# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:02:06 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 2-({[(2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methyl}sulfanyl)-5-(trifluoromethyl)pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc(SC[C@@H]2CO[C@@](CCc3ccc(Cl)cc3)(Cn4ccnc4)O2)nc1
#
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
 Q80  Q80  2-({[(2R,4S)-2-[2-(4-chlorophenyl)ethyl]-2-(1H-imidazol-1-ylmethyl)-1,3-dioxolan-4-yl]methyl}sulfanyl)-5-(trifluoromethyl)pyridine  ligand  53  32  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q80
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
 Q80  CLBF  CL  CL    0  -0.136  -6.9842  -4.5085  -0.8122
 Q80  CAB   C   CR6   0  -0.058  -5.8196  -3.3008  -0.3669
 Q80  CAC   C   CR16  0  -0.195  -4.6104  -3.2379  -1.0408
 Q80  CAD   C   CR16  0  -0.316  -3.6861  -2.2694  -0.6771
 Q80  CAA   C   CR16  0  -0.196  -6.1121  -2.4159   0.6589
 Q80  CAF   C   CR16  0  -0.312  -5.1735  -1.4555   1.0071
 Q80  CAE   C   CR6   0   0.143  -3.9496  -1.3662   0.3488
 Q80  CAG   C   CH2   0  -0.528  -2.9604  -0.2920   0.7034
 Q80  CAH   C   CH2   0  -0.439  -3.2465   0.9881  -0.0809
 Q80  CAI   C   CR5   0   0.496  -2.2414   2.1079   0.1609
 Q80  OAP   O   O     0  -0.505  -0.9668   1.7004  -0.2678
 Q80  CAJ   C   CH2   0  -0.323  -2.6802   3.3690  -0.5957
 Q80  NAK   N   NR5   0  -0.396  -1.6869   4.4096  -0.5292
 Q80  CAO   C   CR15  0   0.095  -0.6884   4.6078  -1.4190
 Q80  NAN   N   N     0  -0.454   0.1228   5.5603  -1.0401
 Q80  CAM   C   CR15  0  -0.217  -0.3682   5.9970   0.1593
 Q80  CAL   C   CR15  0  -0.105  -1.4874   5.2926   0.4965
 Q80  OAS   O   O     0  -0.507  -2.1257   2.4271   1.5276
 Q80  CAR   C   CH2   0  -0.187  -0.8459   2.0597   1.9956
 Q80  CAQ   C   CR15  0  -0.014  -0.0067   2.0120   0.7252
 Q80  CAT   C   CH2   0  -0.580   1.0643   0.9468   0.7565
 Q80  SAU   S   S2    0   0.075   1.8886   0.9075  -0.8574
 Q80  CAV   C   CR6   0   0.104   3.2856  -0.0999  -0.5325
 Q80  CBA   C   CR16  0  -0.288   4.1857  -0.3166  -1.5825
 Q80  NAW   N   N     0  -0.418   3.4480  -0.6219   0.6695
 Q80  CAX   C   CR16  0  -0.058   4.5137  -1.3824   0.8957
 Q80  CAY   C   CR6   0  -0.319   5.4619  -1.6579  -0.0723
 Q80  CAZ   C   CR16  0  -0.146   5.2846  -1.1066  -1.3426
 Q80  CBB   C   CT    0   1.065   6.6561  -2.5072   0.2039
 Q80  FBD   F   F     0  -0.313   6.7318  -3.5437  -0.6430
 Q80  FBE   F   F     0  -0.313   7.7966  -1.8167   0.0585
 Q80  FBC   F   F     0  -0.301   6.6547  -3.0079   1.4417
 Q80  HAC   H   HCR6  0   0.277  -4.3879  -3.9343  -1.8379
 Q80  HAD   H   HCR6  0   0.258  -2.7403  -2.2237  -1.2039
 Q80  HAA   H   HCR6  0   0.277  -7.0566  -2.4714   1.1830
