# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 05:02:58 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: N-{4-[(1E)-N-1H-imidazol-2-ylethanehydrazonoyl]phenyl}-7-nitro-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=N\Nc1[nH]ccn1)/c2ccc(NC(=O)c3[nH]c4c(cccc4[N+]([O-])=O)c3)cc2
#
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
 UPX  UPX  N-{4-[(1E)-N-1H-imidazol-2-ylethanehydrazonoyl]phenyl}-7-nitro-1H-indole-2-carboxamide  ligand  47  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_UPX
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
 UPX  OBB   O  O     -1  -0.379  -6.5012   3.2045   0.9799
 UPX  NAB   N  N      1   0.346  -5.6765   2.3379   0.8109
 UPX  OBC   O  O      0  -0.407  -4.5260   2.4239   1.1923
 UPX  CAJ   C  CR6    0   0.221  -6.0588   1.1351   0.1250
 UPX  CAI   C  CR16   0  -0.313  -7.3624   0.9790  -0.3145
 UPX  CAH   C  CR16   0  -0.270  -7.7566  -0.1815  -0.9796
 UPX  CAM   C  CR16   0  -0.308  -6.8584  -1.2062  -1.2119
 UPX  CAL   C  CR56   0   0.041  -5.5410  -1.0701  -0.7747
 UPX  CAO   C  CR15   0  -0.368  -4.4050  -1.9239  -0.8404
 UPX  CAK   C  CR56   0   0.377  -5.1287   0.1109  -0.1095
 UPX  NAA   N  NR15   0  -0.729  -3.8150  -0.0225   0.1831
 UPX  CAN   C  CR5    0   0.222  -3.3748  -1.2544  -0.2483
 UPX  CAP   C  C      0   0.516  -1.9900  -1.7455  -0.1002
 UPX  OBD   O  O      0  -0.449  -1.7541  -2.9391  -0.1446
 UPX  NAC   N  NH1    0  -0.762  -1.0507  -0.7797   0.0652
 UPX  CAQ   C  CR6    0   0.369   0.3279  -0.9466   0.2373
 UPX  CAV   C  CR16   0  -0.330   1.1432   0.1541  -0.0435
 UPX  CAU   C  CR16   0  -0.275   2.5097   0.0849   0.1216
 UPX  CAR   C  CR16   0  -0.286   0.9230  -2.1177   0.6965
 UPX  CAS   C  CR16   0  -0.316   2.3002  -2.1725   0.8613
 UPX  CAT   C  CR6    0   0.045   3.1256  -1.0855   0.5798
 UPX  CAW   C  C      0   0.192   4.5900  -1.1670   0.7417
 UPX  CAX   C  CH3    0  -0.784   5.1802  -2.3427   1.4650
 UPX  NAD   N  N      0  -0.216   5.2623  -0.2093   0.2237
 UPX  NAE   N  NH1    0  -0.570   6.5911  -0.1908   0.2895
 UPX  CAY   C  CR5    0   0.696   7.2733   0.8474  -0.2898
 UPX  NAF   N  NR15   0  -0.645   8.6227   0.8818  -0.2799
 UPX  CAZ   C  CR15   0  -0.111   9.0013   2.0413  -0.9200
 UPX  CBA   C  CR15   0  -0.207   7.8375   2.6410  -1.2806
 UPX  NAG   N  N      0  -0.481   6.7563   1.8896  -0.8838
 UPX  HAI   H  HCR6   0   0.302  -8.0862   1.7624  -0.1424
 UPX  HAH   H  HCR6   0   0.277  -8.7811  -0.2722  -1.3117
 UPX  HAM   H  HCR6   0   0.276  -7.1728  -2.1063  -1.7236
 UPX  HAO   H  HCR5   0   0.274  -4.3549  -2.9006  -1.2936
 UPX  HAA   H  HNR5   0   0.424  -3.2990   0.6287   0.7523
 UPX  HAC   H  HNH1   0   0.418  -1.3329   0.1723  -0.1139
 UPX  HAV   H  HCR6   0   0.272   0.6977   1.0762  -0.3983
