# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:00:34 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (5,6-dimethyl-1H-benzimidazol-2-yl)methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2[nH]c(CO)nc2cc1C
#
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
 E7S  E7S  (5,6-dimethyl-1H-benzimidazol-2-yl)methanol  ligand  25  13  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E7S
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
 E7S  C10  C  CR56  0   0.133   0.0409   0.8296  -0.0438
 E7S  C01  C  CH3   0  -0.737  -3.4622  -1.6426   0.0700
 E7S  C02  C  CR6   0   0.050  -2.2297  -0.7865   0.0250
 E7S  C03  C  CR16  0  -0.360  -0.9797  -1.3868   0.0456
 E7S  C04  C  CR56  0   0.339   0.1402  -0.5657   0.0128
 E7S  N05  N  NR15  0  -0.688   1.4873  -0.8179   0.0227
 E7S  C06  C  CR5   0   0.404   2.1199   0.3799  -0.0277
 E7S  C07  C  CH2   0  -0.234   3.6068   0.4906   0.0225
 E7S  O08  O  OH1   0  -0.669   4.1628  -0.7267  -0.4036
 E7S  N09  N  N     0  -0.484   1.2972   1.3918  -0.0716
 E7S  C11  C  CR16  0  -0.393  -1.2193   1.4254  -0.0697
 E7S  C12  C  CR6   0   0.060  -2.3502   0.6252  -0.0348
 E7S  C13  C  CH3   0  -0.735  -3.7134   1.2570  -0.0640
 E7S  H1   H  HCH3  0   0.241  -4.0600  -1.4453   0.9627
 E7S  H2   H  HCH3  0   0.240  -4.1138  -1.4650  -0.7880
 E7S  H3   H  HCH3  0   0.249  -3.2061  -2.7012   0.0742
 E7S  H4   H  HCR6  0   0.256  -0.8864  -2.4654   0.0875
 E7S  H5   H  HNR5  0   0.414   1.9361  -1.7191   0.0662
 E7S  H6   H  HCH2  0   0.232   3.9103   1.3375  -0.6031
 E7S  H7   H  HCH2  0   0.243   3.9000   0.7373   1.0506
 E7S  H8   H  HOH1  0   0.469   5.0865  -0.7462  -0.1384
 E7S  H10  H  HCR6  0   0.242  -1.3148   2.5038  -0.1180
 E7S  H11  H  HCH3  0   0.238  -4.3067   0.9871   0.8121
 E7S  H12  H  HCH3  0   0.248  -3.6415   2.3436  -0.0901
 E7S  H13  H  HCH3  0   0.239  -4.2864   0.9437  -0.9395

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
 E7S  C10  C04  aromatic  1.400  0.020  1.400
 E7S  C10  N09  aromatic  1.377  0.020  1.377
 E7S  C10  C11  aromatic  1.394  0.020  1.394
 E7S  C01  C02  single    1.501  0.020  1.501
 E7S  C02  C03  aromatic  1.387  0.020  1.387
 E7S  C02  C12  aromatic  1.418  0.020  1.418
 E7S  C03  C04  aromatic  1.389  0.020  1.389
 E7S  C04  N05  aromatic  1.371  0.020  1.371
 E7S  N05  C06  aromatic  1.356  0.020  1.356
 E7S  C06  C07  single    1.492  0.020  1.492
 E7S  C06  N09  aromatic  1.305  0.020  1.305
 E7S  C07  O08  single    1.405  0.020  1.405
 E7S  C11  C12  aromatic  1.386  0.020  1.386
 E7S  C12  C13  single    1.503  0.020  1.503
 E7S  C01  H1   single    0.970  0.020  1.090
 E7S  C01  H2   single    0.970  0.020  1.090
 E7S  C01  H3   single    0.970  0.020  1.090
 E7S  C03  H4   single    0.930  0.020  1.080
 E7S  N05  H5   single    0.860  0.020  1.020
 E7S  C07  H6   single    0.970  0.020  1.090
 E7S  C07  H7   single    0.970  0.020  1.090
 E7S  O08  H8   single    0.850  0.020  0.980
 E7S  C11  H10  single    0.930  0.020  1.080
 E7S  C13  H11  single    0.970  0.020  1.090
 E7S  C13  H12  single    0.970  0.020  1.090
 E7S  C13  H13  single    0.970  0.020  1.090

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
 E7S  C11  C10  N09  130.54  3.000
 E7S  C11  C10  C04  119.39  3.000
 E7S  N09  C10  C04  110.07  3.000
 E7S  H3   C01  H2   107.55  3.000
 E7S  H3   C01  H1   107.52  3.000
