# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 11:03:49 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-6-nitro-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1c(cccc1[N+]([O-])=O)C(=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
 JOE  JOE  '2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-6-nitro-benzoic acid'  ligand  31  22  .  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_JOE
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
 JOE  C4   C  C      0   0.581   3.7171  -0.0718  -1.0086
 JOE  C5   C  C      0   0.534   0.4573   0.3099  -0.2346
 JOE  C6   C  CR6    0  -0.025  -0.7637  -0.5558  -0.2740
 JOE  C11  C  CR16   0  -0.261  -0.6995  -1.8411  -0.8022
 JOE  C7   C  CR6    0  -0.013  -1.9850  -0.0321   0.1466
 JOE  C8   C  CR6    0   0.263  -3.1093  -0.8399   0.0364
 JOE  C9   C  CR16   0  -0.259  -3.0596  -2.1165  -0.4986
 JOE  C10  C  CR16   0  -0.242  -1.8414  -2.6158  -0.9211
 JOE  C12  C  C      0   0.469  -2.0756   1.3906   0.6268
 JOE  N1   N  NH1    0  -0.679   4.9963  -0.2307  -0.5458
 JOE  N2   N  NH1    0  -0.634   1.5782  -0.3074   0.1749
 JOE  C3   C  CH1    0  -0.234   2.8599   0.3299   0.1888
 JOE  N3   N  N      1   0.331  -4.3895  -0.3677   0.5458
 JOE  C1   C  C      0   0.551   5.1187  -0.1617   0.8248
 JOE  C2   C  CH2    0  -0.603   3.7317   0.0021   1.3968
 JOE  O1   O  O      0  -0.416   6.1578  -0.2483   1.4268
 JOE  O2   O  O      0  -0.404   3.3480  -0.2066  -2.1452
 JOE  O3   O  O      0  -0.462   0.3988   1.4845  -0.5536
 JOE  O4   O  O      0  -0.411  -2.6320   2.2530   0.0048
 JOE  O5   O  OH1    0  -0.575  -1.4657   1.5413   1.7846
 JOE  O6   O  O     -1  -0.369  -4.3673   0.4196   1.4618
 JOE  O7   O  O      0  -0.357  -5.3926  -0.8035   0.0397
 JOE  H1   H  HCR6   0   0.291   0.2449  -2.2377  -1.1518
 JOE  H2   H  HCR6   0   0.312  -3.9515  -2.7224  -0.5683
 JOE  H3   H  HCR6   0   0.295  -1.7828  -3.6097  -1.3411
 JOE  H4   H  HNH1   0   0.430   5.7820  -0.4245  -1.1549
 JOE  H5   H  HNH1   0   0.424   1.5338  -1.2711   0.4700
 JOE  H6   H  HCH1   0   0.337   2.7096   1.4097   0.1173
 JOE  H7   H  HCH2   0   0.315   3.7111   0.7651   2.1721
 JOE  H8   H  HCH2   0   0.315   3.4434  -0.9478   1.8557
 JOE  H9   H  HOH1   0   0.495  -1.4849   2.4713   2.0607

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
 JOE  O1   C1   double    1.204  0.020  1.204
 JOE  N1   C1   single    1.378  0.020  1.378
 JOE  N1   C4   single    1.370  0.020  1.370
 JOE  C1   C2   single    1.509  0.020  1.509
 JOE  O2   C4   double    1.203  0.020  1.203
 JOE  C4   C3   single    1.526  0.020  1.526
 JOE  C2   C3   single    1.525  0.020  1.525
 JOE  C3   N2   single    1.432  0.020  1.432
