# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:05:05 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: N-[(5E)-5-(carbamimidoylhydrazono)-5,6,7,8-tetrahydronaphthalen-2-yl]-7-nitro-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)N/N=C/1CCCc2cc(NC(=O)c3[nH]c4c(cccc4[N+]([O-])=O)c3)ccc/12
#
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
 YIR  YIR  N-[(5E)-5-(carbamimidoylhydrazono)-5,6,7,8-tetrahydronaphthalen-2-yl]-7-nitro-1H-indole-2-carboxamide  ligand  49  30  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YIR
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
 YIR  NAA   N  N      1   0.346  -5.8313  -1.8654  -0.7323
 YIR  NAB   N  NR15   0  -0.731  -3.5607   0.1270  -0.1846
 YIR  NAC   N  NH1    0  -0.767  -0.7221   0.2967   0.1358
 YIR  NAD   N  N      0  -0.225   5.6472   0.3378  -0.1759
 YIR  NAE   N  NH1    0  -0.526   6.9722   0.1527  -0.1674
 YIR  NAF   N  NH2    0  -0.842   9.1404   0.8511  -0.2531
 YIR  NAG   N  N      0  -0.680   7.3685   2.3931  -0.6039
 YIR  CAH   C  CR16   0  -0.314  -7.2702  -0.0401   0.0114
 YIR  CAI   C  CR16   0  -0.271  -7.4567   1.2599   0.4798
 YIR  CAJ   C  CR16   0  -0.309  -6.3794   2.0996   0.6920
 YIR  CAK   C  CR56   0   0.042  -5.0904   1.6342   0.4329
 YIR  CAL   C  CR56   0   0.377  -4.8915   0.3107  -0.0325
 YIR  CAM   C  CR6    0   0.221  -5.9992  -0.5232  -0.2485
 YIR  CAN   C  CR15   0  -0.370  -3.8040   2.2341   0.5288
 YIR  CAO   C  CR5    0   0.221  -2.8987   1.2886   0.1457
 YIR  CAP   C  C      0   0.518  -1.4316   1.4539   0.1080
 YIR  CAQ   C  CR6    0   0.399   0.6678   0.1389   0.1110
 YIR  CAR   C  CR16   0  -0.422   1.1738  -1.0704   0.5787
 YIR  CAS   C  CR6    0   0.098   2.5334  -1.3447   0.5718
 YIR  CAT   C  CR6    0   0.020   3.4281  -0.3874   0.0777
 YIR  CAU   C  CR16   0  -0.280   2.9102   0.8197  -0.3978
 YIR  CAV   C  CR16   0  -0.307   1.5563   1.0941  -0.3887
 YIR  CAW   C  CH2    0  -0.511   3.0420  -2.6576   1.0940
 YIR  CAX   C  CH2    0  -0.450   4.2756  -3.0933   0.3214
 YIR  CAY   C  CH2    0  -0.569   5.3675  -2.0367   0.4114
 YIR  CAZ   C  C      0   0.213   4.8778  -0.6505   0.0829
 YIR  CBA   C  C      0   0.558   7.8201   1.2232  -0.3748
 YIR  OBB   O  O      0  -0.380  -6.8083  -2.5577  -0.8929
 YIR  OBC   O  O     -1  -0.406  -4.6983  -2.2408  -0.9595
 YIR  OBD   O  O      0  -0.449  -0.9396   2.5666   0.0712
 YIR  HNAB  H  HNR5   0   0.427  -3.1520  -0.6939  -0.6003
 YIR  HNAC  H  HNH1   0   0.420  -1.2283  -0.5478   0.3561
 YIR  H1AF  H  HNH2   0   0.388   9.3776  -0.0887  -0.5325
 YIR  H2AF  H  HNH2   0   0.392   9.8050   1.5218  -0.6033
 YIR  HAG   H  H      0   0.322   8.1337   3.0337  -0.7798
 YIR  HAH   H  HCR6   0   0.301  -8.1302  -0.6738  -0.1491
