# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 23:04:24 2021
#   Inital geometry file: a 143 line input string
#   Ligand name: 5-[(2~{R},3~{Z})-3-[azanyl(phenyl)methylidene]-2-(4-nitrophenyl)-4,5-bis(oxidanylidene)pyrrolidin-1-yl]-2-oxidanyl-benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(/c1ccccc1)=C2/[C@H](N(c3ccc(O)c(c3)C(O)=O)C(=O)C2=O)c4ccc(cc4)[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
 NJW  NJW  '5-[(2~{R},3~{Z})-3-[azanyl(phenyl)methylidene]-2-(4-nitrophenyl)-4,5-bis(oxidanylidene)pyrrolidin-1-yl]-2-oxidanyl-benzoic acid'  ligand  51  34  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NJW
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
 NJW  C19   C  C      0   0.602  32.1152  16.7721  12.1669
 NJW  C17   C  CR16   0  -0.342  33.3262  13.3251  13.0491
 NJW  C14   C  CR6    0  -0.232  32.6147  15.6361  12.9534
 NJW  C18   C  CR16   0  -0.255  33.5521  13.4551  14.4013
 NJW  C15   C  CR6    0   0.379  32.8593  14.4107  12.3022
 NJW  C12   C  CR6    0   0.338  33.3089  14.6659  15.0505
 NJW  C10   C  CR15   0  -0.196  32.6657  14.1234  17.4077
 NJW  C22   C  CR5    0   0.453  34.5559  15.4832  16.9812
 NJW  O23   O  O      0  -0.451  35.4156  16.1007  16.3910
 NJW  C03   C  CR6    0  -0.034  31.5263  13.4296  20.0763
 NJW  C04   C  CR16   0  -0.250  30.3353  14.0160  20.4944
 NJW  C05   C  CR16   0  -0.234  29.1698  13.2659  20.5178
 NJW  C06   C  CR16   0  -0.244  29.1955  11.9273  20.1492
 NJW  C07   C  CR16   0  -0.242  30.3893  11.3359  19.7584
 NJW  C08   C  CR16   0  -0.266  31.5543  12.0871  19.7125
 NJW  C09   C  CR5    0  -0.175  33.2815  14.5365  18.7203
 NJW  C13   C  CR16   0  -0.279  32.8410  15.7425  14.3278
 NJW  C24   C  CR5    0   0.220  34.4167  15.3481  18.4910
 NJW  C26   C  CR6    0   0.189  31.2291  14.5652  17.2463
 NJW  C27   C  CR16   0  -0.285  30.8910  15.9100  17.3691
 NJW  C28   C  CR16   0  -0.255  29.5758  16.3177  17.2719
 NJW  C29   C  CR6    0   0.238  28.5929  15.3590  17.0554
 NJW  C30   C  CR16   0  -0.245  28.9055  14.0170  16.9144
 NJW  C31   C  CR16   0  -0.285  30.2327  13.6323  17.0003
 NJW  N01   N  NH2    0  -0.778  33.2562  14.7326  21.0880
 NJW  N11   N  NR5    0  -0.608  33.5321  14.7861  16.4391
 NJW  N32   N  N      1   0.329  27.2029  15.7754  16.9757
 NJW  O16   O  OH1    0  -0.616  32.6661  14.2304  11.0004
 NJW  O20   O  O      0  -0.482  31.9042  16.7067  10.9664
 NJW  O21   O  OH1    0  -0.578  31.9116  17.8696  12.8640
 NJW  O33   O  O     -1  -0.380  26.3581  14.9200  16.8489
 NJW  O34   O  O      0  -0.380  26.9577  16.9574  17.0418
 NJW  H171  H  HCR6   0   0.281  33.5181  12.3840  12.5507
 NJW  H181  H  HCR6   0   0.282  33.9251  12.6068  14.9613
 NJW  H101  H  HCR5   0   0.289  32.7204  13.0402  17.2502
 NJW  H041  H  HCR6   0   0.266  30.3120  15.0634  20.7668
 NJW  H051  H  HCR6   0   0.264  28.2399  13.7275  20.8218
