# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 16:49:13 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-[1-(3-aminopropyl)-1H-indol-3-yl]-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCn1cc(c2ccccc12)C3=C(C(=O)NC3=O)c4c[nH]c5ccccc45
#
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
 BI3  BI3  3-[1-(3-aminopropyl)-1H-indol-3-yl]-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  ligand  49  29  .  2021-08-06  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BI3
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
 BI3  NBC   N  NH2   0  -0.798   2.4779   1.7236   6.1067
 BI3  CBB   C  CH2   0  -0.277   2.5702   0.6310   5.1509
 BI3  CBA   C  CH2   0  -0.446   1.3592   0.6167   4.2301
 BI3  CAY   C  CH2   0  -0.318   1.4527  -0.5126   3.2139
 BI3  NAH   N  NR5   0  -0.521   0.2961  -0.5905   2.3464
 BI3  CAW   C  CR15  0  -0.054   0.1897  -0.0167   1.1245
 BI3  CAE   C  CR56  0   0.371  -0.8990  -1.1853   2.6619
 BI3  CAF   C  CR16  0  -0.306  -1.2544  -1.9063   3.8002
 BI3  CAA   C  CR16  0  -0.283  -2.5260  -2.4429   3.8418
 BI3  CAB   C  CR16  0  -0.264  -3.4198  -2.2699   2.7732
 BI3  CAC   C  CR16  0  -0.393  -3.0654  -1.5466   1.6512
 BI3  CAD   C  CR56  0   0.044  -1.7886  -0.9771   1.5865
 BI3  CAG   C  CR5   0  -0.048  -1.0669  -0.2145   0.6036
 BI3  CAI   C  CR5   0  -0.090  -1.5055   0.2615  -0.6878
 BI3  CAT   C  CR5   0   0.550  -2.8427   0.9045  -0.8883
 BI3  OAZ   O  O     0  -0.396  -3.7011   1.0947  -0.0635
 BI3  NAU   N  NR15  0  -0.737  -2.8993   1.2846  -2.2081
 BI3  CAV   C  CR5   0   0.552  -1.7323   0.9704  -2.8665
 BI3  OAX   O  O     0  -0.396  -1.5106   1.1612  -4.0362
 BI3  CAJ   C  CR5   0  -0.106  -0.8372   0.3250  -1.8591
 BI3  CAK   C  CR5   0  -0.054   0.4680  -0.1888  -2.2128
 BI3  CAM   C  CR56  0   0.045   1.5140   0.4577  -2.9581
 BI3  CAP   C  CR16  0  -0.387   1.6692   1.7204  -3.5419
 BI3  CAQ   C  CR16  0  -0.264   2.8596   2.0232  -4.1727
 BI3  CAR   C  CR16  0  -0.284   3.9096   1.0922  -4.2349
 BI3  CAS   C  CR16  0  -0.301   3.7908  -0.1560  -3.6568
 BI3  CAN   C  CR56  0   0.353   2.5889  -0.4546  -3.0185
 BI3  NAO   N  NR15  0  -0.676   2.2067  -1.5849  -2.3503
 BI3  CAL   C  CR15  0  -0.056   0.9521  -1.4264  -1.8662
 BI3  HBC1  H  HNH2  0   0.339   2.5549   2.6051   5.6138
 BI3  HBC2  H  HNH2  0   0.348   3.2750   1.6913   6.7291
 BI3  HBB1  H  HCH2  0   0.195   3.4839   0.6568   4.5392
 BI3  HBB2  H  HCH2  0   0.220   2.6035  -0.3095   5.7079
 BI3  HBA1  H  HCH2  0   0.235   0.4511   0.5127   4.8295
 BI3  HBA2  H  HCH2  0   0.235   1.2855   1.5709   3.6991
 BI3  HAY1  H  HCH2  0   0.270   2.3326  -0.3869   2.5822
 BI3  HAY2  H  HCH2  0   0.260   1.5650  -1.4748   3.7181
 BI3  HAW   H  HCR5  0   0.293   1.0255   0.5128   0.6938