 YIR  HAI   H  HCR6   0   0.277  -8.4614   1.6072   0.6736
 YIR  HAJ   H  HCR6   0   0.276  -6.5339   3.1086   1.0514
 YIR  HAN   H  HCR5   0   0.274  -3.5777   3.2332   0.8635
 YIR  HAR   H  HCR6   0   0.263   0.4906  -1.8226   0.9598
 YIR  HAU   H  HCR6   0   0.255   3.5888   1.5655  -0.7900
 YIR  HAV   H  HCR6   0   0.274   1.2084   2.0361  -0.7799
 YIR  H1AW  H  HCH2   0   0.251   3.2918  -2.5593   2.1563
 YIR  H2AW  H  HCH2   0   0.256   2.2576  -3.4134   1.0301
 YIR  H1AX  H  HCH2   0   0.249   4.6538  -4.0406   0.7068
 YIR  H2AX  H  HCH2   0   0.236   4.0078  -3.2600  -0.7251
 YIR  H1AY  H  HCH2   0   0.267   5.7906  -2.0333   1.4238
 YIR  H2AY  H  HCH2   0   0.263   6.1876  -2.3101  -0.2596
 YIR  HAE   H  HNH1   0   0.407   7.3653  -0.6844   0.2413

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
 YIR  OBC  NAA   single    1.215  0.020  1.215
 YIR  NAA  OBB   double    1.208  0.020  1.208
 YIR  NAA  CAM   single    1.437  0.020  1.437
 YIR  CAH  CAM   aromatic  1.384  0.020  1.384
 YIR  CAH  CAI   aromatic  1.394  0.020  1.394
 YIR  CAM  CAL   aromatic  1.403  0.020  1.403
 YIR  CAI  CAJ   aromatic  1.382  0.020  1.382
 YIR  CAL  NAB   aromatic  1.352  0.020  1.352
 YIR  CAL  CAK   aromatic  1.417  0.020  1.417
 YIR  CAJ  CAK   aromatic  1.395  0.020  1.395
 YIR  NAB  CAO   aromatic  1.377  0.020  1.377
 YIR  CAK  CAN   aromatic  1.423  0.020  1.423
 YIR  CAO  CAN   aromatic  1.364  0.020  1.364
 YIR  CAO  CAP   single    1.477  0.020  1.477
 YIR  OBD  CAP   double    1.217  0.020  1.217
 YIR  CAP  NAC   single    1.358  0.020  1.358
 YIR  NAC  CAQ   single    1.399  0.020  1.399
 YIR  CAQ  CAR   aromatic  1.392  0.020  1.392
 YIR  CAQ  CAV   aromatic  1.397  0.020  1.397
 YIR  CAR  CAS   aromatic  1.387  0.020  1.387
 YIR  CAV  CAU   aromatic  1.381  0.020  1.381
 YIR  CAS  CAW   single    1.502  0.020  1.502
 YIR  CAS  CAT   aromatic  1.400  0.020  1.400
 YIR  CAW  CAX   single    1.519  0.020  1.519
 YIR  CAU  CAT   aromatic  1.397  0.020  1.397
 YIR  CAX  CAY   single    1.522  0.020  1.522
 YIR  CAT  CAZ   single    1.473  0.020  1.473
 YIR  CAZ  CAY   single    1.506  0.020  1.506
 YIR  CAZ  NAD   double    1.279  0.020  1.279
 YIR  NAD  NAE   single    1.338  0.020  1.338
 YIR  NAE  CBA   single    1.381  0.020  1.381
 YIR  NAG  CBA   double    1.275  0.020  1.275
 YIR  CBA  NAF   single    1.377  0.020  1.377
 YIR  NAB  HNAB  single    0.860  0.020  1.020
 YIR  NAC  HNAC  single    0.860  0.020  1.020
 YIR  NAF  H1AF  single    0.890  0.020  1.040
 YIR  NAF  H2AF  single    0.890  0.020  1.040
 YIR  NAG  HAG   single    0.890  0.020  1.040
 YIR  CAH  HAH   single    0.930  0.020  1.080
 YIR  CAI  HAI   single    0.930  0.020  1.080
 YIR  CAJ  HAJ   single    0.930  0.020  1.080
