# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 17:09:52 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 5-chloro-1-(3-methoxybenzyl)-3-(phenylsulfanyl)-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(Cn2c3ccc(Cl)cc3c(Sc4ccccc4)c2C(O)=O)c1
#
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
 SF2  SF2  '5-chloro-1-(3-methoxybenzyl)-3-(phenylsulfanyl)-1H-indole-2-carboxylic acid'  ligand  46  29  .  2021-08-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SF2
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
 SF2  CAA   C   CH3    0  -0.436  -6.1102   0.5321   1.5620
 SF2  OAR   O   O2     0  -0.472  -5.2458   0.2633   0.4769
 SF2  CAW   C   CR6    0   0.401  -4.2979  -0.6819   0.6290
 SF2  CAO   C   CR16   0  -0.394  -3.4504  -0.8809  -0.4634
 SF2  CAJ   C   CR16   0  -0.393  -4.1279  -1.4444   1.7811
 SF2  CAH   C   CR16   0  -0.228  -3.1161  -2.3979   1.8212
 SF2  CAI   C   CR16   0  -0.325  -2.2751  -2.5954   0.7405
 SF2  CAV   C   CR6    0   0.157  -2.4392  -1.8272  -0.4126
 SF2  CAQ   C   CH2    0  -0.449  -1.5071  -1.9939  -1.5863
 SF2  NBC   N   NR5    0  -0.566  -0.2732  -1.2439  -1.4094
 SF2  CAZ   C   CR5    0   0.236  -0.1090   0.1030  -1.5962
 SF2  CAT   C   C      0   0.393  -1.1361   1.0021  -2.2576
 SF2  OAB   O   OC    -1  -0.590  -1.7431   0.5202  -3.2334
 SF2  OAC   O   O      0  -0.549  -1.2385   2.1358  -1.7735
 SF2  CBB   C   CR56   0   0.362   0.8526  -1.7618  -0.8182
 SF2  CAN   C   CR16   0  -0.315   1.1541  -3.0636  -0.4241
 SF2  CAM   C   CR16   0  -0.242   2.3959  -3.3031   0.1321
 SF2  CAU   C   CR6    0  -0.050   3.3118  -2.2555   0.2929
 SF2  CLAD  CL  CL     0  -0.145   4.8601  -2.6128   1.0017
 SF2  CAP   C   CR16   0  -0.324   3.0292  -0.9623  -0.0886
 SF2  CBA   C   CR56   0   0.151   1.7760  -0.7134  -0.6497
 SF2  CAY   C   CR5    0  -0.334   1.1402   0.4648  -1.1407
 SF2  SAS   S   S2     0   0.045   1.9064   2.0242  -1.2490
 SF2  CAX   C   CR6    0  -0.109   1.5361   2.7876   0.3048
 SF2  CAK   C   CR16   0  -0.219   0.4561   2.4144   1.0980
 SF2  CAF   C   CR16   0  -0.248   0.2250   3.0695   2.2997
 SF2  CAE   C   CR16   0  -0.269   1.0471   4.1117   2.7093
 SF2  CAG   C   CR16   0  -0.247   2.1143   4.4931   1.9064
 SF2  CAL   C   CR16   0  -0.273   2.3648   3.8316   0.7126
 SF2  HAA1  H   HCH3   0   0.259  -6.7777   1.3265   1.2368
 SF2  HAA2  H   HCH3   0   0.227  -6.7103  -0.3405   1.8339
 SF2  HAA3  H   HCH3   0   0.228  -5.5628   0.8719   2.4454
 SF2  HAO   H   HCR6   0   0.257  -3.5952  -0.2872  -1.3583
 SF2  HAJ   H   HCR6   0   0.279  -4.7678  -1.3195   2.6440
 SF2  HAH   H   HCR6   0   0.258  -2.9938  -2.9956   2.7154