 UPX  HAR   H  HCR6   0   0.277   0.3351  -2.9887   0.9359
 UPX  HAU   H  HCR6   0   0.259   3.1122   0.9530  -0.1088
 UPX  HAS   H  HCR6   0   0.258   2.7211  -3.1046   1.2131
 UPX  HAX1  H  HCH3   0   0.271   5.2818  -3.2065   0.8043
 UPX  HAX2  H  HCH3   0   0.259   6.1643  -2.1326   1.8828
 UPX  HAX3  H  HCH3   0   0.266   4.5531  -2.6457   2.3017
 UPX  HAE   H  HNH1   0   0.407   7.1184  -0.9747   0.6490
 UPX  HAF   H  HNR5   0   0.418   9.2443   0.1962   0.1184
 UPX  HAZ   H  HCR5   0   0.281  10.0344   2.3130  -1.0490
 UPX  HBA   H  HCR5   0   0.245   7.7096   3.5746  -1.8061

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
 UPX  OBB  NAB   single    1.208  0.020  1.208
 UPX  NAB  OBC   double    1.215  0.020  1.215
 UPX  NAB  CAJ   single    1.436  0.020  1.436
 UPX  CAJ  CAI   aromatic  1.385  0.020  1.385
 UPX  CAJ  CAK   aromatic  1.403  0.020  1.403
 UPX  CAI  CAH   aromatic  1.394  0.020  1.394
 UPX  CAH  CAM   aromatic  1.382  0.020  1.382
 UPX  CAM  CAL   aromatic  1.395  0.020  1.395
 UPX  CAL  CAO   aromatic  1.423  0.020  1.423
 UPX  CAL  CAK   aromatic  1.417  0.020  1.417
 UPX  CAO  CAN   aromatic  1.364  0.020  1.364
 UPX  CAK  NAA   aromatic  1.352  0.020  1.352
 UPX  NAA  CAN   aromatic  1.378  0.020  1.378
 UPX  CAN  CAP   single    1.477  0.020  1.477
 UPX  CAP  OBD   double    1.218  0.020  1.218
 UPX  CAP  NAC   single    1.357  0.020  1.357
 UPX  NAC  CAQ   single    1.399  0.020  1.399
 UPX  CAQ  CAV   aromatic  1.398  0.020  1.398
 UPX  CAQ  CAR   aromatic  1.392  0.020  1.392
 UPX  CAV  CAU   aromatic  1.378  0.020  1.378
 UPX  CAU  CAT   aromatic  1.400  0.020  1.400
 UPX  CAR  CAS   aromatic  1.388  0.020  1.388
 UPX  CAS  CAT   aromatic  1.394  0.020  1.394
 UPX  CAT  CAW   single    1.476  0.020  1.476
 UPX  CAW  CAX   single    1.501  0.020  1.501
 UPX  CAW  NAD   double    1.280  0.020  1.280
 UPX  NAD  NAE   single    1.331  0.020  1.331
 UPX  NAE  CAY   single    1.371  0.020  1.371
 UPX  CAY  NAF   aromatic  1.350  0.020  1.350
 UPX  CAY  NAG   aromatic  1.306  0.020  1.306
 UPX  NAF  CAZ   aromatic  1.377  0.020  1.377
 UPX  CAZ  CBA   aromatic  1.358  0.020  1.358
 UPX  CBA  NAG   aromatic  1.375  0.020  1.375
 UPX  CAI  HAI   single    0.930  0.020  1.080
 UPX  CAH  HAH   single    0.930  0.020  1.080
 UPX  CAM  HAM   single    0.930  0.020  1.080
 UPX  CAO  HAO   single    0.930  0.020  1.080
 UPX  NAA  HAA   single    0.860  0.020  1.020
 UPX  NAC  HAC   single    0.860  0.020  1.020
 UPX  CAV  HAV   single    0.930  0.020  1.080
 UPX  CAR  HAR   single    0.930  0.020  1.080
 UPX  CAU  HAU   single    0.930  0.020  1.080
 UPX  CAS  HAS   single    0.930  0.020  1.080
 UPX  CAX  HAX1  single    0.970  0.020  1.090