 YIR  CAN  HAN   single    0.930  0.020  1.080
 YIR  CAR  HAR   single    0.930  0.020  1.080
 YIR  CAU  HAU   single    0.930  0.020  1.080
 YIR  CAV  HAV   single    0.930  0.020  1.080
 YIR  CAW  H1AW  single    0.970  0.020  1.090
 YIR  CAW  H2AW  single    0.970  0.020  1.090
 YIR  CAX  H1AX  single    0.970  0.020  1.090
 YIR  CAX  H2AX  single    0.970  0.020  1.090
 YIR  CAY  H1AY  single    0.970  0.020  1.090
 YIR  CAY  H2AY  single    0.970  0.020  1.090
 YIR  NAE  HAE   single    0.860  0.020  1.020

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
 YIR  OBC   NAA  OBB   123.52  3.000
 YIR  OBB   NAA  CAM   119.05  3.000
 YIR  OBC   NAA  CAM   117.43  3.000
 YIR  HNAB  NAB  CAO   126.27  3.000
 YIR  HNAB  NAB  CAL   123.84  3.000
 YIR  CAO   NAB  CAL   109.36  3.000
 YIR  HNAC  NAC  CAQ   114.07  3.000
 YIR  HNAC  NAC  CAP   117.11  3.000
 YIR  CAQ   NAC  CAP   127.95  3.000
 YIR  CAZ   NAD  NAE   119.18  3.000
 YIR  HAE   NAE  CBA   117.63  3.000
 YIR  HAE   NAE  NAD   120.14  3.000
 YIR  CBA   NAE  NAD   119.98  3.000
 YIR  H2AF  NAF  H1AF  111.65  3.000
 YIR  H2AF  NAF  CBA   114.96  3.000
 YIR  H1AF  NAF  CBA   116.92  3.000
 YIR  HAG   NAG  CBA   110.11  3.000
 YIR  HAH   CAH  CAM   119.89  3.000
 YIR  HAH   CAH  CAI   119.36  3.000
 YIR  CAM   CAH  CAI   120.75  3.000
 YIR  HAI   CAI  CAJ   120.12  3.000
 YIR  HAI   CAI  CAH   118.97  3.000
 YIR  CAJ   CAI  CAH   120.91  3.000
 YIR  HAJ   CAJ  CAK   120.32  3.000
 YIR  HAJ   CAJ  CAI   120.41  3.000
 YIR  CAK   CAJ  CAI   119.27  3.000
 YIR  CAN   CAK  CAL   106.80  3.000
 YIR  CAN   CAK  CAJ   133.03  3.000
 YIR  CAL   CAK  CAJ   120.16  3.000
 YIR  CAM   CAL  CAK   119.66  3.000
 YIR  CAK   CAL  NAB   107.58  3.000
 YIR  CAM   CAL  NAB   132.76  3.000
 YIR  CAL   CAM  CAH   119.24  3.000
 YIR  CAL   CAM  NAA   120.98  3.000
 YIR  CAH   CAM  NAA   119.78  3.000
 YIR  HAN   CAN  CAO   126.20  3.000
 YIR  HAN   CAN  CAK   126.99  3.000
 YIR  CAO   CAN  CAK   106.79  3.000
 YIR  CAP   CAO  CAN   126.08  3.000
 YIR  CAP   CAO  NAB   124.45  3.000
 YIR  CAN   CAO  NAB   109.45  3.000
 YIR  OBD   CAP  CAO   120.30  3.000
 YIR  OBD   CAP  NAC   124.65  3.000
 YIR  CAO   CAP  NAC   115.04  3.000
 YIR  CAV   CAQ  CAR   118.89  3.000
 YIR  CAV   CAQ  NAC   124.13  3.000
 YIR  CAR   CAQ  NAC   116.95  3.000
 YIR  HAR   CAR  CAS   118.80  3.000
 YIR  HAR   CAR  CAQ   119.43  3.000
 YIR  CAS   CAR  CAQ   121.77  3.000
 YIR  CAW   CAS  CAT   120.26  3.000
 YIR  CAT   CAS  CAR   119.53  3.000
 YIR  CAW   CAS  CAR   120.22  3.000
 YIR  CAZ   CAT  CAU   121.36  3.000
 YIR  CAZ   CAT  CAS   120.35  3.000
 YIR  CAU   CAT  CAS   118.28  3.000
 YIR  HAU   CAU  CAV   118.70  3.000
 YIR  HAU   CAU  CAT   119.11  3.000
