# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 11:41:26 2022
#   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  50  34  .  2022-03-23  2022-03-23
;
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   0.493  31.9743  16.7869  12.2253
 NJW  C17   C  CR16   0  -0.360  33.3465  13.3302  13.0505
 NJW  C14   C  CR6    0  -0.282  32.5484  15.6194  12.9893
 NJW  C18   C  CR16   0  -0.268  33.5928  13.4557  14.4040
 NJW  C15   C  CR6    0   0.365  32.8245  14.4076  12.3244
 NJW  C12   C  CR6    0   0.313  33.3192  14.6511  15.0636
 NJW  C10   C  CR15   0  -0.191  32.6740  14.1227  17.4244
 NJW  C22   C  CR5    0   0.448  34.5885  15.4426  16.9960
 NJW  O23   O  O      0  -0.451  35.4689  16.0359  16.4094
 NJW  C03   C  CR6    0  -0.018  31.5487  13.4233  20.1292
 NJW  C04   C  CR16   0  -0.264  30.3962  13.9731  20.6845
 NJW  C05   C  CR16   0  -0.241  29.2445  13.2074  20.7855
 NJW  C06   C  CR16   0  -0.247  29.2456  11.8878  20.3526
 NJW  C07   C  CR16   0  -0.238  30.4001  11.3336  19.8162
 NJW  C08   C  CR16   0  -0.267  31.5495  12.1004  19.6978
 NJW  C09   C  CR5    0  -0.181  33.2901  14.5283  18.7381
 NJW  C13   C  CR16   0  -0.302  32.7992  15.7186  14.3507
 NJW  C24   C  CR5    0   0.216  34.4409  15.3203  18.5065
 NJW  C26   C  CR6    0   0.186  31.2445  14.5794  17.2437
 NJW  C27   C  CR16   0  -0.283  30.9020  15.9164  17.4266
 NJW  C28   C  CR16   0  -0.256  29.5963  16.3375  17.2692
 NJW  C29   C  CR6    0   0.237  28.6283  15.4024  16.9234
 NJW  C30   C  CR16   0  -0.254  28.9447  14.0680  16.7263
 NJW  C31   C  CR16   0  -0.294  30.2613  13.6681  16.8856
 NJW  N01   N  NH2    0  -0.784  33.2820  14.7476  21.1007
 NJW  N11   N  NR5    0  -0.598  33.5527  14.7676  16.4544
 NJW  N32   N  N      1   0.327  27.2491  15.8360  16.7634
 NJW  O16   O  OH1    0  -0.649  32.5926  14.2795  11.0252
 NJW  O20   O  O      0  -0.625  31.7866  16.5822  10.9840
 NJW  O21   O  OC    -1  -0.539  31.7273  17.8343  12.8251
 NJW  O33   O  O     -1  -0.376  26.4290  15.0129  16.4311
 NJW  O34   O  O      0  -0.376  26.9917  16.9988  16.9702
 NJW  H171  H  HCR6   0   0.255  33.5606  12.3988  12.5412
 NJW  H181  H  HCR6   0   0.262  34.0013  12.6175  14.9557
 NJW  H101  H  HCR5   0   0.287  32.7148  13.0396  17.2650
 NJW  H041  H  HCR6   0   0.267  30.3917  15.0045  21.0141
 NJW  H051  H  HCR6   0   0.264  28.3454  13.6423  21.2017
 NJW  H061  H  HCR6   0   0.264  28.3468  11.2906  20.4349
 NJW  H071  H  HCR6   0   0.264  30.4068  10.3029  19.4871
 NJW  H081  H  HCR6   0   0.271  32.4488  11.6674  19.2777
 NJW  H131  H  HCR6   0   0.252  32.5748  16.6470  14.8603
 NJW  H271  H  HCR6   0   0.271  31.6598  16.6389  17.7034
 NJW  H281  H  HCR6   0   0.295  29.3427  17.3771  17.4161
 NJW  H301  H  HCR6   0   0.296  28.1899  13.3454  16.4524
