# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:32:20 2022
#   Inital geometry file: a 132 line input string
#   Ligand name: 2-{[3-hydroxy-5-(octyloxy)benzyl]sulfanyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCOc1cc(O)cc(CSc2ccccc2C(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
 HXK  HXK  '2-{[3-hydroxy-5-(octyloxy)benzyl]sulfanyl}benzoic acid'  ligand  54  27  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HXK
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
 HXK  CAA   C  CH3    0  -0.662  11.5357  -2.4778   0.2059
 HXK  OAB   O  OC    -1  -0.586  -6.0325  -2.9756  -1.8149
 HXK  OAC   O  O      0  -0.578  -4.1451  -1.7945  -1.8094
 HXK  CAE   C  CR16   0  -0.244  -6.4975  -0.2922   2.3536
 HXK  CAF   C  CR16   0  -0.263  -7.2940  -1.2458   1.7390
 HXK  CAG   C  CR16   0  -0.262  -5.2905   0.0825   1.7842
 HXK  CAH   C  CR16   0  -0.279  -6.8582  -1.8143   0.5536
 HXK  CAI   C  CR16   0  -0.415  -1.3284   2.8654  -0.3267
 HXK  CAJ   C  CR16   0  -0.537   1.0555   2.5471  -0.6035
 HXK  CAK   C  CR16   0  -0.415  -0.2315   0.9978   0.7311
 HXK  CAL   C  CH2    0  -0.419  10.5744  -1.3432  -0.1211
 HXK  CAM   C  CH2    0  -0.406   9.1379  -1.6497   0.2837
 HXK  CAN   C  CH2    0  -0.412   8.1615  -0.5295  -0.0529
 HXK  CAO   C  CH2    0  -0.412   6.7293  -0.8420   0.3611
 HXK  CAP   C  CH2    0  -0.425   5.7405   0.2565  -0.0095
 HXK  CAQ   C  CH2    0  -0.455   4.3194  -0.0641   0.4385
 HXK  CAR   C  CH2    0  -0.172   3.3348   0.9978  -0.0029
 HXK  OAT   O  O2     0  -0.479   2.0514   0.6380   0.4868
 HXK  SAU   S  S2     0   0.086  -3.3061  -0.0009  -0.1428
 HXK  CAV   C  C      0   0.417  -5.2466  -2.1390  -1.3353
 HXK  CAW   C  CR6    0   0.411  -0.1097   3.2695  -0.8584
 HXK  CAX   C  CR6    0   0.150  -1.3812   1.7309   0.4765
 HXK  CAY   C  CR6    0   0.419   0.9882   1.4062   0.1914
 HXK  CAZ   C  CR6    0  -0.130  -4.8466  -0.4867   0.5860
 HXK  CBA   C  CR6    0  -0.120  -5.6498  -1.4587  -0.0395
 HXK  HAA   H  HCH3   0   0.215  11.5569  -2.6803   1.2783
 HXK  HAAA  H  HCH3   0   0.215  11.2391  -3.4011  -0.2957
 HXK  HAAB  H  HCH3   0   0.225  12.5543  -2.2444  -0.1065
 HXK  HOAD  H  HOH1   0   0.475   0.7909   4.5557  -1.9492
 HXK  HAE   H  HCR6   0   0.255  -6.8078   0.1692   3.2826
 HXK  HAF   H  HCR6   0   0.249  -8.2384  -1.5425   2.1764
 HXK  HAG   H  HCR6   0   0.265  -4.7017   0.8270   2.2983
 HXK  HAH   H  HCR6   0   0.247  -7.4658  -2.5609   0.0601
 HXK  HAI   H  HCR6   0   0.254  -2.2255   3.4363  -0.5341
 HXK  HAJ   H  HCR6   0   0.290   1.9926   2.8870  -1.0274