 NJW  H061  H  HCR6   0   0.264  28.2847  11.3432  20.1666
 NJW  H071  H  HCR6   0   0.265  30.4134  10.2905  19.4808
 NJW  H081  H  HCR6   0   0.270  32.4835  11.6300  19.3955
 NJW  H131  H  HCR6   0   0.277  32.6416  16.6738  14.8402
 NJW  H271  H  HCR6   0   0.268  31.6574  16.6529  17.5539
 NJW  H281  H  HCR6   0   0.296  29.3276  17.3639  17.3735
 NJW  H301  H  HCR6   0   0.295  28.1397  13.2750  16.7427
 NJW  H311  H  HCR6   0   0.269  30.4850  12.5861  16.8900
 NJW  H011  H  HNH2   0   0.421  32.8632  14.4823  21.9800
 NJW  H4    H  HNH2   0   0.421  34.0753  15.3227  21.0754
 NJW  H6    H  HOH1   0   0.496  31.5846  18.5781  12.2889
 NJW  H1    H  HOH1   0   0.481  32.3431  15.0740  10.6175
 NJW  O25   O  O      0  -0.448  35.1822  15.8919  19.2790
 NJW  C02   C  C      0   0.389  32.7490  14.2554  19.9653

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
 NJW  O20  C19   double    1.221  0.020  1.221
 NJW  O16  C15   single    1.328  0.020  1.328
 NJW  C19  O21   single    1.316  0.020  1.316
 NJW  C19  C14   single    1.469  0.020  1.469
 NJW  C15  C14   aromatic  1.409  0.020  1.409
 NJW  C15  C17   aromatic  1.398  0.020  1.398
 NJW  C14  C13   aromatic  1.397  0.020  1.397
 NJW  C17  C18   aromatic  1.377  0.020  1.377
 NJW  C13  C12   aromatic  1.379  0.020  1.379
 NJW  C18  C12   aromatic  1.395  0.020  1.395
 NJW  C12  N11   single    1.412  0.020  1.412
 NJW  N11  C22   single    1.352  0.020  1.352
 NJW  N11  C10   single    1.459  0.020  1.459
 NJW  O33  N32   single    1.209  0.020  1.209
 NJW  O23  C22   double    1.212  0.020  1.212
 NJW  N32  C29   single    1.453  0.020  1.453
 NJW  N32  O34   double    1.209  0.020  1.209
 NJW  C30  C29   aromatic  1.385  0.020  1.385
 NJW  C30  C31   aromatic  1.385  0.020  1.385
 NJW  C22  C24   single    1.522  0.020  1.522
 NJW  C29  C28   aromatic  1.390  0.020  1.390
 NJW  C31  C26   aromatic  1.387  0.020  1.387
 NJW  C28  C27   aromatic  1.380  0.020  1.380
 NJW  C26  C27   aromatic  1.392  0.020  1.392
 NJW  C26  C10   single    1.512  0.020  1.512
 NJW  C10  C09   single    1.508  0.020  1.508
 NJW  C24  C09   single    1.414  0.020  1.414
 NJW  C24  O25   double    1.226  0.020  1.226
 NJW  C09  C02   double    1.383  0.020  1.383
 NJW  C08  C07   aromatic  1.387  0.020  1.387
 NJW  C08  C03   aromatic  1.391  0.020  1.391
 NJW  C07  C06   aromatic  1.388  0.020  1.388
 NJW  C02  C03   single    1.480  0.020  1.480
 NJW  C02  N01   single    1.321  0.020  1.321
 NJW  C03  C04   aromatic  1.392  0.020  1.392
 NJW  C06  C05   aromatic  1.389  0.020  1.389
 NJW  C04  C05   aromatic  1.386  0.020  1.386
 NJW  C17  H171  single    0.930  0.020  1.080
 NJW  C18  H181  single    0.930  0.020  1.080
 NJW  C10  H101  single    0.970  0.020  1.090
 NJW  C04  H041  single    0.930  0.020  1.080
 NJW  C05  H051  single    0.930  0.020  1.080
 NJW  C06  H061  single    0.930  0.020  1.080