 Q80  HAF   H   HCR6  0   0.258  -5.4020  -0.7653   1.8107
 Q80  HAG   H   HCH2  0   0.255  -3.0110  -0.0918   1.7758
 Q80  HAGA  H   HCH2  0   0.253  -1.9492  -0.6439   0.4870
 Q80  HAH   H   HCH2  0   0.251  -3.2614   0.7665  -1.1517
 Q80  HAHA  H   HCH2  0   0.251  -4.2452   1.3563   0.1713
 Q80  HAJ   H   HCH2  0   0.280  -2.8561   3.1254  -1.6437
 Q80  HAJA  H   HCH2  0   0.281  -3.6205   3.7374  -0.1847
 Q80  HAO   H   HCR5  0   0.278  -0.6103   4.0299  -2.3280
 Q80  HAM   H   HCR5  0   0.249   0.1015   6.7954   0.7129
 Q80  HAL   H   HCR5  0   0.286  -2.1477   5.3477   1.3450
 Q80  HAR   H   HCH2  0   0.258  -0.4872   2.8066   2.7037
 Q80  HARA  H   HCH2  0   0.226  -0.8708   1.0858   2.4993
 Q80  HAQ   H   HCR5  0   0.254   0.4514   2.9891   0.5272
 Q80  HAT   H   HCH2  0   0.299   1.7973   1.1881   1.5259
 Q80  HATA  H   HCH2  0   0.283   0.6386  -0.0326   0.9783
 Q80  HBA   H   HCR6  0   0.292   4.0233   0.1260  -2.5559
 Q80  HAX   H   HCR6  0   0.285   4.5976  -1.7820   1.8988
 Q80  HAZ   H   HCR6  0   0.294   5.9948  -1.2877  -2.1394

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
 Q80  CLBF  CAB   single    1.736  0.020  1.736
 Q80  CAC   CAB   aromatic  1.386  0.020  1.386
 Q80  CAB   CAA   aromatic  1.386  0.020  1.386
 Q80  CAC   CAD   aromatic  1.387  0.020  1.387
 Q80  CAC   HAC   single    0.930  0.020  1.080
 Q80  CAD   CAE   aromatic  1.392  0.020  1.392
 Q80  CAD   HAD   single    0.930  0.020  1.080
 Q80  CAA   CAF   aromatic  1.387  0.020  1.387
 Q80  CAA   HAA   single    0.930  0.020  1.080
 Q80  CAE   CAF   aromatic  1.393  0.020  1.393
 Q80  CAF   HAF   single    0.930  0.020  1.080
 Q80  CAE   CAG   single    1.503  0.020  1.503
 Q80  CAG   CAH   single    1.528  0.020  1.528
 Q80  CAG   HAG   single    0.970  0.020  1.090
 Q80  CAG   HAGA  single    0.970  0.020  1.090
 Q80  CAH   CAI   single    1.524  0.020  1.524
 Q80  CAH   HAH   single    0.970  0.020  1.090
 Q80  CAH   HAHA  single    0.970  0.020  1.090
 Q80  OAP   CAI   single    1.405  0.020  1.405
 Q80  CAI   OAS   single    1.408  0.020  1.408
 Q80  CAI   CAJ   single    1.535  0.020  1.535
 Q80  OAP   CAQ   single    1.416  0.020  1.416
 Q80  CAJ   NAK   single    1.440  0.020  1.440
 Q80  CAJ   HAJ   single    0.970  0.020  1.090
 Q80  CAJ   HAJA  single    0.970  0.020  1.090
 Q80  NAK   CAO   aromatic  1.352  0.020  1.352
 Q80  NAK   CAL   aromatic  1.368  0.020  1.368
 Q80  CAO   NAN   aromatic  1.307  0.020  1.307
 Q80  CAO   HAO   single    0.930  0.020  1.080
 Q80  NAN   CAM   aromatic  1.368  0.020  1.368
 Q80  CAL   CAM   aromatic  1.365  0.020  1.365
 Q80  CAM   HAM   single    0.930  0.020  1.080
 Q80  CAL   HAL   single    0.930  0.020  1.080
 Q80  OAS   CAR   single    1.411  0.020  1.411