 BI3  HAF   H  HCR6  0   0.265  -0.5618  -2.0489   4.6202
 BI3  HAA   H  HCR6  0   0.253  -2.8356  -3.0113   4.7091
 BI3  HAB   H  HCR6  0   0.250  -4.4055  -2.7132   2.8315
 BI3  HAC   H  HCR6  0   0.242  -3.7693  -1.4330   0.8385
 BI3  HAU   H  HNR5  0   0.423  -3.6896   1.7461  -2.6347
 BI3  HAP   H  HCR6  0   0.241   0.8763   2.4549  -3.4983
 BI3  HAQ   H  HCR6  0   0.249   2.9887   2.9960  -4.6297
 BI3  HAR   H  HCR6  0   0.252   4.8286   1.3608  -4.7395
 BI3  HAS   H  HCR6  0   0.264   4.6006  -0.8737  -3.6922
 BI3  HAO   H  HNR5  0   0.417   2.7604  -2.4195  -2.2458
 BI3  HAL   H  HCR5  0   0.290   0.4703  -2.2140  -1.3094

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
 BI3  NBC  CBB   single    1.455  0.020  1.455
 BI3  NBC  HBC1  single    0.890  0.020  1.040
 BI3  NBC  HBC2  single    0.890  0.020  1.040
 BI3  CBB  CBA   single    1.521  0.020  1.521
 BI3  CBB  HBB1  single    0.970  0.020  1.090
 BI3  CBB  HBB2  single    0.970  0.020  1.090
 BI3  CBA  CAY   single    1.522  0.020  1.522
 BI3  CBA  HBA1  single    0.970  0.020  1.090
 BI3  CBA  HBA2  single    0.970  0.020  1.090
 BI3  CAY  NAH   single    1.448  0.020  1.448
 BI3  CAY  HAY1  single    0.970  0.020  1.090
 BI3  CAY  HAY2  single    0.970  0.020  1.090
 BI3  NAH  CAW   aromatic  1.354  0.020  1.354
 BI3  NAH  CAE   aromatic  1.372  0.020  1.372
 BI3  CAW  CAG   aromatic  1.375  0.020  1.375
 BI3  CAW  HAW   single    0.930  0.020  1.080
 BI3  CAE  CAF   aromatic  1.394  0.020  1.394
 BI3  CAE  CAD   aromatic  1.411  0.020  1.411
 BI3  CAF  CAA   aromatic  1.381  0.020  1.381
 BI3  CAF  HAF   single    0.930  0.020  1.080
 BI3  CAA  CAB   aromatic  1.404  0.020  1.404
 BI3  CAA  HAA   single    0.930  0.020  1.080
 BI3  CAB  CAC   aromatic  1.381  0.020  1.381
 BI3  CAB  HAB   single    0.930  0.020  1.080
 BI3  CAC  CAD   aromatic  1.400  0.020  1.400
 BI3  CAC  HAC   single    0.930  0.020  1.080
 BI3  CAD  CAG   aromatic  1.438  0.020  1.438
 BI3  CAG  CAI   single    1.444  0.020  1.444
 BI3  CAI  CAT   single    1.497  0.020  1.497
 BI3  CAI  CAJ   double    1.350  0.020  1.350
 BI3  CAT  OAZ   double    1.205  0.020  1.205
 BI3  CAT  NAU   single    1.375  0.020  1.375
 BI3  NAU  CAV   single    1.376  0.020  1.376
 BI3  NAU  HAU   single    0.860  0.020  1.020
 BI3  CAV  OAX   double    1.206  0.020  1.206
 BI3  CAV  CAJ   single    1.494  0.020  1.494
 BI3  CAJ  CAK   single    1.447  0.020  1.447
 BI3  CAK  CAM   aromatic  1.438  0.020  1.438
 BI3  CAK  CAL   aromatic  1.373  0.020  1.373
 BI3  CAM  CAP   aromatic  1.400  0.020  1.400
 BI3  CAM  CAN   aromatic  1.411  0.020  1.411
 BI3  CAP  CAQ   aromatic  1.381  0.020  1.381
 BI3  CAP  HAP   single    0.930  0.020  1.080
 BI3  CAQ  CAR   aromatic  1.405  0.020  1.405
