# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 19:30:15 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 1-[2-(1H-benzimidazol-2-ylsulfanyl)ethyl]-3-methyl-1,3-dihydro-2H-benzimidazole-2-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=S)N(CCSc2[nH]c3ccccc3n2)c4ccccc14
#
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
 BYH  BYH  1-[2-(1H-benzimidazol-2-ylsulfanyl)ethyl]-3-methyl-1,3-dihydro-2H-benzimidazole-2-thione  ligand  39  23  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BYH
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
 BYH  CAA   C  CH3   0  -0.532   4.8796   1.1433  -1.9252
 BYH  CAC   C  CR16  0  -0.281  -6.7066  -0.8243  -0.9877
 BYH  CAD   C  CR16  0  -0.270  -5.8466  -1.2779  -1.9971
 BYH  CAE   C  CR16  0  -0.269   4.5670  -2.9413  -0.1159
 BYH  CAF   C  CR16  0  -0.268   3.5451  -3.0515   0.8282
 BYH  CAG   C  CR16  0  -0.303  -6.2225  -0.1913   0.1463
 BYH  CAH   C  CR16  0  -0.334  -4.4745  -1.1134  -1.9050
 BYH  CAI   C  CR16  0  -0.317   4.8147  -1.7453  -0.7785
 BYH  CAJ   C  CR16  0  -0.312   2.7317  -1.9707   1.1460
 BYH  CAK   C  CH2   0  -0.554  -0.0429   0.5747   0.6014
 BYH  NAM   N  NR15  0  -0.702  -4.0309   0.5318   1.1788
 BYH  NAN   N  N     0  -0.463  -2.6671  -0.1896  -0.4260
 BYH  SAO   S  S2    0   0.057  -1.4317   0.9979   1.6904
 BYH  CAP   C  CR5   0   0.306  -2.7552   0.4030   0.7298
 BYH  CAQ   C  CR5   0   0.374   2.9872   1.3213  -0.3102
 BYH  CAR   C  CR56  0   0.331  -4.8460  -0.0312   0.2286
 BYH  CAS   C  CR56  0   0.146  -3.9688  -0.4793  -0.7724
 BYH  CAT   C  CR56  0   0.327   4.0025  -0.6708  -0.4584
 BYH  CAU   C  CR56  0   0.330   2.9830  -0.7806   0.4850
 BYH  NAV   N  NR5   0  -0.530   3.9796   0.6272  -0.9226
 BYH  NAW   N  NR5   0  -0.537   2.3888   0.4629   0.5614
 BYH  HAA   H  HCH3  0   0.269   4.6721   2.1989  -2.0708
 BYH  HAAA  H  HCH3  0   0.263   5.9120   1.0226  -1.6006
 BYH  HAAB  H  HCH3  0   0.263   4.7373   0.6169  -2.8679
 BYH  HAD   H  HCR6  0   0.253  -6.2669  -1.7664  -2.8662
 BYH  HAE   H  HCR6  0   0.264   5.1796  -3.8045  -0.3386
 BYH  HAF   H  HCR6  0   0.264   3.3806  -3.9984   1.3246
 BYH  HAG   H  HCR6  0   0.268  -6.8867   0.1579   0.9257
 BYH  HAH   H  HCR6  0   0.255  -3.8132  -1.4656  -2.6861
 BYH  HAI   H  HCR6  0   0.281   5.6050  -1.6639  -1.5122
 BYH  HAJ   H  HCR6  0   0.279   1.9413  -2.0641   1.8789
 BYH  HAK   H  HCH2  0   0.294  -0.0644   1.2165  -0.2787
 BYH  HAKA  H  HCH2  0   0.296  -0.1428  -0.4639   0.2895
 BYH  HNAM  H  HNR5  0   0.424  -4.3239   0.9592   2.0435
 BYH  SAB   S  S1    0  -0.385   2.5608   2.9149  -0.5601
 BYH  CAL   C  CH2   0  -0.318   1.2479   0.7915   1.3811
 BYH  HAC   H  HCR6  0   0.256  -7.7730  -0.9720  -1.0961
 BYH  HAL   H  HCH2  0   0.288   1.3455   1.8298   1.6962
 BYH  HALA  H  HCH2  0   0.287   1.2787   0.1656   2.2727