 NJW  H311  H  HCR6   0   0.272  30.5205  12.6282  16.7337
 NJW  H011  H  HNH2   0   0.418  32.9129  14.4916  22.0014
 NJW  H4    H  HNH2   0   0.419  34.0989  15.3407  21.0684
 NJW  H1    H  HOH1   0   0.459  32.2188  15.2049  10.7606
 NJW  C02   C  C      0   0.387  32.7642  14.2548  19.9865
 NJW  O25   O  O      0  -0.444  35.2149  15.8511  19.2954

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   deloc     1.272  0.020  1.272
 NJW  O16  C15   single    1.326  0.020  1.326
 NJW  C19  O21   deloc     1.232  0.020  1.232
 NJW  C19  C14   single    1.509  0.020  1.509
 NJW  C15  C14   aromatic  1.410  0.020  1.410
 NJW  C15  C17   aromatic  1.400  0.020  1.400
 NJW  C14  C13   aromatic  1.388  0.020  1.388
 NJW  C17  C18   aromatic  1.381  0.020  1.381
 NJW  C13  C12   aromatic  1.385  0.020  1.385
 NJW  C18  C12   aromatic  1.393  0.020  1.393
 NJW  C12  N11   single    1.415  0.020  1.415
 NJW  N11  C22   single    1.350  0.020  1.350
 NJW  N11  C10   single    1.459  0.020  1.459
 NJW  O33  N32   single    1.209  0.020  1.209
 NJW  O23  C22   double    1.213  0.020  1.213
 NJW  N32  C29   single    1.455  0.020  1.455
 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    1.523  0.020  1.523
 NJW  C29  C28   aromatic  1.390  0.020  1.390
 NJW  C31  C26   aromatic  1.388  0.020  1.388
 NJW  C28  C27   aromatic  1.381  0.020  1.381
 NJW  C26  C27   aromatic  1.392  0.020  1.392
 NJW  C26  C10   single    1.512  0.020  1.512
 NJW  C10  C09   single    1.507  0.020  1.507
 NJW  C24  C09   single    1.416  0.020  1.416
 NJW  C24  O25   double    1.226  0.020  1.226
 NJW  C09  C02   double    1.382  0.020  1.382
 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    1.324  0.020  1.324
 NJW  C03  C04   aromatic  1.392  0.020  1.392
 NJW  C06  C05   aromatic  1.389  0.020  1.389
 NJW  C04  C05   aromatic  1.387  0.020  1.387
 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  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   125.62  3.000
 NJW  O21   C19  C14   119.18  3.000
 NJW  O20   C19  C14   115.20  3.000
 NJW  H171  C17  C15   119.45  3.000
 NJW  H171  C17  C18   120.24  3.000
 NJW  C15   C17  C18   120.31  3.000
 NJW  C13   C14  C15   119.25  3.000
 NJW  C13   C14  C19   120.68  3.000
 NJW  C15   C14  C19   120.06  3.000
 NJW  H181  C18  C12   119.81  3.000
 NJW  H181  C18  C17   119.73  3.000
 NJW  C12   C18  C17   120.47  3.000
 NJW  O16   C15  C14   120.73  3.000
 NJW  C14   C15  C17   119.34  3.000
 NJW  O16   C15  C17   119.94  3.000
 NJW  N11   C12  C13   120.29  3.000
 NJW  N11   C12  C18   120.25  3.000
 NJW  C13   C12  C18   119.45  3.000
 NJW  H101  C10  N11   108.53  3.000
 NJW  H101  C10  C26   108.46  3.000
 NJW  N11   C10  C26   110.88  3.000
 NJW  H101  C10  C09   112.20  3.000