 HXK  HAK   H  HCR6   0   0.252  -0.2706   0.1090   1.3495
 HXK  HAL   H  HCH2   0   0.210  10.9043  -0.4275   0.3794
 HXK  HALA  H  HCH2   0   0.210  10.6107  -1.1312  -1.1943
 HXK  HAM   H  HCH2   0   0.206   8.8119  -2.5727  -0.2091
 HXK  HAMA  H  HCH2   0   0.206   9.1001  -1.8535   1.3598
 HXK  HAN   H  HCH2   0   0.208   8.4879   0.3964   0.4336
 HXK  HANA  H  HCH2   0   0.207   8.1945  -0.3329  -1.1303
 HXK  HAO   H  HCH2   0   0.210   6.4130  -1.7813  -0.1053
 HXK  HAOA  H  HCH2   0   0.210   6.6927  -1.0138   1.4424
 HXK  HAP   H  HCH2   0   0.217   6.0623   1.2033   0.4369
 HXK  HAPA  H  HCH2   0   0.216   5.7607   0.4081  -1.0940
 HXK  HAQ   H  HCH2   0   0.228   4.0142  -1.0306   0.0268
 HXK  HAQA  H  HCH2   0   0.229   4.2909  -0.1579   1.5280
 HXK  HAR   H  HCH2   0   0.221   3.6267   1.9806   0.3856
 HXK  HARA  H  HCH2   0   0.221   3.3214   1.0662  -1.0969
 HXK  HAS   H  HCH2   0   0.280  -3.3982   2.0959   1.1022
 HXK  HASA  H  HCH2   0   0.280  -2.5622   0.8357   2.0234
 HXK  CAS   C  CH2    0  -0.678  -2.6958   1.2645   1.0288
 HXK  OAD   O  OH1    0  -0.636  -0.0988   4.3780  -1.6245

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
 HXK  CAA  CAL   single    1.523  0.020  1.523
 HXK  CAA  HAA   single    0.970  0.020  1.090
 HXK  CAA  HAAA  single    0.970  0.020  1.090
 HXK  CAA  HAAB  single    0.970  0.020  1.090
 HXK  CAV  OAB   deloc     1.244  0.020  1.244
 HXK  OAC  CAV   deloc     1.248  0.020  1.248
 HXK  OAD  CAW   single    1.347  0.020  1.347
 HXK  OAD  HOAD  single    0.850  0.020  0.980
 HXK  CAG  CAE   aromatic  1.386  0.020  1.386
 HXK  CAF  CAE   aromatic  1.386  0.020  1.386
 HXK  CAE  HAE   single    0.930  0.020  1.080
 HXK  CAH  CAF   aromatic  1.385  0.020  1.385
 HXK  CAF  HAF   single    0.930  0.020  1.080
 HXK  CAZ  CAG   aromatic  1.399  0.020  1.399
 HXK  CAG  HAG   single    0.930  0.020  1.080
 HXK  CBA  CAH   aromatic  1.392  0.020  1.392
 HXK  CAH  HAH   single    0.930  0.020  1.080
 HXK  CAI  CAX   aromatic  1.391  0.020  1.391
 HXK  CAI  CAW   aromatic  1.390  0.020  1.390
 HXK  CAI  HAI   single    0.930  0.020  1.080
 HXK  CAW  CAJ   aromatic  1.394  0.020  1.394
 HXK  CAJ  CAY   aromatic  1.392  0.020  1.392
 HXK  CAJ  HAJ   single    0.930  0.020  1.080
 HXK  CAX  CAK   aromatic  1.387  0.020  1.387
 HXK  CAK  CAY   aromatic  1.395  0.020  1.395
 HXK  CAK  HAK   single    0.930  0.020  1.080
 HXK  CAM  CAL   single    1.524  0.020  1.524
 HXK  CAL  HAL   single    0.970  0.020  1.090
 HXK  CAL  HALA  single    0.970  0.020  1.090
 HXK  CAN  CAM   single    1.524  0.020  1.524