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
 BYH  CAA  NAV   single    1.443  0.020  1.443
 BYH  SAB  CAQ   double    1.668  0.020  1.668
 BYH  CAC  CAD   aromatic  1.402  0.020  1.402
 BYH  CAC  CAG   aromatic  1.386  0.020  1.386
 BYH  CAD  CAH   aromatic  1.385  0.020  1.385
 BYH  CAE  CAF   aromatic  1.396  0.020  1.396
 BYH  CAE  CAI   aromatic  1.389  0.020  1.389
 BYH  CAF  CAJ   aromatic  1.390  0.020  1.390
 BYH  CAG  CAR   aromatic  1.388  0.020  1.388
 BYH  CAH  CAS   aromatic  1.393  0.020  1.393
 BYH  CAI  CAT   aromatic  1.385  0.020  1.385
 BYH  CAJ  CAU   aromatic  1.384  0.020  1.384
 BYH  CAK  CAL   single    1.523  0.020  1.523
 BYH  CAK  SAO   single    1.815  0.020  1.815
 BYH  CAL  NAW   single    1.443  0.020  1.443
 BYH  NAM  CAP   aromatic  1.359  0.020  1.359
 BYH  NAM  CAR   aromatic  1.373  0.020  1.373
 BYH  NAN  CAP   aromatic  1.302  0.020  1.302
 BYH  NAN  CAS   aromatic  1.378  0.020  1.378
 BYH  SAO  CAP   single    1.740  0.020  1.740
 BYH  CAQ  NAV   single    1.357  0.020  1.357
 BYH  CAQ  NAW   single    1.362  0.020  1.362
 BYH  CAR  CAS   aromatic  1.404  0.020  1.404
 BYH  CAT  CAU   aromatic  1.393  0.020  1.393
 BYH  CAT  NAV   single    1.379  0.020  1.379
 BYH  CAU  NAW   single    1.380  0.020  1.380
 BYH  CAA  HAA   single    0.970  0.020  1.090
 BYH  CAA  HAAA  single    0.970  0.020  1.090
 BYH  CAA  HAAB  single    0.970  0.020  1.090
 BYH  CAC  HAC   single    0.930  0.020  1.080
 BYH  CAD  HAD   single    0.930  0.020  1.080
 BYH  CAE  HAE   single    0.930  0.020  1.080
 BYH  CAF  HAF   single    0.930  0.020  1.080
 BYH  CAG  HAG   single    0.930  0.020  1.080
 BYH  CAH  HAH   single    0.930  0.020  1.080
 BYH  CAI  HAI   single    0.930  0.020  1.080
 BYH  CAJ  HAJ   single    0.930  0.020  1.080
 BYH  CAK  HAK   single    0.970  0.020  1.090
 BYH  CAK  HAKA  single    0.970  0.020  1.090
 BYH  CAL  HAL   single    0.970  0.020  1.090
 BYH  CAL  HALA  single    0.970  0.020  1.090
 BYH  NAM  HNAM  single    0.860  0.020  1.020

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
 BYH  HAAB  CAA  HAAA  109.16  3.000
 BYH  HAAB  CAA  HAA   109.20  3.000
 BYH  HAAA  CAA  HAA   109.20  3.000
 BYH  HAAB  CAA  NAV   110.32  3.000
 BYH  HAAA  CAA  NAV   110.16  3.000
 BYH  HAA   CAA  NAV   108.77  3.000
 BYH  HAC   CAC  CAG   119.25  3.000
 BYH  HAC   CAC  CAD   119.24  3.000
 BYH  CAG   CAC  CAD   121.52  3.000
 BYH  HAD   CAD  CAH   119.47  3.000
 BYH  HAD   CAD  CAC   119.09  3.000
 BYH  CAH   CAD  CAC   121.44  3.000
 BYH  HAE   CAE  CAI   119.19  3.000
 BYH  HAE   CAE  CAF   119.40  3.000
 BYH  CAI   CAE  CAF   121.41  3.000
 BYH  HAF   CAF  CAJ   119.14  3.000
 BYH  HAF   CAF  CAE   119.40  3.000
 BYH  CAJ   CAF  CAE   121.46  3.000
 BYH  HAG   CAG  CAR   121.92  3.000
