# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 17:39:34 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 5-bromo-2-{[3-(octyloxy)benzyl]sulfanyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCOc1cccc(CSc2ccc(Br)cc2C(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
 2CN  2CN  '5-bromo-2-{[3-(octyloxy)benzyl]sulfanyl}benzoic acid'  ligand  53  27  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2CN
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
 2CN  CAA   C   CH3    0  -0.661  13.0937   2.6060  -0.2538
 2CN  OAB   O   OC    -1  -0.580  -4.3612   1.7313   3.2855
 2CN  OAC   O   O      0  -0.573  -2.4723   0.6131   2.9043
 2CN  CAE   C   CR16   0  -0.228   1.7323  -3.6953   0.4417
 2CN  CAF   C   CR16   0  -0.316   0.4594  -3.2540   0.1242
 2CN  CAG   C   CR16   0  -0.217  -5.0395   0.1120  -1.3746
 2CN  CAH   C   CR16   0  -0.395   2.8469  -2.8903   0.2326
 2CN  CAI   C   CR16   0  -0.257  -3.7863  -0.3297  -0.9841
 2CN  CAJ   C   CR16   0  -0.388   1.3928  -1.1711  -0.6268
 2CN  CAK   C   CR16   0  -0.255  -5.3159   1.1377   0.7769
 2CN  CAL   C   CH2    0  -0.419  12.1552   1.4402   0.0254
 2CN  CAM   C   CH2    0  -0.406  10.7113   1.7355  -0.3608
 2CN  CAN   C   CH2    0  -0.412   9.7621   0.5789  -0.0738
 2CN  CAO   C   CH2    0  -0.412   8.3175   0.8792  -0.4516
 2CN  CAP   C   CH2    0  -0.425   7.3696  -0.2756  -0.1527
 2CN  CAQ   C   CH2    0  -0.456   5.9243   0.0373  -0.5206
 2CN  CAR   C   CH2    0  -0.169   5.0055  -1.1214  -0.1962
 2CN  OAT   O   O2     0  -0.479   3.6807  -0.7541  -0.5495
 2CN  SAU   S   S2     0   0.097  -1.6658  -0.6153   0.7633
 2CN  CAW   C   CR6    0  -0.113  -5.8014   0.8493  -0.4844
 2CN  CAX   C   CR6    0   0.136   0.2872  -1.9829  -0.4231
 2CN  CAY   C   CR6    0   0.405   2.6762  -1.6168  -0.3054
 2CN  CAZ   C   CR6    0  -0.129  -3.2713  -0.0501   0.2850
 2CN  CBA   C   CR6    0  -0.118  -4.0588   0.6973   1.1791
 2CN  HAA   H   HCH3   0   0.225  14.1180   2.3774   0.0429
 2CN  HAAA  H   HCH3   0   0.215  13.1053   2.8579  -1.3159
 2CN  HAAB  H   HCH3   0   0.215  12.7834   3.4999   0.2910
 2CN  HAE   H   HCR6   0   0.259   1.8716  -4.6837   0.8605
 2CN  HAF   H   HCR6   0   0.248  -0.3990  -3.8923   0.2919
 2CN  HAG   H   HCR6   0   0.279  -5.4000  -0.1264  -2.3663
 2CN  HAH   H   HCR6   0   0.279   3.8258  -3.2708   0.4893
 2CN  HAI   H   HCR6   0   0.278  -3.2238  -0.9046  -1.7036
 2CN  HAJ   H   HCR6   0   0.256   1.2684  -0.1783  -1.0448
 2CN  HAK   H   HCR6   0   0.269  -5.9006   1.7144   1.4807
 2CN  HAL   H   HCH2   0   0.210  12.5004   0.5534  -0.5154