 HXK  CAM  HAM   single    0.970  0.020  1.090
 HXK  CAM  HAMA  single    0.970  0.020  1.090
 HXK  CAO  CAN   single    1.523  0.020  1.523
 HXK  CAN  HAN   single    0.970  0.020  1.090
 HXK  CAN  HANA  single    0.970  0.020  1.090
 HXK  CAO  CAP   single    1.524  0.020  1.524
 HXK  CAO  HAO   single    0.970  0.020  1.090
 HXK  CAO  HAOA  single    0.970  0.020  1.090
 HXK  CAQ  CAP   single    1.524  0.020  1.524
 HXK  CAP  HAP   single    0.970  0.020  1.090
 HXK  CAP  HAPA  single    0.970  0.020  1.090
 HXK  CAR  CAQ   single    1.514  0.020  1.514
 HXK  CAQ  HAQ   single    0.970  0.020  1.090
 HXK  CAQ  HAQA  single    0.970  0.020  1.090
 HXK  OAT  CAR   single    1.420  0.020  1.420
 HXK  CAR  HAR   single    0.970  0.020  1.090
 HXK  CAR  HARA  single    0.970  0.020  1.090
 HXK  SAU  CAS   single    1.829  0.020  1.829
 HXK  CAS  CAX   single    1.500  0.020  1.500
 HXK  CAS  HAS   single    0.970  0.020  1.090
 HXK  CAS  HASA  single    0.970  0.020  1.090
 HXK  CAY  OAT   single    1.344  0.020  1.344
 HXK  SAU  CAZ   single    1.772  0.020  1.772
 HXK  CAV  CBA   single    1.518  0.020  1.518
 HXK  CBA  CAZ   aromatic  1.408  0.020  1.408

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
 HXK  HAAB  CAA  HAAA  107.64  3.000
 HXK  HAAB  CAA  HAA   107.64  3.000
 HXK  HAAA  CAA  HAA   107.44  3.000
 HXK  HAAB  CAA  CAL   111.64  3.000
 HXK  HAAA  CAA  CAL   111.10  3.000
 HXK  HAA   CAA  CAL   111.19  3.000
 HXK  HAE   CAE  CAG   119.13  3.000
 HXK  HAE   CAE  CAF   120.59  3.000
 HXK  CAG   CAE  CAF   120.27  3.000
 HXK  HAF   CAF  CAH   120.53  3.000
 HXK  HAF   CAF  CAE   120.72  3.000
 HXK  CAH   CAF  CAE   118.75  3.000
 HXK  HAG   CAG  CAZ   121.03  3.000
 HXK  HAG   CAG  CAE   117.76  3.000
 HXK  CAZ   CAG  CAE   121.21  3.000
 HXK  HAH   CAH  CBA   117.99  3.000
 HXK  HAH   CAH  CAF   119.80  3.000
 HXK  CBA   CAH  CAF   122.21  3.000
 HXK  HAI   CAI  CAX   120.59  3.000
 HXK  HAI   CAI  CAW   119.98  3.000
 HXK  CAX   CAI  CAW   119.43  3.000
 HXK  HAJ   CAJ  CAY   121.49  3.000
 HXK  HAJ   CAJ  CAW   119.26  3.000
 HXK  CAY   CAJ  CAW   119.25  3.000
 HXK  HAK   CAK  CAY   119.51  3.000
 HXK  HAK   CAK  CAX   120.56  3.000
 HXK  CAY   CAK  CAX   119.93  3.000
 HXK  HALA  CAL  HAL   106.04  3.000
 HXK  HALA  CAL  CAM   109.32  3.000
 HXK  HAL   CAL  CAM   109.33  3.000
 HXK  HALA  CAL  CAA   109.51  3.000
 HXK  HAL   CAL  CAA   109.57  3.000
 HXK  CAM   CAL  CAA   112.85  3.000
 HXK  HAMA  CAM  HAM   105.94  3.000
 HXK  HAMA  CAM  CAN   109.37  3.000
 HXK  HAM   CAM  CAN   109.22  3.000