 SF2  HAI   H   HCR6   0   0.248  -1.5010  -3.3503   0.7928
 SF2  HAQ1  H   HCH2   0   0.282  -1.2398  -3.0421  -1.7176
 SF2  HAQ2  H   HCH2   0   0.297  -1.9769  -1.6634  -2.5071
 SF2  HAN   H   HCR6   0   0.273   0.4580  -3.8826  -0.5468
 SF2  HAM   H   HCR6   0   0.274   2.6615  -4.3043   0.4415
 SF2  HAP   H   HCR6   0   0.266   3.7475  -0.1629   0.0394
 SF2  HAK   H   HCR6   0   0.260  -0.2018   1.6196   0.7754
 SF2  HAF   H   HCR6   0   0.255  -0.6120   2.7653   2.9156
 SF2  HAE   H   HCR6   0   0.254   0.8589   4.6198   3.6460
 SF2  HAG   H   HCR6   0   0.257   2.7654   5.3014   2.2140
 SF2  HAL   H   HCR6   0   0.259   3.2115   4.1265   0.1037

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
 SF2  CAA  OAR   single    1.413  0.020  1.413
 SF2  CAA  HAA1  single    0.970  0.020  1.090
 SF2  CAA  HAA2  single    0.970  0.020  1.090
 SF2  CAA  HAA3  single    0.970  0.020  1.090
 SF2  OAR  CAW   single    1.347  0.020  1.347
 SF2  CAW  CAJ   aromatic  1.392  0.020  1.392
 SF2  CAW  CAO   aromatic  1.397  0.020  1.397
 SF2  CAO  CAV   aromatic  1.386  0.020  1.386
 SF2  CAO  HAO   single    0.930  0.020  1.080
 SF2  CAJ  CAH   aromatic  1.391  0.020  1.391
 SF2  CAJ  HAJ   single    0.930  0.020  1.080
 SF2  CAH  CAI   aromatic  1.384  0.020  1.384
 SF2  CAH  HAH   single    0.930  0.020  1.080
 SF2  CAI  CAV   aromatic  1.395  0.020  1.395
 SF2  CAI  HAI   single    0.930  0.020  1.080
 SF2  CAV  CAQ   single    1.508  0.020  1.508
 SF2  CAQ  NBC   single    1.455  0.020  1.455
 SF2  CAQ  HAQ1  single    0.970  0.020  1.090
 SF2  CAQ  HAQ2  single    0.970  0.020  1.090
 SF2  NBC  CBB   aromatic  1.373  0.020  1.373
 SF2  NBC  CAZ   aromatic  1.370  0.020  1.370
 SF2  CAZ  CAY   aromatic  1.378  0.020  1.378
 SF2  CAZ  CAT   single    1.517  0.020  1.517
 SF2  CAT  OAC   deloc     1.237  0.020  1.237
 SF2  CAT  OAB   deloc     1.246  0.020  1.246
 SF2  CBB  CAN   aromatic  1.393  0.020  1.393
 SF2  CBB  CBA   aromatic  1.407  0.020  1.407
 SF2  CAN  CAM   aromatic  1.382  0.020  1.382
 SF2  CAN  HAN   single    0.930  0.020  1.080
 SF2  CAM  CAU   aromatic  1.401  0.020  1.401
 SF2  CAM  HAM   single    0.930  0.020  1.080
 SF2  CAU  CLAD  single    1.740  0.020  1.740
 SF2  CAU  CAP   aromatic  1.378  0.020  1.378
 SF2  CAP  CBA   aromatic  1.395  0.020  1.395
 SF2  CAP  HAP   single    0.930  0.020  1.080
 SF2  CBA  CAY   aromatic  1.426  0.020  1.426
 SF2  CAY  SAS   single    1.741  0.020  1.741
 SF2  SAS  CAX   single    1.770  0.020  1.770
 SF2  CAX  CAL   aromatic  1.394  0.020  1.394
 SF2  CAX  CAK   aromatic  1.391  0.020  1.391
 SF2  CAK  CAF   aromatic  1.388  0.020  1.388
 SF2  CAK  HAK   single    0.930  0.020  1.080
