# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 10:04:04 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 2-[(2-phenoxyethyl)sulfanyl]-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(CSc1[nH]c2ccccc2n1)Oc3ccccc3
#
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
 17W  17W  2-[(2-phenoxyethyl)sulfanyl]-1H-benzimidazole  ligand  33  19  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_17W
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
 17W  C19  C  CR16  0  -0.380  -4.7625   0.8811   0.0186
 17W  C18  C  CR16  0  -0.241  -6.1511   0.9586   0.0630
 17W  C17  C  CR16  0  -0.281  -6.9308  -0.1864   0.0490
 17W  C16  C  CR16  0  -0.241  -6.3068  -1.4288  -0.0115
 17W  C15  C  CR16  0  -0.342  -4.9271  -1.5238  -0.0560
 17W  C14  C  CR6   0   0.384  -4.1468  -0.3662  -0.0401
 17W  O13  O  O2    0  -0.475  -2.8095  -0.5524  -0.0849
 17W  C12  C  CH2   0  -0.173  -1.9640   0.5775  -0.0381
 17W  C11  C  CH2   0  -0.576  -0.5427   0.0455  -0.0710
 17W  S10  S  S2    0   0.051   0.5736   1.4758  -0.0216
 17W  C8   C  CR5   0   0.307   2.1080   0.6568  -0.0113
 17W  N9   N  NR15  0  -0.702   3.2595   1.3777  -0.0149
 17W  C2   C  CR56  0   0.330   4.2937   0.4753  -0.0018
 17W  N7   N  N     0  -0.462   2.2990  -0.6307   0.0027
 17W  C3   C  CR56  0   0.146   3.6684  -0.7822   0.0090
 17W  C4   C  CR16  0  -0.334   4.4417  -1.9409   0.0243
 17W  C5   C  CR16  0  -0.270   5.8195  -1.8003   0.0275
 17W  C6   C  CR16  0  -0.281   6.4255  -0.5365   0.0154
 17W  C1   C  CR16  0  -0.303   5.6734   0.6275   0.0008
 17W  H1   H  HCR6  0   0.281  -4.1850   1.7957   0.0300
 17W  H2   H  HCR6  0   0.259  -6.6190   1.9337   0.1095
 17W  H3   H  HCR6  0   0.253  -8.0096  -0.1162   0.0841
 17W  H4   H  HCR6  0   0.258  -6.9009  -2.3335  -0.0233
 17W  H5   H  HCR6  0   0.262  -4.4433  -2.4917  -0.1032
 17W  H6   H  HCH2  0   0.241  -2.1471   1.2392  -0.8922
 17W  H7   H  HCH2  0   0.242  -2.1347   1.1555   0.8769
 17W  H8   H  HCH2  0   0.295  -0.3477  -0.5918   0.7905
 17W  H9   H  HCH2  0   0.295  -0.3598  -0.5209  -0.9834
 17W  H10  H  HNR5  0   0.424   3.3404   2.3824  -0.0299
 17W  H12  H  HCR6  0   0.255   3.9770  -2.9185   0.0344
 17W  H13  H  HCR6  0   0.253   6.4455  -2.6828   0.0395
 17W  H14  H  HCR6  0   0.256   7.5053  -0.4676   0.0174
 17W  H15  H  HCR6  0   0.268   6.1414   1.6032  -0.0089

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
 17W  C4   C3   aromatic  1.393  0.020  1.393
 17W  C4   C5   aromatic  1.385  0.020  1.385
 17W  N7   C3   aromatic  1.378  0.020  1.378
 17W  N7   C8   aromatic  1.302  0.020  1.302
 17W  C3   C2   aromatic  1.404  0.020  1.404
 17W  C5   C6   aromatic  1.402  0.020  1.402
 17W  C11  S10  single    1.815  0.020  1.815
 17W  C11  C12  single    1.518  0.020  1.518
 17W  S10  C8   single    1.739  0.020  1.739
 17W  C8   N9   aromatic  1.359  0.020  1.359
 17W  C6   C1   aromatic  1.386  0.020  1.386
 17W  C2   N9   aromatic  1.373  0.020  1.373