 Q80  CAQ   CAR   single    1.523  0.020  1.523
 Q80  CAR   HAR   single    0.970  0.020  1.090
 Q80  CAR   HARA  single    0.970  0.020  1.090
 Q80  CAT   CAQ   single    1.511  0.020  1.511
 Q80  CAQ   HAQ   single    0.970  0.020  1.090
 Q80  CAT   SAU   single    1.813  0.020  1.813
 Q80  CAT   HAT   single    0.970  0.020  1.090
 Q80  CAT   HATA  single    0.970  0.020  1.090
 Q80  CAV   SAU   single    1.753  0.020  1.753
 Q80  NAW   CAV   aromatic  1.320  0.020  1.320
 Q80  CAV   CBA   aromatic  1.400  0.020  1.400
 Q80  CAZ   CBA   aromatic  1.374  0.020  1.374
 Q80  CBA   HBA   single    0.930  0.020  1.080
 Q80  CAX   NAW   aromatic  1.329  0.020  1.329
 Q80  CAX   CAY   aromatic  1.383  0.020  1.383
 Q80  CAX   HAX   single    0.930  0.020  1.080
 Q80  CBB   CAY   single    1.491  0.020  1.491
 Q80  CAY   CAZ   aromatic  1.396  0.020  1.396
 Q80  CAZ   HAZ   single    0.930  0.020  1.080
 Q80  FBE   CBB   single    1.341  0.020  1.341
 Q80  FBD   CBB   single    1.341  0.020  1.341
 Q80  CBB   FBC   single    1.335  0.020  1.335

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
 Q80  CAA   CAB  CAC   121.00  3.000
 Q80  CAA   CAB  CLBF  119.51  3.000
 Q80  CAC   CAB  CLBF  119.49  3.000
 Q80  HAC   CAC  CAD   120.37  3.000
 Q80  HAC   CAC  CAB   120.58  3.000
 Q80  CAD   CAC  CAB   119.05  3.000
 Q80  HAD   CAD  CAE   119.75  3.000
 Q80  HAD   CAD  CAC   118.92  3.000
 Q80  CAE   CAD  CAC   121.33  3.000
 Q80  HAA   CAA  CAF   120.31  3.000
 Q80  HAA   CAA  CAB   120.67  3.000
 Q80  CAF   CAA  CAB   119.02  3.000
 Q80  HAF   CAF  CAE   119.67  3.000
 Q80  HAF   CAF  CAA   118.97  3.000
 Q80  CAE   CAF  CAA   121.36  3.000
 Q80  CAG   CAE  CAF   120.85  3.000
 Q80  CAG   CAE  CAD   120.87  3.000
 Q80  CAF   CAE  CAD   118.24  3.000
 Q80  HAGA  CAG  HAG   107.25  3.000
 Q80  HAGA  CAG  CAH   109.96  3.000
 Q80  HAG   CAG  CAH   109.98  3.000
 Q80  HAGA  CAG  CAE   109.41  3.000
 Q80  HAG   CAG  CAE   109.41  3.000
 Q80  CAH   CAG  CAE   110.76  3.000
 Q80  HAHA  CAH  HAH   106.35  3.000
 Q80  HAHA  CAH  CAI   108.56  3.000
 Q80  HAH   CAH  CAI   108.26  3.000
 Q80  HAHA  CAH  CAG   109.54  3.000
 Q80  HAH   CAH  CAG   109.59  3.000
 Q80  CAI   CAH  CAG   114.24  3.000
 Q80  OAS   CAI  CAJ   108.40  3.000
 Q80  CAJ   CAI  OAP   110.32  3.000
 Q80  OAS   CAI  OAP   106.70  3.000
 Q80  CAJ   CAI  CAH   109.69  3.000
 Q80  OAS   CAI  CAH   112.01  3.000
 Q80  OAP   CAI  CAH   109.68  3.000
 Q80  CAQ   OAP  CAI   109.71  3.000
 Q80  HAJA  CAJ  HAJ   107.38  3.000
 Q80  HAJA  CAJ  NAK   109.47  3.000
 Q80  HAJ   CAJ  NAK   108.49  3.000
 Q80  HAJA  CAJ  CAI   109.78  3.000
 Q80  HAJ   CAJ  CAI   109.66  3.000
 Q80  NAK   CAJ  CAI   111.95  3.000
 Q80  CAL   NAK  CAO   106.92  3.000