 SF2  CAF  CAE   aromatic  1.389  0.020  1.389
 SF2  CAF  HAF   single    0.930  0.020  1.080
 SF2  CAE  CAG   aromatic  1.389  0.020  1.389
 SF2  CAE  HAE   single    0.930  0.020  1.080
 SF2  CAG  CAL   aromatic  1.388  0.020  1.388
 SF2  CAG  HAG   single    0.930  0.020  1.080
 SF2  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
 SF2  HAA3  CAA  HAA2  108.78  3.000
 SF2  HAA3  CAA  HAA1  108.78  3.000
 SF2  HAA2  CAA  HAA1  108.70  3.000
 SF2  HAA3  CAA  OAR   111.91  3.000
 SF2  HAA2  CAA  OAR   112.02  3.000
 SF2  HAA1  CAA  OAR   106.55  3.000
 SF2  CAW   OAR  CAA   118.50  3.000
 SF2  CAJ   CAW  CAO   119.68  3.000
 SF2  CAO   CAW  OAR   116.01  3.000
 SF2  CAJ   CAW  OAR   124.31  3.000
 SF2  HAO   CAO  CAV   120.12  3.000
 SF2  HAO   CAO  CAW   119.12  3.000
 SF2  CAV   CAO  CAW   120.75  3.000
 SF2  HAJ   CAJ  CAH   119.12  3.000
 SF2  HAJ   CAJ  CAW   121.65  3.000
 SF2  CAH   CAJ  CAW   119.22  3.000
 SF2  HAH   CAH  CAI   119.85  3.000
 SF2  HAH   CAH  CAJ   118.98  3.000
 SF2  CAI   CAH  CAJ   121.16  3.000
 SF2  HAI   CAI  CAV   120.53  3.000
 SF2  HAI   CAI  CAH   119.76  3.000
 SF2  CAV   CAI  CAH   119.70  3.000
 SF2  CAQ   CAV  CAI   120.64  3.000
 SF2  CAQ   CAV  CAO   119.87  3.000
 SF2  CAI   CAV  CAO   119.48  3.000
 SF2  HAQ2  CAQ  HAQ1  107.27  3.000
 SF2  HAQ2  CAQ  NBC   108.26  3.000
 SF2  HAQ1  CAQ  NBC   107.61  3.000
 SF2  HAQ2  CAQ  CAV   111.04  3.000
 SF2  HAQ1  CAQ  CAV   110.60  3.000
 SF2  NBC   CAQ  CAV   111.88  3.000
 SF2  CBB   NBC  CAZ   109.35  3.000
 SF2  CAZ   NBC  CAQ   126.30  3.000
 SF2  CBB   NBC  CAQ   123.60  3.000
 SF2  CAY   CAZ  CAT   127.04  3.000
 SF2  CAT   CAZ  NBC   124.14  3.000
 SF2  CAY   CAZ  NBC   108.77  3.000
 SF2  OAC   CAT  OAB   128.36  3.000
 SF2  OAB   CAT  CAZ   116.24  3.000
 SF2  OAC   CAT  CAZ   115.38  3.000
 SF2  CBA   CBB  CAN   121.35  3.000
 SF2  CBA   CBB  NBC   107.97  3.000
 SF2  CAN   CBB  NBC   130.67  3.000
 SF2  HAN   CAN  CAM   119.53  3.000
 SF2  HAN   CAN  CBB   122.41  3.000
 SF2  CAM   CAN  CBB   118.06  3.000
 SF2  HAM   CAM  CAU   119.94  3.000
 SF2  HAM   CAM  CAN   119.78  3.000
 SF2  CAU   CAM  CAN   120.29  3.000
 SF2  CAP   CAU  CLAD  119.22  3.000
 SF2  CAP   CAU  CAM   122.42  3.000
 SF2  CLAD  CAU  CAM   118.36  3.000
 SF2  HAP   CAP  CBA   120.78  3.000
 SF2  HAP   CAP  CAU   121.63  3.000
 SF2  CBA   CAP  CAU   117.59  3.000
 SF2  CAY   CBA  CAP   133.34  3.000
 SF2  CAY   CBA  CBB   106.37  3.000
 SF2  CAP   CBA  CBB   120.30  3.000
 SF2  SAS   CAY  CBA   124.42  3.000
 SF2  SAS   CAY  CAZ   127.85  3.000
 SF2  CBA   CAY  CAZ   107.53  3.000
 SF2  CAX   SAS  CAY   103.86  3.000