 NJW  C07  H071  single    0.930  0.020  1.080
 NJW  C08  H081  single    0.930  0.020  1.080
 NJW  C13  H131  single    0.930  0.020  1.080
 NJW  C27  H271  single    0.930  0.020  1.080
 NJW  C28  H281  single    0.930  0.020  1.080
 NJW  C30  H301  single    0.930  0.020  1.080
 NJW  C31  H311  single    0.930  0.020  1.080
 NJW  N01  H011  single    0.860  0.020  1.020
 NJW  N01  H4    single    0.860  0.020  1.020
 NJW  O21  H6    single    0.850  0.020  0.980
 NJW  O16  H1    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
 NJW  O21   C19  O20   122.61  3.000
 NJW  O21   C19  C14   114.45  3.000
 NJW  O20   C19  C14   122.95  3.000
 NJW  H171  C17  C15   119.24  3.000
 NJW  H171  C17  C18   120.35  3.000
 NJW  C15   C17  C18   120.40  3.000
 NJW  C13   C14  C15   119.53  3.000
 NJW  C13   C14  C19   121.52  3.000
 NJW  C15   C14  C19   118.95  3.000
 NJW  H181  C18  C12   119.95  3.000
 NJW  H181  C18  C17   119.37  3.000
 NJW  C12   C18  C17   120.68  3.000
 NJW  O16   C15  C14   123.07  3.000
 NJW  C14   C15  C17   119.11  3.000
 NJW  O16   C15  C17   117.82  3.000
 NJW  N11   C12  C13   120.19  3.000
 NJW  N11   C12  C18   120.27  3.000
 NJW  C13   C12  C18   119.54  3.000
 NJW  H101  C10  N11   108.91  3.000
 NJW  H101  C10  C26   108.72  3.000
 NJW  N11   C10  C26   111.15  3.000
 NJW  H101  C10  C09   112.06  3.000
 NJW  C26   C10  C09   113.64  3.000
 NJW  N11   C10  C09   102.19  3.000
 NJW  N11   C22  C24   106.42  3.000
 NJW  C24   C22  O23   126.38  3.000
 NJW  N11   C22  O23   127.20  3.000
 NJW  C08   C03  C04   120.16  3.000
 NJW  C04   C03  C02   119.63  3.000
 NJW  C08   C03  C02   120.16  3.000
 NJW  H041  C04  C05   120.08  3.000
 NJW  H041  C04  C03   120.12  3.000
 NJW  C05   C04  C03   119.77  3.000
 NJW  H051  C05  C06   120.13  3.000
 NJW  H051  C05  C04   119.77  3.000
 NJW  C06   C05  C04   120.10  3.000
 NJW  H061  C06  C07   119.89  3.000
 NJW  H061  C06  C05   120.03  3.000
 NJW  C07   C06  C05   120.08  3.000
 NJW  H071  C07  C08   119.75  3.000
 NJW  H071  C07  C06   120.19  3.000
 NJW  C08   C07  C06   120.06  3.000
 NJW  H081  C08  C07   120.12  3.000
 NJW  H081  C08  C03   120.08  3.000
 NJW  C07   C08  C03   119.81  3.000
 NJW  C24   C09  C02   124.87  3.000
 NJW  C02   C09  C10   124.81  3.000
 NJW  C24   C09  C10   110.12  3.000
 NJW  H131  C13  C12   119.13  3.000
 NJW  H131  C13  C14   120.12  3.000
 NJW  C12   C13  C14   120.75  3.000
 NJW  O25   C24  C09   130.67  3.000
 NJW  O25   C24  C22   122.76  3.000
 NJW  C09   C24  C22   106.57  3.000
 NJW  C31   C26  C27   119.40  3.000
 NJW  C27   C26  C10   120.25  3.000
 NJW  C31   C26  C10   120.34  3.000
 NJW  H271  C27  C28   118.92  3.000
 NJW  H271  C27  C26   120.38  3.000
 NJW  C28   C27  C26   120.69  3.000
 NJW  H281  C28  C29   121.35  3.000
 NJW  H281  C28  C27   119.89  3.000
 NJW  C29   C28  C27   118.75  3.000
