# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 10:15:44 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 3-azanyl-2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(C(O)=O)c1C(=O)N[C@H]2CC(=O)NC2=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
 JO8  JO8  '3-azanyl-2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]benzoic acid'  ligand  31  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JO8
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
 JO8  O2   O  O     0  -0.416  -5.3161   0.9902  -0.9778
 JO8  C4   C  C     0   0.552  -4.2685   0.5601  -0.5689
 JO8  N2   N  NH1   0  -0.677  -4.1053  -0.6699   0.0316
 JO8  C5   C  C     0   0.589  -2.8263  -0.9269   0.4454
 JO8  O3   O  O     0  -0.413  -2.4131  -1.9753   0.8720
 JO8  C3   C  CH2   0  -0.604  -2.9108   1.2155  -0.6381
 JO8  C2   C  CH1   0  -0.226  -2.0374   0.3680   0.2815
 JO8  N1   N  NH1   0  -0.610  -0.7023   0.1397  -0.1730
 JO8  C1   C  C     0   0.474   0.3548   0.0798   0.6590
 JO8  O1   O  O     0  -0.459   0.2823   0.2582   1.8621
 JO8  C6   C  CR6   0  -0.114   1.6417  -0.3245  -0.0003
 JO8  C11  C  CR6   0  -0.074   2.7037   0.5758  -0.1372
 JO8  C12  C  C     0   0.509   2.4693   2.0124   0.1646
 JO8  O4   O  OH1   0  -0.589   3.5900   2.6856   0.3760
 JO8  O5   O  O     0  -0.432   1.3745   2.5197   0.1975
 JO8  C7   C  CR6   0   0.336   1.8133  -1.6742  -0.3470
 JO8  N3   N  NH2   0  -0.870   0.7961  -2.5914  -0.2674
 JO8  C8   C  CR16  0  -0.316   3.0652  -2.0775  -0.8373
 JO8  C9   C  CR16  0  -0.238   4.1018  -1.1789  -0.9714
 JO8  C10  C  CR16  0  -0.301   3.9347   0.1555  -0.6242
 JO8  H1   H  HNH1  0   0.429  -4.8613  -1.3376   0.1219
 JO8  H2   H  HCH2  0   0.314  -2.5680   1.1716  -1.6755
 JO8  H3   H  HCH2  0   0.313  -2.9645   2.2632  -0.3501
 JO8  H4   H  HCH1  0   0.333  -1.9907   0.8281   1.2722
 JO8  H5   H  HNH1  0   0.416  -0.5552  -0.0319  -1.1562
 JO8  H6   H  HOH1  0   0.489   3.3903   3.6225   0.5216
 JO8  H7   H  HNH2  0   0.388   0.0060  -2.4006   0.3272
 JO8  H8   H  HNH2  0   0.391   1.0745  -3.5585  -0.2430
 JO8  H9   H  HCR6  0   0.272   3.2130  -3.1157  -1.1093
 JO8  H10  H  HCR6  0   0.267   5.0542  -1.5202  -1.3545
 JO8  H11  H  HCR6  0   0.266   4.7515   0.8505  -0.7502

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
 JO8  O2   C4   double    1.204  0.020  1.204
 JO8  N2   C4   single    1.378  0.020  1.378
 JO8  N2   C5   single    1.369  0.020  1.369
 JO8  C4   C3   single    1.509  0.020  1.509
 JO8  O3   C5   double    1.205  0.020  1.205
 JO8  C5   C2   single    1.525  0.020  1.525
 JO8  C3   C2   single    1.525  0.020  1.525
 JO8  C2   N1   single    1.429  0.020  1.429
 JO8  O1   C1   double    1.218  0.020  1.218