 SF2  CAL   CAX  CAK   119.72  3.000
 SF2  CAK   CAX  SAS   123.18  3.000
 SF2  CAL   CAX  SAS   117.09  3.000
 SF2  HAK   CAK  CAF   120.27  3.000
 SF2  HAK   CAK  CAX   119.97  3.000
 SF2  CAF   CAK  CAX   119.76  3.000
 SF2  HAF   CAF  CAE   120.03  3.000
 SF2  HAF   CAF  CAK   119.25  3.000
 SF2  CAE   CAF  CAK   120.72  3.000
 SF2  HAE   CAE  CAG   120.34  3.000
 SF2  HAE   CAE  CAF   120.30  3.000
 SF2  CAG   CAE  CAF   119.36  3.000
 SF2  HAG   CAG  CAL   119.46  3.000
 SF2  HAG   CAG  CAE   120.19  3.000
 SF2  CAL   CAG  CAE   120.34  3.000
 SF2  HAL   CAL  CAG   119.65  3.000
 SF2  HAL   CAL  CAX   120.26  3.000
 SF2  CAG   CAL  CAX   120.09  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
 SF2  CONST_01  CAI   CAH  CAJ  CAW     0.00   0.0  0
 SF2  CONST_02  CAI   CAV  CAO  CAW     0.00   0.0  0
 SF2  CONST_03  CAH   CAJ  CAW  CAO     0.00   0.0  0
 SF2  CONST_04  CAH   CAI  CAV  CAO     0.00   0.0  0
 SF2  CONST_05  CAV   CAO  CAW  CAJ     0.00   0.0  0
 SF2  CONST_06  CAV   CAI  CAH  CAJ     0.00   0.0  0
 SF2  CONST_07  CAM   CAN  CBB  NBC   180.00   0.0  0
 SF2  CONST_08  CAP   CBA  CBB  NBC   180.00   0.0  0
 SF2  CONST_09  CAY   CBA  CBB  NBC     0.00   0.0  0
 SF2  CONST_10  CBA   CAY  CAZ  NBC     0.00   0.0  0
 SF2  CONST_11  CAN   CBB  NBC  CAZ   180.00   0.0  0
 SF2  CONST_12  CBA   CBB  NBC  CAZ     0.00   0.0  0
 SF2  CONST_13  CBB   CBA  CAY  CAZ     0.00   0.0  0
 SF2  CONST_14  CAP   CBA  CAY  CAZ   180.00   0.0  0
 SF2  CONST_15  CAY   CAZ  NBC  CBB     0.00   0.0  0
 SF2  CONST_16  CAU   CAM  CAN  CBB     0.00   0.0  0
 SF2  CONST_17  CAU   CAP  CBA  CBB     0.00   0.0  0
 SF2  CONST_18  CAP   CBA  CBB  CAN     0.00   0.0  0
 SF2  CONST_19  CAY   CBA  CBB  CAN   180.00   0.0  0
 SF2  CONST_20  CAP   CAU  CAM  CAN     0.00   0.0  0
 SF2  CONST_21  CBA   CBB  CAN  CAM     0.00   0.0  0
 SF2  CONST_22  CBA   CAP  CAU  CAM     0.00   0.0  0
 SF2  CONST_23  CAY   CBA  CAP  CAU   180.00   0.0  0
 SF2  CONST_24  CAE   CAG  CAL  CAX     0.00   0.0  0
 SF2  CONST_25  CAE   CAF  CAK  CAX     0.00   0.0  0
 SF2  CONST_26  CAG   CAL  CAX  CAK     0.00   0.0  0
 SF2  CONST_27  CAG   CAE  CAF  CAK     0.00   0.0  0
 SF2  CONST_28  CAL   CAX  CAK  CAF     0.00   0.0  0
 SF2  CONST_29  CAL   CAG  CAE  CAF     0.00   0.0  0
 SF2  CONST_30  CAH   CAJ  CAW  OAR   180.00   0.0  0
 SF2  CONST_31  CAV   CAO  CAW  OAR   180.00   0.0  0
 SF2  CONST_32  CAQ   CAV  CAO  CAW   180.00   0.0  0
 SF2  CONST_33  CAQ   CAV  CAI  CAH   180.00   0.0  0
 SF2  CONST_34  CAN   CBB  NBC  CAQ     0.00   0.0  0
 SF2  CONST_35  CBA   CBB  NBC  CAQ   180.00   0.0  0
 SF2  CONST_36  CAY   CAZ  NBC  CAQ   180.00   0.0  0
