# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:01:07 2021
#   Inital geometry file: a 66 line input string
#   Ligand name: 2-(1H-benzimidazol-1-yl)-N-methylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)Cn1cnc2ccccc12
#
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
 WRM  WRM  2-(1H-benzimidazol-1-yl)-N-methylacetamide  ligand  25  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WRM
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
 WRM  N1   N  NR5   0  -0.491  -6.9858  14.3244   1.4048
 WRM  C4   C  CR16  0  -0.306  -4.5689  14.8691   1.8951
 WRM  C5   C  CR16  0  -0.274  -3.4255  15.3094   1.2508
 WRM  C6   C  CR16  0  -0.273  -3.4235  15.6042  -0.1212
 WRM  C7   C  CR16  0  -0.322  -4.5661  15.4714  -0.8897
 WRM  C8   C  CR56  0   0.124  -5.7298  15.0329  -0.2588
 WRM  O    O  O     0  -0.480  -7.9991  16.3557   2.9458
 WRM  C1   C  C     0   0.538  -7.7539  15.2992   3.5039
 WRM  N    N  NH1   0  -0.622  -7.7186  15.1448   4.8290
 WRM  C    C  CH3   0  -0.513  -8.0091  16.2254   5.7432
 WRM  C2   C  CH2   0  -0.459  -7.5024  14.0221   2.7062
 WRM  C9   C  CR15  0   0.112  -7.6942  14.4183   0.2506
 WRM  N2   N  N     0  -0.468  -6.9916  14.8214  -0.7670
 WRM  C3   C  CR56  0   0.347  -5.7106  14.7363   1.1135
 WRM  H1   H  HCR6  0   0.267  -4.5623  14.6470   2.9548
 WRM  H2   H  HCR6  0   0.257  -2.5121  15.4300   1.8184
 WRM  H3   H  HCR6  0   0.254  -2.5063  15.9446  -0.5837
 WRM  H4   H  HCR6  0   0.256  -4.5610  15.7006  -1.9475
 WRM  H5   H  HNH1  0   0.411  -7.4609  14.2516   5.2146
 WRM  H6   H  HCH3  0   0.254  -8.0164  15.8271   6.7533
 WRM  H7   H  HCH3  0   0.242  -7.2571  17.0131   5.6883
 WRM  H8   H  HCH3  0   0.243  -8.9846  16.6658   5.5392
 WRM  H9   H  HCH2  0   0.321  -8.4509  13.4930   2.5932
 WRM  H10  H  HCH2  0   0.295  -6.8254  13.3422   3.2259
 WRM  H11  H  HCR5  0   0.290  -8.7433  14.1599   0.2207

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
 WRM  C7  C6   aromatic  1.383  0.020  1.383
 WRM  C7  C8   aromatic  1.394  0.020  1.394
 WRM  N2  C8   aromatic  1.377  0.020  1.377
 WRM  N2  C9   aromatic  1.301  0.020  1.301
 WRM  C6  C5   aromatic  1.403  0.020  1.403
 WRM  C8  C3   aromatic  1.404  0.020  1.404
 WRM  C9  N1   aromatic  1.357  0.020  1.357
 WRM  C5  C4   aromatic  1.384  0.020  1.384
 WRM  C3  N1   aromatic  1.371  0.020  1.371
 WRM  C3  C4   aromatic  1.390  0.020  1.390
 WRM  N1  C2   single    1.432  0.020  1.432
 WRM  C2  C1   single    1.527  0.020  1.527
 WRM  O   C1   double    1.220  0.020  1.220
 WRM  C1  N    single    1.335  0.020  1.335
 WRM  N   C    single    1.445  0.020  1.445
 WRM  C4  H1   single    0.930  0.020  1.080
 WRM  C5  H2   single    0.930  0.020  1.080
 WRM  C6  H3   single    0.930  0.020  1.080
 WRM  C7  H4   single    0.930  0.020  1.080
 WRM  N   H5   single    0.860  0.020  1.020
 WRM  C   H6   single    0.970  0.020  1.090
 WRM  C   H7   single    0.970  0.020  1.090
 WRM  C   H8   single    0.970  0.020  1.090
 WRM  C2  H9   single    0.970  0.020  1.090
 WRM  C2  H10  single    0.970  0.020  1.090
 WRM  C9  H11  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
 WRM  C3   N1  C9  106.49  3.000
 WRM  C3   N1  C2  126.28  3.000
 WRM  C9   N1  C2  126.79  3.000
 WRM  H1   C4  C3  122.39  3.000
 WRM  H1   C4  C5  121.05  3.000
 WRM  C3   C4  C5  116.56  3.000