 2CN  HALA  H   HCH2   0   0.210  12.1992   1.1820   1.0881
 2CN  HAM   H   HCH2   0   0.206  10.3682   2.6276   0.1754
 2CN  HAMA  H   HCH2   0   0.206  10.6649   1.9880  -1.4260
 2CN  HAN   H   HCH2   0   0.208  10.1020  -0.3124  -0.6132
 2CN  HANA  H   HCH2   0   0.207   9.8131   0.3250   0.9908
 2CN  HAO   H   HCH2   0   0.210   7.9795   1.7727   0.0848
 2CN  HAOA  H   HCH2   0   0.210   8.2629   1.1270  -1.5172
 2CN  HAP   H   HCH2   0   0.216   7.7030  -1.1675  -0.6941
 2CN  HAPA  H   HCH2   0   0.216   7.4305  -0.5258   0.9118
 2CN  HAQ   H   HCH2   0   0.228   5.5919   0.9272   0.0223
 2CN  HAQA  H   HCH2   0   0.228   5.8573   0.2703  -1.5873
 2CN  HAR   H   HCH2   0   0.219   5.3139  -2.0169  -0.7491
 2CN  HARA  H   HCH2   0   0.219   5.0624  -1.3595   0.8726
 2CN  HAS   H   HCH2   0   0.283  -1.7500  -2.3009  -0.9968
 2CN  HASA  H   HCH2   0   0.283  -1.0528  -0.7836  -1.5902
 2CN  CAV   C   C      0   0.430  -3.5947   1.0498   2.5837
 2CN  CAS   C   CH2    0  -0.680  -1.0860  -1.4726  -0.7447
 2CN  BRAD  BR  BR     0  -0.062  -7.5144   1.4629  -0.9984

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
 2CN  CAA   CAL   single    1.522  0.020  1.522
 2CN  CAA   HAA   single    0.970  0.020  1.090
 2CN  CAA   HAAA  single    0.970  0.020  1.090
 2CN  CAA   HAAB  single    0.970  0.020  1.090
 2CN  OAB   CAV   deloc     1.243  0.020  1.243
 2CN  OAC   CAV   deloc     1.246  0.020  1.246
 2CN  BRAD  CAW   single    1.891  0.020  1.891
 2CN  CAE   CAF   aromatic  1.384  0.020  1.384
 2CN  CAE   CAH   aromatic  1.391  0.020  1.391
 2CN  CAE   HAE   single    0.930  0.020  1.080
 2CN  CAF   CAX   aromatic  1.395  0.020  1.395
 2CN  CAF   HAF   single    0.930  0.020  1.080
 2CN  CAG   CAI   aromatic  1.385  0.020  1.385
 2CN  CAG   CAW   aromatic  1.384  0.020  1.384
 2CN  CAG   HAG   single    0.930  0.020  1.080
 2CN  CAH   CAY   aromatic  1.393  0.020  1.393
 2CN  CAH   HAH   single    0.930  0.020  1.080
 2CN  CAI   CAZ   aromatic  1.398  0.020  1.398
 2CN  CAI   HAI   single    0.930  0.020  1.080
 2CN  CAJ   CAX   aromatic  1.387  0.020  1.387
 2CN  CAJ   CAY   aromatic  1.396  0.020  1.396
 2CN  CAJ   HAJ   single    0.930  0.020  1.080
 2CN  CAK   CAW   aromatic  1.382  0.020  1.382
 2CN  CAK   CBA   aromatic  1.391  0.020  1.391
 2CN  CAK   HAK   single    0.930  0.020  1.080
 2CN  CAL   CAM   single    1.524  0.020  1.524
 2CN  CAL   HAL   single    0.970  0.020  1.090
 2CN  CAL   HALA  single    0.970  0.020  1.090
 2CN  CAM   CAN   single    1.524  0.020  1.524
 2CN  CAM   HAM   single    0.970  0.020  1.090