 E7S  H2   C01  H1   106.63  3.000
 E7S  H3   C01  C02  111.18  3.000
 E7S  H2   C01  C02  111.93  3.000
 E7S  H1   C01  C02  111.76  3.000
 E7S  C12  C02  C03  120.54  3.000
 E7S  C12  C02  C01  119.95  3.000
 E7S  C03  C02  C01  119.51  3.000
 E7S  H4   C03  C04  121.34  3.000
 E7S  H4   C03  C02  120.60  3.000
 E7S  C04  C03  C02  118.06  3.000
 E7S  N05  C04  C03  133.11  3.000
 E7S  N05  C04  C10  104.68  3.000
 E7S  C03  C04  C10  122.21  3.000
 E7S  H5   N05  C06  125.73  3.000
 E7S  H5   N05  C04  127.06  3.000
 E7S  C06  N05  C04  107.20  3.000
 E7S  N09  C06  C07  124.89  3.000
 E7S  N09  C06  N05  113.09  3.000
 E7S  C07  C06  N05  121.97  3.000
 E7S  H7   C07  H6   106.69  3.000
 E7S  H7   C07  O08  111.93  3.000
 E7S  H6   C07  O08  112.77  3.000
 E7S  H7   C07  C06  108.33  3.000
 E7S  H6   C07  C06  108.31  3.000
 E7S  O08  C07  C06  108.66  3.000
 E7S  H8   O08  C07  108.31  3.000
 E7S  C06  N09  C10  104.95  3.000
 E7S  H10  C11  C12  120.25  3.000
 E7S  H10  C11  C10  120.38  3.000
 E7S  C12  C11  C10  119.37  3.000
 E7S  C13  C12  C11  119.80  3.000
 E7S  C13  C12  C02  119.77  3.000
 E7S  C11  C12  C02  120.43  3.000
 E7S  H13  C13  H12  107.55  3.000
 E7S  H13  C13  H11  106.69  3.000
 E7S  H12  C13  H11  107.56  3.000
 E7S  H13  C13  C12  111.77  3.000
 E7S  H12  C13  C12  111.10  3.000
 E7S  H11  C13  C12  111.92  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
 E7S  CONST_01  C02  C03  C04  C10    0.00   0.0  0
 E7S  CONST_02  C06  N05  C04  C10    0.00   0.0  0
 E7S  CONST_03  N05  C06  N09  C10    0.00   0.0  0
 E7S  CONST_04  C02  C12  C11  C10    0.00   0.0  0
 E7S  CONST_05  N05  C04  C03  C02  180.00   0.0  0
 E7S  CONST_06  C11  C12  C02  C03    0.00   0.0  0
 E7S  CONST_07  N09  C10  C04  C03  180.00   0.0  0
 E7S  CONST_08  C11  C10  C04  C03    0.00   0.0  0
 E7S  CONST_09  C06  N05  C04  C03  180.00   0.0  0
 E7S  CONST_10  C06  N09  C10  C04    0.00   0.0  0
 E7S  CONST_11  C12  C11  C10  C04    0.00   0.0  0
 E7S  CONST_12  C12  C02  C03  C04    0.00   0.0  0
 E7S  CONST_13  N09  C06  N05  C04    0.00   0.0  0
 E7S  CONST_14  N09  C10  C04  N05    0.00   0.0  0
 E7S  CONST_15  C11  C10  C04  N05  180.00   0.0  0
 E7S  CONST_16  C11  C10  N09  C06  180.00   0.0  0
 E7S  CONST_17  C12  C11  C10  N09  180.00   0.0  0
 E7S  CONST_18  C07  C06  N09  C10  180.00   0.0  0
 E7S  CONST_19  C13  C12  C11  C10  180.00   0.0  0
 E7S  CONST_20  C04  C03  C02  C01  180.00   0.0  0
 E7S  CONST_21  C11  C12  C02  C01  180.00   0.0  0
 E7S  CONST_22  C13  C12  C02  C03  180.00   0.0  0
 E7S  CONST_23  C07  C06  N05  C04  180.00   0.0  0
 E7S  CONST_24  H4   C03  C04  C10  180.00   0.0  0
 E7S  CONST_25  H5   N05  C04  C10  180.00   0.0  0
 E7S  CONST_26  H10  C11  C12  C02  180.00   0.0  0
 E7S  Var_01    O08  C07  C06  N05   23.10  30.0  2
 E7S  Var_02    H11  C13  C12  C02   58.64  30.0  2
 E7S  Var_03    H1   C01  C02  C03  117.78  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
 E7S  plan-1  C10  0.020
 E7S  plan-1  C01  0.020
 E7S  plan-1  C02  0.020
 E7S  plan-1  C03  0.020
 E7S  plan-1  C04  0.020
 E7S  plan-1  N05  0.020
 E7S  plan-1  C06  0.020
 E7S  plan-1  C07  0.020
 E7S  plan-1  N09  0.020
 E7S  plan-1  C11  0.020
 E7S  plan-1  C12  0.020
 E7S  plan-1  C13  0.020
 E7S  plan-1  H4   0.020
 E7S  plan-1  H5   0.020
 E7S  plan-1  H10  0.020