 Q80  CAL   NAK  CAJ   126.98  3.000
 Q80  CAO   NAK  CAJ   125.80  3.000
 Q80  HAO   CAO  NAN   126.08  3.000
 Q80  HAO   CAO  NAK   121.93  3.000
 Q80  NAN   CAO  NAK   111.98  3.000
 Q80  CAM   NAN  CAO   105.31  3.000
 Q80  HAM   CAM  CAL   127.74  3.000
 Q80  HAM   CAM  NAN   122.00  3.000
 Q80  CAL   CAM  NAN   110.26  3.000
 Q80  HAL   CAL  CAM   132.17  3.000
 Q80  HAL   CAL  NAK   122.31  3.000
 Q80  CAM   CAL  NAK   105.52  3.000
 Q80  CAR   OAS  CAI   109.71  3.000
 Q80  HARA  CAR  HAR   108.51  3.000
 Q80  HARA  CAR  CAQ   111.57  3.000
 Q80  HAR   CAR  CAQ   112.46  3.000
 Q80  HARA  CAR  OAS   111.28  3.000
 Q80  HAR   CAR  OAS   109.60  3.000
 Q80  CAQ   CAR  OAS   103.37  3.000
 Q80  HAQ   CAQ  CAT   109.61  3.000
 Q80  HAQ   CAQ  CAR   110.64  3.000
 Q80  CAT   CAQ  CAR   113.29  3.000
 Q80  HAQ   CAQ  OAP   110.65  3.000
 Q80  CAT   CAQ  OAP   109.88  3.000
 Q80  CAR   CAQ  OAP   102.60  3.000
 Q80  HATA  CAT  HAT   108.53  3.000
 Q80  HATA  CAT  SAU   109.82  3.000
 Q80  HAT   CAT  SAU   109.13  3.000
 Q80  HATA  CAT  CAQ   111.14  3.000
 Q80  HAT   CAT  CAQ   109.60  3.000
 Q80  SAU   CAT  CAQ   108.61  3.000
 Q80  CAV   SAU  CAT   102.12  3.000
 Q80  NAW   CAV  CBA   122.85  3.000
 Q80  CBA   CAV  SAU   117.55  3.000
 Q80  NAW   CAV  SAU   119.60  3.000
 Q80  HBA   CBA  CAZ   120.82  3.000
 Q80  HBA   CBA  CAV   121.01  3.000
 Q80  CAZ   CBA  CAV   118.17  3.000
 Q80  CAX   NAW  CAV   118.68  3.000
 Q80  HAX   CAX  CAY   121.45  3.000
 Q80  HAX   CAX  NAW   115.53  3.000
 Q80  CAY   CAX  NAW   123.02  3.000
 Q80  CBB   CAY  CAZ   119.68  3.000
 Q80  CAZ   CAY  CAX   118.11  3.000
 Q80  CBB   CAY  CAX   122.20  3.000
 Q80  HAZ   CAZ  CAY   121.35  3.000
 Q80  HAZ   CAZ  CBA   119.49  3.000
 Q80  CAY   CAZ  CBA   119.16  3.000
 Q80  FBC   CBB  FBE   107.12  3.000
 Q80  FBC   CBB  FBD   107.21  3.000
 Q80  FBE   CBB  FBD   106.35  3.000
 Q80  FBC   CBB  CAY   112.61  3.000
 Q80  FBD   CBB  CAY   111.63  3.000
 Q80  FBE   CBB  CAY   111.57  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
 Q80  CONST_01  CAE  CAD  CAC  CAB      0.00   0.0  0
 Q80  CONST_02  CAE  CAF  CAA  CAB      0.00   0.0  0
 Q80  CONST_03  CAF  CAA  CAB  CAC      0.00   0.0  0
 Q80  CONST_04  CAF  CAE  CAD  CAC      0.00   0.0  0
 Q80  CONST_05  CAA  CAB  CAC  CAD      0.00   0.0  0
 Q80  CONST_06  CAA  CAF  CAE  CAD      0.00   0.0  0
 Q80  CONST_07  CAM  NAN  CAO  NAK      0.00   0.0  0
 Q80  CONST_08  NAN  CAM  CAL  NAK      0.00   0.0  0
 Q80  CONST_09  CAM  CAL  NAK  CAO      0.00   0.0  0
 Q80  CONST_10  CAL  CAM  NAN  CAO      0.00   0.0  0
 Q80  CONST_11  CAL  NAK  CAO  NAN      0.00   0.0  0
 Q80  CONST_12  CAY  CAX  NAW  CAV      0.00   0.0  0