 UPX  CAX  HAX2  single    0.970  0.020  1.090
 UPX  CAX  HAX3  single    0.970  0.020  1.090
 UPX  NAE  HAE   single    0.860  0.020  1.020
 UPX  NAF  HAF   single    0.860  0.020  1.020
 UPX  CAZ  HAZ   single    0.930  0.020  1.080
 UPX  CBA  HBA   single    0.930  0.020  1.080

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
 UPX  CAJ   NAB  OBC   117.46  3.000
 UPX  CAJ   NAB  OBB   119.07  3.000
 UPX  OBC   NAB  OBB   123.48  3.000
 UPX  CAK   CAJ  CAI   119.26  3.000
 UPX  CAK   CAJ  NAB   120.97  3.000
 UPX  CAI   CAJ  NAB   119.77  3.000
 UPX  HAI   CAI  CAH   119.34  3.000
 UPX  HAI   CAI  CAJ   119.90  3.000
 UPX  CAH   CAI  CAJ   120.76  3.000
 UPX  HAH   CAH  CAM   120.14  3.000
 UPX  HAH   CAH  CAI   118.97  3.000
 UPX  CAM   CAH  CAI   120.89  3.000
 UPX  HAM   CAM  CAL   120.25  3.000
 UPX  HAM   CAM  CAH   120.49  3.000
 UPX  CAL   CAM  CAH   119.26  3.000
 UPX  CAK   CAL  CAO   106.83  3.000
 UPX  CAK   CAL  CAM   120.23  3.000
 UPX  CAO   CAL  CAM   132.95  3.000
 UPX  HAO   CAO  CAN   126.31  3.000
 UPX  HAO   CAO  CAL   126.89  3.000
 UPX  CAN   CAO  CAL   106.77  3.000
 UPX  NAA   CAK  CAL   107.58  3.000
 UPX  NAA   CAK  CAJ   132.82  3.000
 UPX  CAL   CAK  CAJ   119.60  3.000
 UPX  HAA   NAA  CAN   126.26  3.000
 UPX  HAA   NAA  CAK   123.79  3.000
 UPX  CAN   NAA  CAK   109.32  3.000
 UPX  CAP   CAN  NAA   124.45  3.000
 UPX  CAP   CAN  CAO   126.06  3.000
 UPX  NAA   CAN  CAO   109.48  3.000
 UPX  NAC   CAP  OBD   124.61  3.000
 UPX  NAC   CAP  CAN   115.12  3.000
 UPX  OBD   CAP  CAN   120.27  3.000
 UPX  HAC   NAC  CAQ   114.20  3.000
 UPX  HAC   NAC  CAP   117.14  3.000
 UPX  CAQ   NAC  CAP   127.73  3.000
 UPX  CAR   CAQ  CAV   118.64  3.000
 UPX  CAR   CAQ  NAC   124.21  3.000
 UPX  CAV   CAQ  NAC   117.13  3.000
 UPX  HAV   CAV  CAU   119.31  3.000
 UPX  HAV   CAV  CAQ   119.72  3.000
 UPX  CAU   CAV  CAQ   120.97  3.000
 UPX  HAU   CAU  CAT   119.73  3.000
 UPX  HAU   CAU  CAV   119.11  3.000
 UPX  CAT   CAU  CAV   121.16  3.000
 UPX  HAR   CAR  CAS   118.87  3.000
 UPX  HAR   CAR  CAQ   121.34  3.000
 UPX  CAS   CAR  CAQ   119.78  3.000
 UPX  HAS   CAS  CAT   120.49  3.000
 UPX  HAS   CAS  CAR   117.31  3.000
 UPX  CAT   CAS  CAR   122.20  3.000
 UPX  CAW   CAT  CAS   121.51  3.000
 UPX  CAW   CAT  CAU   121.25  3.000
 UPX  CAS   CAT  CAU   117.25  3.000
 UPX  NAD   CAW  CAX   125.07  3.000
 UPX  NAD   CAW  CAT   115.83  3.000
 UPX  CAX   CAW  CAT   119.09  3.000
 UPX  HAX3  CAX  HAX2  106.21  3.000
 UPX  HAX3  CAX  HAX1  107.36  3.000
 UPX  HAX2  CAX  HAX1  107.48  3.000
 UPX  HAX3  CAX  CAW   111.21  3.000
 UPX  HAX2  CAX  CAW   112.88  3.000
 UPX  HAX1  CAX  CAW   111.38  3.000
 UPX  NAE   NAD  CAW   121.00  3.000
 UPX  HAE   NAE  CAY   118.56  3.000
