# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 19:57:21 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-[2-(4-phenylpiperidin-1-yl)ethyl]-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CN(CCC1c2ccccc2)CCc3[nH]c4ccccc4c3
#
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
 VU3  VU3  2-[2-(4-phenylpiperidin-1-yl)ethyl]-1H-indole  ligand  47  23  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VU3
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
 VU3  CAW   C  CH2   0  -0.547  -1.5706   0.1306  -0.8767
 VU3  CAO   C  CR5   0   0.368  -3.0361   0.0016  -0.6490
 VU3  NAQ   N  NR15  0  -0.725  -3.7417   0.9736   0.0124
 VU3  CAX   C  CR56  0   0.332  -5.0540   0.6097   0.1126
 VU3  CAN   C  CR16  0  -0.313  -6.1354   1.2770   0.6834
 VU3  CAJ   C  CR16  0  -0.287  -7.3692   0.6550   0.6306
 VU3  CAF   C  CR16  0  -0.273  -7.5246  -0.6019   0.0239
 VU3  CAI   C  CR16  0  -0.352  -6.4489  -1.2594  -0.5420
 VU3  CAM   C  CR56  0   0.076  -5.1873  -0.6543  -0.5060
 VU3  CAP   C  CH2   0  -0.250  -0.7606  -0.0926   0.4047
 VU3  CAV   C  CR16  0  -0.343   5.9867  -0.9002   0.6490
 VU3  CAD   C  CR16  0  -0.237   7.3226  -0.6269   0.3805
 VU3  CAC   C  CR16  0  -0.277   7.6646   0.4580  -0.4143
 VU3  CAR   C  CR16  0  -0.238   6.6602   1.2639  -0.9373
 VU3  CAE   C  CR16  0  -0.322   5.3280   0.9850  -0.6666
 VU3  CAU   C  CR6   0   0.203   4.9697  -0.1018   0.1315
 VU3  CAS   C  CH1   0  -0.349   3.5256  -0.4129   0.4266
 VU3  CAT   C  CH2   0  -0.410   2.7258  -0.7403  -0.8359
 VU3  CAK   C  CH2   0  -0.414   2.8200   0.7153   1.1804
 VU3  CAG   C  CH2   0  -0.283   1.3622   0.3669   1.4404
 VU3  CAL   C  CH2   0  -0.290   1.2723  -1.0275  -0.4928
 VU3  C17   C  CR15  0  -0.466  -3.8883  -1.0157  -0.9800
 VU3  N1    N  NT    0  -0.423   0.6612   0.0955   0.1967
 VU3  HAW1  H  HCH2  0   0.256  -1.2849  -0.5890  -1.6449
 VU3  HAW2  H  HCH2  0   0.251  -1.3351   1.1238  -1.2692
 VU3  HAP1  H  HCH2  0   0.231  -1.0897   0.6305   1.1551
 VU3  HAP2  H  HCH2  0   0.203  -0.9939  -1.0895   0.8131
 VU3  HAQ   H  HNR5  0   0.403  -3.3544   1.8405   0.3471
 VU3  H17   H  HCR5  0   0.244  -3.6123  -1.9184  -1.5032
 VU3  HAN   H  HCR6  0   0.256  -6.0152   2.2454   1.1528
 VU3  HAJ   H  HCR6  0   0.247  -8.2310   1.1461   1.0637
 VU3  HAF   H  HCR6  0   0.244  -8.5055  -1.0591  -0.0013
 VU3  HAI   H  HCR6  0   0.243  -6.5822  -2.2278  -1.0088
 VU3  HAD   H  HCR6  0   0.252   8.0948  -1.2646   0.7921
