# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 07:30:25 2021
#   Inital geometry file: a 101 line input string
#   Ligand name: 3-(4-fluorophenyl)-2-(4-hydroxyphenoxy)-1-benzothiophene-6-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(Oc2sc3cc(O)ccc3c2c4ccc(F)cc4)cc1
#
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
 V9J  V9J  3-(4-fluorophenyl)-2-(4-hydroxyphenoxy)-1-benzothiophene-6-ol  ligand  38  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V9J
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
 V9J  CAM  C  CR16  0  -0.282  17.7369  -11.4258   6.5202
 V9J  CAN  C  CR16  0  -0.331  18.5182  -12.4308   7.0641
 V9J  CAO  C  CR6   0   0.352  19.4601  -12.1315   8.0460
 V9J  OAR  O  OH1   0  -0.636  20.2017  -13.1461   8.5393
 V9J  CAP  C  CR16  0  -0.374  19.6009  -10.8180   8.4823
 V9J  CAQ  C  CR16  0  -0.280  18.8229   -9.8106   7.9318
 V9J  CAL  C  CR6   0   0.310  17.8985  -10.1189   6.9523
 V9J  OAK  O  O2    0  -0.499  17.1299   -9.0946   6.4208
 V9J  CAH  C  CR5   0  -0.002  17.1390   -8.9841   5.0790
 V9J  SAG  S  S2    0   0.197  15.5913   -8.9056   4.2768
 V9J  CAE  C  CR56  0  -0.216  16.3799   -8.8119   2.7327
 V9J  CAD  C  CR16  0  -0.417  15.7546   -8.6943   1.4964
 V9J  CAC  C  CR6   0   0.349  16.5521   -8.6368   0.3631
 V9J  OAS  O  OH1   0  -0.632  16.0393   -8.5325  -0.8796
 V9J  CAB  C  CR16  0  -0.334  17.9504   -8.6866   0.4750
 V9J  CAA  C  CR16  0  -0.335  18.5536   -8.7937   1.7098
 V9J  CAF  C  CR56  0   0.194  17.7756   -8.8610   2.8684
 V9J  CAI  C  CR5   0   0.103  18.2005   -8.9524   4.2414
 V9J  CAJ  C  CR6   0   0.016  19.6022   -9.0005   4.6930
 V9J  CAT  C  CR16  0  -0.260  20.1559   -7.9235   5.3797
 V9J  CAU  C  CR16  0  -0.400  21.4583   -7.9734   5.8532
 V9J  CAV  C  CR6   0   0.521  22.1955   -9.1189   5.6294
 V9J  FAY  F  F     0  -0.317  23.4562   -9.1790   6.0897
 V9J  CAW  C  CR16  0  -0.394  21.6834  -10.2039   4.9442
 V9J  CAX  C  CR16  0  -0.245  20.3806  -10.1352   4.4762
 V9J  H1   H  HCR6  0   0.274  17.0095  -11.6677   5.7547
 V9J  H2   H  HCR6  0   0.268  18.3975  -13.4522   6.7261
 V9J  H3   H  HOH1  0   0.473  20.8235  -12.8152   9.1964
 V9J  H4   H  HCR6  0   0.273  20.3288  -10.5708   9.2467
 V9J  H5   H  HCR6  0   0.269  18.9511   -8.7870   8.2581
 V9J  H6   H  HCR6  0   0.284  14.6739   -8.6551   1.4206
 V9J  H7   H  HOH1  0   0.476  15.0765   -8.5093  -0.8476
 V9J  H8   H  HCR6  0   0.267  18.5546   -8.6367  -0.4218
 V9J  H9   H  HCR6  0   0.253  19.6338   -8.8231   1.7799
 V9J  H10  H  HCR6  0   0.261  19.5637   -7.0337   5.5506
 V9J  H11  H  HCR6  0   0.279  21.8888   -7.1367   6.3875
 V9J  H12  H  HCR6  0   0.278  22.2864  -11.0883   4.7856
 V9J  H13  H  HCR6  0   0.259  19.9598  -10.9848   3.9540

