# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 10:20:42 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 1-[2-(4-methylphenoxy)ethyl]-2-[(2-phenoxyethyl)sulfanyl]-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(OCCn2c(SCCOc3ccccc3)nc4ccccc24)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
 YLO  YLO  1-[2-(4-methylphenoxy)ethyl]-2-[(2-phenoxyethyl)sulfanyl]-1H-benzimidazole  ligand  53  29  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YLO
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
 YLO  C01   C  CH3   0  -0.721   6.8959   4.6073  -1.5454
 YLO  C02   C  CR6   0   0.075   5.9603   3.6441  -0.8731
 YLO  C03   C  CR16  0  -0.282   5.8774   3.5644   0.5176
 YLO  C04   C  CR16  0  -0.331   5.0397   2.6582   1.1434
 YLO  C05   C  CR6   0   0.366   4.2501   1.7951   0.3844
 YLO  C06   C  CR16  0  -0.364   4.3132   1.8599  -1.0031
 YLO  C07   C  CR16  0  -0.285   5.1621   2.7789  -1.6110
 YLO  O08   O  O2    0  -0.476   3.4583   0.9402   1.0730
 YLO  C09   C  CH2   0  -0.165   2.6638   0.0295   0.3495
 YLO  C10   C  CH2   0  -0.377   1.9110  -0.8085   1.3731
 YLO  N11   N  NR5   0  -0.552   1.0941  -1.7989   0.7134
 YLO  C12   C  CR56  0   0.340   1.5139  -3.0349   0.2741
 YLO  C13   C  CR16  0  -0.307   2.7268  -3.6998   0.3881
 YLO  C14   C  CR16  0  -0.277   2.7966  -4.9632  -0.1780
 YLO  C15   C  CR16  0  -0.271   1.6962  -5.5342  -0.8308
 YLO  C16   C  CR16  0  -0.331   0.4910  -4.8604  -0.9402
 YLO  C17   C  CR56  0   0.143   0.4031  -3.5891  -0.3784
 YLO  N18   N  N     0  -0.466  -0.6531  -2.7064  -0.3441
 YLO  C19   C  CR5   0   0.320  -0.2001  -1.6710   0.2989
 YLO  S20   S  S2    0   0.041  -1.0824  -0.2124   0.6516
 YLO  C21   C  CH2   0  -0.571  -2.6689  -0.6135  -0.1346
 YLO  C22   C  CH2   0  -0.173  -3.6520   0.4748   0.2565
 YLO  O23   O  O2    0  -0.475  -4.8583   0.1795  -0.4152
 YLO  C24   C  CR6   0   0.383  -5.9229   0.9880  -0.2190
 YLO  C25   C  CR16  0  -0.342  -7.0874   0.6464  -0.9090
 YLO  C26   C  CR16  0  -0.241  -8.2272   1.4186  -0.7687
 YLO  C27   C  CR16  0  -0.280  -8.2275   2.5382   0.0576
 YLO  C28   C  CR16  0  -0.241  -7.0686   2.8719   0.7391
 YLO  C29   C  CR16  0  -0.379  -5.9135   2.1068   0.6095
 YLO  H011  H  HCH3  0   0.245   7.8777   4.1573  -1.7073
 YLO  H012  H  HCH3  0   0.241   6.5185   4.9161  -2.5200
 YLO  H013  H  HCH3  0   0.241   7.0486   5.5042  -0.9456
 YLO  H03   H  HCR6  0   0.249   6.4794   4.2264   1.1292
 YLO  H07   H  HCR6  0   0.250   5.1937   2.8137  -2.6938
 YLO  H04   H  HCR6  0   0.260   4.9902   2.6159   2.2247
 YLO  H06   H  HCR6  0   0.277   3.7144   1.2137  -1.6305
 YLO  H091  H  HCH2  0   0.232   1.9524   0.5514  -0.3010
 YLO  H092  H  HCH2  0   0.235   3.2810  -0.6200  -0.2822
 YLO  H101  H  HCH2  0   0.291   2.6078  -1.3212   2.0371
 YLO  H102  H  HCH2  0   0.288   1.2800  -0.1779   2.0013