 VU3  HAC   H  HCR6  0   0.252   8.7037   0.6752  -0.6256
 VU3  HAR   H  HCR6  0   0.252   6.9151   2.1136  -1.5580
 VU3  HAE   H  HCR6  0   0.242   4.5596   1.6242  -1.0862
 VU3  HAS   H  HCH1  0   0.234   3.5027  -1.3018   1.0694
 VU3  HAT1  H  HCH2  0   0.219   2.7728   0.0988  -1.5360
 VU3  HAT2  H  HCH2  0   0.236   3.1564  -1.6068  -1.3429
 VU3  HAK1  H  HCH2  0   0.237   3.3235   0.9124   2.1298
 VU3  HAK2  H  HCH2  0   0.218   2.8622   1.6392   0.5958
 VU3  HAL1  H  HCH2  0   0.238   0.7231  -1.2386  -1.4118
 VU3  HAL2  H  HCH2  0   0.190   1.2226  -1.9445   0.1228
 VU3  HAG1  H  HCH2  0   0.188   1.3092  -0.4953   2.1287
 VU3  HAG2  H  HCH2  0   0.237   0.8726   1.2036   1.9448
 VU3  HAV   H  HCR6  0   0.245   5.7300  -1.7506   1.2705

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
 VU3  CAW  CAO   single    1.489  0.020  1.489
 VU3  CAW  CAP   single    1.532  0.020  1.532
 VU3  CAO  NAQ   aromatic  1.371  0.020  1.371
 VU3  CAO  C17   aromatic  1.368  0.020  1.368
 VU3  NAQ  CAX   aromatic  1.366  0.020  1.366
 VU3  CAX  CAN   aromatic  1.393  0.020  1.393
 VU3  CAX  CAM   aromatic  1.413  0.020  1.413
 VU3  CAN  CAJ   aromatic  1.383  0.020  1.383
 VU3  CAJ  CAF   aromatic  1.404  0.020  1.404
 VU3  CAF  CAI   aromatic  1.382  0.020  1.382
 VU3  CAI  CAM   aromatic  1.400  0.020  1.400
 VU3  CAM  C17   aromatic  1.429  0.020  1.429
 VU3  CAP  N1    single    1.449  0.020  1.449
 VU3  CAV  CAD   aromatic  1.390  0.020  1.390
 VU3  CAV  CAU   aromatic  1.393  0.020  1.393
 VU3  CAD  CAC   aromatic  1.388  0.020  1.388
 VU3  CAC  CAR   aromatic  1.390  0.020  1.390
 VU3  CAR  CAE   aromatic  1.388  0.020  1.388
 VU3  CAE  CAU   aromatic  1.395  0.020  1.395
 VU3  CAU  CAS   single    1.506  0.020  1.506
 VU3  CAS  CAT   single    1.530  0.020  1.530
 VU3  CAS  CAK   single    1.529  0.020  1.529
 VU3  CAT  CAL   single    1.521  0.020  1.521
 VU3  CAK  CAG   single    1.521  0.020  1.521
 VU3  CAG  N1    single    1.453  0.020  1.453
 VU3  CAL  N1    single    1.453  0.020  1.453
 VU3  CAW  HAW1  single    0.970  0.020  1.090
 VU3  CAW  HAW2  single    0.970  0.020  1.090
 VU3  CAP  HAP1  single    0.970  0.020  1.090
 VU3  CAP  HAP2  single    0.970  0.020  1.090
 VU3  NAQ  HAQ   single    0.860  0.020  1.020
 VU3  C17  H17   single    0.930  0.020  1.080
 VU3  CAN  HAN   single    0.930  0.020  1.080
 VU3  CAJ  HAJ   single    0.930  0.020  1.080
 VU3  CAF  HAF   single    0.930  0.020  1.080
