# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 09:12:21 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-4-nitro-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(cc1C(=O)N[C@H]2CC(=O)NC2=O)[N+]([O-])=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
 JO2  JO2  '2-[[(3~{S})-2,5-bis(oxidanylidene)pyrrolidin-3-yl]carbamoyl]-4-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_JO2
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
 JO2  C4   C  CH2    0  -0.603   3.5779   0.4499   1.1659
 JO2  C5   C  CR6    0  -0.060  -2.0394   1.4445   0.2571
 JO2  C6   C  CR6    0  -0.030  -1.1032   0.4797  -0.1199
 JO2  C11  C  CR16   0  -0.270  -1.4957  -0.8378  -0.2860
 JO2  C7   C  C      0   0.509   0.3072   0.8301  -0.5021
 JO2  C8   C  CR16   0  -0.252  -3.3651   1.0786   0.4567
 JO2  C9   C  CR16   0  -0.252  -3.7679  -0.2363   0.2915
 JO2  C10  C  CR6    0   0.281  -2.8234  -1.1761  -0.0769
 JO2  N1   N  NR15   0  -0.679   4.3533  -1.2435  -0.2353
 JO2  N2   N  NH1    0  -0.616   1.2468   0.2707   0.2781
 JO2  C3   C  CR5    0   0.552   4.7309  -0.4685   0.8393
 JO2  N3   N  N      1   0.330  -3.2334  -2.5659  -0.2567
 JO2  C1   C  CR15   0  -0.232   2.6426   0.3224  -0.0320
 JO2  C2   C  CR5    0   0.581   3.1155  -0.9445  -0.7392
 JO2  O1   O  O      0  -0.416   5.7884  -0.5525   1.4089
 JO2  O2   O  O      0  -0.405   2.5228  -1.5575  -1.5879
 JO2  O3   O  O      0  -0.455   0.5341   1.5087  -1.4854
 JO2  O4   O  O     -1  -0.366  -2.3949  -3.3592  -0.6082
 JO2  O5   O  O      0  -0.365  -4.3877  -2.8438  -0.0431
 JO2  O6   O  O      0  -0.418  -0.4548   3.1015   0.8587
 JO2  O7   O  OH1    0  -0.580  -2.5542   3.7224   0.4077
 JO2  H1   H  HCH2   0   0.313   3.1110   0.0907   2.0873
 JO2  H2   H  HCH2   0   0.314   3.9233   1.4658   1.3464
 JO2  H3   H  HCR6   0   0.308  -0.7723  -1.5833  -0.5880
 JO2  H4   H  HCR6   0   0.296  -4.0991   1.8112   0.7603
 JO2  H5   H  HCR6   0   0.312  -4.8009  -0.5050   0.4548
 JO2  H6   H  HNR5   0   0.429   4.9297  -1.9935  -0.5973
 JO2  H7   H  HNH1   0   0.422   0.9569  -0.2800   1.0724
 JO2  H8   H  HCR5   0   0.336   2.8100   1.1488  -0.7273
 JO2  H9   H  HOH1   0   0.497  -2.2356   4.6091   0.6373
 JO2  C12  C  C      0   0.516  -1.5838   2.8371   0.5340

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
 JO2  O5   N3   double    1.206  0.020  1.206
 JO2  O4   N3   single    1.207  0.020  1.207
 JO2  N3   C10  single    1.460  0.020  1.460
 JO2  C10  C11  aromatic  1.386  0.020  1.386
 JO2  C10  C9   aromatic  1.382  0.020  1.382
 JO2  C11  C6   aromatic  1.385  0.020  1.385
 JO2  C9   C8   aromatic  1.385  0.020  1.385
 JO2  O2   C2   double    1.203  0.020  1.203
 JO2  N1   C2   single    1.370  0.020  1.370
 JO2  N1   C3   single    1.378  0.020  1.378
