# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 16:51:56 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 1-benzyl-5-chloro-3-(phenylsulfanyl)-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1n(Cc2ccccc2)c3ccc(Cl)cc3c1Sc4ccccc4
#
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
 SF1  SF1  '1-benzyl-5-chloro-3-(phenylsulfanyl)-1H-indole-2-carboxylic acid'  ligand  42  27  .  2021-08-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SF1
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
 SF1  CAJ   C   CR16   0  -0.293  -3.3222  -0.0380  -0.6326
 SF1  CAF   C   CR16   0  -0.240  -3.9775  -0.0986  -1.8532
 SF1  CAD   C   CR16   0  -0.266  -4.5448   1.0468  -2.4011
 SF1  CAG   C   CR16   0  -0.239  -4.4517   2.2517  -1.7205
 SF1  CAK   C   CR16   0  -0.317  -3.7901   2.3105  -0.4993
 SF1  CAU   C   CR6    0   0.133  -3.2209   1.1702   0.0550
 SF1  CAQ   C   CH2    0  -0.435  -2.5039   1.2402   1.3803
 SF1  NBA   N   NR5    0  -0.565  -1.1250   0.8062   1.2810
 SF1  CAX   C   CR5    0   0.263  -0.6407  -0.4370   1.5797
 SF1  CAS   C   C      0   0.373  -1.4822  -1.5024   2.2538
 SF1  OAB   O   OC    -1  -0.576  -1.9492  -1.1982   3.3642
 SF1  OAA   O   O      0  -0.555  -1.6110  -2.5613   1.6216
 SF1  CAZ   C   CR56   0   0.365  -0.1384   1.5431   0.6726
 SF1  CAO   C   CR16   0  -0.304  -0.1648   2.8377   0.1652
 SF1  CAN   C   CR16   0  -0.242   1.0018   3.3424  -0.3797
 SF1  CAT   C   CR6    0  -0.051   2.1607   2.5580  -0.4134
 SF1  CLAC  CL  CL     0  -0.145   3.6021   3.2435  -1.1067
 SF1  CAP   C   CR16   0  -0.326   2.1992   1.2699   0.0784
 SF1  CAY   C   CR56   0   0.155   1.0249   0.7526   0.6240
 SF1  CAW   C   CR5    0  -0.349   0.6774  -0.5094   1.1952
 SF1  SAR   S   S2     0   0.027   1.7729  -1.8336   1.4774
 SF1  CAV   C   CR6    0  -0.123   1.8546  -2.6318  -0.1074
 SF1  CAL   C   CR16   0  -0.224   0.7317  -2.7780  -0.9165
 SF1  CAH   C   CR16   0  -0.247   0.8432  -3.4305  -2.1356
 SF1  CAE   C   CR16   0  -0.264   2.0614  -3.9621  -2.5435
 SF1  CAI   C   CR16   0  -0.247   3.1748  -3.8301  -1.7249
 SF1  CAM   C   CR16   0  -0.267   3.0773  -3.1585  -0.5130
 SF1  HAJ   H   HCR6   0   0.251  -2.8893  -0.9403  -0.2150
 SF1  HAF   H   HCR6   0   0.257  -4.0513  -1.0430  -2.3769
 SF1  HAD   H   HCR6   0   0.257  -5.0573   0.9971  -3.3531
 SF1  HAG   H   HCR6   0   0.257  -4.8878   3.1492  -2.1394
 SF1  HAK   H   HCR6   0   0.253  -3.7154   3.2567   0.0245
 SF1  HAQ1  H   HCH2   0   0.282  -2.5222   2.2604   1.7677