 UPX  HAE   NAE  NAD   121.85  3.000
 UPX  CAY   NAE  NAD   119.12  3.000
 UPX  NAG   CAY  NAF   112.25  3.000
 UPX  NAG   CAY  NAE   126.84  3.000
 UPX  NAF   CAY  NAE   120.91  3.000
 UPX  HAF   NAF  CAZ   125.94  3.000
 UPX  HAF   NAF  CAY   127.03  3.000
 UPX  CAZ   NAF  CAY   107.03  3.000
 UPX  HAZ   CAZ  CBA   132.81  3.000
 UPX  HAZ   CAZ  NAF   122.15  3.000
 UPX  CBA   CAZ  NAF   105.04  3.000
 UPX  HBA   CBA  NAG   121.34  3.000
 UPX  HBA   CBA  CAZ   127.80  3.000
 UPX  NAG   CBA  CAZ   110.85  3.000
 UPX  CBA   NAG  CAY   104.83  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
 UPX  CONST_01  CAM   CAH  CAI  CAJ    0.00   0.0  0
 UPX  CONST_02  CAM   CAL  CAK  CAJ    0.00   0.0  0
 UPX  CONST_03  CAO   CAL  CAK  CAJ  180.00   0.0  0
 UPX  CONST_04  CAN   NAA  CAK  CAJ  180.00   0.0  0
 UPX  CONST_05  CAL   CAK  CAJ  CAI    0.00   0.0  0
 UPX  CONST_06  NAA   CAK  CAJ  CAI  180.00   0.0  0
 UPX  CONST_07  CAL   CAM  CAH  CAI    0.00   0.0  0
 UPX  CONST_08  CAK   CAJ  CAI  CAH    0.00   0.0  0
 UPX  CONST_09  CAO   CAL  CAM  CAH  180.00   0.0  0
 UPX  CONST_10  CAK   CAL  CAM  CAH    0.00   0.0  0
 UPX  CONST_11  CAN   CAO  CAL  CAM  180.00   0.0  0
 UPX  CONST_12  NAA   CAK  CAL  CAM  180.00   0.0  0
 UPX  CONST_13  NAA   CAN  CAO  CAL    0.00   0.0  0
 UPX  CONST_14  CAN   NAA  CAK  CAL    0.00   0.0  0
 UPX  CONST_15  NAA   CAK  CAL  CAO    0.00   0.0  0
 UPX  CONST_16  CAK   NAA  CAN  CAO    0.00   0.0  0
 UPX  CONST_17  CAN   CAO  CAL  CAK    0.00   0.0  0
 UPX  CONST_18  CAT   CAU  CAV  CAQ    0.00   0.0  0
 UPX  CONST_19  CAT   CAS  CAR  CAQ    0.00   0.0  0
 UPX  CONST_20  CAS   CAR  CAQ  CAV    0.00   0.0  0
 UPX  CONST_21  CAS   CAT  CAU  CAV    0.00   0.0  0
 UPX  CONST_22  CAR   CAQ  CAV  CAU    0.00   0.0  0
 UPX  CONST_23  CAR   CAS  CAT  CAU    0.00   0.0  0
 UPX  CONST_24  CBA   CAZ  NAF  CAY    0.00   0.0  0
 UPX  CONST_25  CAZ   CBA  NAG  CAY    0.00   0.0  0
 UPX  CONST_26  CBA   NAG  CAY  NAF    0.00   0.0  0
 UPX  CONST_27  NAG   CBA  CAZ  NAF    0.00   0.0  0
 UPX  CONST_28  NAG   CAY  NAF  CAZ    0.00   0.0  0
 UPX  CONST_29  CAH   CAI  CAJ  NAB  180.00   0.0  0
 UPX  CONST_30  CAL   CAK  CAJ  NAB  180.00   0.0  0
 UPX  CONST_31  NAA   CAK  CAJ  NAB    0.00   0.0  0
 UPX  CONST_32  CAP   CAN  CAO  CAL  180.00   0.0  0
 UPX  CONST_33  CAP   CAN  NAA  CAK  180.00   0.0  0
 UPX  CONST_34  CAU   CAV  CAQ  NAC  180.00   0.0  0
 UPX  CONST_35  CAS   CAR  CAQ  NAC  180.00   0.0  0
 UPX  CONST_36  CAW   CAT  CAU  CAV  180.00   0.0  0
 UPX  CONST_37  CAW   CAT  CAS  CAR  180.00   0.0  0
 UPX  CONST_38  CAZ   NAF  CAY  NAE  180.00   0.0  0
 UPX  CONST_39  CBA   NAG  CAY  NAE  180.00   0.0  0
 UPX  CONST_40  HAH   CAH  CAI  CAJ  180.00   0.0  0
 UPX  CONST_41  HAA   NAA  CAK  CAJ    0.00   0.0  0