 BYH  HAG   CAG  CAC   121.49  3.000
 BYH  CAR   CAG  CAC   116.59  3.000
 BYH  HAH   CAH  CAS   120.87  3.000
 BYH  HAH   CAH  CAD   121.24  3.000
 BYH  CAS   CAH  CAD   117.89  3.000
 BYH  HAI   CAI  CAT   121.81  3.000
 BYH  HAI   CAI  CAE   121.24  3.000
 BYH  CAT   CAI  CAE   116.95  3.000
 BYH  HAJ   CAJ  CAU   122.03  3.000
 BYH  HAJ   CAJ  CAF   121.03  3.000
 BYH  CAU   CAJ  CAF   116.95  3.000
 BYH  HAKA  CAK  HAK   109.19  3.000
 BYH  HAKA  CAK  SAO   108.91  3.000
 BYH  HAK   CAK  SAO   109.40  3.000
 BYH  HAKA  CAK  CAL   111.10  3.000
 BYH  HAK   CAK  CAL   110.27  3.000
 BYH  SAO   CAK  CAL   107.94  3.000
 BYH  HNAM  NAM  CAR   126.51  3.000
 BYH  HNAM  NAM  CAP   126.63  3.000
 BYH  CAR   NAM  CAP   106.86  3.000
 BYH  CAS   NAN  CAP   104.77  3.000
 BYH  CAP   SAO  CAK    99.85  3.000
 BYH  SAO   CAP  NAN   126.46  3.000
 BYH  SAO   CAP  NAM   119.96  3.000
 BYH  NAN   CAP  NAM   113.58  3.000
 BYH  NAW   CAQ  NAV   106.72  3.000
 BYH  NAW   CAQ  SAB   125.85  3.000
 BYH  NAV   CAQ  SAB   127.43  3.000
 BYH  CAS   CAR  NAM   104.67  3.000
 BYH  CAS   CAR  CAG   122.70  3.000
 BYH  NAM   CAR  CAG   132.62  3.000
 BYH  CAR   CAS  NAN   110.11  3.000
 BYH  CAR   CAS  CAH   119.86  3.000
 BYH  NAN   CAS  CAH   130.02  3.000
 BYH  NAV   CAT  CAU   106.86  3.000
 BYH  NAV   CAT  CAI   131.50  3.000
 BYH  CAU   CAT  CAI   121.64  3.000
 BYH  NAW   CAU  CAT   106.35  3.000
 BYH  NAW   CAU  CAJ   132.05  3.000
 BYH  CAT   CAU  CAJ   121.59  3.000
 BYH  CAT   NAV  CAQ   109.98  3.000
 BYH  CAT   NAV  CAA   124.08  3.000
 BYH  CAQ   NAV  CAA   125.93  3.000
 BYH  CAU   NAW  CAQ   110.07  3.000
 BYH  CAU   NAW  CAL   125.25  3.000
 BYH  CAQ   NAW  CAL   124.57  3.000
 BYH  HALA  CAL  HAL   107.95  3.000
 BYH  HALA  CAL  NAW   108.16  3.000
 BYH  HAL   CAL  NAW   108.09  3.000
 BYH  HALA  CAL  CAK   111.16  3.000
 BYH  HAL   CAL  CAK   111.07  3.000
 BYH  NAW   CAL  CAK   110.29  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
 BYH  CONST_01  CAS   CAH  CAD  CAC     0.00   0.0  0
 BYH  CONST_02  NAM   CAR  CAG  CAC   180.00   0.0  0
 BYH  CONST_03  CAS   CAR  CAG  CAC     0.00   0.0  0
 BYH  CONST_04  CAR   CAG  CAC  CAD     0.00   0.0  0
 BYH  CONST_05  NAN   CAS  CAH  CAD   180.00   0.0  0
 BYH  CONST_06  CAR   CAS  CAH  CAD     0.00   0.0  0
 BYH  CONST_07  CAU   CAJ  CAF  CAE     0.00   0.0  0
 BYH  CONST_08  CAU   CAT  CAI  CAE     0.00   0.0  0
 BYH  CONST_09  CAT   CAI  CAE  CAF     0.00   0.0  0
 BYH  CONST_10  CAT   CAU  CAJ  CAF     0.00   0.0  0
 BYH  CONST_11  CAH   CAD  CAC  CAG     0.00   0.0  0
 BYH  CONST_12  CAP   NAM  CAR  CAG   180.00   0.0  0
 BYH  CONST_13  CAH   CAS  CAR  CAG     0.00   0.0  0
 BYH  CONST_14  NAN   CAS  CAR  CAG   180.00   0.0  0
 BYH  CONST_15  CAP   NAN  CAS  CAH   180.00   0.0  0
 BYH  CONST_16  NAM   CAR  CAS  CAH   180.00   0.0  0