 WRM  H2   C5  C6  119.22  3.000
 WRM  H2   C5  C4  119.24  3.000
 WRM  C6   C5  C4  121.54  3.000
 WRM  H3   C6  C7  119.53  3.000
 WRM  H3   C6  C5  119.02  3.000
 WRM  C7   C6  C5  121.45  3.000
 WRM  H4   C7  C8  120.84  3.000
 WRM  H4   C7  C6  121.24  3.000
 WRM  C8   C7  C6  117.92  3.000
 WRM  C3   C8  N2  109.93  3.000
 WRM  C3   C8  C7  119.81  3.000
 WRM  N2   C8  C7  130.26  3.000
 WRM  C2   C1  N   114.68  3.000
 WRM  N    C1  O   124.05  3.000
 WRM  C2   C1  O   121.24  3.000
 WRM  H5   N   C   118.22  3.000
 WRM  H5   N   C1  119.34  3.000
 WRM  C    N   C1  122.43  3.000
 WRM  H8   C   H7  108.42  3.000
 WRM  H8   C   H6  108.45  3.000
 WRM  H7   C   H6  108.45  3.000
 WRM  H8   C   N   111.34  3.000
 WRM  H7   C   N   111.70  3.000
 WRM  H6   C   N   108.40  3.000
 WRM  H10  C2  H9  106.63  3.000
 WRM  H10  C2  C1  112.00  3.000
 WRM  H9   C2  C1  108.44  3.000
 WRM  H10  C2  N1  109.90  3.000
 WRM  H9   C2  N1  108.76  3.000
 WRM  C1   C2  N1  110.95  3.000
 WRM  H11  C9  N2  125.22  3.000
 WRM  H11  C9  N1  120.90  3.000
 WRM  N2   C9  N1  113.88  3.000
 WRM  C9   N2  C8  104.71  3.000
 WRM  C8   C3  C4  122.73  3.000
 WRM  C4   C3  N1  132.30  3.000
 WRM  C8   C3  N1  104.97  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
 WRM  CONST_01  C8   N2  C9  N1    0.00   0.0  0
 WRM  CONST_02  C7   C8  C3  N1  180.00   0.0  0
 WRM  CONST_03  N2   C8  C3  N1    0.00   0.0  0
 WRM  CONST_04  C5   C4  C3  N1  180.00   0.0  0
 WRM  CONST_05  C7   C6  C5  C4    0.00   0.0  0
 WRM  CONST_06  C7   C8  C3  C4    0.00   0.0  0
 WRM  CONST_07  N2   C8  C3  C4  180.00   0.0  0
 WRM  CONST_08  C9   N1  C3  C4  180.00   0.0  0
 WRM  CONST_09  C8   C7  C6  C5    0.00   0.0  0
 WRM  CONST_10  C8   C3  C4  C5    0.00   0.0  0
 WRM  CONST_11  N2   C8  C7  C6  180.00   0.0  0
 WRM  CONST_12  C3   C8  C7  C6    0.00   0.0  0
 WRM  CONST_13  C3   C4  C5  C6    0.00   0.0  0
 WRM  CONST_14  C9   N2  C8  C7  180.00   0.0  0
 WRM  CONST_15  C9   N1  C3  C8    0.00   0.0  0
 WRM  CONST_16  C3   C8  N2  C9    0.00   0.0  0
 WRM  CONST_17  C3   N1  C9  N2    0.00   0.0  0
 WRM  CONST_18  C2   N1  C3  C4    0.00   0.0  0
 WRM  CONST_19  C2   N1  C3  C8  180.00   0.0  0
 WRM  CONST_20  N2   C9  N1  C2  180.00   0.0  0
 WRM  CONST_21  H1   C4  C3  N1    0.00   0.0  0
 WRM  CONST_22  H3   C6  C5  C4  180.00   0.0  0
 WRM  CONST_23  H4   C7  C6  C5  180.00   0.0  0
 WRM  CONST_24  H2   C5  C6  C7  180.00   0.0  0
 WRM  CONST_25  H11  C9  N2  C8  180.00   0.0  0
 WRM  CONST_26  C    N   C1  O     0.00   0.0  0
 WRM  CONST_27  C2   C1  N   C   180.00   0.0  0
 WRM  CONST_28  H5   N   C1  O   180.00   0.0  0
 WRM  Var_01    C9   N1  C2  C1  -96.62  30.0  2
 WRM  Var_02    O    C1  C2  N1   27.00  30.0  3
 WRM  Var_03    H6   C   N   C1  174.15  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
 WRM  plan-1  N1   0.020
 WRM  plan-1  C4   0.020
 WRM  plan-1  C5   0.020
 WRM  plan-1  C6   0.020
 WRM  plan-1  C7   0.020
 WRM  plan-1  C8   0.020
 WRM  plan-1  C2   0.020
 WRM  plan-1  C9   0.020
 WRM  plan-1  N2   0.020
 WRM  plan-1  C3   0.020
 WRM  plan-1  H1   0.020
 WRM  plan-1  H2   0.020
 WRM  plan-1  H3   0.020
 WRM  plan-1  H4   0.020
 WRM  plan-1  H11  0.020
 WRM  plan-2  O    0.020
 WRM  plan-2  C1   0.020
 WRM  plan-2  N    0.020
 WRM  plan-2  C    0.020
 WRM  plan-2  C2   0.020
 WRM  plan-2  H5   0.020