 YIR  CAV   CAU  CAT   122.20  3.000
 YIR  HAV   CAV  CAU   119.19  3.000
 YIR  HAV   CAV  CAQ   121.48  3.000
 YIR  CAU   CAV  CAQ   119.33  3.000
 YIR  H2AW  CAW  H1AW  106.42  3.000
 YIR  H2AW  CAW  CAX   110.81  3.000
 YIR  H1AW  CAW  CAX   109.49  3.000
 YIR  H2AW  CAW  CAS   109.98  3.000
 YIR  H1AW  CAW  CAS   109.63  3.000
 YIR  CAX   CAW  CAS   110.42  3.000
 YIR  H2AX  CAX  H1AX  106.91  3.000
 YIR  H2AX  CAX  CAY   109.77  3.000
 YIR  H1AX  CAX  CAY   109.48  3.000
 YIR  H2AX  CAX  CAW   109.37  3.000
 YIR  H1AX  CAX  CAW   110.55  3.000
 YIR  CAY   CAX  CAW   110.69  3.000
 YIR  H2AY  CAY  H1AY  106.11  3.000
 YIR  H2AY  CAY  CAZ   109.87  3.000
 YIR  H1AY  CAY  CAZ   108.89  3.000
 YIR  H2AY  CAY  CAX   109.14  3.000
 YIR  H1AY  CAY  CAX   109.47  3.000
 YIR  CAZ   CAY  CAX   113.12  3.000
 YIR  CAY   CAZ  CAT   119.01  3.000
 YIR  CAY   CAZ  NAD   124.03  3.000
 YIR  CAT   CAZ  NAD   116.95  3.000
 YIR  NAG   CBA  NAF   127.12  3.000
 YIR  NAF   CBA  NAE   111.46  3.000
 YIR  NAG   CBA  NAE   121.39  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
 YIR  CONST_01  CAH   CAM  CAL  NAB   180.00   0.0  0
 YIR  CONST_02  CAJ   CAK  CAL  NAB   180.00   0.0  0
 YIR  CONST_03  CAN   CAK  CAL  NAB     0.00   0.0  0
 YIR  CONST_04  CAK   CAN  CAO  NAB     0.00   0.0  0
 YIR  CONST_05  CAK   CAL  CAM  CAH     0.00   0.0  0
 YIR  CONST_06  CAK   CAJ  CAI  CAH     0.00   0.0  0
 YIR  CONST_07  CAL   CAM  CAH  CAI     0.00   0.0  0
 YIR  CONST_08  CAL   CAK  CAJ  CAI     0.00   0.0  0
 YIR  CONST_09  CAN   CAK  CAJ  CAI   180.00   0.0  0
 YIR  CONST_10  CAM   CAH  CAI  CAJ     0.00   0.0  0
 YIR  CONST_11  CAM   CAL  CAK  CAJ     0.00   0.0  0
 YIR  CONST_12  CAO   CAN  CAK  CAJ   180.00   0.0  0
 YIR  CONST_13  CAO   NAB  CAL  CAK     0.00   0.0  0
 YIR  CONST_14  CAN   CAO  NAB  CAL     0.00   0.0  0
 YIR  CONST_15  CAO   CAN  CAK  CAL     0.00   0.0  0
 YIR  CONST_16  CAO   NAB  CAL  CAM   180.00   0.0  0
 YIR  CONST_17  CAN   CAK  CAL  CAM   180.00   0.0  0
 YIR  CONST_18  CAT   CAS  CAR  CAQ     0.00   0.0  0
 YIR  CONST_19  CAT   CAU  CAV  CAQ     0.00   0.0  0
 YIR  CONST_20  CAU   CAV  CAQ  CAR     0.00   0.0  0
 YIR  CONST_21  CAU   CAT  CAS  CAR     0.00   0.0  0
 YIR  CONST_22  CAV   CAQ  CAR  CAS     0.00   0.0  0
 YIR  CONST_23  CAV   CAU  CAT  CAS     0.00   0.0  0
 YIR  CONST_24  CAI   CAH  CAM  NAA   180.00   0.0  0
 YIR  CONST_25  NAB   CAL  CAM  NAA     0.00   0.0  0
 YIR  CONST_26  CAK   CAL  CAM  NAA   180.00   0.0  0
 YIR  CONST_27  CAS   CAR  CAQ  NAC   180.00   0.0  0
 YIR  CONST_28  CAU   CAV  CAQ  NAC   180.00   0.0  0
 YIR  CONST_29  CAP   CAO  CAN  CAK   180.00   0.0  0
 YIR  CONST_30  CAP   CAO  NAB  CAL   180.00   0.0  0
 YIR  CONST_31  HAN   CAN  CAO  NAB   180.00   0.0  0