 YLO  H13   H  HCR6  0   0.269   3.5812  -3.2612   0.8876
 YLO  H14   H  HCR6  0   0.257   3.7227  -5.5194  -0.1175
 YLO  H15   H  HCR6  0   0.254   1.7951  -6.5225  -1.2604
 YLO  H16   H  HCR6  0   0.257  -0.3564  -5.3026  -1.4477
 YLO  H211  H  HCH2  0   0.297  -2.5322  -0.6516  -1.2145
 YLO  H212  H  HCH2  0   0.298  -3.0048  -1.5868   0.2197
 YLO  H221  H  HCH2  0   0.243  -3.7981   0.4778   1.3419
 YLO  H222  H  HCH2  0   0.241  -3.2768   1.4621  -0.0364
 YLO  H25   H  HCR6  0   0.263  -7.0880  -0.2248  -1.5523
 YLO  H29   H  HCR6  0   0.280  -5.0288   2.3993   1.1592
 YLO  H26   H  HCR6  0   0.258  -9.1226   1.1434  -1.3113
 YLO  H27   H  HCR6  0   0.253  -9.1203   3.1393   0.1661
 YLO  H28   H  HCR6  0   0.260  -7.0506   3.7397   1.3859

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
 YLO  C01  C02   single    1.502  0.020  1.502
 YLO  C02  C03   aromatic  1.396  0.020  1.396
 YLO  C02  C07   aromatic  1.389  0.020  1.389
 YLO  C03  C04   aromatic  1.384  0.020  1.384
 YLO  C04  C05   aromatic  1.394  0.020  1.394
 YLO  C05  C06   aromatic  1.391  0.020  1.391
 YLO  C05  O08   single    1.353  0.020  1.353
 YLO  C06  C07   aromatic  1.391  0.020  1.391
 YLO  O08  C09   single    1.409  0.020  1.409
 YLO  C09  C10   single    1.522  0.020  1.522
 YLO  C10  N11   single    1.443  0.020  1.443
 YLO  N11  C12   aromatic  1.377  0.020  1.377
 YLO  N11  C19   aromatic  1.365  0.020  1.365
 YLO  C12  C13   aromatic  1.388  0.020  1.388
 YLO  C12  C17   aromatic  1.402  0.020  1.402
 YLO  C13  C14   aromatic  1.386  0.020  1.386
 YLO  C14  C15   aromatic  1.401  0.020  1.401
 YLO  C15  C16   aromatic  1.385  0.020  1.385
 YLO  C16  C17   aromatic  1.393  0.020  1.393
 YLO  C17  N18   aromatic  1.377  0.020  1.377
 YLO  N18  C19   aromatic  1.300  0.020  1.300
 YLO  C19  S20   single    1.741  0.020  1.741
 YLO  S20  C21   single    1.816  0.020  1.816
 YLO  C21  C22   single    1.518  0.020  1.518
 YLO  C22  O23   single    1.412  0.020  1.412
 YLO  O23  C24   single    1.351  0.020  1.351
 YLO  C24  C25   aromatic  1.396  0.020  1.396
 YLO  C24  C29   aromatic  1.392  0.020  1.392
 YLO  C25  C26   aromatic  1.384  0.020  1.384
 YLO  C26  C27   aromatic  1.391  0.020  1.391
 YLO  C27  C28   aromatic  1.385  0.020  1.385
 YLO  C28  C29   aromatic  1.392  0.020  1.392
 YLO  C01  H011  single    0.970  0.020  1.090
 YLO  C01  H012  single    0.970  0.020  1.090
 YLO  C01  H013  single    0.970  0.020  1.090
 YLO  C03  H03   single    0.930  0.020  1.080
 YLO  C07  H07   single    0.930  0.020  1.080
 YLO  C04  H04   single    0.930  0.020  1.080
 YLO  C06  H06   single    0.930  0.020  1.080
 YLO  C09  H091  single    0.970  0.020  1.090
 YLO  C09  H092  single    0.970  0.020  1.090
 YLO  C10  H101  single    0.970  0.020  1.090
 YLO  C10  H102  single    0.970  0.020  1.090