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
 V9J  OAS  CAC  single    1.348  0.020  1.348
 V9J  CAC  CAB  aromatic  1.404  0.020  1.404
 V9J  CAC  CAD  aromatic  1.387  0.020  1.387
 V9J  CAB  CAA  aromatic  1.378  0.020  1.378
 V9J  CAD  CAE  aromatic  1.390  0.020  1.390
 V9J  CAA  CAF  aromatic  1.397  0.020  1.397
 V9J  CAE  CAF  aromatic  1.403  0.020  1.403
 V9J  CAE  SAG  aromatic  1.736  0.020  1.736
 V9J  CAF  CAI  aromatic  1.440  0.020  1.440
 V9J  SAG  CAH  aromatic  1.745  0.020  1.745
 V9J  CAI  CAJ  single    1.473  0.020  1.473
 V9J  CAI  CAH  aromatic  1.353  0.020  1.353
 V9J  CAJ  CAX  aromatic  1.393  0.020  1.393
 V9J  CAJ  CAT  aromatic  1.392  0.020  1.392
 V9J  CAX  CAW  aromatic  1.386  0.020  1.386
 V9J  CAT  CAU  aromatic  1.387  0.020  1.387
 V9J  CAW  CAV  aromatic  1.382  0.020  1.382
 V9J  CAH  OAK  single    1.346  0.020  1.346
 V9J  CAU  CAV  aromatic  1.380  0.020  1.380
 V9J  CAV  FAY  single    1.343  0.020  1.343
 V9J  OAK  CAL  single    1.386  0.020  1.386
 V9J  CAM  CAL  aromatic  1.386  0.020  1.386
 V9J  CAM  CAN  aromatic  1.384  0.020  1.384
 V9J  CAL  CAQ  aromatic  1.382  0.020  1.382
 V9J  CAN  CAO  aromatic  1.393  0.020  1.393
 V9J  CAQ  CAP  aromatic  1.387  0.020  1.387
 V9J  CAO  CAP  aromatic  1.391  0.020  1.391
 V9J  CAO  OAR  single    1.350  0.020  1.350
 V9J  CAM  H1   single    0.930  0.020  1.080
 V9J  CAN  H2   single    0.930  0.020  1.080
 V9J  OAR  H3   single    0.850  0.020  0.980
 V9J  CAP  H4   single    0.930  0.020  1.080
 V9J  CAQ  H5   single    0.930  0.020  1.080
 V9J  CAD  H6   single    0.930  0.020  1.080
 V9J  OAS  H7   single    0.850  0.020  0.980
 V9J  CAB  H8   single    0.930  0.020  1.080
 V9J  CAA  H9   single    0.930  0.020  1.080
 V9J  CAT  H10  single    0.930  0.020  1.080
 V9J  CAU  H11  single    0.930  0.020  1.080
 V9J  CAW  H12  single    0.930  0.020  1.080
 V9J  CAX  H13  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
 V9J  H1   CAM  CAL  120.61  3.000
 V9J  H1   CAM  CAN  119.64  3.000
 V9J  CAL  CAM  CAN  119.75  3.000
 V9J  H2   CAN  CAO  119.87  3.000
 V9J  H2   CAN  CAM  119.96  3.000
 V9J  CAO  CAN  CAM  120.17  3.000
 V9J  CAP  CAO  OAR  122.64  3.000
 V9J  OAR  CAO  CAN  117.87  3.000
 V9J  CAP  CAO  CAN  119.49  3.000
 V9J  H3   OAR  CAO  110.22  3.000
 V9J  H4   CAP  CAQ  119.40  3.000
 V9J  H4   CAP  CAO  120.29  3.000
 V9J  CAQ  CAP  CAO  120.30  3.000
 V9J  H5   CAQ  CAL  120.27  3.000
 V9J  H5   CAQ  CAP  120.07  3.000
 V9J  CAL  CAQ  CAP  119.65  3.000
 V9J  OAK  CAL  CAQ  118.54  3.000
 V9J  CAQ  CAL  CAM  120.63  3.000
 V9J  OAK  CAL  CAM  120.83  3.000
 V9J  CAH  OAK  CAL  116.04  3.000
 V9J  CAI  CAH  SAG  114.23  3.000
 V9J  CAI  CAH  OAK  128.64  3.000
