# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 15:45:06 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 1-(3,4-dichlorobenzyl)-5,6-dimethyl-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2ncn(Cc3ccc(Cl)c(Cl)c3)c2cc1C
#
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
 09T  09T  1-(3,4-dichlorobenzyl)-5,6-dimethyl-1H-benzimidazole  ligand  34  20  .  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_09T
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
 09T  C4   C   CR16  0  -0.277   1.2969   1.3991  -0.3011
 09T  C5   C   CR6   0   0.104   0.9624   1.1463   1.0251
 09T  C6   C   CR16  0  -0.270   1.7121   0.2309   1.7478
 09T  C7   C   CR6   0   0.023   2.7873  -0.4202   1.1600
 09T  N12  N   N     0  -0.471  -3.0137   2.7483  -0.3790
 09T  C13  C   CR56  0   0.120  -3.1283   1.3761  -0.3447
 09T  C15  C   CR6   0   0.057  -3.9614  -0.8370  -0.7473
 09T  C17  C   CR6   0   0.053  -2.9115  -1.3751   0.0417
 09T  C20  C   CR56  0   0.353  -2.0995   0.8273   0.4279
 09T  CL8  CL  CL    0  -0.094   3.6956  -1.5511   2.0876
 09T  C2   C   CR6   0  -0.017   3.1159  -0.1629  -0.1645
 09T  CL1  CL  CL    0  -0.095   4.4417  -0.9649  -0.9149
 09T  C3   C   CR16  0  -0.201   2.3647   0.7493  -0.8931
 09T  C9   C   CH2   0  -0.380  -0.1858   1.8629   1.6900
 09T  N10  N   NR5   0  -0.512  -1.3639   1.9037   0.8595
 09T  C11  C   CR15  0   0.097  -1.9620   3.0090   0.3413
 09T  C19  C   CR16  0  -0.344  -1.9737  -0.5419   0.6313
 09T  C16  C   CH3   0  -0.737  -4.9609  -1.7585  -1.3860
 09T  C14  C   CR16  0  -0.374  -4.0667   0.5310  -0.9364
 09T  H1   H   HCR6  0   0.270   0.7232   2.1044  -0.8887
 09T  H2   H   HCR6  0   0.289   1.4597   0.0133   2.7779
 09T  H3   H   HCR6  0   0.292   2.6195   0.9487  -1.9249
 09T  H4   H   HCH2  0   0.287  -0.4267   1.3861   2.6420
 09T  H5   H   HCH2  0   0.300   0.0956   2.8930   1.9144
 09T  H6   H   HCR5  0   0.291  -1.5666   3.9956   0.5376
 09T  H7   H   HCR6  0   0.258  -1.1693  -0.9597   1.2243
 09T  H8   H   HCH3  0   0.242  -2.7112  -3.3896  -0.7086
 09T  H9   H   HCH3  0   0.250  -1.9492  -3.1175   0.8553
 09T  H10  H   HCH3  0   0.242  -3.6994  -3.2626   0.7322
 09T  H11  H   HCH3  0   0.241  -5.5063  -2.3456  -0.6442
 09T  H12  H   HCH3  0   0.250  -5.6948  -1.2002  -1.9654
 09T  H13  H   HCH3  0   0.241  -4.4805  -2.4725  -2.0588
 09T  H14  H   HCR6  0   0.245  -4.8704   0.9415  -1.5364
 09T  C18  C   CH3   0  -0.736  -2.8109  -2.8597   0.2410

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
 09T  N12  C13  aromatic  1.377  0.020  1.377
 09T  N12  C11  aromatic  1.301  0.020  1.301
 09T  C14  C13  aromatic  1.395  0.020  1.395
 09T  C14  C15  aromatic  1.385  0.020  1.385
 09T  C13  C20  aromatic  1.399  0.020  1.399
 09T  C16  C15  single    1.502  0.020  1.502
 09T  C11  N10  aromatic  1.359  0.020  1.359
 09T  C15  C17  aromatic  1.419  0.020  1.419
 09T  C20  N10  aromatic  1.373  0.020  1.373
 09T  C20  C19  aromatic  1.390  0.020  1.390
 09T  N10  C9   single    1.442  0.020  1.442
 09T  C17  C19  aromatic  1.386  0.020  1.386
 09T  C17  C18  single    1.501  0.020  1.501
 09T  C9   C5   single    1.508  0.020  1.508
 09T  C4   C5   aromatic  1.391  0.020  1.391