 BI3  CAQ  HAQ   single    0.930  0.020  1.080
 BI3  CAR  CAS   aromatic  1.381  0.020  1.381
 BI3  CAR  HAR   single    0.930  0.020  1.080
 BI3  CAS  CAN   aromatic  1.393  0.020  1.393
 BI3  CAS  HAS   single    0.930  0.020  1.080
 BI3  CAN  NAO   aromatic  1.368  0.020  1.368
 BI3  NAO  CAL   aromatic  1.354  0.020  1.354
 BI3  NAO  HAO   single    0.860  0.020  1.020
 BI3  CAL  HAL   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
 BI3  HBC2  NBC  HBC1  105.50  3.000
 BI3  HBC2  NBC  CBB   109.28  3.000
 BI3  HBC1  NBC  CBB   109.21  3.000
 BI3  HBB2  CBB  HBB1  106.15  3.000
 BI3  HBB2  CBB  CBA   108.94  3.000
 BI3  HBB1  CBB  CBA   108.96  3.000
 BI3  HBB2  CBB  NBC   108.26  3.000
 BI3  HBB1  CBB  NBC   113.61  3.000
 BI3  CBA   CBB  NBC   110.75  3.000
 BI3  HBA2  CBA  HBA1  107.04  3.000
 BI3  HBA2  CBA  CAY   109.09  3.000
 BI3  HBA1  CBA  CAY   110.28  3.000
 BI3  HBA2  CBA  CBB   109.82  3.000
 BI3  HBA1  CBA  CBB   109.29  3.000
 BI3  CAY   CBA  CBB   111.23  3.000
 BI3  HAY2  CAY  HAY1  106.63  3.000
 BI3  HAY2  CAY  NAH   108.14  3.000
 BI3  HAY1  CAY  NAH   107.68  3.000
 BI3  HAY2  CAY  CBA   110.59  3.000
 BI3  HAY1  CAY  CBA   110.54  3.000
 BI3  NAH   CAY  CBA   113.01  3.000
 BI3  CAE   NAH  CAW   108.83  3.000
 BI3  CAE   NAH  CAY   125.56  3.000
 BI3  CAW   NAH  CAY   125.49  3.000
 BI3  HAW   CAW  CAG   128.86  3.000
 BI3  HAW   CAW  NAH   120.48  3.000
 BI3  CAG   CAW  NAH   110.66  3.000
 BI3  CAD   CAE  CAF   122.55  3.000
 BI3  CAD   CAE  NAH   108.06  3.000
 BI3  CAF   CAE  NAH   129.38  3.000
 BI3  HAF   CAF  CAA   121.00  3.000
 BI3  HAF   CAF  CAE   121.58  3.000
 BI3  CAA   CAF  CAE   117.42  3.000
 BI3  HAA   CAA  CAB   119.52  3.000
 BI3  HAA   CAA  CAF   119.45  3.000
 BI3  CAB   CAA  CAF   121.03  3.000
 BI3  HAB   CAB  CAC   119.47  3.000
 BI3  HAB   CAB  CAA   119.23  3.000
 BI3  CAC   CAB  CAA   121.30  3.000
 BI3  HAC   CAC  CAD   121.10  3.000
 BI3  HAC   CAC  CAB   119.91  3.000
 BI3  CAD   CAC  CAB   118.99  3.000
 BI3  CAG   CAD  CAC   134.84  3.000
 BI3  CAG   CAD  CAE   106.42  3.000
 BI3  CAC   CAD  CAE   118.68  3.000
 BI3  CAI   CAG  CAD   129.30  3.000
 BI3  CAI   CAG  CAW   124.68  3.000
 BI3  CAD   CAG  CAW   106.02  3.000
 BI3  CAJ   CAI  CAT   107.80  3.000
 BI3  CAJ   CAI  CAG   129.85  3.000
 BI3  CAT   CAI  CAG   122.17  3.000
 BI3  NAU   CAT  OAZ   125.73  3.000
 BI3  NAU   CAT  CAI   106.51  3.000
 BI3  OAZ   CAT  CAI   127.74  3.000
 BI3  HAU   NAU  CAV   124.47  3.000
 BI3  HAU   NAU  CAT   124.35  3.000
 BI3  CAV   NAU  CAT   111.18  3.000
 BI3  CAJ   CAV  OAX   127.75  3.000
 BI3  CAJ   CAV  NAU   106.50  3.000
 BI3  OAX   CAV  NAU   125.73  3.000
 BI3  CAK   CAJ  CAV   121.95  3.000
 BI3  CAK   CAJ  CAI   129.94  3.000
 BI3  CAV   CAJ  CAI   107.98  3.000