 HXK  HAMA  CAM  CAL   109.32  3.000
 HXK  HAM   CAM  CAL   109.29  3.000
 HXK  CAN   CAM  CAL   113.43  3.000
 HXK  HANA  CAN  HAN   106.02  3.000
 HXK  HANA  CAN  CAO   109.41  3.000
 HXK  HAN   CAN  CAO   109.44  3.000
 HXK  HANA  CAN  CAM   109.26  3.000
 HXK  HAN   CAN  CAM   109.41  3.000
 HXK  CAO   CAN  CAM   113.05  3.000
 HXK  HAOA  CAO  HAO   106.03  3.000
 HXK  HAOA  CAO  CAP   109.36  3.000
 HXK  HAO   CAO  CAP   109.10  3.000
 HXK  HAOA  CAO  CAN   109.38  3.000
 HXK  HAO   CAO  CAN   109.37  3.000
 HXK  CAP   CAO  CAN   113.34  3.000
 HXK  HAPA  CAP  HAP   106.17  3.000
 HXK  HAPA  CAP  CAQ   109.72  3.000
 HXK  HAP   CAP  CAQ   109.63  3.000
 HXK  HAPA  CAP  CAO   109.19  3.000
 HXK  HAP   CAP  CAO   109.48  3.000
 HXK  CAQ   CAP  CAO   112.45  3.000
 HXK  HAQA  CAQ  HAQ   106.97  3.000
 HXK  HAQA  CAQ  CAR   109.49  3.000
 HXK  HAQ   CAQ  CAR   109.18  3.000
 HXK  HAQA  CAQ  CAP   109.58  3.000
 HXK  HAQ   CAQ  CAP   109.59  3.000
 HXK  CAR   CAQ  CAP   111.91  3.000
 HXK  HARA  CAR  HAR   107.51  3.000
 HXK  HARA  CAR  OAT   110.42  3.000
 HXK  HAR   CAR  OAT   110.22  3.000
 HXK  HARA  CAR  CAQ   110.04  3.000
 HXK  HAR   CAR  CAQ   110.62  3.000
 HXK  OAT   CAR  CAQ   108.03  3.000
 HXK  CAY   OAT  CAR   119.62  3.000
 HXK  CAZ   SAU  CAS   102.49  3.000
 HXK  CBA   CAV  OAC   115.79  3.000
 HXK  CBA   CAV  OAB   117.56  3.000
 HXK  OAC   CAV  OAB   126.65  3.000
 HXK  CAJ   CAW  CAI   120.81  3.000
 HXK  CAJ   CAW  OAD   121.56  3.000
 HXK  CAI   CAW  OAD   117.63  3.000
 HXK  CAS   CAX  CAK   119.63  3.000
 HXK  CAS   CAX  CAI   119.96  3.000
 HXK  CAK   CAX  CAI   120.37  3.000
 HXK  OAT   CAY  CAK   116.05  3.000
 HXK  OAT   CAY  CAJ   123.74  3.000
 HXK  CAK   CAY  CAJ   120.21  3.000
 HXK  CBA   CAZ  SAU   120.17  3.000
 HXK  CBA   CAZ  CAG   118.72  3.000
 HXK  SAU   CAZ  CAG   121.11  3.000
 HXK  CAZ   CBA  CAV   122.50  3.000
 HXK  CAZ   CBA  CAH   118.83  3.000
 HXK  CAV   CBA  CAH   118.67  3.000
 HXK  HASA  CAS  HAS   108.48  3.000
 HXK  HASA  CAS  CAX   110.51  3.000
 HXK  HAS   CAS  CAX   110.61  3.000
 HXK  HASA  CAS  SAU   110.66  3.000
 HXK  HAS   CAS  SAU   110.82  3.000
 HXK  CAX   CAS  SAU   105.76  3.000
 HXK  HOAD  OAD  CAW   110.53  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
 HXK  CONST_01  CBA  CAZ  CAG  CAE     0.00   0.0  0
 HXK  CONST_02  CBA  CAH  CAF  CAE     0.00   0.0  0
 HXK  CONST_03  CAZ  CAG  CAE  CAF     0.00   0.0  0
 HXK  CONST_04  CAZ  CBA  CAH  CAF     0.00   0.0  0
 HXK  CONST_05  CAH  CAF  CAE  CAG     0.00   0.0  0
 HXK  CONST_06  CAH  CBA  CAZ  CAG     0.00   0.0  0