 JO8  N1   C1   single    1.347  0.020  1.347
 JO8  C1   C6   single    1.501  0.020  1.501
 JO8  O5   C12  double    1.207  0.020  1.207
 JO8  N3   C7   single    1.372  0.020  1.372
 JO8  C6   C7   aromatic  1.404  0.020  1.404
 JO8  C6   C11  aromatic  1.399  0.020  1.399
 JO8  C12  O4   single    1.324  0.020  1.324
 JO8  C12  C11  single    1.487  0.020  1.487
 JO8  C7   C8   aromatic  1.404  0.020  1.404
 JO8  C11  C10  aromatic  1.389  0.020  1.389
 JO8  C8   C9   aromatic  1.378  0.020  1.378
 JO8  C10  C9   aromatic  1.389  0.020  1.389
 JO8  N2   H1   single    0.860  0.020  1.020
 JO8  C3   H2   single    0.970  0.020  1.090
 JO8  C3   H3   single    0.970  0.020  1.090
 JO8  C2   H4   single    0.970  0.020  1.090
 JO8  N1   H5   single    0.860  0.020  1.020
 JO8  O4   H6   single    0.850  0.020  0.980
 JO8  N3   H7   single    0.890  0.020  1.040
 JO8  N3   H8   single    0.890  0.020  1.040
 JO8  C8   H9   single    0.930  0.020  1.080
 JO8  C9   H10  single    0.930  0.020  1.080
 JO8  C10  H11  single    0.930  0.020  1.080

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
 JO8  C3   C4   N2   107.51  3.000
 JO8  C3   C4   O2   127.73  3.000
 JO8  N2   C4   O2   124.74  3.000
 JO8  H1   N2   C5   123.15  3.000
 JO8  H1   N2   C4   122.60  3.000
 JO8  C5   N2   C4   114.20  3.000
 JO8  C2   C5   O3   126.83  3.000
 JO8  C2   C5   N2   106.94  3.000
 JO8  O3   C5   N2   126.23  3.000
 JO8  H3   C3   H2   107.78  3.000
 JO8  H3   C3   C2   113.81  3.000
 JO8  H2   C3   C2   111.72  3.000
 JO8  H3   C3   C4   111.20  3.000
 JO8  H2   C3   C4   107.95  3.000
 JO8  C2   C3   C4   104.25  3.000
 JO8  H4   C2   N1   108.39  3.000
 JO8  H4   C2   C3   109.69  3.000
 JO8  N1   C2   C3   115.60  3.000
 JO8  H4   C2   C5   106.38  3.000
 JO8  N1   C2   C5   112.45  3.000
 JO8  C3   C2   C5   103.91  3.000
 JO8  H5   N1   C1   118.70  3.000
 JO8  H5   N1   C2   118.26  3.000
 JO8  C1   N1   C2   122.96  3.000
 JO8  C6   C1   O1   121.61  3.000
 JO8  C6   C1   N1   114.42  3.000
 JO8  O1   C1   N1   123.84  3.000
 JO8  C7   C6   C11  120.11  3.000
 JO8  C11  C6   C1   121.36  3.000
 JO8  C7   C6   C1   118.17  3.000
 JO8  C10  C11  C12  120.23  3.000
 JO8  C10  C11  C6   120.82  3.000
 JO8  C12  C11  C6   118.84  3.000
 JO8  O5   C12  O4   123.33  3.000
 JO8  O4   C12  C11  112.97  3.000
 JO8  O5   C12  C11  123.70  3.000
 JO8  H6   O4   C12  109.94  3.000
 JO8  C8   C7   N3   119.31  3.000
 JO8  C8   C7   C6   118.13  3.000
 JO8  N3   C7   C6   122.53  3.000
 JO8  H8   N3   H7   112.62  3.000
 JO8  H8   N3   C7   116.01  3.000
 JO8  H7   N3   C7   119.29  3.000
 JO8  H9   C8   C9   119.85  3.000
 JO8  H9   C8   C7   118.99  3.000