 JOE  O3   C5   double    1.219  0.020  1.219
 JOE  N2   C5   single    1.344  0.020  1.344
 JOE  C5   C6   single    1.497  0.020  1.497
 JOE  O4   C12  double    1.200  0.020  1.200
 JOE  O5   C12  single    1.317  0.020  1.317
 JOE  C12  C7   single    1.504  0.020  1.504
 JOE  C6   C7   aromatic  1.394  0.020  1.394
 JOE  C6   C11  aromatic  1.391  0.020  1.391
 JOE  C7   C8   aromatic  1.389  0.020  1.389
 JOE  C11  C10  aromatic  1.385  0.020  1.385
 JOE  C8   C9   aromatic  1.385  0.020  1.385
 JOE  C8   N3   single    1.456  0.020  1.456
 JOE  C10  C9   aromatic  1.383  0.020  1.383
 JOE  O6   N3   single    1.208  0.020  1.208
 JOE  N3   O7   double    1.205  0.020  1.205
 JOE  C11  H1   single    0.930  0.020  1.080
 JOE  C9   H2   single    0.930  0.020  1.080
 JOE  C10  H3   single    0.930  0.020  1.080
 JOE  N1   H4   single    0.860  0.020  1.020
 JOE  N2   H5   single    0.860  0.020  1.020
 JOE  C3   H6   single    0.970  0.020  1.090
 JOE  C2   H7   single    0.970  0.020  1.090
 JOE  C2   H8   single    0.970  0.020  1.090
 JOE  O5   H9   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
 JOE  O2   C4   C3   126.77  3.000
 JOE  C3   C4   N1   106.86  3.000
 JOE  O2   C4   N1   126.37  3.000
 JOE  O3   C5   N2   124.25  3.000
 JOE  N2   C5   C6   115.00  3.000
 JOE  O3   C5   C6   120.75  3.000
 JOE  C7   C6   C11  120.15  3.000
 JOE  C11  C6   C5   120.43  3.000
 JOE  C7   C6   C5   119.30  3.000
 JOE  H1   C11  C10  119.13  3.000
 JOE  H1   C11  C6   120.10  3.000
 JOE  C10  C11  C6   120.75  3.000
 JOE  C12  C7   C8   121.78  3.000
 JOE  C8   C7   C6   117.83  3.000
 JOE  C12  C7   C6   120.30  3.000
 JOE  N3   C8   C9   117.74  3.000
 JOE  N3   C8   C7   119.69  3.000
 JOE  C9   C8   C7   122.53  3.000
 JOE  H2   C9   C10  120.34  3.000
 JOE  H2   C9   C8   120.80  3.000
 JOE  C10  C9   C8   118.85  3.000
 JOE  H3   C10  C9   119.91  3.000
 JOE  H3   C10  C11  120.21  3.000
 JOE  C9   C10  C11  119.88  3.000
 JOE  O5   C12  O4   126.01  3.000
 JOE  O5   C12  C7   111.15  3.000
 JOE  O4   C12  C7   122.83  3.000
 JOE  H4   N1   C1   122.61  3.000
 JOE  H4   N1   C4   122.93  3.000
 JOE  C1   N1   C4   114.41  3.000
 JOE  H5   N2   C3   117.50  3.000
 JOE  H5   N2   C5   119.43  3.000
 JOE  C3   N2   C5   123.05  3.000
 JOE  H6   C3   C2   110.05  3.000
 JOE  H6   C3   N2   108.43  3.000
 JOE  C2   C3   N2   115.07  3.000
 JOE  H6   C3   C4   106.62  3.000
 JOE  N2   C3   C4   112.21  3.000
 JOE  C2   C3   C4   104.11  3.000
 JOE  O7   N3   O6   124.71  3.000
 JOE  O7   N3   C8   117.88  3.000
 JOE  O6   N3   C8   117.41  3.000
 JOE  O1   C1   C2   127.69  3.000
 JOE  C2   C1   N1   107.51  3.000
 JOE  O1   C1   N1   124.78  3.000
