# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:57:20 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  30  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  CR5    0   0.571   3.4153   1.0227  -0.6640
 JOE  C5   C  C      0   0.533   0.4828   0.0048   0.8357
 JOE  C6   C  C      0  -0.088  -0.7542  -0.7470   0.4517
 JOE  C11  C  C1     0  -0.246  -0.7666  -2.1323   0.5673
 JOE  C7   C  C      0  -0.039  -1.9004  -0.0462   0.0735
 JOE  C8   C  C      0   0.213  -3.0385  -0.8028  -0.1683
 JOE  C9   C  C1     0  -0.256  -3.0806  -2.1838  -0.0423
 JOE  C10  C  C1     0  -0.264  -1.9273  -2.8524   0.3227
 JOE  C12  C  C      0   0.383  -1.8797   1.4808  -0.0248
 JOE  N1   N  NR15   0  -0.679   4.7508   0.7439  -0.8064
 JOE  N2   N  NH1    0  -0.627   1.5983  -0.3980   0.1953
 JOE  C3   C  CR15   0  -0.233   2.8963   0.1369   0.4650
 JOE  N3   N  N      1   0.332  -4.2547  -0.1443  -0.6204
 JOE  C1   C  CR5    0   0.548   5.1967  -0.3173  -0.0518
 JOE  C2   C  CH2    0  -0.595   4.0015  -0.8998   0.6605
 JOE  O1   O  O      0  -0.420   6.3383  -0.7004  -0.0115
 JOE  O2   O  O      0  -0.400   2.7890   1.8287  -1.2992
 JOE  O3   O  O      0  -0.471   0.4662   0.8573   1.7051
 JOE  O4   O  O      0  -0.573  -1.0493   1.9386  -0.8206
 JOE  O5   O  OC    -1  -0.585  -2.6803   2.0717   0.7136
 JOE  O6   O  O     -1  -0.370  -4.1535   0.7167  -1.4594
 JOE  O7   O  O      0  -0.379  -5.3027  -0.5220  -0.1507
 JOE  H1   H  H      0   0.276   0.1300  -2.6583   0.8708
 JOE  H2   H  H      0   0.294  -3.9887  -2.7331  -0.2495
 JOE  H3   H  H      0   0.278  -1.9322  -3.9291   0.4158
 JOE  H4   H  HNR5   0   0.428   5.3531   1.2533  -1.4411
 JOE  H5   H  HNH1   0   0.416   1.5066  -1.0438  -0.5743
 JOE  H6   H  HCR5   0   0.331   2.8233   0.7741   1.3496
 JOE  H7   H  HCH2   0   0.311   4.2279  -1.1072   1.7046
 JOE  H8   H  HCH2   0   0.310   3.7497  -1.8491   0.1802

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    1.205  0.020  1.205
 JOE  N1   C1   single    1.376  0.020  1.376
 JOE  N1   C4   single    1.372  0.020  1.372
 JOE  C1   C2   single    1.508  0.020  1.508
 JOE  O2   C4   double    1.202  0.020  1.202
 JOE  C4   C3   single    1.526  0.020  1.526
 JOE  C2   C3   single    1.528  0.020  1.528
 JOE  C3   N2   single    1.430  0.020  1.430
 JOE  O3   C5   double    1.218  0.020  1.218
 JOE  N2   C5   single    1.348  0.020  1.348
 JOE  C5   C6   single    1.498  0.020  1.498
 JOE  O4   C12  deloc     1.238  0.020  1.238
 JOE  O5   C12  deloc     1.239  0.020  1.239
 JOE  C12  C7   single    1.530  0.020  1.530
 JOE  C6   C7   aromatic  1.396  0.020  1.396
 JOE  C6   C11  aromatic  1.390  0.020  1.390
 JOE  C7   C8   aromatic  1.388  0.020  1.388
 JOE  C11  C10  aromatic  1.388  0.020  1.388
 JOE  C8   C9   aromatic  1.387  0.020  1.387
 JOE  C8   N3   single    1.455  0.020  1.455
 JOE  C10  C9   aromatic  1.382  0.020  1.382
 JOE  O6   N3   single    1.206  0.020  1.206
 JOE  N3   O7   double    1.209  0.020  1.209
 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

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   127.08  3.000
 JOE  C3   C4   N1   106.86  3.000
 JOE  O2   C4   N1   126.05  3.000
 JOE  O3   C5   N2   124.03  3.000
 JOE  N2   C5   C6   114.32  3.000
 JOE  O3   C5   C6   121.55  3.000
 JOE  C7   C6   C11  121.03  3.000
 JOE  C11  C6   C5   119.10  3.000
 JOE  C7   C6   C5   119.72  3.000
 JOE  H1   C11  C10  119.34  3.000
 JOE  H1   C11  C6   119.99  3.000
 JOE  C10  C11  C6   120.65  3.000
 JOE  C12  C7   C8   122.95  3.000
 JOE  C8   C7   C6   116.55  3.000
 JOE  C12  C7   C6   120.49  3.000
 JOE  N3   C8   C9   116.96  3.000
 JOE  N3   C8   C7   119.53  3.000
 JOE  C9   C8   C7   123.49  3.000
 JOE  H2   C9   C10  120.37  3.000
 JOE  H2   C9   C8   120.91  3.000
 JOE  C10  C9   C8   118.70  3.000
 JOE  H3   C10  C9   120.06  3.000
 JOE  H3   C10  C11  120.37  3.000
 JOE  C9   C10  C11  119.57  3.000
 JOE  O5   C12  O4   129.80  3.000
 JOE  O5   C12  C7   115.39  3.000
 JOE  O4   C12  C7   114.80  3.000
 JOE  H4   N1   C1   122.61  3.000
 JOE  H4   N1   C4   122.82  3.000
 JOE  C1   N1   C4   114.53  3.000
 JOE  H5   N2   C3   117.77  3.000
 JOE  H5   N2   C5   118.59  3.000
 JOE  C3   N2   C5   123.37  3.000
 JOE  H6   C3   C2   109.90  3.000
 JOE  H6   C3   N2   108.08  3.000
 JOE  C2   C3   N2   115.28  3.000
 JOE  H6   C3   C4   106.45  3.000
 JOE  N2   C3   C4   112.73  3.000
 JOE  C2   C3   C4   104.04  3.000
 JOE  O7   N3   O6   124.45  3.000
 JOE  O7   N3   C8   117.55  3.000
 JOE  O6   N3   C8   117.97  3.000
 JOE  O1   C1   C2   127.75  3.000
 JOE  C2   C1   N1   107.46  3.000
 JOE  O1   C1   N1   124.78  3.000
 JOE  H8   C2   H7   107.69  3.000
 JOE  H8   C2   C1   108.08  3.000
 JOE  H7   C2   C1   111.21  3.000
 JOE  H8   C2   C3   111.49  3.000
 JOE  H7   C2   C3   113.74  3.000
 JOE  C1   C2   C3   104.52  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  Var_01    C2   C1   N1   C4      3.13  30.0  1
 JOE  Var_02    C3   C2   C1   N1    -12.13  30.0  1
 JOE  Var_03    O4   C12  C7   C6     58.93  30.0  2
 JOE  Var_04    O3   C5   C6   C11  -121.01  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