 BI3  CAL   CAK  CAM   106.24  3.000
 BI3  CAL   CAK  CAJ   125.20  3.000
 BI3  CAM   CAK  CAJ   128.56  3.000
 BI3  CAN   CAM  CAP   118.74  3.000
 BI3  CAN   CAM  CAK   106.60  3.000
 BI3  CAP   CAM  CAK   134.62  3.000
 BI3  HAP   CAP  CAQ   120.10  3.000
 BI3  HAP   CAP  CAM   120.96  3.000
 BI3  CAQ   CAP  CAM   118.94  3.000
 BI3  HAQ   CAQ  CAR   119.19  3.000
 BI3  HAQ   CAQ  CAP   119.52  3.000
 BI3  CAR   CAQ  CAP   121.28  3.000
 BI3  HAR   CAR  CAS   119.51  3.000
 BI3  HAR   CAR  CAQ   119.40  3.000
 BI3  CAS   CAR  CAQ   121.09  3.000
 BI3  HAS   CAS  CAN   121.21  3.000
 BI3  HAS   CAS  CAR   121.42  3.000
 BI3  CAN   CAS  CAR   117.37  3.000
 BI3  NAO   CAN  CAS   129.94  3.000
 BI3  NAO   CAN  CAM   107.49  3.000
 BI3  CAS   CAN  CAM   122.56  3.000
 BI3  HAO   NAO  CAL   124.70  3.000
 BI3  HAO   NAO  CAN   125.60  3.000
 BI3  CAL   NAO  CAN   109.68  3.000
 BI3  HAL   CAL  NAO   120.87  3.000
 BI3  HAL   CAL  CAK   129.14  3.000
 BI3  NAO   CAL  CAK   109.99  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
 BI3  CONST_01  CAD   CAG  CAW  NAH     0.00   0.0  0
 BI3  CONST_02  CAA   CAF  CAE  NAH   180.00   0.0  0
 BI3  CONST_03  CAC   CAD  CAE  NAH   180.00   0.0  0
 BI3  CONST_04  CAG   CAD  CAE  NAH     0.00   0.0  0
 BI3  CONST_05  CAF   CAE  NAH  CAW   180.00   0.0  0
 BI3  CONST_06  CAD   CAE  NAH  CAW     0.00   0.0  0
 BI3  CONST_07  CAE   CAD  CAG  CAW     0.00   0.0  0
 BI3  CONST_08  CAC   CAD  CAG  CAW   180.00   0.0  0
 BI3  CONST_09  CAG   CAW  NAH  CAE     0.00   0.0  0
 BI3  CONST_10  CAB   CAA  CAF  CAE     0.00   0.0  0
 BI3  CONST_11  CAB   CAC  CAD  CAE     0.00   0.0  0
 BI3  CONST_12  CAC   CAD  CAE  CAF     0.00   0.0  0
 BI3  CONST_13  CAG   CAD  CAE  CAF   180.00   0.0  0
 BI3  CONST_14  CAC   CAB  CAA  CAF     0.00   0.0  0
 BI3  CONST_15  CAD   CAE  CAF  CAA     0.00   0.0  0
 BI3  CONST_16  CAD   CAC  CAB  CAA     0.00   0.0  0
 BI3  CONST_17  CAG   CAD  CAC  CAB   180.00   0.0  0
 BI3  CONST_18  CAQ   CAP  CAM  CAK   180.00   0.0  0
 BI3  CONST_19  CAS   CAN  CAM  CAK   180.00   0.0  0
 BI3  CONST_20  NAO   CAN  CAM  CAK     0.00   0.0  0
 BI3  CONST_21  CAN   NAO  CAL  CAK     0.00   0.0  0
 BI3  CONST_22  NAO   CAL  CAK  CAM     0.00   0.0  0
 BI3  CONST_23  CAR   CAQ  CAP  CAM     0.00   0.0  0
 BI3  CONST_24  CAR   CAS  CAN  CAM     0.00   0.0  0
 BI3  CONST_25  CAL   NAO  CAN  CAM     0.00   0.0  0
 BI3  CONST_26  CAL   CAK  CAM  CAP   180.00   0.0  0
 BI3  CONST_27  CAS   CAN  CAM  CAP     0.00   0.0  0
 BI3  CONST_28  NAO   CAN  CAM  CAP   180.00   0.0  0
 BI3  CONST_29  CAS   CAR  CAQ  CAP     0.00   0.0  0
 BI3  CONST_30  CAN   CAM  CAP  CAQ     0.00   0.0  0
 BI3  CONST_31  CAN   CAS  CAR  CAQ     0.00   0.0  0
 BI3  CONST_32  NAO   CAN  CAS  CAR   180.00   0.0  0