 JOE  H8   C2   H7   107.76  3.000
 JOE  H8   C2   C1   107.88  3.000
 JOE  H7   C2   C1   111.32  3.000
 JOE  H8   C2   C3   111.61  3.000
 JOE  H7   C2   C3   113.75  3.000
 JOE  C1   C2   C3   104.39  3.000
 JOE  H9   O5   C12  110.52  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
 JOE  CONST_01  C9   C8   C7   C6     0.00   0.0  0
 JOE  CONST_02  C9   C10  C11  C6     0.00   0.0  0
 JOE  CONST_03  C8   C7   C6   C11    0.00   0.0  0
 JOE  CONST_04  C8   C9   C10  C11    0.00   0.0  0
 JOE  CONST_05  C10  C11  C6   C7     0.00   0.0  0
 JOE  CONST_06  C10  C9   C8   C7     0.00   0.0  0
 JOE  CONST_07  C1   N1   C4   C3     0.00   0.0  0
 JOE  CONST_08  C8   C7   C6   C5   180.00   0.0  0
 JOE  CONST_09  C10  C11  C6   C5   180.00   0.0  0
 JOE  CONST_10  N3   C8   C7   C6   180.00   0.0  0
 JOE  CONST_11  C12  C7   C6   C11  180.00   0.0  0
 JOE  CONST_12  C12  C7   C8   C9   180.00   0.0  0
 JOE  CONST_13  N3   C8   C9   C10  180.00   0.0  0
 JOE  CONST_14  O2   C4   N1   C1   180.00   0.0  0
 JOE  CONST_15  H3   C10  C11  C6   180.00   0.0  0
 JOE  CONST_16  H2   C9   C10  C11  180.00   0.0  0
 JOE  CONST_17  H1   C11  C6   C7   180.00   0.0  0
 JOE  CONST_18  H4   N1   C4   C3   180.00   0.0  0
 JOE  CONST_19  C3   N2   C5   C6   180.00   0.0  0
 JOE  CONST_24  O3   C5   N2   C3     0.00   0.0  0
 JOE  CONST_25  H5   N2   C5   C6     0.00   0.0  0
 JOE  CONST_26  H9   O5   C12  C7   180.00   0.0  0
 JOE  Var_01    C2   C1   N1   C4     3.01  30.0  1
 JOE  Var_02    C3   C2   C1   N1   -12.31  30.0  1
 JOE  Var_03    O4   C12  C7   C6   109.86  30.0  2
 JOE  Var_04    O3   C5   C6   C11  136.16  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
 JOE  chir_01  C3  C4  C2  N2  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
 JOE  plan-1  C5   0.020
 JOE  plan-1  C6   0.020
 JOE  plan-1  C11  0.020
 JOE  plan-1  C7   0.020
 JOE  plan-1  C8   0.020
 JOE  plan-1  C9   0.020
 JOE  plan-1  C10  0.020
 JOE  plan-1  C12  0.020
 JOE  plan-1  N3   0.020
 JOE  plan-1  H1   0.020
 JOE  plan-1  H2   0.020
 JOE  plan-1  H3   0.020
 JOE  plan-2  C8   0.020
 JOE  plan-2  N3   0.020
 JOE  plan-2  O6   0.020
 JOE  plan-2  O7   0.020
 JOE  plan-3  C5   0.020
 JOE  plan-3  C6   0.020
 JOE  plan-3  N2   0.020
 JOE  plan-3  C3   0.020
 JOE  plan-3  O3   0.020
 JOE  plan-3  H5   0.020
 JOE  plan-4  N1   0.020
 JOE  plan-4  C1   0.020
 JOE  plan-4  C2   0.020
 JOE  plan-4  O1   0.020
 JOE  plan-5  C4   0.020
 JOE  plan-5  N1   0.020
 JOE  plan-5  C3   0.020
 JOE  plan-5  C1   0.020
 JOE  plan-5  O2   0.020
 JOE  plan-5  H4   0.020
 JOE  plan-6  C7   0.020
 JOE  plan-6  C12  0.020
 JOE  plan-6  O4   0.020
 JOE  plan-6  O5   0.020
 JOE  plan-6  H9   0.020