 YLO  C13  H13   single    0.930  0.020  1.080
 YLO  C14  H14   single    0.930  0.020  1.080
 YLO  C15  H15   single    0.930  0.020  1.080
 YLO  C16  H16   single    0.930  0.020  1.080
 YLO  C21  H211  single    0.970  0.020  1.090
 YLO  C21  H212  single    0.970  0.020  1.090
 YLO  C22  H221  single    0.970  0.020  1.090
 YLO  C22  H222  single    0.970  0.020  1.090
 YLO  C25  H25   single    0.930  0.020  1.080
 YLO  C29  H29   single    0.930  0.020  1.080
 YLO  C26  H26   single    0.930  0.020  1.080
 YLO  C27  H27   single    0.930  0.020  1.080
 YLO  C28  H28   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
 YLO  H013  C01  H012  107.91  3.000
 YLO  H013  C01  H011  107.14  3.000
 YLO  H012  C01  H011  107.19  3.000
 YLO  H013  C01  C02   111.64  3.000
 YLO  H012  C01  C02   111.49  3.000
 YLO  H011  C01  C02   111.24  3.000
 YLO  C07   C02  C03   117.36  3.000
 YLO  C07   C02  C01   121.31  3.000
 YLO  C03   C02  C01   121.32  3.000
 YLO  H03   C03  C04   118.76  3.000
 YLO  H03   C03  C02   119.63  3.000
 YLO  C04   C03  C02   121.60  3.000
 YLO  H04   C04  C05   119.55  3.000
 YLO  H04   C04  C03   120.31  3.000
 YLO  C05   C04  C03   120.14  3.000
 YLO  O08   C05  C06   124.31  3.000
 YLO  O08   C05  C04   116.45  3.000
 YLO  C06   C05  C04   119.24  3.000
 YLO  H06   C06  C07   118.63  3.000
 YLO  H06   C06  C05   121.72  3.000
 YLO  C07   C06  C05   119.65  3.000
 YLO  H07   C07  C06   118.40  3.000
 YLO  H07   C07  C02   119.60  3.000
 YLO  C06   C07  C02   122.01  3.000
 YLO  C09   O08  C05   118.49  3.000
 YLO  H092  C09  H091  107.79  3.000
 YLO  H092  C09  C10   109.87  3.000
 YLO  H091  C09  C10   109.89  3.000
 YLO  H092  C09  O08   111.19  3.000
 YLO  H091  C09  O08   111.29  3.000
 YLO  C10   C09  O08   106.83  3.000
 YLO  H102  C10  H101  106.90  3.000
 YLO  H102  C10  N11   109.42  3.000
 YLO  H101  C10  N11   108.50  3.000
 YLO  H102  C10  C09   110.80  3.000
 YLO  H101  C10  C09   110.63  3.000
 YLO  N11   C10  C09   110.51  3.000
 YLO  C19   N11  C12   106.04  3.000
 YLO  C19   N11  C10   127.66  3.000
 YLO  C12   N11  C10   126.09  3.000
 YLO  C17   C12  C13   122.76  3.000
 YLO  C17   C12  N11   105.17  3.000
 YLO  C13   C12  N11   132.07  3.000
 YLO  H13   C13  C14   121.20  3.000
 YLO  H13   C13  C12   122.25  3.000
 YLO  C14   C13  C12   116.55  3.000
 YLO  H14   C14  C15   119.26  3.000
 YLO  H14   C14  C13   119.26  3.000
 YLO  C15   C14  C13   121.48  3.000
 YLO  H15   C15  C16   119.50  3.000
 YLO  H15   C15  C14   119.04  3.000
 YLO  C16   C15  C14   121.46  3.000
 YLO  H16   C16  C17   120.85  3.000
 YLO  H16   C16  C15   121.30  3.000
 YLO  C17   C16  C15   117.85  3.000
 YLO  N18   C17  C16   130.07  3.000
 YLO  N18   C17  C12   110.04  3.000
 YLO  C16   C17  C12   119.90  3.000
 YLO  C19   N18  C17   104.81  3.000