 SF1  HAQ2  H   HCH2   0   0.295  -2.9952   0.6168   2.1250
 SF1  HAO   H   HCR6   0   0.267  -1.0561   3.4503   0.1860
 SF1  HAN   H   HCR6   0   0.273   1.0173   4.3464  -0.7806
 SF1  HAP   H   HCR6   0   0.265   3.1038   0.6762   0.0439
 SF1  HAL   H   HCR6   0   0.273  -0.2231  -2.3957  -0.5806
 SF1  HAH   H   HCR6   0   0.256  -0.0317  -3.5362  -2.7645
 SF1  HAE   H   HCR6   0   0.256   2.1414  -4.4758  -3.4927
 SF1  HAI   H   HCR6   0   0.258   4.1292  -4.2360  -2.0346
 SF1  HAM   H   HCR6   0   0.261   3.9554  -3.0357   0.1091

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
 SF1  CAJ  CAF   aromatic  1.387  0.020  1.387
 SF1  CAJ  CAU   aromatic  1.394  0.020  1.394
 SF1  CAJ  HAJ   single    0.930  0.020  1.080
 SF1  CAF  CAD   aromatic  1.391  0.020  1.391
 SF1  CAF  HAF   single    0.930  0.020  1.080
 SF1  CAD  CAG   aromatic  1.387  0.020  1.387
 SF1  CAD  HAD   single    0.930  0.020  1.080
 SF1  CAG  CAK   aromatic  1.390  0.020  1.390
 SF1  CAG  HAG   single    0.930  0.020  1.080
 SF1  CAK  CAU   aromatic  1.390  0.020  1.390
 SF1  CAK  HAK   single    0.930  0.020  1.080
 SF1  CAU  CAQ   single    1.508  0.020  1.508
 SF1  CAQ  NBA   single    1.449  0.020  1.449
 SF1  CAQ  HAQ1  single    0.970  0.020  1.090
 SF1  CAQ  HAQ2  single    0.970  0.020  1.090
 SF1  NBA  CAZ   aromatic  1.373  0.020  1.373
 SF1  NBA  CAX   aromatic  1.367  0.020  1.367
 SF1  CAX  CAS   single    1.516  0.020  1.516
 SF1  CAX  CAW   aromatic  1.375  0.020  1.375
 SF1  CAS  OAA   deloc     1.240  0.020  1.240
 SF1  CAS  OAB   deloc     1.242  0.020  1.242
 SF1  CAZ  CAO   aromatic  1.391  0.020  1.391
 SF1  CAZ  CAY   aromatic  1.407  0.020  1.407
 SF1  CAO  CAN   aromatic  1.383  0.020  1.383
 SF1  CAO  HAO   single    0.930  0.020  1.080
 SF1  CAN  CAT   aromatic  1.400  0.020  1.400
 SF1  CAN  HAN   single    0.930  0.020  1.080
 SF1  CAT  CLAC  single    1.740  0.020  1.740
 SF1  CAT  CAP   aromatic  1.379  0.020  1.379
 SF1  CAP  CAY   aromatic  1.394  0.020  1.394
 SF1  CAP  HAP   single    0.930  0.020  1.080
 SF1  CAY  CAW   aromatic  1.428  0.020  1.428
 SF1  CAW  SAR   single    1.742  0.020  1.742
 SF1  SAR  CAV   single    1.776  0.020  1.776
 SF1  CAV  CAM   aromatic  1.392  0.020  1.392
 SF1  CAV  CAL   aromatic  1.392  0.020  1.392
 SF1  CAL  CAH   aromatic  1.387  0.020  1.387
 SF1  CAL  HAL   single    0.930  0.020  1.080
 SF1  CAH  CAE   aromatic  1.390  0.020  1.390
 SF1  CAH  HAH   single    0.930  0.020  1.080