 BYH  CONST_17  CAJ   CAF  CAE  CAI     0.00   0.0  0
 BYH  CONST_18  CAJ   CAU  CAT  CAI     0.00   0.0  0
 BYH  CONST_19  CAS   NAN  CAP  NAM     0.00   0.0  0
 BYH  CONST_20  NAN   CAS  CAR  NAM     0.00   0.0  0
 BYH  CONST_21  CAR   NAM  CAP  NAN     0.00   0.0  0
 BYH  CONST_22  CAS   CAR  NAM  CAP     0.00   0.0  0
 BYH  CONST_23  CAR   CAS  NAN  CAP     0.00   0.0  0
 BYH  CONST_24  CAU   CAT  NAV  CAQ     0.00   0.0  0
 BYH  CONST_25  CAT   CAU  NAW  CAQ     0.00   0.0  0
 BYH  CONST_26  NAW   CAQ  NAV  CAT     0.00   0.0  0
 BYH  CONST_27  NAV   CAQ  NAW  CAU     0.00   0.0  0
 BYH  CONST_28  NAW   CAU  CAT  NAV     0.00   0.0  0
 BYH  CONST_29  CAR   NAM  CAP  SAO   180.00   0.0  0
 BYH  CONST_30  CAS   NAN  CAP  SAO   180.00   0.0  0
 BYH  CONST_31  NAW   CAQ  NAV  CAA   180.00   0.0  0
 BYH  CONST_32  CAU   CAT  NAV  CAA   180.00   0.0  0
 BYH  CONST_33  CAT   NAV  CAQ  SAB   180.00   0.0  0
 BYH  CONST_34  CAU   NAW  CAQ  SAB   180.00   0.0  0
 BYH  CONST_35  NAV   CAQ  NAW  CAL   180.00   0.0  0
 BYH  CONST_36  CAT   CAU  NAW  CAL   180.00   0.0  0
 BYH  CONST_37  HAH   CAH  CAD  CAC   180.00   0.0  0
 BYH  CONST_38  HAG   CAG  CAC  CAD   180.00   0.0  0
 BYH  CONST_39  HAJ   CAJ  CAF  CAE   180.00   0.0  0
 BYH  CONST_40  HAI   CAI  CAE  CAF   180.00   0.0  0
 BYH  CONST_41  HAD   CAD  CAC  CAG   180.00   0.0  0
 BYH  CONST_42  HNAM  NAM  CAR  CAG     0.00   0.0  0
 BYH  CONST_43  HAC   CAC  CAD  CAH   180.00   0.0  0
 BYH  CONST_44  HAF   CAF  CAE  CAI   180.00   0.0  0
 BYH  CONST_45  HAE   CAE  CAF  CAJ   180.00   0.0  0
 BYH  CONST_46  SAB   CAQ  NAV  CAA     0.00   0.0  0
 BYH  CONST_47  CAL   NAW  CAQ  SAB     0.00   0.0  0
 BYH  Var_01    CAQ   NAW  CAL  CAK    85.36  30.0  3
 BYH  Var_02    NAM   CAP  SAO  CAK  -179.33  30.0  2
 BYH  Var_03    HAA   CAA  NAV  CAQ     3.27  30.0  3
 BYH  Var_04    NAW   CAL  CAK  SAO   179.74  30.0  3
 BYH  Var_05    HAK   CAK  SAO  CAP    70.10  30.0  1

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
 BYH  plan-1  CAC   0.020
 BYH  plan-1  CAD   0.020
 BYH  plan-1  CAG   0.020
 BYH  plan-1  CAH   0.020
 BYH  plan-1  NAM   0.020
 BYH  plan-1  NAN   0.020
 BYH  plan-1  SAO   0.020
 BYH  plan-1  CAP   0.020
 BYH  plan-1  CAR   0.020
 BYH  plan-1  CAS   0.020
 BYH  plan-1  HAD   0.020
 BYH  plan-1  HAG   0.020
 BYH  plan-1  HAH   0.020
 BYH  plan-1  HNAM  0.020
 BYH  plan-1  HAC   0.020
 BYH  plan-2  CAA   0.020
 BYH  plan-2  CAE   0.020
 BYH  plan-2  CAF   0.020
 BYH  plan-2  CAI   0.020
 BYH  plan-2  CAJ   0.020
 BYH  plan-2  CAQ   0.020
 BYH  plan-2  CAT   0.020
 BYH  plan-2  CAU   0.020
 BYH  plan-2  NAV   0.020
 BYH  plan-2  NAW   0.020
 BYH  plan-2  HAE   0.020
 BYH  plan-2  HAF   0.020
 BYH  plan-2  HAI   0.020
 BYH  plan-2  HAJ   0.020
 BYH  plan-2  SAB   0.020
 BYH  plan-2  CAL   0.020