 YLO  S20   C19  N18   126.21  3.000
 YLO  S20   C19  N11   119.84  3.000
 YLO  N18   C19  N11   113.94  3.000
 YLO  C21   S20  C19    99.79  3.000
 YLO  H212  C21  H211  109.28  3.000
 YLO  H212  C21  C22   110.93  3.000
 YLO  H211  C21  C22   111.22  3.000
 YLO  H212  C21  S20   109.03  3.000
 YLO  H211  C21  S20   109.11  3.000
 YLO  C22   C21  S20   107.22  3.000
 YLO  H222  C22  H221  107.94  3.000
 YLO  H222  C22  O23   110.72  3.000
 YLO  H221  C22  O23   110.98  3.000
 YLO  H222  C22  C21   110.81  3.000
 YLO  H221  C22  C21   110.10  3.000
 YLO  O23   C22  C21   106.31  3.000
 YLO  C24   O23  C22   118.62  3.000
 YLO  C29   C24  C25   119.76  3.000
 YLO  C29   C24  O23   124.19  3.000
 YLO  C25   C24  O23   116.05  3.000
 YLO  H25   C25  C26   120.58  3.000
 YLO  H25   C25  C24   119.40  3.000
 YLO  C26   C25  C24   120.03  3.000
 YLO  H26   C26  C27   120.13  3.000
 YLO  H26   C26  C25   119.25  3.000
 YLO  C27   C26  C25   120.62  3.000
 YLO  H27   C27  C28   120.48  3.000
 YLO  H27   C27  C26   120.45  3.000
 YLO  C28   C27  C26   119.06  3.000
 YLO  H28   C28  C29   118.86  3.000
 YLO  H28   C28  C27   120.07  3.000
 YLO  C29   C28  C27   121.07  3.000
 YLO  H29   C29  C28   118.86  3.000
 YLO  H29   C29  C24   121.68  3.000
 YLO  C28   C29  C24   119.45  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
 YLO  CONST_01  C05   C04  C03  C02     0.00   0.0  0
 YLO  CONST_02  C05   C06  C07  C02     0.00   0.0  0
 YLO  CONST_03  C06   C07  C02  C03     0.00   0.0  0
 YLO  CONST_04  C06   C05  C04  C03     0.00   0.0  0
 YLO  CONST_05  C07   C02  C03  C04     0.00   0.0  0
 YLO  CONST_06  C07   C06  C05  C04     0.00   0.0  0
 YLO  CONST_07  C14   C13  C12  N11   180.00   0.0  0
 YLO  CONST_08  C16   C17  C12  N11   180.00   0.0  0
 YLO  CONST_09  N18   C17  C12  N11     0.00   0.0  0
 YLO  CONST_10  C17   N18  C19  N11     0.00   0.0  0
 YLO  CONST_11  N18   C19  N11  C12     0.00   0.0  0
 YLO  CONST_12  C15   C14  C13  C12     0.00   0.0  0
 YLO  CONST_13  C15   C16  C17  C12     0.00   0.0  0
 YLO  CONST_14  C19   N18  C17  C12     0.00   0.0  0
 YLO  CONST_15  C19   N11  C12  C13   180.00   0.0  0
 YLO  CONST_16  C16   C17  C12  C13     0.00   0.0  0
 YLO  CONST_17  N18   C17  C12  C13   180.00   0.0  0
 YLO  CONST_18  C16   C15  C14  C13     0.00   0.0  0
 YLO  CONST_19  C17   C12  C13  C14     0.00   0.0  0
 YLO  CONST_20  C17   C16  C15  C14     0.00   0.0  0
 YLO  CONST_21  N18   C17  C16  C15   180.00   0.0  0
 YLO  CONST_22  C19   N18  C17  C16   180.00   0.0  0
 YLO  CONST_23  C19   N11  C12  C17     0.00   0.0  0
 YLO  CONST_24  C27   C26  C25  C24     0.00   0.0  0
 YLO  CONST_25  C27   C28  C29  C24     0.00   0.0  0
 YLO  CONST_26  C28   C29  C24  C25     0.00   0.0  0
 YLO  CONST_27  C28   C27  C26  C25     0.00   0.0  0