 2CN  CAM   HAMA  single    0.970  0.020  1.090
 2CN  CAN   CAO   single    1.523  0.020  1.523
 2CN  CAN   HAN   single    0.970  0.020  1.090
 2CN  CAN   HANA  single    0.970  0.020  1.090
 2CN  CAO   CAP   single    1.524  0.020  1.524
 2CN  CAO   HAO   single    0.970  0.020  1.090
 2CN  CAO   HAOA  single    0.970  0.020  1.090
 2CN  CAP   CAQ   single    1.524  0.020  1.524
 2CN  CAP   HAP   single    0.970  0.020  1.090
 2CN  CAP   HAPA  single    0.970  0.020  1.090
 2CN  CAQ   CAR   single    1.514  0.020  1.514
 2CN  CAQ   HAQ   single    0.970  0.020  1.090
 2CN  CAQ   HAQA  single    0.970  0.020  1.090
 2CN  CAR   OAT   single    1.419  0.020  1.419
 2CN  CAR   HAR   single    0.970  0.020  1.090
 2CN  CAR   HARA  single    0.970  0.020  1.090
 2CN  CAS   SAU   single    1.829  0.020  1.829
 2CN  CAS   CAX   single    1.500  0.020  1.500
 2CN  CAS   HAS   single    0.970  0.020  1.090
 2CN  CAS   HASA  single    0.970  0.020  1.090
 2CN  OAT   CAY   single    1.346  0.020  1.346
 2CN  SAU   CAZ   single    1.768  0.020  1.768
 2CN  CAV   CBA   single    1.521  0.020  1.521
 2CN  CAZ   CBA   aromatic  1.406  0.020  1.406

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
 2CN  HAAB  CAA  HAAA  107.43  3.000
 2CN  HAAB  CAA  HAA   107.63  3.000
 2CN  HAAA  CAA  HAA   107.64  3.000
 2CN  HAAB  CAA  CAL   111.11  3.000
 2CN  HAAA  CAA  CAL   111.20  3.000
 2CN  HAA   CAA  CAL   111.62  3.000
 2CN  HAE   CAE  CAH   118.92  3.000
 2CN  HAE   CAE  CAF   119.88  3.000
 2CN  CAH   CAE  CAF   121.20  3.000
 2CN  HAF   CAF  CAX   120.01  3.000
 2CN  HAF   CAF  CAE   120.37  3.000
 2CN  CAX   CAF  CAE   119.62  3.000
 2CN  HAG   CAG  CAW   121.57  3.000
 2CN  HAG   CAG  CAI   119.32  3.000
 2CN  CAW   CAG  CAI   119.11  3.000
 2CN  HAH   CAH  CAY   121.63  3.000
 2CN  HAH   CAH  CAE   119.09  3.000
 2CN  CAY   CAH  CAE   119.28  3.000
 2CN  HAI   CAI  CAZ   121.32  3.000
 2CN  HAI   CAI  CAG   116.97  3.000
 2CN  CAZ   CAI  CAG   121.71  3.000
 2CN  HAJ   CAJ  CAY   119.11  3.000
 2CN  HAJ   CAJ  CAX   120.07  3.000
 2CN  CAY   CAJ  CAX   120.82  3.000
 2CN  HAK   CAK  CBA   117.98  3.000
 2CN  HAK   CAK  CAW   121.02  3.000
 2CN  CBA   CAK  CAW   121.00  3.000
 2CN  HALA  CAL  HAL   106.02  3.000
 2CN  HALA  CAL  CAM   109.27  3.000
 2CN  HAL   CAL  CAM   109.31  3.000
 2CN  HALA  CAL  CAA   109.51  3.000
 2CN  HAL   CAL  CAA   109.59  3.000
 2CN  CAM   CAL  CAA   112.91  3.000
 2CN  HAMA  CAM  HAM   105.95  3.000
 2CN  HAMA  CAM  CAN   109.37  3.000
 2CN  HAM   CAM  CAN   109.31  3.000
 2CN  HAMA  CAM  CAL   109.35  3.000