 YIR  CONST_32  HAJ   CAJ  CAI  CAH   180.00   0.0  0
 YIR  CONST_33  HAH   CAH  CAI  CAJ   180.00   0.0  0
 YIR  CONST_34  HNAB  NAB  CAL  CAK   180.00   0.0  0
 YIR  CONST_35  HAI   CAI  CAJ  CAK   180.00   0.0  0
 YIR  CONST_36  HAU   CAU  CAV  CAQ   180.00   0.0  0
 YIR  CONST_37  HAV   CAV  CAQ  CAR   180.00   0.0  0
 YIR  CONST_38  HAR   CAR  CAS  CAT   180.00   0.0  0
 YIR  CONST_39  CAQ   NAC  CAP  CAO   180.00   0.0  0
 YIR  CONST_40  OBC   NAA  CAM  CAH   180.00   0.0  0
 YIR  CONST_41  OBB   NAA  CAM  CAH     0.00   0.0  0
 YIR  CONST_42  OBC   NAA  CAM  CAL     0.00   0.0  0
 YIR  CONST_43  OBB   NAA  CAM  CAL   180.00   0.0  0
 YIR  CONST_46  HNAC  NAC  CAQ  CAR     0.00   0.0  0
 YIR  CONST_47  OBD   CAP  NAC  CAQ     0.00   0.0  0
 YIR  CONST_48  NAG   CBA  NAE  NAD     0.00   0.0  0
 YIR  CONST_49  NAF   CBA  NAE  NAD   180.00   0.0  0
 YIR  CONST_50  HAG   NAG  CBA  NAE   180.00   0.0  0
 YIR  CONST_52  H2AF  NAF  CBA  NAE   180.00   0.0  0
 YIR  CONST_53  HAE   NAE  CBA  NAF     0.00   0.0  0
 YIR  Var_01    CAX   CAW  CAS  CAR   147.04  30.0  1
 YIR  Var_02    CAY   CAX  CAW  CAS    57.84  30.0  1
 YIR  Var_03    CAY   CAZ  CAT  CAS     9.94  30.0  1
 YIR  Var_04    CAX   CAY  CAZ  CAT    16.16  30.0  1
 YIR  Var_05    CAZ   CAY  CAX  CAW   -49.77  30.0  1
 YIR  Var_06    OBD   CAP  CAO  NAB   160.88  30.0  2
 YIR  Var_07    CAT   CAZ  NAD  NAE   179.21  30.0  2
 YIR  Var_08    CBA   NAE  NAD  CAZ  -176.58  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
 YIR  plan-1  NAA   0.020
 YIR  plan-1  NAB   0.020
 YIR  plan-1  CAH   0.020
 YIR  plan-1  CAI   0.020
 YIR  plan-1  CAJ   0.020
 YIR  plan-1  CAK   0.020
 YIR  plan-1  CAL   0.020
 YIR  plan-1  CAM   0.020
 YIR  plan-1  CAN   0.020
 YIR  plan-1  CAO   0.020
 YIR  plan-1  CAP   0.020
 YIR  plan-1  HNAB  0.020
 YIR  plan-1  HAH   0.020
 YIR  plan-1  HAI   0.020
 YIR  plan-1  HAJ   0.020
 YIR  plan-1  HAN   0.020
 YIR  plan-2  NAC   0.020
 YIR  plan-2  CAQ   0.020
 YIR  plan-2  CAR   0.020
 YIR  plan-2  CAS   0.020
 YIR  plan-2  CAT   0.020
 YIR  plan-2  CAU   0.020
 YIR  plan-2  CAV   0.020
 YIR  plan-2  CAW   0.020
 YIR  plan-2  CAZ   0.020
 YIR  plan-2  HAR   0.020
 YIR  plan-2  HAU   0.020
 YIR  plan-2  HAV   0.020
 YIR  plan-3  NAC   0.020
 YIR  plan-3  CAO   0.020
 YIR  plan-3  CAP   0.020
 YIR  plan-3  CAQ   0.020
 YIR  plan-3  OBD   0.020
 YIR  plan-3  HNAC  0.020
 YIR  plan-4  NAA   0.020
 YIR  plan-4  CAM   0.020
 YIR  plan-4  OBB   0.020
 YIR  plan-4  OBC   0.020
 YIR  plan-5  NAD   0.020
 YIR  plan-5  NAE   0.020
 YIR  plan-5  NAF   0.020
 YIR  plan-5  NAG   0.020
 YIR  plan-5  CBA   0.020
 YIR  plan-5  H1AF  0.020
 YIR  plan-5  H2AF  0.020
 YIR  plan-5  HAG   0.020
 YIR  plan-5  HAE   0.020