 SF2  CONST_37  SAS   CAY  CAZ  NBC   180.00   0.0  0
 SF2  CONST_38  CBB   NBC  CAZ  CAT   180.00   0.0  0
 SF2  CONST_39  CBA   CAY  CAZ  CAT   180.00   0.0  0
 SF2  CONST_40  SAS   CAY  CBA  CBB   180.00   0.0  0
 SF2  CONST_41  CLAD  CAU  CAM  CAN   180.00   0.0  0
 SF2  CONST_42  CBA   CAP  CAU  CLAD  180.00   0.0  0
 SF2  CONST_43  SAS   CAY  CBA  CAP     0.00   0.0  0
 SF2  CONST_44  CAG   CAL  CAX  SAS   180.00   0.0  0
 SF2  CONST_45  CAF   CAK  CAX  SAS   180.00   0.0  0
 SF2  CONST_46  HAH   CAH  CAJ  CAW   180.00   0.0  0
 SF2  CONST_47  HAJ   CAJ  CAW  CAO   180.00   0.0  0
 SF2  CONST_48  HAI   CAI  CAV  CAO   180.00   0.0  0
 SF2  CONST_49  HAO   CAO  CAW  CAJ   180.00   0.0  0
 SF2  CONST_50  HAN   CAN  CBB  NBC     0.00   0.0  0
 SF2  CONST_51  HAM   CAM  CAN  CBB   180.00   0.0  0
 SF2  CONST_52  HAP   CAP  CBA  CBB   180.00   0.0  0
 SF2  CONST_53  HAG   CAG  CAL  CAX   180.00   0.0  0
 SF2  CONST_54  HAF   CAF  CAK  CAX   180.00   0.0  0
 SF2  CONST_55  HAL   CAL  CAX  CAK   180.00   0.0  0
 SF2  CONST_56  HAE   CAE  CAF  CAK   180.00   0.0  0
 SF2  CONST_57  HAK   CAK  CAF  CAE   180.00   0.0  0
 SF2  Var_01    NBC   CAQ  CAV  CAO    96.12  30.0  2
 SF2  Var_02    CBB   NBC  CAQ  CAV    90.53  30.0  2
 SF2  Var_03    CAL   CAX  SAS  CAY   158.69  30.0  2
 SF2  Var_04    CAJ   CAW  OAR  CAA     1.65  30.0  2
 SF2  Var_05    OAC   CAT  CAZ  NBC   143.03  30.0  2
 SF2  Var_06    HAA1  CAA  OAR  CAW   179.12  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
 SF2  plan-1  OAR   0.020
 SF2  plan-1  CAW   0.020
 SF2  plan-1  CAO   0.020
 SF2  plan-1  CAJ   0.020
 SF2  plan-1  CAH   0.020
 SF2  plan-1  CAI   0.020
 SF2  plan-1  CAV   0.020
 SF2  plan-1  CAQ   0.020
 SF2  plan-1  HAO   0.020
 SF2  plan-1  HAJ   0.020
 SF2  plan-1  HAH   0.020
 SF2  plan-1  HAI   0.020
 SF2  plan-2  SAS   0.020
 SF2  plan-2  CAX   0.020
 SF2  plan-2  CAK   0.020
 SF2  plan-2  CAF   0.020
 SF2  plan-2  CAE   0.020
 SF2  plan-2  CAG   0.020
 SF2  plan-2  CAL   0.020
 SF2  plan-2  HAK   0.020
 SF2  plan-2  HAF   0.020
 SF2  plan-2  HAE   0.020
 SF2  plan-2  HAG   0.020
 SF2  plan-2  HAL   0.020
 SF2  plan-3  CAQ   0.020
 SF2  plan-3  NBC   0.020
 SF2  plan-3  CAZ   0.020
 SF2  plan-3  CAT   0.020
 SF2  plan-3  CBB   0.020
 SF2  plan-3  CAN   0.020
 SF2  plan-3  CAM   0.020
 SF2  plan-3  CAU   0.020
 SF2  plan-3  CLAD  0.020
 SF2  plan-3  CAP   0.020
 SF2  plan-3  CBA   0.020
 SF2  plan-3  CAY   0.020
 SF2  plan-3  SAS   0.020
 SF2  plan-3  HAN   0.020
 SF2  plan-3  HAM   0.020
 SF2  plan-3  HAP   0.020
 SF2  plan-4  CAZ   0.020
 SF2  plan-4  CAT   0.020
 SF2  plan-4  OAB   0.020
 SF2  plan-4  OAC   0.020