 2CN  HAM   CAM  CAL   109.30  3.000
 2CN  CAN   CAM  CAL   113.30  3.000
 2CN  HANA  CAN  HAN   105.98  3.000
 2CN  HANA  CAN  CAO   109.32  3.000
 2CN  HAN   CAN  CAO   109.42  3.000
 2CN  HANA  CAN  CAM   109.26  3.000
 2CN  HAN   CAN  CAM   109.36  3.000
 2CN  CAO   CAN  CAM   113.24  3.000
 2CN  HAOA  CAO  HAO   106.05  3.000
 2CN  HAOA  CAO  CAP   109.35  3.000
 2CN  HAO   CAO  CAP   109.27  3.000
 2CN  HAOA  CAO  CAN   109.46  3.000
 2CN  HAO   CAO  CAN   109.39  3.000
 2CN  CAP   CAO  CAN   113.08  3.000
 2CN  HAPA  CAP  HAP   106.11  3.000
 2CN  HAPA  CAP  CAQ   109.52  3.000
 2CN  HAP   CAP  CAQ   109.67  3.000
 2CN  HAPA  CAP  CAO   109.23  3.000
 2CN  HAP   CAP  CAO   109.32  3.000
 2CN  CAQ   CAP  CAO   112.77  3.000
 2CN  HAQA  CAQ  HAQ   106.98  3.000
 2CN  HAQA  CAQ  CAR   109.56  3.000
 2CN  HAQ   CAQ  CAR   109.38  3.000
 2CN  HAQA  CAQ  CAP   109.71  3.000
 2CN  HAQ   CAQ  CAP   109.60  3.000
 2CN  CAR   CAQ  CAP   111.51  3.000
 2CN  HARA  CAR  HAR   107.43  3.000
 2CN  HARA  CAR  OAT   110.32  3.000
 2CN  HAR   CAR  OAT   110.38  3.000
 2CN  HARA  CAR  CAQ   110.09  3.000
 2CN  HAR   CAR  CAQ   110.26  3.000
 2CN  OAT   CAR  CAQ   108.36  3.000
 2CN  CAY   OAT  CAR   119.04  3.000
 2CN  CAZ   SAU  CAS   102.40  3.000
 2CN  CAK   CAW  CAG   120.31  3.000
 2CN  CAK   CAW  BRAD  119.91  3.000
 2CN  CAG   CAW  BRAD  119.78  3.000
 2CN  CAS   CAX  CAJ   119.96  3.000
 2CN  CAS   CAX  CAF   120.49  3.000
 2CN  CAJ   CAX  CAF   119.52  3.000
 2CN  OAT   CAY  CAJ   116.08  3.000
 2CN  OAT   CAY  CAH   124.36  3.000
 2CN  CAJ   CAY  CAH   119.56  3.000
 2CN  CBA   CAZ  SAU   120.42  3.000
 2CN  CBA   CAZ  CAI   118.50  3.000
 2CN  SAU   CAZ  CAI   121.08  3.000
 2CN  CAZ   CBA  CAV   122.65  3.000
 2CN  CAZ   CBA  CAK   119.36  3.000
 2CN  CAV   CBA  CAK   117.99  3.000
 2CN  CBA   CAV  OAC   115.54  3.000
 2CN  CBA   CAV  OAB   117.42  3.000
 2CN  OAC   CAV  OAB   127.04  3.000
 2CN  HASA  CAS  HAS   108.60  3.000
 2CN  HASA  CAS  CAX   110.67  3.000
 2CN  HAS   CAS  CAX   110.39  3.000
 2CN  HASA  CAS  SAU   110.65  3.000
 2CN  HAS   CAS  SAU   110.70  3.000
 2CN  CAX   CAS  SAU   105.84  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
 2CN  CONST_01  CAJ  CAX  CAF  CAE      0.00   0.0  0
 2CN  CONST_02  CAJ  CAY  CAH  CAE      0.00   0.0  0
 2CN  CONST_03  CAY  CAH  CAE  CAF      0.00   0.0  0
 2CN  CONST_04  CAY  CAJ  CAX  CAF      0.00   0.0  0
 2CN  CONST_05  CBA  CAZ  CAI  CAG      0.00   0.0  0
 2CN  CONST_06  CBA  CAK  CAW  CAG      0.00   0.0  0
 2CN  CONST_07  CAX  CAF  CAE  CAH      0.00   0.0  0