 YLO  CONST_28  C29   C24  C25  C26     0.00   0.0  0
 YLO  CONST_29  C29   C28  C27  C26     0.00   0.0  0
 YLO  CONST_30  C04   C03  C02  C01   180.00   0.0  0
 YLO  CONST_31  C06   C07  C02  C01   180.00   0.0  0
 YLO  CONST_32  O08   C05  C04  C03   180.00   0.0  0
 YLO  CONST_33  O08   C05  C06  C07   180.00   0.0  0
 YLO  CONST_34  C13   C12  N11  C10     0.00   0.0  0
 YLO  CONST_35  C17   C12  N11  C10   180.00   0.0  0
 YLO  CONST_36  N18   C19  N11  C10   180.00   0.0  0
 YLO  CONST_37  S20   C19  N11  C12   180.00   0.0  0
 YLO  CONST_38  S20   C19  N18  C17   180.00   0.0  0
 YLO  CONST_39  C26   C25  C24  O23   180.00   0.0  0
 YLO  CONST_40  C28   C29  C24  O23   180.00   0.0  0
 YLO  CONST_41  H04   C04  C03  C02   180.00   0.0  0
 YLO  CONST_42  H06   C06  C07  C02   180.00   0.0  0
 YLO  CONST_43  H07   C07  C02  C03   180.00   0.0  0
 YLO  CONST_44  H03   C03  C04  C05   180.00   0.0  0
 YLO  CONST_45  H13   C13  C12  N11     0.00   0.0  0
 YLO  CONST_46  H14   C14  C13  C12   180.00   0.0  0
 YLO  CONST_47  H16   C16  C17  C12   180.00   0.0  0
 YLO  CONST_48  H15   C15  C14  C13   180.00   0.0  0
 YLO  CONST_49  H26   C26  C25  C24   180.00   0.0  0
 YLO  CONST_50  H28   C28  C29  C24   180.00   0.0  0
 YLO  CONST_51  H29   C29  C24  C25   180.00   0.0  0
 YLO  CONST_52  H27   C27  C26  C25   180.00   0.0  0
 YLO  CONST_53  H25   C25  C26  C27   180.00   0.0  0
 YLO  Var_01    C12   N11  C10  C09    84.12  30.0  2
 YLO  Var_02    C25   C24  O23  C22  -179.99  30.0  2
 YLO  Var_03    H011  C01  C02  C03    89.23  30.0  2
 YLO  Var_04    C10   C09  O08  C05   178.98  30.0  3
 YLO  Var_05    N11   C10  C09  O08  -178.45  30.0  3
 YLO  Var_06    C22   C21  S20  C19   171.49  30.0  3
 YLO  Var_07    H221  C22  O23  C24    59.00  30.0  1
 YLO  Var_08    O23   C22  C21  S20   177.27  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
 YLO  plan-1  C01  0.020
 YLO  plan-1  C02  0.020
 YLO  plan-1  C03  0.020
 YLO  plan-1  C04  0.020
 YLO  plan-1  C05  0.020
 YLO  plan-1  C06  0.020
 YLO  plan-1  C07  0.020
 YLO  plan-1  O08  0.020
 YLO  plan-1  H03  0.020
 YLO  plan-1  H07  0.020
 YLO  plan-1  H04  0.020
 YLO  plan-1  H06  0.020
 YLO  plan-2  O23  0.020
 YLO  plan-2  C24  0.020
 YLO  plan-2  C25  0.020
 YLO  plan-2  C26  0.020
 YLO  plan-2  C27  0.020
 YLO  plan-2  C28  0.020
 YLO  plan-2  C29  0.020
 YLO  plan-2  H25  0.020
 YLO  plan-2  H29  0.020
 YLO  plan-2  H26  0.020
 YLO  plan-2  H27  0.020
 YLO  plan-2  H28  0.020
 YLO  plan-3  C10  0.020
 YLO  plan-3  N11  0.020
 YLO  plan-3  C12  0.020
 YLO  plan-3  C13  0.020
 YLO  plan-3  C14  0.020
 YLO  plan-3  C15  0.020
 YLO  plan-3  C16  0.020
 YLO  plan-3  C17  0.020
 YLO  plan-3  N18  0.020
 YLO  plan-3  C19  0.020
 YLO  plan-3  S20  0.020
 YLO  plan-3  H13  0.020
 YLO  plan-3  H14  0.020
 YLO  plan-3  H15  0.020
 YLO  plan-3  H16  0.020