 VU3  CAI  HAI   single    0.930  0.020  1.080
 VU3  CAV  HAV   single    0.930  0.020  1.080
 VU3  CAD  HAD   single    0.930  0.020  1.080
 VU3  CAC  HAC   single    0.930  0.020  1.080
 VU3  CAR  HAR   single    0.930  0.020  1.080
 VU3  CAE  HAE   single    0.930  0.020  1.080
 VU3  CAS  HAS   single    0.970  0.020  1.090
 VU3  CAT  HAT1  single    0.970  0.020  1.090
 VU3  CAT  HAT2  single    0.970  0.020  1.090
 VU3  CAK  HAK1  single    0.970  0.020  1.090
 VU3  CAK  HAK2  single    0.970  0.020  1.090
 VU3  CAL  HAL1  single    0.970  0.020  1.090
 VU3  CAL  HAL2  single    0.970  0.020  1.090
 VU3  CAG  HAG1  single    0.970  0.020  1.090
 VU3  CAG  HAG2  single    0.970  0.020  1.090

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
 VU3  HAW2  CAW  HAW1  106.86  3.000
 VU3  HAW2  CAW  CAP   108.58  3.000
 VU3  HAW1  CAW  CAP   110.76  3.000
 VU3  HAW2  CAW  CAO   110.22  3.000
 VU3  HAW1  CAW  CAO   107.97  3.000
 VU3  CAP   CAW  CAO   112.33  3.000
 VU3  C17   CAO  NAQ   108.87  3.000
 VU3  C17   CAO  CAW   129.85  3.000
 VU3  NAQ   CAO  CAW   121.26  3.000
 VU3  HAQ   NAQ  CAX   125.09  3.000
 VU3  HAQ   NAQ  CAO   124.95  3.000
 VU3  CAX   NAQ  CAO   109.94  3.000
 VU3  CAM   CAX  CAN   122.31  3.000
 VU3  CAM   CAX  NAQ   107.27  3.000
 VU3  CAN   CAX  NAQ   130.42  3.000
 VU3  HAN   CAN  CAJ   121.19  3.000
 VU3  HAN   CAN  CAX   121.32  3.000
 VU3  CAJ   CAN  CAX   117.49  3.000
 VU3  HAJ   CAJ  CAF   119.40  3.000
 VU3  HAJ   CAJ  CAN   119.42  3.000
 VU3  CAF   CAJ  CAN   121.19  3.000
 VU3  HAF   CAF  CAI   119.66  3.000
 VU3  HAF   CAF  CAJ   119.24  3.000
 VU3  CAI   CAF  CAJ   121.11  3.000
 VU3  HAI   CAI  CAM   120.57  3.000
 VU3  HAI   CAI  CAF   120.40  3.000
 VU3  CAM   CAI  CAF   119.04  3.000
 VU3  C17   CAM  CAI   134.53  3.000
 VU3  C17   CAM  CAX   106.59  3.000
 VU3  CAI   CAM  CAX   118.87  3.000
 VU3  HAP2  CAP  HAP1  106.28  3.000
 VU3  HAP2  CAP  N1    112.23  3.000
 VU3  HAP1  CAP  N1    107.95  3.000
 VU3  HAP2  CAP  CAW   109.25  3.000
 VU3  HAP1  CAP  CAW   108.58  3.000
 VU3  N1    CAP  CAW   112.31  3.000
 VU3  HAV   CAV  CAU   119.33  3.000
 VU3  HAV   CAV  CAD   119.51  3.000
 VU3  CAU   CAV  CAD   121.16  3.000
 VU3  HAD   CAD  CAC   120.16  3.000
 VU3  HAD   CAD  CAV   119.76  3.000
 VU3  CAC   CAD  CAV   120.09  3.000
 VU3  HAC   CAC  CAR   120.26  3.000
 VU3  HAC   CAC  CAD   120.35  3.000
 VU3  CAR   CAC  CAD   119.39  3.000