 HXK  CONST_07  CAY  CAK  CAX  CAI     0.00   0.0  0
 HXK  CONST_08  CAY  CAJ  CAW  CAI     0.00   0.0  0
 HXK  CONST_09  CAX  CAI  CAW  CAJ     0.00   0.0  0
 HXK  CONST_10  CAX  CAK  CAY  CAJ     0.00   0.0  0
 HXK  CONST_11  CAW  CAI  CAX  CAK     0.00   0.0  0
 HXK  CONST_12  CAW  CAJ  CAY  CAK     0.00   0.0  0
 HXK  CONST_13  CAX  CAI  CAW  OAD   180.00   0.0  0
 HXK  CONST_14  CAY  CAJ  CAW  OAD   180.00   0.0  0
 HXK  CONST_15  SAU  CAZ  CAG  CAE   180.00   0.0  0
 HXK  CONST_16  CAV  CBA  CAH  CAF   180.00   0.0  0
 HXK  CONST_17  CAV  CBA  CAZ  CAG   180.00   0.0  0
 HXK  CONST_18  SAU  CAZ  CBA  CAH   180.00   0.0  0
 HXK  CONST_19  CAW  CAI  CAX  CAS   180.00   0.0  0
 HXK  CONST_20  CAY  CAK  CAX  CAS   180.00   0.0  0
 HXK  CONST_21  CAW  CAJ  CAY  OAT   180.00   0.0  0
 HXK  CONST_22  CAX  CAK  CAY  OAT   180.00   0.0  0
 HXK  CONST_23  HAH  CAH  CAF  CAE   180.00   0.0  0
 HXK  CONST_24  HAG  CAG  CAE  CAF   180.00   0.0  0
 HXK  CONST_25  HAF  CAF  CAE  CAG   180.00   0.0  0
 HXK  CONST_26  HAE  CAE  CAF  CAH   180.00   0.0  0
 HXK  CONST_27  HAK  CAK  CAX  CAI   180.00   0.0  0
 HXK  CONST_28  HAJ  CAJ  CAW  CAI   180.00   0.0  0
 HXK  CONST_29  HAI  CAI  CAW  CAJ   180.00   0.0  0
 HXK  Var_01    CAH  CBA  CAV  OAB     0.91  30.0  2
 HXK  Var_02    SAU  CAS  CAX  CAI    94.91  30.0  3
 HXK  Var_03    CBA  CAZ  SAU  CAS   179.33  30.0  2
 HXK  Var_04    HAR  CAR  OAT  CAY    61.08  30.0  3
 HXK  Var_05    CAN  CAM  CAL  CAA  -179.31  30.0  2
 HXK  Var_06    CAO  CAN  CAM  CAL  -179.74  30.0  1
 HXK  Var_07    CAP  CAO  CAN  CAM  -178.30  30.0  1
 HXK  Var_08    CAQ  CAP  CAO  CAN  -178.85  30.0  3
 HXK  Var_09    CAR  CAQ  CAP  CAO  -176.82  30.0  1
 HXK  Var_10    OAT  CAR  CAQ  CAP  -178.41  30.0  1
 HXK  Var_11    HAA  CAA  CAL  CAM   -60.70  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
 HXK  plan-1  CAE  0.020
 HXK  plan-1  CAF  0.020
 HXK  plan-1  CAG  0.020
 HXK  plan-1  CAH  0.020
 HXK  plan-1  SAU  0.020
 HXK  plan-1  CAV  0.020
 HXK  plan-1  CAZ  0.020
 HXK  plan-1  CBA  0.020
 HXK  plan-1  HAE  0.020
 HXK  plan-1  HAF  0.020
 HXK  plan-1  HAG  0.020
 HXK  plan-1  HAH  0.020
 HXK  plan-2  CAI  0.020
 HXK  plan-2  CAJ  0.020
 HXK  plan-2  CAK  0.020
 HXK  plan-2  OAT  0.020
 HXK  plan-2  CAW  0.020
 HXK  plan-2  CAX  0.020
 HXK  plan-2  CAY  0.020
 HXK  plan-2  HAI  0.020
 HXK  plan-2  HAJ  0.020
 HXK  plan-2  HAK  0.020
 HXK  plan-2  CAS  0.020
 HXK  plan-2  OAD  0.020
 HXK  plan-3  OAB  0.020
 HXK  plan-3  OAC  0.020
 HXK  plan-3  CAV  0.020
 HXK  plan-3  CBA  0.020