 17W  C2   C1   aromatic  1.388  0.020  1.388
 17W  C12  O13  single    1.412  0.020  1.412
 17W  O13  C14  single    1.351  0.020  1.351
 17W  C14  C15  aromatic  1.396  0.020  1.396
 17W  C14  C19  aromatic  1.392  0.020  1.392
 17W  C15  C16  aromatic  1.384  0.020  1.384
 17W  C19  C18  aromatic  1.392  0.020  1.392
 17W  C16  C17  aromatic  1.392  0.020  1.392
 17W  C18  C17  aromatic  1.385  0.020  1.385
 17W  C19  H1   single    0.930  0.020  1.080
 17W  C18  H2   single    0.930  0.020  1.080
 17W  C17  H3   single    0.930  0.020  1.080
 17W  C16  H4   single    0.930  0.020  1.080
 17W  C15  H5   single    0.930  0.020  1.080
 17W  C12  H6   single    0.970  0.020  1.090
 17W  C12  H7   single    0.970  0.020  1.090
 17W  C11  H8   single    0.970  0.020  1.090
 17W  C11  H9   single    0.970  0.020  1.090
 17W  N9   H10  single    0.860  0.020  1.020
 17W  C4   H12  single    0.930  0.020  1.080
 17W  C5   H13  single    0.930  0.020  1.080
 17W  C6   H14  single    0.930  0.020  1.080
 17W  C1   H15  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
 17W  H1   C19  C14  121.45  3.000
 17W  H1   C19  C18  119.03  3.000
 17W  C14  C19  C18  119.51  3.000
 17W  H2   C18  C17  120.11  3.000
 17W  H2   C18  C19  118.87  3.000
 17W  C17  C18  C19  121.02  3.000
 17W  H3   C17  C16  120.43  3.000
 17W  H3   C17  C18  120.49  3.000
 17W  C16  C17  C18  119.08  3.000
 17W  H4   C16  C15  119.31  3.000
 17W  H4   C16  C17  120.04  3.000
 17W  C15  C16  C17  120.65  3.000
 17W  H5   C15  C14  119.45  3.000
 17W  H5   C15  C16  120.54  3.000
 17W  C14  C15  C16  120.00  3.000
 17W  O13  C14  C15  116.02  3.000
 17W  C15  C14  C19  119.74  3.000
 17W  O13  C14  C19  124.24  3.000
 17W  C12  O13  C14  118.78  3.000
 17W  H7   C12  H6   107.84  3.000
 17W  H7   C12  C11  110.42  3.000
 17W  H6   C12  C11  110.56  3.000
 17W  H7   C12  O13  110.88  3.000
 17W  H6   C12  O13  110.93  3.000
 17W  C11  C12  O13  106.23  3.000
 17W  H9   C11  H8   109.16  3.000
 17W  H9   C11  S10  109.22  3.000
 17W  H8   C11  S10  109.24  3.000
 17W  H9   C11  C12  110.95  3.000
 17W  H8   C11  C12  110.83  3.000
 17W  S10  C11  C12  107.40  3.000
 17W  C8   S10  C11   99.89  3.000
 17W  N7   C8   N9   113.61  3.000
 17W  N9   C8   S10  119.86  3.000
 17W  N7   C8   S10  126.53  3.000
 17W  H10  N9   C2   126.50  3.000
 17W  H10  N9   C8   126.65  3.000
 17W  C2   N9   C8   106.85  3.000
 17W  C1   C2   C3   122.73  3.000
 17W  C1   C2   N9   132.60  3.000
 17W  C3   C2   N9   104.67  3.000
 17W  C3   N7   C8   104.75  3.000
 17W  C4   C3   N7   130.03  3.000
 17W  N7   C3   C2   110.12  3.000
 17W  C4   C3   C2   119.85  3.000
 17W  H12  C4   C5   121.25  3.000
 17W  H12  C4   C3   120.87  3.000
 17W  C5   C4   C3   117.89  3.000
 17W  H13  C5   C6   119.04  3.000
 17W  H13  C5   C4   119.52  3.000
 17W  C6   C5   C4   121.44  3.000
 17W  H14  C6   C1   119.21  3.000
 17W  H14  C6   C5   119.27  3.000
 17W  C1   C6   C5   121.52  3.000
 17W  H15  C1   C6   121.52  3.000