 VU3  HAR   CAR  CAE   119.71  3.000
 VU3  HAR   CAR  CAC   120.04  3.000
 VU3  CAE   CAR  CAC   120.25  3.000
 VU3  HAE   CAE  CAU   119.91  3.000
 VU3  HAE   CAE  CAR   119.11  3.000
 VU3  CAU   CAE  CAR   120.98  3.000
 VU3  CAS   CAU  CAE   121.28  3.000
 VU3  CAS   CAU  CAV   120.59  3.000
 VU3  CAE   CAU  CAV   118.14  3.000
 VU3  HAS   CAS  CAK   107.41  3.000
 VU3  HAS   CAS  CAT   107.41  3.000
 VU3  CAK   CAS  CAT   108.87  3.000
 VU3  HAS   CAS  CAU   107.58  3.000
 VU3  CAK   CAS  CAU   112.73  3.000
 VU3  CAT   CAS  CAU   112.57  3.000
 VU3  HAT2  CAT  HAT1  107.13  3.000
 VU3  HAT2  CAT  CAL   109.37  3.000
 VU3  HAT1  CAT  CAL   109.30  3.000
 VU3  HAT2  CAT  CAS   110.28  3.000
 VU3  HAT1  CAT  CAS   109.97  3.000
 VU3  CAL   CAT  CAS   110.73  3.000
 VU3  HAK2  CAK  HAK1  107.11  3.000
 VU3  HAK2  CAK  CAG   108.77  3.000
 VU3  HAK1  CAK  CAG   109.54  3.000
 VU3  HAK2  CAK  CAS   109.99  3.000
 VU3  HAK1  CAK  CAS   110.41  3.000
 VU3  CAG   CAK  CAS   110.94  3.000
 VU3  HAG2  CAG  HAG1  106.77  3.000
 VU3  HAG2  CAG  N1    108.78  3.000
 VU3  HAG1  CAG  N1    111.37  3.000
 VU3  HAG2  CAG  CAK   109.44  3.000
 VU3  HAG1  CAG  CAK   109.35  3.000
 VU3  N1    CAG  CAK   111.03  3.000
 VU3  HAL2  CAL  HAL1  106.61  3.000
 VU3  HAL2  CAL  N1    110.98  3.000
 VU3  HAL1  CAL  N1    109.73  3.000
 VU3  HAL2  CAL  CAT   108.98  3.000
 VU3  HAL1  CAL  CAT   109.13  3.000
 VU3  N1    CAL  CAT   111.29  3.000
 VU3  H17   C17  CAM   127.21  3.000
 VU3  H17   C17  CAO   125.46  3.000
 VU3  CAM   C17  CAO   107.33  3.000
 VU3  CAL   N1   CAG   110.34  3.000
 VU3  CAL   N1   CAP   112.37  3.000
 VU3  CAG   N1   CAP   112.00  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
 VU3  CONST_01  CAN  CAX  NAQ  CAO   180.00   0.0  0
 VU3  CONST_02  CAM  CAX  NAQ  CAO     0.00   0.0  0
 VU3  CONST_03  CAX  CAM  C17  CAO     0.00   0.0  0
 VU3  CONST_04  CAI  CAM  C17  CAO   180.00   0.0  0
 VU3  CONST_05  CAM  C17  CAO  NAQ     0.00   0.0  0
 VU3  CONST_06  CAJ  CAN  CAX  NAQ   180.00   0.0  0
 VU3  CONST_07  CAI  CAM  CAX  NAQ   180.00   0.0  0
 VU3  CONST_08  C17  CAM  CAX  NAQ     0.00   0.0  0
 VU3  CONST_09  C17  CAO  NAQ  CAX     0.00   0.0  0
 VU3  CONST_10  CAF  CAJ  CAN  CAX     0.00   0.0  0
 VU3  CONST_11  CAF  CAI  CAM  CAX     0.00   0.0  0
 VU3  CONST_12  CAI  CAM  CAX  CAN     0.00   0.0  0
 VU3  CONST_13  C17  CAM  CAX  CAN   180.00   0.0  0
 VU3  CONST_14  CAI  CAF  CAJ  CAN     0.00   0.0  0