 Q80  CONST_13  CAY  CAZ  CBA  CAV      0.00   0.0  0
 Q80  CONST_14  CAX  NAW  CAV  CBA      0.00   0.0  0
 Q80  CONST_15  CAX  CAY  CAZ  CBA      0.00   0.0  0
 Q80  CONST_16  CAZ  CBA  CAV  NAW      0.00   0.0  0
 Q80  CONST_17  CAZ  CAY  CAX  NAW      0.00   0.0  0
 Q80  CONST_18  CAD  CAC  CAB  CLBF   180.00   0.0  0
 Q80  CONST_19  CAF  CAA  CAB  CLBF   180.00   0.0  0
 Q80  CONST_20  CAG  CAE  CAD  CAC    180.00   0.0  0
 Q80  CONST_21  CAG  CAE  CAF  CAA    180.00   0.0  0
 Q80  CONST_22  NAN  CAO  NAK  CAJ    180.00   0.0  0
 Q80  CONST_23  CAM  CAL  NAK  CAJ    180.00   0.0  0
 Q80  CONST_24  CAX  NAW  CAV  SAU    180.00   0.0  0
 Q80  CONST_25  CAZ  CBA  CAV  SAU    180.00   0.0  0
 Q80  CONST_26  CBB  CAY  CAZ  CBA    180.00   0.0  0
 Q80  CONST_27  CBB  CAY  CAX  NAW    180.00   0.0  0
 Q80  CONST_28  HAD  CAD  CAC  CAB    180.00   0.0  0
 Q80  CONST_29  HAF  CAF  CAA  CAB    180.00   0.0  0
 Q80  CONST_30  HAA  CAA  CAB  CAC    180.00   0.0  0
 Q80  CONST_31  HAC  CAC  CAB  CAA    180.00   0.0  0
 Q80  CONST_32  HAM  CAM  CAL  NAK    180.00   0.0  0
 Q80  CONST_33  HAL  CAL  NAK  CAO    180.00   0.0  0
 Q80  CONST_34  HAO  CAO  NAN  CAM    180.00   0.0  0
 Q80  CONST_35  HAX  CAX  NAW  CAV    180.00   0.0  0
 Q80  CONST_36  HAZ  CAZ  CBA  CAV    180.00   0.0  0
 Q80  CONST_37  HBA  CBA  CAV  NAW    180.00   0.0  0
 Q80  Var_01    CAQ  CAR  OAS  CAI     22.00  30.0  1
 Q80  Var_02    CAO  NAK  CAJ  CAI     91.15  30.0  2
 Q80  Var_03    CAH  CAG  CAE  CAD     91.35  30.0  2
 Q80  Var_04    CAI  CAH  CAG  CAE   -176.78  30.0  3
 Q80  Var_05    NAW  CAV  SAU  CAT      1.90  30.0  2
 Q80  Var_06    FBE  CBB  CAY  CAX   -117.27  30.0  3
 Q80  Var_07    HAT  CAT  SAU  CAV     48.80  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 Q80  chir_01  CAI  OAP  OAS  CAJ  negativ
 Q80  chir_02  CAQ  OAP  CAT  CAR  positiv

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
 Q80  plan-1  CAJ   0.020
 Q80  plan-1  NAK   0.020
 Q80  plan-1  CAO   0.020
 Q80  plan-1  NAN   0.020
 Q80  plan-1  CAM   0.020
 Q80  plan-1  CAL   0.020
 Q80  plan-1  HAO   0.020
 Q80  plan-1  HAM   0.020
 Q80  plan-1  HAL   0.020
 Q80  plan-2  CLBF  0.020
 Q80  plan-2  CAB   0.020
 Q80  plan-2  CAC   0.020
 Q80  plan-2  CAD   0.020
 Q80  plan-2  CAA   0.020
 Q80  plan-2  CAF   0.020
 Q80  plan-2  CAE   0.020
 Q80  plan-2  CAG   0.020
 Q80  plan-2  HAC   0.020
 Q80  plan-2  HAD   0.020
 Q80  plan-2  HAA   0.020
 Q80  plan-2  HAF   0.020
 Q80  plan-3  SAU   0.020
 Q80  plan-3  CAV   0.020
 Q80  plan-3  CBA   0.020
 Q80  plan-3  NAW   0.020
 Q80  plan-3  CAX   0.020
 Q80  plan-3  CAY   0.020
 Q80  plan-3  CAZ   0.020
 Q80  plan-3  CBB   0.020
 Q80  plan-3  HBA   0.020
 Q80  plan-3  HAX   0.020
 Q80  plan-3  HAZ   0.020