 JO8  C9   C8   C7   121.16  3.000
 JO8  H10  C9   C10  119.84  3.000
 JO8  H10  C9   C8   119.40  3.000
 JO8  C10  C9   C8   120.77  3.000
 JO8  H11  C10  C9   119.88  3.000
 JO8  H11  C10  C11  121.10  3.000
 JO8  C9   C10  C11  119.02  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
 JO8  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 JO8  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 JO8  CONST_03  C8   C7   C6   C11    0.00   0.0  0
 JO8  CONST_04  C8   C9   C10  C11    0.00   0.0  0
 JO8  CONST_05  C10  C11  C6   C7     0.00   0.0  0
 JO8  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 JO8  CONST_07  C3   C4   N2   C5     0.00   0.0  0
 JO8  CONST_08  C8   C7   C6   C1   180.00   0.0  0
 JO8  CONST_09  C10  C11  C6   C1   180.00   0.0  0
 JO8  CONST_10  N3   C7   C6   C11  180.00   0.0  0
 JO8  CONST_11  C7   C6   C11  C12  180.00   0.0  0
 JO8  CONST_12  C9   C10  C11  C12  180.00   0.0  0
 JO8  CONST_13  C9   C8   C7   N3   180.00   0.0  0
 JO8  CONST_14  C5   N2   C4   O2   180.00   0.0  0
 JO8  CONST_15  H9   C8   C7   C6   180.00   0.0  0
 JO8  CONST_16  H11  C10  C11  C6   180.00   0.0  0
 JO8  CONST_17  H10  C9   C10  C11  180.00   0.0  0
 JO8  CONST_18  H1   N2   C4   C3   180.00   0.0  0
 JO8  CONST_19  C6   C1   N1   C2   180.00   0.0  0
 JO8  CONST_22  O1   C1   N1   C2     0.00   0.0  0
 JO8  CONST_23  H5   N1   C1   C6     0.00   0.0  0
 JO8  CONST_24  H6   O4   C12  C11  180.00   0.0  0
 JO8  Var_01    C2   C5   N2   C4     8.62  30.0  1
 JO8  Var_02    C2   C3   C4   N2   -13.08  30.0  1
 JO8  Var_03    C7   C6   C1   N1   -74.91  30.0  2
 JO8  Var_04    O5   C12  C11  C6   -19.21  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
 JO8  chir_01  C2  C5  C3  N1  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
 JO8  plan-1  C1   0.020
 JO8  plan-1  C6   0.020
 JO8  plan-1  C11  0.020
 JO8  plan-1  C12  0.020
 JO8  plan-1  C7   0.020
 JO8  plan-1  N3   0.020
 JO8  plan-1  C8   0.020
 JO8  plan-1  C9   0.020
 JO8  plan-1  C10  0.020
 JO8  plan-1  H9   0.020
 JO8  plan-1  H10  0.020
 JO8  plan-1  H11  0.020
 JO8  plan-2  C7   0.020
 JO8  plan-2  N3   0.020
 JO8  plan-2  H7   0.020
 JO8  plan-2  H8   0.020
 JO8  plan-3  N2   0.020
 JO8  plan-3  C5   0.020
 JO8  plan-3  O3   0.020
 JO8  plan-3  C2   0.020
 JO8  plan-4  C2   0.020
 JO8  plan-4  N1   0.020
 JO8  plan-4  C1   0.020
 JO8  plan-4  O1   0.020
 JO8  plan-4  C6   0.020
 JO8  plan-4  H5   0.020
 JO8  plan-5  O2   0.020
 JO8  plan-5  C4   0.020
 JO8  plan-5  N2   0.020
 JO8  plan-5  C5   0.020
 JO8  plan-5  C3   0.020
 JO8  plan-5  H1   0.020
 JO8  plan-6  C11  0.020
 JO8  plan-6  C12  0.020
 JO8  plan-6  O4   0.020
 JO8  plan-6  O5   0.020
 JO8  plan-6  H6   0.020