 VU3  CONST_15  CAM  CAX  CAN  CAJ     0.00   0.0  0
 VU3  CONST_16  CAM  CAI  CAF  CAJ     0.00   0.0  0
 VU3  CONST_17  C17  CAM  CAI  CAF   180.00   0.0  0
 VU3  CONST_18  CAR  CAC  CAD  CAV     0.00   0.0  0
 VU3  CONST_19  CAR  CAE  CAU  CAV     0.00   0.0  0
 VU3  CONST_20  CAE  CAU  CAV  CAD     0.00   0.0  0
 VU3  CONST_21  CAE  CAR  CAC  CAD     0.00   0.0  0
 VU3  CONST_22  CAU  CAV  CAD  CAC     0.00   0.0  0
 VU3  CONST_23  CAU  CAE  CAR  CAC     0.00   0.0  0
 VU3  CONST_24  CAS  CAU  CAV  CAD   180.00   0.0  0
 VU3  CONST_25  CAS  CAU  CAE  CAR   180.00   0.0  0
 VU3  CONST_26  CAX  NAQ  CAO  CAW   180.00   0.0  0
 VU3  CONST_27  CAM  C17  CAO  CAW   180.00   0.0  0
 VU3  CONST_28  H17  C17  CAO  NAQ   180.00   0.0  0
 VU3  CONST_29  HAN  CAN  CAX  NAQ     0.00   0.0  0
 VU3  CONST_30  HAJ  CAJ  CAN  CAX   180.00   0.0  0
 VU3  CONST_31  HAI  CAI  CAM  CAX   180.00   0.0  0
 VU3  CONST_32  HAQ  NAQ  CAX  CAN     0.00   0.0  0
 VU3  CONST_33  HAF  CAF  CAJ  CAN   180.00   0.0  0
 VU3  CONST_34  HAC  CAC  CAD  CAV   180.00   0.0  0
 VU3  CONST_35  HAE  CAE  CAU  CAV   180.00   0.0  0
 VU3  CONST_36  HAR  CAR  CAC  CAD   180.00   0.0  0
 VU3  CONST_37  HAV  CAV  CAD  CAC   180.00   0.0  0
 VU3  CONST_38  HAD  CAD  CAC  CAR   180.00   0.0  0
 VU3  Var_01    N1   CAL  CAT  CAS    57.70  30.0  1
 VU3  Var_02    N1   CAG  CAK  CAS   -57.74  30.0  1
 VU3  Var_03    CAG  N1   CAL  CAT   -60.55  30.0  1
 VU3  Var_04    CAL  N1   CAG  CAK    60.43  30.0  1
 VU3  Var_05    N1   CAP  CAW  CAO  -177.25  30.0  3
 VU3  Var_06    CAP  CAW  CAO  NAQ    73.45  30.0  3

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
 VU3  chir_01  CAS  CAU  CAT  CAK  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
 VU3  plan-1  CAV  0.020
 VU3  plan-1  CAD  0.020
 VU3  plan-1  CAC  0.020
 VU3  plan-1  CAR  0.020
 VU3  plan-1  CAE  0.020
 VU3  plan-1  CAU  0.020
 VU3  plan-1  CAS  0.020
 VU3  plan-1  HAD  0.020
 VU3  plan-1  HAC  0.020
 VU3  plan-1  HAR  0.020
 VU3  plan-1  HAE  0.020
 VU3  plan-1  HAV  0.020
 VU3  plan-2  CAW  0.020
 VU3  plan-2  CAO  0.020
 VU3  plan-2  NAQ  0.020
 VU3  plan-2  CAX  0.020
 VU3  plan-2  CAN  0.020
 VU3  plan-2  CAJ  0.020
 VU3  plan-2  CAF  0.020
 VU3  plan-2  CAI  0.020
 VU3  plan-2  CAM  0.020
 VU3  plan-2  C17  0.020
 VU3  plan-2  HAQ  0.020
 VU3  plan-2  H17  0.020
 VU3  plan-2  HAN  0.020
 VU3  plan-2  HAJ  0.020
 VU3  plan-2  HAF  0.020
 VU3  plan-2  HAI  0.020