 BI3  CONST_33  CAL   NAO  CAN  CAS   180.00   0.0  0
 BI3  CONST_34  CAL   CAK  CAM  CAN     0.00   0.0  0
 BI3  CONST_35  CAI   CAG  CAW  NAH   180.00   0.0  0
 BI3  CONST_36  CAI   CAG  CAD  CAE   180.00   0.0  0
 BI3  CONST_37  CAI   CAG  CAD  CAC     0.00   0.0  0
 BI3  CONST_38  CAP   CAM  CAK  CAJ     0.00   0.0  0
 BI3  CONST_39  CAN   CAM  CAK  CAJ   180.00   0.0  0
 BI3  CONST_40  NAO   CAL  CAK  CAJ   180.00   0.0  0
 BI3  CONST_41  CAV   NAU  CAT  CAI     0.00   0.0  0
 BI3  CONST_42  CAG   CAW  NAH  CAY   180.00   0.0  0
 BI3  CONST_43  CAF   CAE  NAH  CAY     0.00   0.0  0
 BI3  CONST_44  CAD   CAE  NAH  CAY   180.00   0.0  0
 BI3  CONST_45  CAV   NAU  CAT  OAZ   180.00   0.0  0
 BI3  CONST_46  HAF   CAF  CAE  NAH     0.00   0.0  0
 BI3  CONST_47  HAW   CAW  NAH  CAE   180.00   0.0  0
 BI3  CONST_48  HAA   CAA  CAF  CAE   180.00   0.0  0
 BI3  CONST_49  HAC   CAC  CAD  CAE   180.00   0.0  0
 BI3  CONST_50  HAB   CAB  CAA  CAF   180.00   0.0  0
 BI3  CONST_51  HAL   CAL  CAK  CAJ     0.00   0.0  0
 BI3  CONST_52  HAP   CAP  CAM  CAK     0.00   0.0  0
 BI3  CONST_53  HAO   NAO  CAL  CAK   180.00   0.0  0
 BI3  CONST_54  HAQ   CAQ  CAP  CAM   180.00   0.0  0
 BI3  CONST_55  HAS   CAS  CAN  CAM   180.00   0.0  0
 BI3  CONST_56  HAR   CAR  CAQ  CAP   180.00   0.0  0
 BI3  CONST_57  HAU   NAU  CAT  CAI   180.00   0.0  0
 BI3  Var_01    CAT   CAI  CAG  CAW  -136.21  30.0  2
 BI3  Var_02    CAM   CAK  CAJ  CAI  -135.93  30.0  2
 BI3  Var_03    CAW   NAH  CAY  CBA    94.31  30.0  2
 BI3  Var_04    NAH   CAY  CBA  CBB   177.99  30.0  3
 BI3  Var_05    CAY   CBA  CBB  NBC   179.30  30.0  3
 BI3  Var_06    HBC1  NBC  CBB  CBA   -67.18  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
 BI3  plan-1  CAG  0.020
 BI3  plan-1  CAI  0.020
 BI3  plan-1  CAT  0.020
 BI3  plan-1  OAZ  0.020
 BI3  plan-1  NAU  0.020
 BI3  plan-1  CAV  0.020
 BI3  plan-1  OAX  0.020
 BI3  plan-1  CAJ  0.020
 BI3  plan-1  CAK  0.020
 BI3  plan-1  HAU  0.020
 BI3  plan-2  CAY  0.020
 BI3  plan-2  NAH  0.020
 BI3  plan-2  CAW  0.020
 BI3  plan-2  CAE  0.020
 BI3  plan-2  CAF  0.020
 BI3  plan-2  CAA  0.020
 BI3  plan-2  CAB  0.020
 BI3  plan-2  CAC  0.020
 BI3  plan-2  CAD  0.020
 BI3  plan-2  CAG  0.020
 BI3  plan-2  CAI  0.020
 BI3  plan-2  HAW  0.020
 BI3  plan-2  HAF  0.020
 BI3  plan-2  HAA  0.020
 BI3  plan-2  HAB  0.020
 BI3  plan-2  HAC  0.020
 BI3  plan-3  CAJ  0.020
 BI3  plan-3  CAK  0.020
 BI3  plan-3  CAM  0.020
 BI3  plan-3  CAP  0.020
 BI3  plan-3  CAQ  0.020
 BI3  plan-3  CAR  0.020
 BI3  plan-3  CAS  0.020
 BI3  plan-3  CAN  0.020
 BI3  plan-3  NAO  0.020
 BI3  plan-3  CAL  0.020
 BI3  plan-3  HAP  0.020
 BI3  plan-3  HAQ  0.020
 BI3  plan-3  HAR  0.020
 BI3  plan-3  HAS  0.020
 BI3  plan-3  HAO  0.020
 BI3  plan-3  HAL  0.020