 UPX  CONST_42  HAM   CAM  CAH  CAI  180.00   0.0  0
 UPX  CONST_43  HAI   CAI  CAH  CAM  180.00   0.0  0
 UPX  CONST_44  HAO   CAO  CAL  CAM    0.00   0.0  0
 UPX  CONST_45  HAU   CAU  CAV  CAQ  180.00   0.0  0
 UPX  CONST_46  HAS   CAS  CAR  CAQ  180.00   0.0  0
 UPX  CONST_47  HAR   CAR  CAQ  CAV  180.00   0.0  0
 UPX  CONST_48  HAV   CAV  CAQ  CAR  180.00   0.0  0
 UPX  CONST_49  HAZ   CAZ  NAF  CAY  180.00   0.0  0
 UPX  CONST_50  HBA   CBA  NAG  CAY  180.00   0.0  0
 UPX  CONST_51  HAF   NAF  CAZ  CBA  180.00   0.0  0
 UPX  CONST_52  CAQ   NAC  CAP  CAN  180.00   0.0  0
 UPX  CONST_53  CAI   CAJ  NAB  OBB    0.00   0.0  0
 UPX  CONST_54  CAK   CAJ  NAB  OBB  180.00   0.0  0
 UPX  CONST_55  CAI   CAJ  NAB  OBC  180.00   0.0  0
 UPX  CONST_56  CAK   CAJ  NAB  OBC    0.00   0.0  0
 UPX  CONST_59  NAF   CAY  NAE  NAD  180.00   0.0  0
 UPX  CONST_60  NAG   CAY  NAE  NAD    0.00   0.0  0
 UPX  CONST_61  HAC   NAC  CAQ  CAV    0.00   0.0  0
 UPX  CONST_62  HAE   NAE  CAY  NAF    0.00   0.0  0
 UPX  CONST_63  CAQ   NAC  CAP  OBD    0.00   0.0  0
 UPX  CONST_64  CAY   NAE  NAD  CAW  180.00   0.0  0
 UPX  Var_01    OBD   CAP  CAN  CAO  -21.98  30.0  2
 UPX  Var_02    CAX   CAW  CAT  CAU  169.00  30.0  2
 UPX  Var_03    HAX1  CAX  CAW  CAT   82.40  30.0  3

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
 UPX  plan-1  NAE  0.020
 UPX  plan-1  CAY  0.020
 UPX  plan-1  NAF  0.020
 UPX  plan-1  CAZ  0.020
 UPX  plan-1  CBA  0.020
 UPX  plan-1  NAG  0.020
 UPX  plan-1  HAF  0.020
 UPX  plan-1  HAZ  0.020
 UPX  plan-1  HBA  0.020
 UPX  plan-2  CAT  0.020
 UPX  plan-2  CAW  0.020
 UPX  plan-2  CAX  0.020
 UPX  plan-2  NAD  0.020
 UPX  plan-2  NAE  0.020
 UPX  plan-3  NAC  0.020
 UPX  plan-3  CAQ  0.020
 UPX  plan-3  CAV  0.020
 UPX  plan-3  CAU  0.020
 UPX  plan-3  CAR  0.020
 UPX  plan-3  CAS  0.020
 UPX  plan-3  CAT  0.020
 UPX  plan-3  CAW  0.020
 UPX  plan-3  HAV  0.020
 UPX  plan-3  HAR  0.020
 UPX  plan-3  HAU  0.020
 UPX  plan-3  HAS  0.020
 UPX  plan-4  NAB  0.020
 UPX  plan-4  CAJ  0.020
 UPX  plan-4  CAI  0.020
 UPX  plan-4  CAH  0.020
 UPX  plan-4  CAM  0.020
 UPX  plan-4  CAL  0.020
 UPX  plan-4  CAO  0.020
 UPX  plan-4  CAK  0.020
 UPX  plan-4  NAA  0.020
 UPX  plan-4  CAN  0.020
 UPX  plan-4  CAP  0.020
 UPX  plan-4  HAI  0.020
 UPX  plan-4  HAH  0.020
 UPX  plan-4  HAM  0.020
 UPX  plan-4  HAO  0.020
 UPX  plan-4  HAA  0.020
 UPX  plan-5  CAN  0.020
 UPX  plan-5  CAP  0.020
 UPX  plan-5  OBD  0.020
 UPX  plan-5  NAC  0.020
 UPX  plan-5  CAQ  0.020
 UPX  plan-5  HAC  0.020
 UPX  plan-6  OBB  0.020
 UPX  plan-6  NAB  0.020
 UPX  plan-6  OBC  0.020
 UPX  plan-6  CAJ  0.020
 UPX  plan-7  NAD  0.020
 UPX  plan-7  NAE  0.020
 UPX  plan-7  CAY  0.020
 UPX  plan-7  HAE  0.020