 V9J  SAG  CAH  OAK  117.12  3.000
 V9J  CAE  SAG  CAH   90.48  3.000
 V9J  CAF  CAE  CAD  122.43  3.000
 V9J  CAF  CAE  SAG  111.34  3.000
 V9J  CAD  CAE  SAG  126.23  3.000
 V9J  H6   CAD  CAC  120.97  3.000
 V9J  H6   CAD  CAE  120.90  3.000
 V9J  CAC  CAD  CAE  118.13  3.000
 V9J  CAB  CAC  OAS  117.07  3.000
 V9J  CAB  CAC  CAD  120.41  3.000
 V9J  OAS  CAC  CAD  122.52  3.000
 V9J  H7   OAS  CAC  110.56  3.000
 V9J  H8   CAB  CAA  120.10  3.000
 V9J  H8   CAB  CAC  119.23  3.000
 V9J  CAA  CAB  CAC  120.67  3.000
 V9J  H9   CAA  CAF  120.03  3.000
 V9J  H9   CAA  CAB  119.78  3.000
 V9J  CAF  CAA  CAB  120.19  3.000
 V9J  CAI  CAF  CAA  129.00  3.000
 V9J  CAI  CAF  CAE  112.83  3.000
 V9J  CAA  CAF  CAE  118.16  3.000
 V9J  CAJ  CAI  CAF  125.10  3.000
 V9J  CAJ  CAI  CAH  123.78  3.000
 V9J  CAF  CAI  CAH  111.12  3.000
 V9J  CAX  CAJ  CAT  118.99  3.000
 V9J  CAT  CAJ  CAI  120.29  3.000
 V9J  CAX  CAJ  CAI  120.70  3.000
 V9J  H10  CAT  CAU  119.31  3.000
 V9J  H10  CAT  CAJ  119.74  3.000
 V9J  CAU  CAT  CAJ  120.94  3.000
 V9J  H11  CAU  CAV  120.62  3.000
 V9J  H11  CAU  CAT  120.96  3.000
 V9J  CAV  CAU  CAT  118.43  3.000
 V9J  CAW  CAV  FAY  118.86  3.000
 V9J  FAY  CAV  CAU  118.86  3.000
 V9J  CAW  CAV  CAU  122.28  3.000
 V9J  H12  CAW  CAX  120.98  3.000
 V9J  H12  CAW  CAV  120.53  3.000
 V9J  CAX  CAW  CAV  118.49  3.000
 V9J  H13  CAX  CAW  119.30  3.000
 V9J  H13  CAX  CAJ  119.82  3.000
 V9J  CAW  CAX  CAJ  120.87  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
 V9J  CONST_01  CAP  CAQ  CAL  CAM    0.00   0.0  0
 V9J  CONST_02  CAP  CAO  CAN  CAM    0.00   0.0  0
 V9J  CONST_03  CAQ  CAL  CAM  CAN    0.00   0.0  0
 V9J  CONST_04  CAQ  CAP  CAO  CAN    0.00   0.0  0
 V9J  CONST_05  CAL  CAM  CAN  CAO    0.00   0.0  0
 V9J  CONST_06  CAL  CAQ  CAP  CAO    0.00   0.0  0
 V9J  CONST_07  CAD  CAE  SAG  CAH  180.00   0.0  0
 V9J  CONST_08  CAF  CAE  SAG  CAH    0.00   0.0  0
 V9J  CONST_09  CAA  CAF  CAI  CAH  180.00   0.0  0
 V9J  CONST_10  CAE  CAF  CAI  CAH    0.00   0.0  0
 V9J  CONST_13  CAC  CAD  CAE  SAG  180.00   0.0  0
 V9J  CONST_14  CAA  CAF  CAE  SAG  180.00   0.0  0
 V9J  CONST_15  CAI  CAF  CAE  SAG    0.00   0.0  0
 V9J  CONST_16  CAF  CAI  CAH  SAG    0.00   0.0  0
 V9J  CONST_17  CAJ  CAI  CAH  SAG  180.00   0.0  0
 V9J  CONST_18  CAB  CAC  CAD  CAE    0.00   0.0  0
 V9J  CONST_19  CAB  CAA  CAF  CAE    0.00   0.0  0
 V9J  CONST_20  CAJ  CAI  CAF  CAE  180.00   0.0  0
 V9J  CONST_21  CAI  CAH  SAG  CAE    0.00   0.0  0
 V9J  CONST_22  CAA  CAB  CAC  CAD    0.00   0.0  0
 V9J  CONST_23  CAA  CAF  CAE  CAD    0.00   0.0  0
 V9J  CONST_24  CAI  CAF  CAE  CAD  180.00   0.0  0
 V9J  CONST_25  CAF  CAA  CAB  CAC    0.00   0.0  0
 V9J  CONST_26  CAF  CAE  CAD  CAC    0.00   0.0  0