 2CN  CONST_08  CAX  CAJ  CAY  CAH      0.00   0.0  0
 2CN  CONST_09  CAK  CAW  CAG  CAI      0.00   0.0  0
 2CN  CONST_10  CAK  CBA  CAZ  CAI      0.00   0.0  0
 2CN  CONST_11  CAZ  CAI  CAG  CAW      0.00   0.0  0
 2CN  CONST_12  CAZ  CBA  CAK  CAW      0.00   0.0  0
 2CN  CONST_13  CAI  CAG  CAW  BRAD   180.00   0.0  0
 2CN  CONST_14  CBA  CAK  CAW  BRAD   180.00   0.0  0
 2CN  CONST_15  CAS  CAX  CAF  CAE    180.00   0.0  0
 2CN  CONST_16  OAT  CAY  CAH  CAE    180.00   0.0  0
 2CN  CONST_17  SAU  CAZ  CAI  CAG    180.00   0.0  0
 2CN  CONST_18  CAV  CBA  CAZ  CAI    180.00   0.0  0
 2CN  CONST_19  SAU  CAZ  CBA  CAK    180.00   0.0  0
 2CN  CONST_20  CAY  CAJ  CAX  CAS    180.00   0.0  0
 2CN  CONST_21  CAX  CAJ  CAY  OAT    180.00   0.0  0
 2CN  CONST_22  CAW  CAK  CBA  CAV    180.00   0.0  0
 2CN  CONST_23  HAH  CAH  CAE  CAF    180.00   0.0  0
 2CN  CONST_24  HAJ  CAJ  CAX  CAF    180.00   0.0  0
 2CN  CONST_25  HAK  CAK  CAW  CAG    180.00   0.0  0
 2CN  CONST_26  HAF  CAF  CAE  CAH    180.00   0.0  0
 2CN  CONST_27  HAG  CAG  CAW  CAK    180.00   0.0  0
 2CN  CONST_28  HAI  CAI  CAG  CAW    180.00   0.0  0
 2CN  CONST_29  HAE  CAE  CAF  CAX    180.00   0.0  0
 2CN  Var_01    CAK  CBA  CAV  OAB     -1.09  30.0  2
 2CN  Var_02    SAU  CAS  CAX  CAF     90.30  30.0  1
 2CN  Var_03    CBA  CAZ  SAU  CAS   -178.72  30.0  2
 2CN  Var_04    HAR  CAR  OAT  CAY     61.50  30.0  1
 2CN  Var_05    CAN  CAM  CAL  CAA   -179.50  30.0  3
 2CN  Var_06    CAO  CAN  CAM  CAL    179.60  30.0  3
 2CN  Var_07    CAP  CAO  CAN  CAM   -179.53  30.0  3
 2CN  Var_08    CAQ  CAP  CAO  CAN    179.43  30.0  3
 2CN  Var_09    CAR  CAQ  CAP  CAO   -179.29  30.0  3
 2CN  Var_10    OAT  CAR  CAQ  CAP    179.34  30.0  3
 2CN  Var_11    HAA  CAA  CAL  CAM    179.21  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
 2CN  plan-1  CAE   0.020
 2CN  plan-1  CAF   0.020
 2CN  plan-1  CAH   0.020
 2CN  plan-1  CAJ   0.020
 2CN  plan-1  OAT   0.020
 2CN  plan-1  CAX   0.020
 2CN  plan-1  CAY   0.020
 2CN  plan-1  HAE   0.020
 2CN  plan-1  HAF   0.020
 2CN  plan-1  HAH   0.020
 2CN  plan-1  HAJ   0.020
 2CN  plan-1  CAS   0.020
 2CN  plan-2  CAG   0.020
 2CN  plan-2  CAI   0.020
 2CN  plan-2  CAK   0.020
 2CN  plan-2  SAU   0.020
 2CN  plan-2  CAW   0.020
 2CN  plan-2  CAZ   0.020
 2CN  plan-2  CBA   0.020
 2CN  plan-2  HAG   0.020
 2CN  plan-2  HAI   0.020
 2CN  plan-2  HAK   0.020
 2CN  plan-2  CAV   0.020
 2CN  plan-2  BRAD  0.020
 2CN  plan-3  OAB   0.020
 2CN  plan-3  OAC   0.020
 2CN  plan-3  CBA   0.020
 2CN  plan-3  CAV   0.020

