C5B   C6B  C1B  C2B    0.00   0.0  0
 9LO  CONST_04  C5B   C4B  C3B  C2B    0.00   0.0  0
 9LO  CONST_05  C6B   C1B  C2B  C3B    0.00   0.0  0
 9LO  CONST_06  C6B   C5B  C4B  C3B    0.00   0.0  0
 9LO  CONST_07  C4    N3   C2   N1     0.00   0.0  0
 9LO  CONST_08  C5    C6   N1   C2     0.00   0.0  0
 9LO  CONST_09  C5    C4   N3   C2     0.00   0.0  0
 9LO  CONST_10  C6    N1   C2   N3     0.00   0.0  0
 9LO  CONST_11  C3B   C2B  C1B  N9   180.00   0.0  0
 9LO  CONST_12  C5B   C6B  C1B  N9   180.00   0.0  0
 9LO  CONST_13  C7B   C4B  C3B  C2B  180.00   0.0  0
 9LO  CONST_14  C7B   C4B  C5B  C6B  180.00   0.0  0
 9LO  CONST_15  C6    N1   C2   N2A  180.00   0.0  0
 9LO  CONST_16  C4    N3   C2   N2A  180.00   0.0  0
 9LO  CONST_17  N7    C6   N1   C2   180.00   0.0  0
 9LO  CONST_18  O4A   C4   N3   C2   180.00   0.0  0
 9LO  CONST_19  H3B   C3B  C2B  C1B  180.00   0.0  0
 9LO  CONST_20  H5B   C5B  C6B  C1B  180.00   0.0  0
 9LO  CONST_21  H6B   C6B  C1B  C2B  180.00   0.0  0
 9LO  CONST_22  H2B   C2B  C3B  C4B  180.00   0.0  0
 9LO  CONST_23  HN3   N3   C2   N1   180.00   0.0  0
 9LO  CONST_24  CAW   N9   C1B  C2B  180.00   0.0  0
 9LO  CONST_25  CAW   N9   C1B  C6B    0.00   0.0  0
 9LO  CONST_26  H9    N9   C1B  C2B    0.00   0.0  0
 9LO  CONST_27  H2A1  N2A  C2   N1     0.00   0.0  0
 9LO  CONST_28  H2A2  N2A  C2   N1   180.00   0.0  0
 9LO  CONST_29  H71N  N7   C6   N1     0.00   0.0  0
 9LO  CONST_30  H72N  N7   C6   N1   180.00   0.0  0
 9LO  CONST_31  O8A   CAW  N5A  C5     0.00   0.0  0
 9LO  CONST_32  C1B   N9   CAW  O8A    0.00   0.0  0
 9LO  CONST_33  C1B   N9   CAW  N5A  180.00   0.0  0
 9LO  CONST_34  N9    CAW  N5A  C5   180.00   0.0  0
 9LO  CONST_35  HXT   OXT  C7B  C4B  180.00   0.0  0
 9LO  CONST_36  H5A   N5A  CAW  O8A  180.00   0.0  0
 9LO  Var_01    CAW   N5A  C5   C4   -74.72  30.0  2
 9LO  Var_02    O7B   C7B  C4B  C3B   -0.26  30.0  2

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
 9LO  plan-1  N2A   0.020
 9LO  plan-1  N1    0.020
 9LO  plan-1  C2    0.020
 9LO  plan-1  N3    0.020
 9LO  plan-1  C4    0.020
 9LO  plan-1  O4A   0.020
 9LO  plan-1  C5    0.020
 9LO  plan-1  C6    0.020
 9LO  plan-1  N7    0.020
 9LO  plan-1  H2A1  0.020
 9LO  plan-1  H2A2  0.020
 9LO  plan-1  H71N  0.020
 9LO  plan-1  H72N  0.020
 9LO  plan-1  HN3   0.020
 9LO  plan-1  N5A   0.020
 9LO  plan-2  C4B   0.020
 9LO  plan-2  C7B   0.020
 9LO  plan-2  O7B   0.020
 9LO  plan-2  OXT   0.020
 9LO  plan-2  HXT   0.020
 9LO  plan-3  N9    0.020
 9LO  plan-3  C1B   0.020
 9LO  plan-3  C2B   0.020
 9LO  plan-3  C3B   0.020
 9LO  plan-3  C4B   0.020
 9LO  plan-3  C5B   0.020
 9LO  plan-3  C6B   0.020
 9LO  plan-3  C7B   0.020
 9LO  plan-3  H2B   0.020
 9LO  plan-3  H6B   0.020
 9LO  plan-3  H3B   0.020
 9LO  plan-3  H5B   0.020
 9LO  plan-4  C5    0.020
 9LO  plan-4  O8A   0.020
 9LO  plan-4  N9    0.020
 9LO  plan-4  C1B   0.020
 9LO  plan-4  CAW   0.020
 9LO  plan-4  H9    0.020
 9LO  plan-4  H5A   0.020
 9LO  plan-4  N5A   0.020