 NJW  C26   C10  C09   114.18  3.000
 NJW  N11   C10  C09   102.38  3.000
 NJW  N11   C22  C24   106.47  3.000
 NJW  C24   C22  O23   126.12  3.000
 NJW  N11   C22  O23   127.41  3.000
 NJW  C08   C03  C04   119.96  3.000
 NJW  C04   C03  C02   119.77  3.000
 NJW  C08   C03  C02   120.26  3.000
 NJW  H041  C04  C05   120.02  3.000
 NJW  H041  C04  C03   120.06  3.000
 NJW  C05   C04  C03   119.90  3.000
 NJW  H051  C05  C06   120.17  3.000
 NJW  H051  C05  C04   119.74  3.000
 NJW  C06   C05  C04   120.08  3.000
 NJW  H061  C06  C07   119.98  3.000
 NJW  H061  C06  C05   119.99  3.000
 NJW  C07   C06  C05   120.03  3.000
 NJW  H071  C07  C08   119.71  3.000
 NJW  H071  C07  C06   120.19  3.000
 NJW  C08   C07  C06   120.09  3.000
 NJW  H081  C08  C07   120.02  3.000
 NJW  H081  C08  C03   120.06  3.000
 NJW  C07   C08  C03   119.92  3.000
 NJW  C24   C09  C02   124.58  3.000
 NJW  C02   C09  C10   125.36  3.000
 NJW  C24   C09  C10   109.90  3.000
 NJW  H131  C13  C12   119.77  3.000
 NJW  H131  C13  C14   119.05  3.000
 NJW  C12   C13  C14   121.18  3.000
 NJW  O25   C24  C09   130.54  3.000
 NJW  O25   C24  C22   122.84  3.000
 NJW  C09   C24  C22   106.61  3.000
 NJW  C31   C26  C27   119.37  3.000
 NJW  C27   C26  C10   120.47  3.000
 NJW  C31   C26  C10   120.16  3.000
 NJW  H271  C27  C28   119.17  3.000
 NJW  H271  C27  C26   120.14  3.000
 NJW  C28   C27  C26   120.69  3.000
 NJW  H281  C28  C29   121.20  3.000
 NJW  H281  C28  C27   120.00  3.000
 NJW  C29   C28  C27   118.81  3.000
 NJW  N32   C29  C30   119.21  3.000
 NJW  C30   C29  C28   121.63  3.000
 NJW  N32   C29  C28   119.16  3.000
 NJW  H301  C30  C31   120.01  3.000
 NJW  H301  C30  C29   121.38  3.000
 NJW  C31   C30  C29   118.61  3.000
 NJW  H311  C31  C30   119.26  3.000
 NJW  H311  C31  C26   119.84  3.000
 NJW  C30   C31  C26   120.90  3.000
 NJW  H4    N01  H011  118.33  3.000
 NJW  H4    N01  C02   120.53  3.000
 NJW  H011  N01  C02   121.01  3.000
 NJW  C22   N11  C10   114.61  3.000
 NJW  C10   N11  C12   121.17  3.000
 NJW  C22   N11  C12   124.21  3.000
 NJW  O34   N32  O33   123.90  3.000
 NJW  O34   N32  C29   118.03  3.000
 NJW  O33   N32  C29   118.07  3.000
 NJW  H1    O16  C15   103.17  3.000
 NJW  N01   C02  C09   122.54  3.000
 NJW  N01   C02  C03   116.70  3.000
 NJW  C09   C02  C03   120.73  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  Var_01    C22   N11  C12  C18   105.04  30.0  2
 NJW  Var_02    C22   C24  C09  C10     0.06  30.0  1
 NJW  Var_03    N11   C22  C24  C09     1.00  30.0  1
 NJW  Var_04    C03   C02  C09  C10     4.46   0.0  2
 NJW  Var_05    C09   C02  C03  C04  -117.40  30.0  3
 NJW  Var_06    O20   C19  C14  C15    -0.61  30.0  2
 NJW  Var_07    H011  N01  C02  C03     5.68  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