 SF1  CAE  CAI   aromatic  1.388  0.020  1.388
 SF1  CAE  HAE   single    0.930  0.020  1.080
 SF1  CAI  CAM   aromatic  1.389  0.020  1.389
 SF1  CAI  HAI   single    0.930  0.020  1.080
 SF1  CAM  HAM   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
 SF1  HAJ   CAJ  CAU   120.15  3.000
 SF1  HAJ   CAJ  CAF   119.42  3.000
 SF1  CAU   CAJ  CAF   120.43  3.000
 SF1  HAF   CAF  CAD   120.01  3.000
 SF1  HAF   CAF  CAJ   119.75  3.000
 SF1  CAD   CAF  CAJ   120.24  3.000
 SF1  HAD   CAD  CAG   120.22  3.000
 SF1  HAD   CAD  CAF   120.13  3.000
 SF1  CAG   CAD  CAF   119.65  3.000
 SF1  HAG   CAG  CAK   119.78  3.000
 SF1  HAG   CAG  CAD   120.23  3.000
 SF1  CAK   CAG  CAD   119.99  3.000
 SF1  HAK   CAK  CAU   119.68  3.000
 SF1  HAK   CAK  CAG   119.62  3.000
 SF1  CAU   CAK  CAG   120.70  3.000
 SF1  CAQ   CAU  CAK   120.47  3.000
 SF1  CAQ   CAU  CAJ   120.54  3.000
 SF1  CAK   CAU  CAJ   118.99  3.000
 SF1  HAQ2  CAQ  HAQ1  106.55  3.000
 SF1  HAQ2  CAQ  NBA   107.75  3.000
 SF1  HAQ1  CAQ  NBA   108.68  3.000
 SF1  HAQ2  CAQ  CAU   111.10  3.000
 SF1  HAQ1  CAQ  CAU   110.32  3.000
 SF1  NBA   CAQ  CAU   112.23  3.000
 SF1  CAZ   NBA  CAX   109.28  3.000
 SF1  CAX   NBA  CAQ   126.48  3.000
 SF1  CAZ   NBA  CAQ   123.59  3.000
 SF1  CAW   CAX  CAS   128.28  3.000
 SF1  CAW   CAX  NBA   109.05  3.000
 SF1  CAS   CAX  NBA   122.65  3.000
 SF1  OAA   CAS  OAB   128.73  3.000
 SF1  OAB   CAS  CAX   115.72  3.000
 SF1  OAA   CAS  CAX   115.54  3.000
 SF1  CAY   CAZ  CAO   121.73  3.000
 SF1  CAY   CAZ  NBA   107.92  3.000
 SF1  CAO   CAZ  NBA   130.34  3.000
 SF1  HAO   CAO  CAN   119.73  3.000
 SF1  HAO   CAO  CAZ   122.40  3.000
 SF1  CAN   CAO  CAZ   117.87  3.000
 SF1  HAN   CAN  CAT   119.97  3.000
 SF1  HAN   CAN  CAO   119.81  3.000
 SF1  CAT   CAN  CAO   120.22  3.000
 SF1  CAP   CAT  CLAC  119.13  3.000
 SF1  CAP   CAT  CAN   122.54  3.000
 SF1  CLAC  CAT  CAN   118.33  3.000
 SF1  HAP   CAP  CAY   120.84  3.000
 SF1  HAP   CAP  CAT   121.61  3.000
 SF1  CAY   CAP  CAT   117.54  3.000
 SF1  CAW   CAY  CAP   133.57  3.000
 SF1  CAW   CAY  CAZ   106.35  3.000
 SF1  CAP   CAY  CAZ   120.08  3.000
 SF1  SAR   CAW  CAY   125.71  3.000
 SF1  SAR   CAW  CAX   126.71  3.000
 SF1  CAY   CAW  CAX   107.37  3.000
 SF1  CAV   SAR  CAW   103.07  3.000
 SF1  CAM   CAV  CAL   119.98  3.000
 SF1  CAL   CAV  SAR   121.92  3.000
 SF1  CAM   CAV  SAR   118.07  3.000
 SF1  HAL   CAL  CAH   120.66  3.000
 SF1  HAL   CAL  CAV   119.63  3.000