 V9J  CONST_27  CAI  CAF  CAA  CAB  180.00   0.0  0
 V9J  CONST_28  CAJ  CAI  CAF  CAA    0.00   0.0  0
 V9J  CONST_31  CAW  CAX  CAJ  CAI  180.00   0.0  0
 V9J  CONST_32  CAU  CAT  CAJ  CAI  180.00   0.0  0
 V9J  CONST_33  CAV  CAW  CAX  CAJ    0.00   0.0  0
 V9J  CONST_34  CAV  CAU  CAT  CAJ    0.00   0.0  0
 V9J  CONST_35  CAW  CAX  CAJ  CAT    0.00   0.0  0
 V9J  CONST_36  CAW  CAV  CAU  CAT    0.00   0.0  0
 V9J  CONST_37  CAX  CAJ  CAT  CAU    0.00   0.0  0
 V9J  CONST_38  CAX  CAW  CAV  CAU    0.00   0.0  0
 V9J  CONST_39  OAR  CAO  CAN  CAM  180.00   0.0  0
 V9J  CONST_40  OAK  CAL  CAM  CAN  180.00   0.0  0
 V9J  CONST_41  CAQ  CAP  CAO  OAR  180.00   0.0  0
 V9J  CONST_42  OAK  CAL  CAQ  CAP  180.00   0.0  0
 V9J  CONST_43  CAE  SAG  CAH  OAK  180.00   0.0  0
 V9J  CONST_44  CAF  CAI  CAH  OAK  180.00   0.0  0
 V9J  CONST_45  CAJ  CAI  CAH  OAK    0.00   0.0  0
 V9J  CONST_46  OAS  CAC  CAD  CAE  180.00   0.0  0
 V9J  CONST_47  CAA  CAB  CAC  OAS  180.00   0.0  0
 V9J  CONST_48  FAY  CAV  CAU  CAT  180.00   0.0  0
 V9J  CONST_49  CAX  CAW  CAV  FAY  180.00   0.0  0
 V9J  CONST_50  H5   CAQ  CAL  CAM  180.00   0.0  0
 V9J  CONST_51  H4   CAP  CAO  CAN  180.00   0.0  0
 V9J  CONST_52  H1   CAM  CAN  CAO  180.00   0.0  0
 V9J  CONST_53  H2   CAN  CAO  CAP  180.00   0.0  0
 V9J  CONST_54  H6   CAD  CAE  SAG    0.00   0.0  0
 V9J  CONST_55  H9   CAA  CAF  CAE  180.00   0.0  0
 V9J  CONST_56  H8   CAB  CAC  CAD  180.00   0.0  0
 V9J  CONST_57  H13  CAX  CAJ  CAI    0.00   0.0  0
 V9J  CONST_58  H10  CAT  CAJ  CAI    0.00   0.0  0
 V9J  CONST_59  H12  CAW  CAX  CAJ  180.00   0.0  0
 V9J  CONST_60  H11  CAU  CAT  CAJ  180.00   0.0  0
 V9J  Var_01    SAG  CAH  OAK  CAL  128.79  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
 V9J  plan-1  CAM  0.020
 V9J  plan-1  CAN  0.020
 V9J  plan-1  CAO  0.020
 V9J  plan-1  OAR  0.020
 V9J  plan-1  CAP  0.020
 V9J  plan-1  CAQ  0.020
 V9J  plan-1  CAL  0.020
 V9J  plan-1  OAK  0.020
 V9J  plan-1  H1   0.020
 V9J  plan-1  H2   0.020
 V9J  plan-1  H4   0.020
 V9J  plan-1  H5   0.020
 V9J  plan-2  CAI  0.020
 V9J  plan-2  CAJ  0.020
 V9J  plan-2  CAT  0.020
 V9J  plan-2  CAU  0.020
 V9J  plan-2  CAV  0.020
 V9J  plan-2  FAY  0.020
 V9J  plan-2  CAW  0.020
 V9J  plan-2  CAX  0.020
 V9J  plan-2  H10  0.020
 V9J  plan-2  H11  0.020
 V9J  plan-2  H12  0.020
 V9J  plan-2  H13  0.020
 V9J  plan-3  OAK  0.020
 V9J  plan-3  CAH  0.020
 V9J  plan-3  SAG  0.020
 V9J  plan-3  CAE  0.020
 V9J  plan-3  CAD  0.020
 V9J  plan-3  CAC  0.020
 V9J  plan-3  OAS  0.020
 V9J  plan-3  CAB  0.020
 V9J  plan-3  CAA  0.020
 V9J  plan-3  CAF  0.020
 V9J  plan-3  CAI  0.020
 V9J  plan-3  CAJ  0.020
 V9J  plan-3  H6   0.020
 V9J  plan-3  H8   0.020
 V9J  plan-3  H9   0.020