 NJW  N32   C29  C30   119.20  3.000
 NJW  C30   C29  C28   121.64  3.000
 NJW  N32   C29  C28   119.16  3.000
 NJW  H301  C30  C31   119.91  3.000
 NJW  H301  C30  C29   121.45  3.000
 NJW  C31   C30  C29   118.63  3.000
 NJW  H311  C31  C30   119.07  3.000
 NJW  H311  C31  C26   120.07  3.000
 NJW  C30   C31  C26   120.85  3.000
 NJW  H4    N01  H011  118.25  3.000
 NJW  H4    N01  C02   120.79  3.000
 NJW  H011  N01  C02   120.90  3.000
 NJW  C22   N11  C10   114.69  3.000
 NJW  C10   N11  C12   121.38  3.000
 NJW  C22   N11  C12   123.92  3.000
 NJW  O34   N32  O33   123.77  3.000
 NJW  O34   N32  C29   118.11  3.000
 NJW  O33   N32  C29   118.12  3.000
 NJW  H1    O16  C15   108.28  3.000
 NJW  H6    O21  C19   110.33  3.000
 NJW  N01   C02  C09   122.95  3.000
 NJW  N01   C02  C03   117.07  3.000
 NJW  C09   C02  C03   119.94  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
 NJW  CONST_01  C13   C14  C15  C17     0.00   0.0  0
 NJW  CONST_02  C13   C12  C18  C17     0.00   0.0  0
 NJW  CONST_03  C18   C17  C15  C14     0.00   0.0  0
 NJW  CONST_04  C18   C12  C13  C14     0.00   0.0  0
 NJW  CONST_05  C12   C13  C14  C15     0.00   0.0  0
 NJW  CONST_06  C12   C18  C17  C15     0.00   0.0  0
 NJW  CONST_07  C06   C07  C08  C03     0.00   0.0  0
 NJW  CONST_08  C06   C05  C04  C03     0.00   0.0  0
 NJW  CONST_09  C07   C08  C03  C04     0.00   0.0  0
 NJW  CONST_10  C07   C06  C05  C04     0.00   0.0  0
 NJW  CONST_11  C08   C07  C06  C05     0.00   0.0  0
 NJW  CONST_12  C08   C03  C04  C05     0.00   0.0  0
 NJW  CONST_13  C29   C30  C31  C26     0.00   0.0  0
 NJW  CONST_14  C29   C28  C27  C26     0.00   0.0  0
 NJW  CONST_15  C30   C29  C28  C27     0.00   0.0  0
 NJW  CONST_16  C30   C31  C26  C27     0.00   0.0  0
 NJW  CONST_17  C31   C30  C29  C28     0.00   0.0  0
 NJW  CONST_18  C31   C26  C27  C28     0.00   0.0  0
 NJW  CONST_19  N11   C12  C18  C17   180.00   0.0  0
 NJW  CONST_20  N11   C12  C13  C14   180.00   0.0  0
 NJW  CONST_21  C30   C31  C26  C10   180.00   0.0  0
 NJW  CONST_22  C28   C27  C26  C10   180.00   0.0  0
 NJW  CONST_23  C24   C22  N11  C12   180.00   0.0  0
 NJW  CONST_24  C24   C22  N11  C10     0.00   0.0  0
 NJW  CONST_25  C17   C15  C14  C19   180.00   0.0  0
 NJW  CONST_26  C12   C13  C14  C19   180.00   0.0  0
 NJW  CONST_27  O16   C15  C17  C18   180.00   0.0  0
 NJW  CONST_28  C07   C08  C03  C02   180.00   0.0  0
 NJW  CONST_29  C05   C04  C03  C02   180.00   0.0  0
 NJW  CONST_30  O16   C15  C14  C13   180.00   0.0  0
 NJW  CONST_31  N32   C29  C28  C27   180.00   0.0  0
 NJW  CONST_32  N32   C29  C30  C31   180.00   0.0  0
 NJW  CONST_33  O23   C22  N11  C12     0.00   0.0  0
 NJW  CONST_34  O23   C22  N11  C10   180.00   0.0  0
 NJW  CONST_35  H171  C17  C15  C14   180.00   0.0  0
 NJW  CONST_36  H131  C13  C12  C18   180.00   0.0  0
 NJW  CONST_37  H181  C18  C17  C15   180.00   0.0  0