 17W  H15  C1   C2   121.91  3.000
 17W  C6   C1   C2   116.57  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
 17W  CONST_01  C16  C15  C14  C19    0.00   0.0  0
 17W  CONST_02  C16  C17  C18  C19    0.00   0.0  0
 17W  CONST_03  C15  C14  C19  C18    0.00   0.0  0
 17W  CONST_04  C15  C16  C17  C18    0.00   0.0  0
 17W  CONST_05  C14  C15  C16  C17    0.00   0.0  0
 17W  CONST_06  C14  C19  C18  C17    0.00   0.0  0
 17W  CONST_07  C4   C3   N7   C8   180.00   0.0  0
 17W  CONST_08  C2   C3   N7   C8     0.00   0.0  0
 17W  CONST_09  C3   C2   N9   C8     0.00   0.0  0
 17W  CONST_10  C1   C2   N9   C8   180.00   0.0  0
 17W  CONST_11  C3   N7   C8   N9     0.00   0.0  0
 17W  CONST_12  C4   C3   C2   N9   180.00   0.0  0
 17W  CONST_13  N7   C3   C2   N9     0.00   0.0  0
 17W  CONST_14  C6   C1   C2   N9   180.00   0.0  0
 17W  CONST_15  C5   C4   C3   C2     0.00   0.0  0
 17W  CONST_16  N7   C8   N9   C2     0.00   0.0  0
 17W  CONST_17  C5   C6   C1   C2     0.00   0.0  0
 17W  CONST_18  C5   C4   C3   N7   180.00   0.0  0
 17W  CONST_19  C1   C2   C3   N7   180.00   0.0  0
 17W  CONST_20  C6   C5   C4   C3     0.00   0.0  0
 17W  CONST_21  C6   C1   C2   C3     0.00   0.0  0
 17W  CONST_22  C1   C2   C3   C4     0.00   0.0  0
 17W  CONST_23  C1   C6   C5   C4     0.00   0.0  0
 17W  CONST_24  O13  C14  C19  C18  180.00   0.0  0
 17W  CONST_25  O13  C14  C15  C16  180.00   0.0  0
 17W  CONST_26  C3   N7   C8   S10  180.00   0.0  0
 17W  CONST_27  C2   N9   C8   S10  180.00   0.0  0
 17W  CONST_28  H5   C15  C14  C19  180.00   0.0  0
 17W  CONST_29  H3   C17  C18  C19  180.00   0.0  0
 17W  CONST_30  H4   C16  C17  C18  180.00   0.0  0
 17W  CONST_31  H1   C19  C18  C17  180.00   0.0  0
 17W  CONST_32  H2   C18  C17  C16  180.00   0.0  0
 17W  CONST_33  H15  C1   C2   N9     0.00   0.0  0
 17W  CONST_34  H12  C4   C3   C2   180.00   0.0  0
 17W  CONST_35  H14  C6   C1   C2   180.00   0.0  0
 17W  CONST_36  H10  N9   C8   N7   180.00   0.0  0
 17W  CONST_37  H13  C5   C4   C3   180.00   0.0  0
 17W  Var_01    N7   C8   S10  C11   -2.04  30.0  2
 17W  Var_02    C11  C12  O13  C14  178.64  30.0  1
 17W  Var_03    H8   C11  S10  C8    57.87  30.0  1
 17W  Var_04    S10  C11  C12  O13  179.68  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
 17W  plan-1  C19  0.020
 17W  plan-1  C18  0.020
 17W  plan-1  C17  0.020
 17W  plan-1  C16  0.020
 17W  plan-1  C15  0.020
 17W  plan-1  C14  0.020
 17W  plan-1  O13  0.020
 17W  plan-1  H1   0.020
 17W  plan-1  H2   0.020
 17W  plan-1  H3   0.020
 17W  plan-1  H4   0.020
 17W  plan-1  H5   0.020
 17W  plan-2  S10  0.020
 17W  plan-2  C8   0.020
 17W  plan-2  N9   0.020
 17W  plan-2  C2   0.020
 17W  plan-2  N7   0.020
 17W  plan-2  C3   0.020
 17W  plan-2  C4   0.020
 17W  plan-2  C5   0.020
 17W  plan-2  C6   0.020
 17W  plan-2  C1   0.020
 17W  plan-2  H10  0.020
 17W  plan-2  H12  0.020
 17W  plan-2  H13  0.020
 17W  plan-2  H14  0.020
 17W  plan-2  H15  0.020

