# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 05:11:19 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  30  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  -0.420  -5.2191   1.1954  -1.0770
 JO8  C4   C  CR5    0   0.550  -4.2106   0.6977  -0.6451
 JO8  N2   N  NR15   0  -0.678  -4.1153  -0.5894  -0.1636
 JO8  C5   C  CR5    0   0.581  -2.8727  -0.9265   0.3042
 JO8  O3   O  O      0  -0.413  -2.5262  -2.0224   0.6652
 JO8  C3   C  CH2    0  -0.603  -2.8392   1.3196  -0.5543
 JO8  C2   C  CR15   0  -0.222  -2.0317   0.3463   0.3006
 JO8  N1   N  NH1    0  -0.605  -0.6914   0.1134  -0.1305
 JO8  C1   C  C      0   0.493   0.3483  -0.0008   0.7223
 JO8  O1   O  O      0  -0.482   0.2212   0.0262   1.9363
 JO8  C6   C  C      0  -0.140   1.6466  -0.3749   0.0677
 JO8  C11  C  C      0  -0.120   2.6586   0.5590  -0.1598
 JO8  C12  C  C      0   0.401   2.4209   2.0410   0.1062
 JO8  O4   O  OC    -1  -0.588   3.4021   2.7983  -0.0065
 JO8  O5   O  O      0  -0.575   1.2553   2.3644   0.4033
 JO8  C7   C  C      0   0.312   1.8501  -1.7385  -0.2107
 JO8  N3   N  NH2    0  -0.869   0.8513  -2.6782  -0.0621
 JO8  C8   C  C1     0  -0.336   3.0947  -2.1356  -0.7149
 JO8  C9   C  C1     0  -0.242   4.0947  -1.2070  -0.9356
 JO8  C10  C  C1     0  -0.329   3.8828   0.1371  -0.6656
 JO8  H1   H  HNR5   0   0.427  -4.8913  -1.2394  -0.1874
 JO8  H2   H  HCH2   0   0.311  -2.4360   1.4001  -1.5675
 JO8  H3   H  HCH2   0   0.310  -2.8920   2.3256  -0.1426
 JO8  H4   H  HCR5   0   0.325  -2.0031   0.6963   1.3358
 JO8  H5   H  HNH1   0   0.405  -0.5112   0.0561  -1.1203
 JO8  H7   H  HNH2   0   0.382   0.0758  -2.4645   0.5435
 JO8  H8   H  HNH2   0   0.381   1.1637  -3.6292   0.0467
 JO8  H9   H  H      0   0.255   3.2686  -3.1831  -0.9320
 JO8  H10  H  H      0   0.249   5.0481  -1.5398  -1.3264
 JO8  H11  H  H      0   0.238   4.6627   0.8634  -0.8449

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    1.205  0.020  1.205
 JO8  N2   C4   single    1.378  0.020  1.378
 JO8  N2   C5   single    1.370  0.020  1.370
 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    1.527  0.020  1.527
 JO8  C2   N1   single    1.427  0.020  1.427
 JO8  O1   C1   double    1.221  0.020  1.221
 JO8  N1   C1   single    1.350  0.020  1.350
 JO8  C1   C6   single    1.501  0.020  1.501
 JO8  O5   C12  deloc     1.246  0.020  1.246
 JO8  N3   C7   single    1.379  0.020  1.379
 JO8  C6   C7   aromatic  1.406  0.020  1.406
 JO8  C6   C11  aromatic  1.396  0.020  1.396
 JO8  C12  O4   deloc     1.245  0.020  1.245
 JO8  C12  C11  single    1.524  0.020  1.524
 JO8  C7   C8   aromatic  1.400  0.020  1.400
 JO8  C11  C10  aromatic  1.390  0.020  1.390
 JO8  C8   C9   aromatic  1.382  0.020  1.382
 JO8  C10  C9   aromatic  1.387  0.020  1.387
 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  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   107.54  3.000
 JO8  C3   C4   O2   127.76  3.000
 JO8  N2   C4   O2   124.69  3.000
 JO8  H1   N2   C5   123.04  3.000
 JO8  H1   N2   C4   122.59  3.000
 JO8  C5   N2   C4   114.33  3.000
 JO8  C2   C5   O3   126.95  3.000
 JO8  C2   C5   N2   107.10  3.000
 JO8  O3   C5   N2   125.94  3.000
 JO8  H3   C3   H2   107.48  3.000
 JO8  H3   C3   C2   113.78  3.000
 JO8  H2   C3   C2   111.77  3.000
 JO8  H3   C3   C4   111.08  3.000
 JO8  H2   C3   C4   108.05  3.000
 JO8  C2   C3   C4   104.58  3.000
 JO8  H4   C2   N1   108.29  3.000
 JO8  H4   C2   C3   109.88  3.000
 JO8  N1   C2   C3   115.57  3.000
 JO8  H4   C2   C5   106.22  3.000
 JO8  N1   C2   C5   112.48  3.000
 JO8  C3   C2   C5   103.99  3.000
 JO8  H5   N1   C1   118.56  3.000
 JO8  H5   N1   C2   118.29  3.000
 JO8  C1   N1   C2   123.13  3.000
 JO8  C6   C1   O1   121.94  3.000
 JO8  C6   C1   N1   114.32  3.000
 JO8  O1   C1   N1   123.11  3.000
 JO8  C7   C6   C11  120.77  3.000
 JO8  C11  C6   C1   122.10  3.000
 JO8  C7   C6   C1   116.94  3.000
 JO8  C10  C11  C12  119.73  3.000
 JO8  C10  C11  C6   119.65  3.000
 JO8  C12  C11  C6   120.60  3.000
 JO8  O5   C12  O4   126.97  3.000
 JO8  O4   C12  C11  116.92  3.000
 JO8  O5   C12  C11  116.10  3.000
 JO8  C8   C7   N3   119.29  3.000
 JO8  C8   C7   C6   118.34  3.000
 JO8  N3   C7   C6   122.30  3.000
 JO8  H8   N3   H7   111.99  3.000
 JO8  H8   N3   C7   115.49  3.000
 JO8  H7   N3   C7   118.55  3.000
 JO8  H9   C8   C9   120.08  3.000
 JO8  H9   C8   C7   119.26  3.000
 JO8  C9   C8   C7   120.66  3.000
 JO8  H10  C9   C10  120.16  3.000
 JO8  H10  C9   C8   119.22  3.000
 JO8  C10  C9   C8   120.62  3.000
 JO8  H11  C10  C9   120.57  3.000
 JO8  H11  C10  C11  119.47  3.000
 JO8  C9   C10  C11  119.96  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  Var_01    C2   C5   N2   C4     7.55  30.0  1
 JO8  Var_02    C2   C3   C4   N2   -11.61  30.0  1
 JO8  Var_03    C7   C6   C1   N1   -81.64  30.0  2
 JO8  Var_04    O5   C12  C11  C6    -6.74  30.0  2

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