 SF1  CAH   CAL  CAV   119.70  3.000
 SF1  HAH   CAH  CAE   120.02  3.000
 SF1  HAH   CAH  CAL   119.44  3.000
 SF1  CAE   CAH  CAL   120.54  3.000
 SF1  HAE   CAE  CAI   120.20  3.000
 SF1  HAE   CAE  CAH   120.24  3.000
 SF1  CAI   CAE  CAH   119.56  3.000
 SF1  HAI   CAI  CAM   119.53  3.000
 SF1  HAI   CAI  CAE   120.19  3.000
 SF1  CAM   CAI  CAE   120.28  3.000
 SF1  HAM   CAM  CAI   119.93  3.000
 SF1  HAM   CAM  CAV   120.13  3.000
 SF1  CAI   CAM  CAV   119.93  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
 SF1  CONST_01  CAG   CAD  CAF  CAJ     0.00   0.0  0
 SF1  CONST_02  CAG   CAK  CAU  CAJ     0.00   0.0  0
 SF1  CONST_03  CAK   CAU  CAJ  CAF     0.00   0.0  0
 SF1  CONST_04  CAK   CAG  CAD  CAF     0.00   0.0  0
 SF1  CONST_05  CAU   CAJ  CAF  CAD     0.00   0.0  0
 SF1  CONST_06  CAU   CAK  CAG  CAD     0.00   0.0  0
 SF1  CONST_07  CAN   CAO  CAZ  NBA   180.00   0.0  0
 SF1  CONST_08  CAP   CAY  CAZ  NBA   180.00   0.0  0
 SF1  CONST_09  CAW   CAY  CAZ  NBA     0.00   0.0  0
 SF1  CONST_10  CAY   CAW  CAX  NBA     0.00   0.0  0
 SF1  CONST_11  CAO   CAZ  NBA  CAX   180.00   0.0  0
 SF1  CONST_12  CAY   CAZ  NBA  CAX     0.00   0.0  0
 SF1  CONST_13  CAZ   CAY  CAW  CAX     0.00   0.0  0
 SF1  CONST_14  CAP   CAY  CAW  CAX   180.00   0.0  0
 SF1  CONST_15  CAW   CAX  NBA  CAZ     0.00   0.0  0
 SF1  CONST_16  CAT   CAN  CAO  CAZ     0.00   0.0  0
 SF1  CONST_17  CAT   CAP  CAY  CAZ     0.00   0.0  0
 SF1  CONST_18  CAP   CAY  CAZ  CAO     0.00   0.0  0
 SF1  CONST_19  CAW   CAY  CAZ  CAO   180.00   0.0  0
 SF1  CONST_20  CAP   CAT  CAN  CAO     0.00   0.0  0
 SF1  CONST_21  CAY   CAZ  CAO  CAN     0.00   0.0  0
 SF1  CONST_22  CAY   CAP  CAT  CAN     0.00   0.0  0
 SF1  CONST_23  CAW   CAY  CAP  CAT   180.00   0.0  0
 SF1  CONST_24  CAE   CAI  CAM  CAV     0.00   0.0  0
 SF1  CONST_25  CAE   CAH  CAL  CAV     0.00   0.0  0
 SF1  CONST_26  CAI   CAM  CAV  CAL     0.00   0.0  0
 SF1  CONST_27  CAI   CAE  CAH  CAL     0.00   0.0  0
 SF1  CONST_28  CAM   CAV  CAL  CAH     0.00   0.0  0
 SF1  CONST_29  CAM   CAI  CAE  CAH     0.00   0.0  0
 SF1  CONST_30  CAQ   CAU  CAJ  CAF   180.00   0.0  0
 SF1  CONST_31  CAQ   CAU  CAK  CAG   180.00   0.0  0
 SF1  CONST_32  CAO   CAZ  NBA  CAQ     0.00   0.0  0
 SF1  CONST_33  CAY   CAZ  NBA  CAQ   180.00   0.0  0
 SF1  CONST_34  CAW   CAX  NBA  CAQ   180.00   0.0  0
 SF1  CONST_35  SAR   CAW  CAX  NBA   180.00   0.0  0
 SF1  CONST_36  CAZ   NBA  CAX  CAS   180.00   0.0  0