 09T  C4   C3   aromatic  1.383  0.020  1.383
 09T  C5   C6   aromatic  1.387  0.020  1.387
 09T  C3   C2   aromatic  1.388  0.020  1.388
 09T  C6   C7   aromatic  1.388  0.020  1.388
 09T  C2   C7   aromatic  1.389  0.020  1.389
 09T  C2   CL1  single    1.722  0.020  1.722
 09T  C7   CL8  single    1.722  0.020  1.722
 09T  C4   H1   single    0.930  0.020  1.080
 09T  C6   H2   single    0.930  0.020  1.080
 09T  C3   H3   single    0.930  0.020  1.080
 09T  C9   H4   single    0.970  0.020  1.090
 09T  C9   H5   single    0.970  0.020  1.090
 09T  C11  H6   single    0.930  0.020  1.080
 09T  C19  H7   single    0.930  0.020  1.080
 09T  C18  H8   single    0.970  0.020  1.090
 09T  C18  H9   single    0.970  0.020  1.090
 09T  C18  H10  single    0.970  0.020  1.090
 09T  C16  H11  single    0.970  0.020  1.090
 09T  C16  H12  single    0.970  0.020  1.090
 09T  C16  H13  single    0.970  0.020  1.090
 09T  C14  H14  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
 09T  H1   C4   C3   118.88  3.000
 09T  H1   C4   C5   120.56  3.000
 09T  C3   C4   C5   120.56  3.000
 09T  C9   C5   C6   119.71  3.000
 09T  C6   C5   C4   119.14  3.000
 09T  C9   C5   C4   121.14  3.000
 09T  H2   C6   C7   119.30  3.000
 09T  H2   C6   C5   120.17  3.000
 09T  C7   C6   C5   120.53  3.000
 09T  C2   C7   CL8  120.71  3.000
 09T  CL8  C7   C6   119.25  3.000
 09T  C2   C7   C6   120.03  3.000
 09T  C11  N12  C13  104.66  3.000
 09T  C14  C13  C20  119.44  3.000
 09T  C20  C13  N12  110.09  3.000
 09T  C14  C13  N12  130.48  3.000
 09T  C14  C15  C16  119.82  3.000
 09T  C16  C15  C17  119.74  3.000
 09T  C14  C15  C17  120.44  3.000
 09T  C18  C17  C19  119.52  3.000
 09T  C18  C17  C15  119.89  3.000
 09T  C19  C17  C15  120.60  3.000
 09T  C19  C20  N10  132.66  3.000
 09T  C19  C20  C13  122.27  3.000
 09T  N10  C20  C13  105.07  3.000
 09T  C3   C2   CL1  119.60  3.000
 09T  CL1  C2   C7   120.77  3.000
 09T  C3   C2   C7   119.62  3.000
 09T  H3   C3   C2   119.64  3.000
 09T  H3   C3   C4   120.24  3.000
 09T  C2   C3   C4   120.12  3.000
 09T  H5   C9   H4   106.84  3.000
 09T  H5   C9   N10  107.60  3.000
 09T  H4   C9   N10  109.54  3.000
 09T  H5   C9   C5   110.06  3.000
 09T  H4   C9   C5   110.18  3.000
 09T  N10  C9   C5   112.43  3.000
 09T  C11  N10  C9   127.02  3.000
 09T  C9   N10  C20  126.62  3.000
 09T  C11  N10  C20  106.37  3.000
 09T  H6   C11  N10  120.79  3.000
 09T  H6   C11  N12  125.39  3.000
 09T  N10  C11  N12  113.82  3.000
 09T  H7   C19  C20  121.82  3.000
 09T  H7   C19  C17  120.22  3.000
 09T  C20  C19  C17  117.95  3.000
 09T  H13  C16  H12  107.68  3.000
 09T  H13  C16  H11  106.66  3.000
 09T  H12  C16  H11  107.48  3.000
 09T  H13  C16  C15  111.73  3.000
 09T  H12  C16  C15  111.11  3.000
 09T  H11  C16  C15  111.93  3.000
 09T  H14  C14  C15  120.40  3.000
 09T  H14  C14  C13  120.29  3.000
 09T  C15  C14  C13  119.31  3.000
 09T  H10  C18  H9   107.62  3.000
 09T  H10  C18  H8   106.64  3.000
 09T  H9   C18  H8   107.66  3.000
 09T  H10  C18  C17  111.71  3.000
 09T  H9   C18  C17  111.22  3.000
 09T  H8   C18  C17  111.75  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
