# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 08:01:29 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 6-methyl-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2nc[nH]c2c1
#
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
 5MB  5MB  6-methyl-1H-benzimidazole  ligand  18  10  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5MB
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
 5MB  N3    N  NR15  0  -0.662  -1.2605  -0.0145  -1.6942
 5MB  N1    N  N     0  -0.462   0.9124   0.0811  -2.1484
 5MB  C2    C  CR15  0   0.097  -0.2923   0.0308  -2.6410
 5MB  C7A   C  CR56  0   0.112   0.7322   0.0684  -0.7837
 5MB  C3A   C  CR56  0   0.348  -0.6354   0.0079  -0.4769
 5MB  C4    C  CR16  0  -0.356  -1.1137  -0.0172   0.8303
 5MB  C5    C  CR6   0   0.075  -0.1830   0.0196   1.8562
 5MB  C6    C  CR16  0  -0.303   1.1934   0.0818   1.5522
 5MB  C7    C  CR16  0  -0.314   1.6641   0.1064   0.2548
 5MB  C8    C  CH3   0  -0.723  -0.6217  -0.0111   3.2927
 5MB  HN31  H  HNR5  0   0.420  -2.2522  -0.0543  -1.8674
 5MB  H21   H  HCR5  0   0.284  -0.5370   0.0243  -3.6927
 5MB  H41   H  HCR6  0   0.259  -2.1752  -0.0641   1.0401
 5MB  H61   H  HCR6  0   0.244   1.9037   0.1112   2.3698
 5MB  H71   H  HCR6  0   0.251   2.7258   0.1543   0.0479
 5MB  H81   H  HCH3  0   0.243  -0.2417   0.8515   3.8426
 5MB  H82   H  HCH3  0   0.243  -1.7075  -0.0095   3.3808
 5MB  H83   H  HCH3  0   0.244  -0.2494  -0.9022   3.8016

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
 5MB  N3   C2    aromatic  1.355  0.020  1.355
 5MB  N3   C3A   aromatic  1.369  0.020  1.369
 5MB  N3   HN31  single    0.860  0.020  1.020
 5MB  N1   C2    aromatic  1.303  0.020  1.303
 5MB  N1   C7A   aromatic  1.377  0.020  1.377
 5MB  C2   H21   single    0.930  0.020  1.080
 5MB  C7A  C3A   aromatic  1.403  0.020  1.403
 5MB  C7A  C7    aromatic  1.396  0.020  1.396
 5MB  C3A  C4    aromatic  1.392  0.020  1.392
 5MB  C4   C5    aromatic  1.386  0.020  1.386
 5MB  C4   H41   single    0.930  0.020  1.080
 5MB  C5   C6    aromatic  1.411  0.020  1.411
 5MB  C5   C8    single    1.502  0.020  1.502
 5MB  C6   C7    aromatic  1.380  0.020  1.380
 5MB  C6   H61   single    0.930  0.020  1.080
 5MB  C7   H71   single    0.930  0.020  1.080
 5MB  C8   H81   single    0.970  0.020  1.090
 5MB  C8   H82   single    0.970  0.020  1.090
 5MB  C8   H83   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
 5MB  HN31  N3   C3A  127.10  3.000
 5MB  HN31  N3   C2   125.77  3.000
 5MB  C3A   N3   C2   107.13  3.000
 5MB  C7A   N1   C2   104.68  3.000
 5MB  H21   C2   N1   125.32  3.000
 5MB  H21   C2   N3   121.23  3.000
 5MB  N1    C2   N3   113.45  3.000
 5MB  C7    C7A  C3A  119.30  3.000
 5MB  C7    C7A  N1   130.53  3.000
 5MB  C3A   C7A  N1   110.17  3.000
 5MB  C4    C3A  C7A  122.75  3.000
 5MB  C4    C3A  N3   132.68  3.000
 5MB  C7A   C3A  N3   104.57  3.000
 5MB  H41   C4   C5   121.07  3.000
 5MB  H41   C4   C3A  121.29  3.000
 5MB  C5    C4   C3A  117.64  3.000
 5MB  C8    C5   C6   119.46  3.000
 5MB  C8    C5   C4   120.75  3.000
 5MB  C6    C5   C4   119.79  3.000
 5MB  H61   C6   C7   119.03  3.000
 5MB  H61   C6   C5   118.56  3.000
 5MB  C7    C6   C5   122.41  3.000
 5MB  H71   C7   C6   120.98  3.000
 5MB  H71   C7   C7A  120.91  3.000
 5MB  C6    C7   C7A  118.11  3.000
 5MB  H83   C8   H82  107.66  3.000
 5MB  H83   C8   H81  106.95  3.000
 5MB  H82   C8   H81  107.77  3.000
 5MB  H83   C8   C5   111.28  3.000
 5MB  H82   C8   C5   111.61  3.000
 5MB  H81   C8   C5   111.35  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
 5MB  CONST_01  C7A   N1   C2   N3      0.00   0.0  0
 5MB  CONST_02  N1    C7A  C3A  N3      0.00   0.0  0
 5MB  CONST_03  C7    C7A  C3A  N3    180.00   0.0  0
 5MB  CONST_04  C5    C4   C3A  N3    180.00   0.0  0
 5MB  CONST_05  C3A   N3   C2   N1      0.00   0.0  0
 5MB  CONST_06  C4    C3A  C7A  N1    180.00   0.0  0
 5MB  CONST_07  C6    C7   C7A  N1    180.00   0.0  0
 5MB  CONST_08  C7A   C3A  N3   C2      0.00   0.0  0
 5MB  CONST_09  C4    C3A  N3   C2    180.00   0.0  0
 5MB  CONST_10  C3A   C7A  N1   C2      0.00   0.0  0
 5MB  CONST_11  C7    C7A  N1   C2    180.00   0.0  0
 5MB  CONST_12  C5    C4   C3A  C7A     0.00   0.0  0
 5MB  CONST_13  C5    C6   C7   C7A     0.00   0.0  0
 5MB  CONST_14  C6    C7   C7A  C3A     0.00   0.0  0
 5MB  CONST_15  C6    C5   C4   C3A     0.00   0.0  0
 5MB  CONST_16  C7    C7A  C3A  C4      0.00   0.0  0
 5MB  CONST_17  C7    C6   C5   C4      0.00   0.0  0
 5MB  CONST_18  C8    C5   C4   C3A   180.00   0.0  0
 5MB  CONST_19  C8    C5   C6   C7    180.00   0.0  0
 5MB  CONST_20  H41   C4   C3A  N3      0.00   0.0  0
 5MB  CONST_21  HN31  N3   C2   N1    180.00   0.0  0
 5MB  CONST_22  H71   C7   C7A  N1      0.00   0.0  0
 5MB  CONST_23  H21   C2   N1   C7A   180.00   0.0  0
 5MB  CONST_24  H61   C6   C7   C7A   180.00   0.0  0
 5MB  Var_01    H81   C8   C5   C4   -123.51  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
 5MB  plan-1  N3    0.020
 5MB  plan-1  N1    0.020
 5MB  plan-1  C2    0.020
 5MB  plan-1  C7A   0.020
 5MB  plan-1  C3A   0.020
 5MB  plan-1  C4    0.020
 5MB  plan-1  C5    0.020
 5MB  plan-1  C6    0.020
 5MB  plan-1  C7    0.020
 5MB  plan-1  C8    0.020
 5MB  plan-1  HN31  0.020
 5MB  plan-1  H21   0.020
 5MB  plan-1  H41   0.020
 5MB  plan-1  H61   0.020
 5MB  plan-1  H71   0.020