 SF1  CONST_37  CAY   CAW  CAX  CAS   180.00   0.0  0
 SF1  CONST_38  SAR   CAW  CAY  CAZ   180.00   0.0  0
 SF1  CONST_39  CLAC  CAT  CAN  CAO   180.00   0.0  0
 SF1  CONST_40  CAY   CAP  CAT  CLAC  180.00   0.0  0
 SF1  CONST_41  SAR   CAW  CAY  CAP     0.00   0.0  0
 SF1  CONST_42  CAI   CAM  CAV  SAR   180.00   0.0  0
 SF1  CONST_43  CAH   CAL  CAV  SAR   180.00   0.0  0
 SF1  CONST_44  HAD   CAD  CAF  CAJ   180.00   0.0  0
 SF1  CONST_45  HAK   CAK  CAU  CAJ   180.00   0.0  0
 SF1  CONST_46  HAG   CAG  CAD  CAF   180.00   0.0  0
 SF1  CONST_47  HAJ   CAJ  CAF  CAD   180.00   0.0  0
 SF1  CONST_48  HAF   CAF  CAD  CAG   180.00   0.0  0
 SF1  CONST_49  HAO   CAO  CAZ  NBA     0.00   0.0  0
 SF1  CONST_50  HAN   CAN  CAO  CAZ   180.00   0.0  0
 SF1  CONST_51  HAP   CAP  CAY  CAZ   180.00   0.0  0
 SF1  CONST_52  HAI   CAI  CAM  CAV   180.00   0.0  0
 SF1  CONST_53  HAH   CAH  CAL  CAV   180.00   0.0  0
 SF1  CONST_54  HAM   CAM  CAV  CAL   180.00   0.0  0
 SF1  CONST_55  HAE   CAE  CAH  CAL   180.00   0.0  0
 SF1  CONST_56  HAL   CAL  CAH  CAE   180.00   0.0  0
 SF1  Var_01    NBA   CAQ  CAU  CAJ    58.51  30.0  2
 SF1  Var_02    CAZ   NBA  CAQ  CAU    72.48  30.0  2
 SF1  Var_03    CAM   CAV  SAR  CAW   143.03  30.0  2
 SF1  Var_04    OAA   CAS  CAX  NBA   121.39  30.0  2

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
 SF1  plan-1  CAJ   0.020
 SF1  plan-1  CAF   0.020
 SF1  plan-1  CAD   0.020
 SF1  plan-1  CAG   0.020
 SF1  plan-1  CAK   0.020
 SF1  plan-1  CAU   0.020
 SF1  plan-1  CAQ   0.020
 SF1  plan-1  HAJ   0.020
 SF1  plan-1  HAF   0.020
 SF1  plan-1  HAD   0.020
 SF1  plan-1  HAG   0.020
 SF1  plan-1  HAK   0.020
 SF1  plan-2  SAR   0.020
 SF1  plan-2  CAV   0.020
 SF1  plan-2  CAL   0.020
 SF1  plan-2  CAH   0.020
 SF1  plan-2  CAE   0.020
 SF1  plan-2  CAI   0.020
 SF1  plan-2  CAM   0.020
 SF1  plan-2  HAL   0.020
 SF1  plan-2  HAH   0.020
 SF1  plan-2  HAE   0.020
 SF1  plan-2  HAI   0.020
 SF1  plan-2  HAM   0.020
 SF1  plan-3  CAQ   0.020
 SF1  plan-3  NBA   0.020
 SF1  plan-3  CAX   0.020
 SF1  plan-3  CAS   0.020
 SF1  plan-3  CAZ   0.020
 SF1  plan-3  CAO   0.020
 SF1  plan-3  CAN   0.020
 SF1  plan-3  CAT   0.020
 SF1  plan-3  CLAC  0.020
 SF1  plan-3  CAP   0.020
 SF1  plan-3  CAY   0.020
 SF1  plan-3  CAW   0.020
 SF1  plan-3  SAR   0.020
 SF1  plan-3  HAO   0.020
 SF1  plan-3  HAN   0.020
 SF1  plan-3  HAP   0.020
 SF1  plan-4  CAX   0.020
 SF1  plan-4  CAS   0.020
 SF1  plan-4  OAB   0.020
 SF1  plan-4  OAA   0.020