 09T  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 09T  CONST_02  C7   C2   C3   C4      0.00   0.0  0
 09T  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 09T  CONST_04  C2   C7   C6   C5      0.00   0.0  0
 09T  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 09T  CONST_06  C3   C2   C7   C6      0.00   0.0  0
 09T  CONST_07  C15  C14  C13  N12   180.00   0.0  0
 09T  CONST_08  N10  C20  C13  N12     0.00   0.0  0
 09T  CONST_09  C19  C20  C13  N12   180.00   0.0  0
 09T  CONST_10  C20  N10  C11  N12     0.00   0.0  0
 09T  CONST_11  N10  C11  N12  C13     0.00   0.0  0
 09T  CONST_12  C17  C15  C14  C13     0.00   0.0  0
 09T  CONST_13  C11  N10  C20  C13     0.00   0.0  0
 09T  CONST_14  C17  C19  C20  C13     0.00   0.0  0
 09T  CONST_15  C20  C13  C14  C15     0.00   0.0  0
 09T  CONST_16  C20  C19  C17  C15     0.00   0.0  0
 09T  CONST_17  N10  C20  C19  C17   180.00   0.0  0
 09T  CONST_18  C11  N12  C13  C20     0.00   0.0  0
 09T  CONST_19  C14  C13  C20  N10   180.00   0.0  0
 09T  CONST_20  C14  C13  N12  C11   180.00   0.0  0
 09T  CONST_21  C19  C20  N10  C11   180.00   0.0  0
 09T  CONST_22  C14  C13  C20  C19     0.00   0.0  0
 09T  CONST_23  C14  C15  C17  C19     0.00   0.0  0
 09T  CONST_24  CL1  C2   C3   C4    180.00   0.0  0
 09T  CONST_25  CL8  C7   C6   C5    180.00   0.0  0
 09T  CONST_26  CL1  C2   C7   C6    180.00   0.0  0
 09T  CONST_27  C9   C5   C6   C7    180.00   0.0  0
 09T  CONST_28  C9   N10  C11  N12   180.00   0.0  0
 09T  CONST_29  C16  C15  C14  C13   180.00   0.0  0
 09T  CONST_30  C9   N10  C20  C13   180.00   0.0  0
 09T  CONST_31  C18  C17  C19  C20   180.00   0.0  0
 09T  CONST_32  C3   C2   C7   CL8   180.00   0.0  0
 09T  CONST_33  C9   C5   C4   C3    180.00   0.0  0
 09T  CONST_34  C19  C20  N10  C9      0.00   0.0  0
 09T  CONST_35  C16  C15  C17  C19   180.00   0.0  0
 09T  CONST_36  C14  C15  C17  C18   180.00   0.0  0
 09T  CONST_37  H2   C6   C5   C4    180.00   0.0  0
 09T  CONST_38  H3   C3   C4   C5    180.00   0.0  0
 09T  CONST_39  H1   C4   C5   C6    180.00   0.0  0
 09T  CONST_40  H14  C14  C13  N12     0.00   0.0  0
 09T  CONST_41  H6   C11  N12  C13   180.00   0.0  0
 09T  CONST_42  H7   C19  C20  C13   180.00   0.0  0
 09T  Var_01    N10  C9   C5   C4     45.44  30.0  3
 09T  Var_02    C11  N10  C9   C5   -116.00  30.0  2
 09T  Var_03    H8   C18  C17  C15    58.85  30.0  2
 09T  Var_04    H11  C16  C15  C17    60.45  30.0  2

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
 09T  plan-1  C4   0.020
 09T  plan-1  C5   0.020
 09T  plan-1  C6   0.020
 09T  plan-1  C7   0.020
 09T  plan-1  CL8  0.020
 09T  plan-1  C2   0.020
 09T  plan-1  CL1  0.020
 09T  plan-1  C3   0.020
 09T  plan-1  C9   0.020
 09T  plan-1  H1   0.020
 09T  plan-1  H2   0.020
 09T  plan-1  H3   0.020
 09T  plan-2  N12  0.020
 09T  plan-2  C13  0.020
 09T  plan-2  C15  0.020
 09T  plan-2  C17  0.020
 09T  plan-2  C20  0.020
 09T  plan-2  C9   0.020
 09T  plan-2  N10  0.020
 09T  plan-2  C11  0.020
 09T  plan-2  C19  0.020
 09T  plan-2  C16  0.020
 09T  plan-2  C14  0.020
 09T  plan-2  H6   0.020
 09T  plan-2  H7   0.020
 09T  plan-2  H14  0.020
 09T  plan-2  C18  0.020