 NJW  CONST_38  H311  C31  C26  C10     0.00   0.0  0
 NJW  CONST_39  H271  C27  C26  C10     0.00   0.0  0
 NJW  CONST_40  H071  C07  C08  C03   180.00   0.0  0
 NJW  CONST_41  H051  C05  C04  C03   180.00   0.0  0
 NJW  CONST_42  H081  C08  C03  C04   180.00   0.0  0
 NJW  CONST_43  H061  C06  C05  C04   180.00   0.0  0
 NJW  CONST_44  H041  C04  C05  C06   180.00   0.0  0
 NJW  CONST_45  H301  C30  C31  C26   180.00   0.0  0
 NJW  CONST_46  H281  C28  C27  C26   180.00   0.0  0
 NJW  CONST_47  O33   N32  C29  C28   180.00   0.0  0
 NJW  CONST_48  O34   N32  C29  C28     0.00   0.0  0
 NJW  CONST_49  O33   N32  C29  C30     0.00   0.0  0
 NJW  CONST_50  O34   N32  C29  C30   180.00   0.0  0
 NJW  CONST_51  H6    O21  C19  C14   180.00   0.0  0
 NJW  Var_01    C22   N11  C12  C18   107.94  30.0  2
 NJW  Var_02    C22   C24  C09  C10     0.25  30.0  1
 NJW  Var_03    N11   C22  C24  C09     0.60  30.0  1
 NJW  Var_04    C03   C02  C09  C10     3.54   0.0  2
 NJW  Var_05    C09   C02  C03  C04  -110.80  30.0  2
 NJW  Var_06    O20   C19  C14  C15    -0.25  30.0  3
 NJW  Var_07    H011  N01  C02  C03     4.55  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
 NJW  chir_01  C10  N11  C26  C09  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
 NJW  plan-1  C10   0.020
 NJW  plan-1  C03   0.020
 NJW  plan-1  C09   0.020
 NJW  plan-1  C24   0.020
 NJW  plan-1  N01   0.020
 NJW  plan-1  C02   0.020
 NJW  plan-2  C19   0.020
 NJW  plan-2  C17   0.020
 NJW  plan-2  C14   0.020
 NJW  plan-2  C18   0.020
 NJW  plan-2  C15   0.020
 NJW  plan-2  C12   0.020
 NJW  plan-2  C13   0.020
 NJW  plan-2  N11   0.020
 NJW  plan-2  O16   0.020
 NJW  plan-2  H171  0.020
 NJW  plan-2  H181  0.020
 NJW  plan-2  H131  0.020
 NJW  plan-3  C03   0.020
 NJW  plan-3  C04   0.020
 NJW  plan-3  C05   0.020
 NJW  plan-3  C06   0.020
 NJW  plan-3  C07   0.020
 NJW  plan-3  C08   0.020
 NJW  plan-3  H041  0.020
 NJW  plan-3  H051  0.020
 NJW  plan-3  H061  0.020
 NJW  plan-3  H071  0.020
 NJW  plan-3  H081  0.020
 NJW  plan-3  C02   0.020
 NJW  plan-4  C10   0.020
 NJW  plan-4  C26   0.020
 NJW  plan-4  C27   0.020
 NJW  plan-4  C28   0.020
 NJW  plan-4  C29   0.020
 NJW  plan-4  C30   0.020
 NJW  plan-4  C31   0.020
 NJW  plan-4  N32   0.020
 NJW  plan-4  H271  0.020
 NJW  plan-4  H281  0.020
 NJW  plan-4  H301  0.020
 NJW  plan-4  H311  0.020
 NJW  plan-5  C29   0.020
 NJW  plan-5  N32   0.020
 NJW  plan-5  O33   0.020
 NJW  plan-5  O34   0.020
 NJW  plan-6  C22   0.020
 NJW  plan-6  C09   0.020
 NJW  plan-6  C24   0.020
 NJW  plan-6  O25   0.020
 NJW  plan-7  C12   0.020
 NJW  plan-7  C10   0.020
 NJW  plan-7  C22   0.020
 NJW  plan-7  O23   0.020
 NJW  plan-7  C24   0.020
 NJW  plan-7  N11   0.020
 NJW  plan-8  C19   0.020
 NJW  plan-8  C14   0.020
 NJW  plan-8  O20   0.020
 NJW  plan-8  O21   0.020
 NJW  plan-8  H6    0.020