 JO2  C2   C1   single    1.526  0.020  1.526
 JO2  C3   O1   double    1.204  0.020  1.204
 JO2  C3   C4   single    1.510  0.020  1.510
 JO2  C6   C7   single    1.503  0.020  1.503
 JO2  C6   C5   aromatic  1.396  0.020  1.396
 JO2  C8   C5   aromatic  1.390  0.020  1.390
 JO2  N2   C1   single    1.431  0.020  1.431
 JO2  N2   C7   single    1.343  0.020  1.343
 JO2  C1   C4   single    1.525  0.020  1.525
 JO2  C7   O3   double    1.216  0.020  1.216
 JO2  C5   C12  single    1.491  0.020  1.491
 JO2  C12  O6   double    1.204  0.020  1.204
 JO2  C12  O7   single    1.320  0.020  1.320
 JO2  C4   H1   single    0.970  0.020  1.090
 JO2  C4   H2   single    0.970  0.020  1.090
 JO2  C11  H3   single    0.930  0.020  1.080
 JO2  C8   H4   single    0.930  0.020  1.080
 JO2  C9   H5   single    0.930  0.020  1.080
 JO2  N1   H6   single    0.860  0.020  1.020
 JO2  N2   H7   single    0.860  0.020  1.020
 JO2  C1   H8   single    0.970  0.020  1.090
 JO2  O7   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
 JO2  H2   C4   H1   107.60  3.000
 JO2  H2   C4   C1   113.77  3.000
 JO2  H1   C4   C1   111.87  3.000
 JO2  H2   C4   C3   111.18  3.000
 JO2  H1   C4   C3   107.97  3.000
 JO2  C1   C4   C3   104.34  3.000
 JO2  C12  C5   C8   120.71  3.000
 JO2  C12  C5   C6   119.38  3.000
 JO2  C8   C5   C6   119.77  3.000
 JO2  C7   C6   C11  117.22  3.000
 JO2  C7   C6   C5   122.47  3.000
 JO2  C11  C6   C5   119.99  3.000
 JO2  H3   C11  C10  120.96  3.000
 JO2  H3   C11  C6   119.98  3.000
 JO2  C10  C11  C6   119.06  3.000
 JO2  O3   C7   N2   124.86  3.000
 JO2  O3   C7   C6   120.72  3.000
 JO2  N2   C7   C6   114.31  3.000
 JO2  H4   C8   C9   118.66  3.000
 JO2  H4   C8   C5   120.65  3.000
 JO2  C9   C8   C5   120.68  3.000
 JO2  H5   C9   C10  121.65  3.000
 JO2  H5   C9   C8   119.76  3.000
 JO2  C10  C9   C8   118.59  3.000
 JO2  N3   C10  C9   119.21  3.000
 JO2  C9   C10  C11  121.92  3.000
 JO2  N3   C10  C11  118.87  3.000
 JO2  H6   N1   C2   122.99  3.000
 JO2  H6   N1   C3   122.64  3.000
 JO2  C2   N1   C3   114.33  3.000
 JO2  H7   N2   C1   118.07  3.000
 JO2  H7   N2   C7   118.92  3.000
 JO2  C1   N2   C7   122.78  3.000
 JO2  O1   C3   N1   124.78  3.000
 JO2  O1   C3   C4   127.65  3.000
 JO2  N1   C3   C4   107.55  3.000
 JO2  O5   N3   O4   124.41  3.000
 JO2  O4   N3   C10  117.81  3.000
 JO2  O5   N3   C10  117.79  3.000
 JO2  H8   C1   C2   106.59  3.000
 JO2  H8   C1   N2   108.34  3.000
 JO2  C2   C1   N2   111.89  3.000
 JO2  H8   C1   C4   110.03  3.000
 JO2  N2   C1   C4   115.54  3.000
 JO2  C2   C1   C4   104.09  3.000
 JO2  O2   C2   C1   126.67  3.000
 JO2  C1   C2   N1   106.90  3.000
 JO2  O2   C2   N1   126.42  3.000
 JO2  H9   O7   C12  110.44  3.000
 JO2  O7   C12  O6   124.61  3.000
 JO2  O7   C12  C5   112.59  3.000
 JO2  O6   C12  C5   122.79  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
 JO2  CONST_01  C10  C11  C6   C5     0.00   0.0  0
 JO2  CONST_02  C10  C9   C8   C5     0.00   0.0  0
 JO2  CONST_03  C9   C10  C11  C6     0.00   0.0  0
 JO2  CONST_04  C9   C8   C5   C6     0.00   0.0  0
 JO2  CONST_05  C8   C9   C10  C11    0.00   0.0  0
 JO2  CONST_06  C8   C5   C6   C11    0.00   0.0  0
 JO2  CONST_07  C2   N1   C3   C4     0.00   0.0  0
 JO2  CONST_08  N3   C10  C11  C6   180.00   0.0  0
 JO2  CONST_09  C12  C5   C6   C11  180.00   0.0  0
 JO2  CONST_10  C10  C11  C6   C7   180.00   0.0  0
 JO2  CONST_11  C8   C5   C6   C7   180.00   0.0  0
 JO2  CONST_12  N3   C10  C9   C8   180.00   0.0  0
 JO2  CONST_13  C12  C5   C8   C9   180.00   0.0  0
 JO2  CONST_14  O1   C3   N1   C2   180.00   0.0  0
 JO2  CONST_15  H3   C11  C6   C5   180.00   0.0  0
 JO2  CONST_16  H5   C9   C8   C5   180.00   0.0  0
 JO2  CONST_17  H4   C8   C5   C6   180.00   0.0  0
 JO2  CONST_18  H6   N1   C3   C4   180.00   0.0  0
 JO2  CONST_19  C1   N2   C7   C6   180.00   0.0  0
 JO2  CONST_20  O5   N3   C10  C11  180.00   0.0  0
 JO2  CONST_21  O4   N3   C10  C11    0.00   0.0  0
 JO2  CONST_22  O5   N3   C10  C9     0.00   0.0  0
 JO2  CONST_23  O4   N3   C10  C9   180.00   0.0  0
 JO2  CONST_24  O3   C7   N2   C1     0.00   0.0  0
 JO2  CONST_25  H7   N2   C7   C6     0.00   0.0  0
 JO2  CONST_26  H9   O7   C12  C5   180.00   0.0  0
 JO2  Var_01    C1   C4   C3   N1   -12.33  30.0  1
 JO2  Var_02    C1   C2   N1   C3     8.00  30.0  1
 JO2  Var_03    N2   C7   C6   C5   119.53  30.0  2
 JO2  Var_04    O6   C12  C5   C6   -23.87  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
 JO2  chir_01  C1  C2  N2  C4  negativ

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
 JO2  plan-1  C5   0.020
 JO2  plan-1  C6   0.020
 JO2  plan-1  C11  0.020
 JO2  plan-1  C7   0.020
 JO2  plan-1  C8   0.020
 JO2  plan-1  C9   0.020
 JO2  plan-1  C10  0.020
 JO2  plan-1  N3   0.020
 JO2  plan-1  H3   0.020
 JO2  plan-1  H4   0.020
 JO2  plan-1  H5   0.020
 JO2  plan-1  C12  0.020
 JO2  plan-2  C10  0.020
 JO2  plan-2  N3   0.020
 JO2  plan-2  O4   0.020
 JO2  plan-2  O5   0.020
 JO2  plan-3  C6   0.020
 JO2  plan-3  C7   0.020
 JO2  plan-3  N2   0.020
 JO2  plan-3  C1   0.020
 JO2  plan-3  O3   0.020
 JO2  plan-3  H7   0.020
 JO2  plan-4  N1   0.020
 JO2  plan-4  C1   0.020
 JO2  plan-4  C2   0.020
 JO2  plan-4  O2   0.020
 JO2  plan-5  C4   0.020
 JO2  plan-5  N1   0.020
 JO2  plan-5  C3   0.020
 JO2  plan-5  C2   0.020
 JO2  plan-5  O1   0.020
 JO2  plan-5  H6   0.020
 JO2  plan-6  C5   0.020
 JO2  plan-6  O6   0.020
 JO2  plan-6  O7   0.020
 JO2  plan-6  H9   0.020
 JO2  plan-6  C12  0.020

