# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:53:17 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: 5,6-dimethyl-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc2[nH]cnc2cc1C
#
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
 DMD  DMD  5,6-dimethyl-1H-benzimidazole  ligand  21  11  .  2021-08-08  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DMD
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
 DMD  N3    N  NR15  0  -0.663   1.0521  -0.0367  -2.2445
 DMD  N1    N  N     0  -0.466  -1.1673   0.0777  -2.2420
 DMD  C2    C  CR15  0   0.095  -0.0888   0.0215  -2.9717
 DMD  C7A   C  CR56  0   0.128  -0.7107   0.0538  -0.9431
 DMD  C3A   C  CR56  0   0.336   0.6874  -0.0189  -0.9244
 DMD  C4    C  CR16  0  -0.354   1.4108  -0.0593   0.2624
 DMD  C5    C  CR6   0   0.051   0.7073  -0.0242   1.4558
 DMD  C6    C  CR6   0   0.061  -0.7097   0.0549   1.4566
 DMD  C7    C  CR16  0  -0.380  -1.4108   0.0911   0.2632
 DMD  C8    C  CH3   0  -0.736   1.4535  -0.0800   2.7575
 DMD  C9    C  CH3   0  -0.736  -1.4530   0.1053   2.7611
 DMD  HN31  H  HNR5  0   0.419   1.9868  -0.0931  -2.6162
 DMD  H21   H  HCR5  0   0.282  -0.0659   0.0210  -4.0512
 DMD  H41   H  HCR6  0   0.258   2.4923  -0.1162   0.2616
 DMD  H71   H  HCR6  0   0.244  -2.4930   0.1480   0.2660
 DMD  H81   H  HCH3  0   0.241   1.2467   0.7893   3.3851
 DMD  H82   H  HCH3  0   0.241   1.1795  -0.9615   3.3411
 DMD  H83   H  HCH3  0   0.250   2.5295  -0.1174   2.5925
 DMD  H91   H  HCH3  0   0.239  -1.2457  -0.7667   3.3849
 DMD  H92   H  HCH3  0   0.240  -1.1787   0.9841   3.3490
 DMD  H93   H  HCH3  0   0.249  -2.5292   0.1429   2.5974

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
 DMD  N3   C2    aromatic  1.354  0.020  1.354
 DMD  N3   C3A   aromatic  1.370  0.020  1.370
 DMD  N3   HN31  single    0.860  0.020  1.020
 DMD  N1   C2    aromatic  1.303  0.020  1.303
 DMD  N1   C7A   aromatic  1.377  0.020  1.377
 DMD  C2   H21   single    0.930  0.020  1.080
 DMD  C7A  C3A   aromatic  1.400  0.020  1.400
 DMD  C7A  C7    aromatic  1.395  0.020  1.395
 DMD  C3A  C4    aromatic  1.390  0.020  1.390
 DMD  C4   C5    aromatic  1.386  0.020  1.386
 DMD  C4   H41   single    0.930  0.020  1.080
 DMD  C5   C6    aromatic  1.419  0.020  1.419
 DMD  C5   C8    single    1.501  0.020  1.501
 DMD  C6   C7    aromatic  1.385  0.020  1.385
 DMD  C6   C9    single    1.502  0.020  1.502
 DMD  C7   H71   single    0.930  0.020  1.080
 DMD  C8   H81   single    0.970  0.020  1.090
 DMD  C8   H82   single    0.970  0.020  1.090
 DMD  C8   H83   single    0.970  0.020  1.090
 DMD  C9   H91   single    0.970  0.020  1.090
 DMD  C9   H92   single    0.970  0.020  1.090
 DMD  C9   H93   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
 DMD  HN31  N3   C3A  127.11  3.000
 DMD  HN31  N3   C2   125.87  3.000
 DMD  C3A   N3   C2   107.02  3.000
 DMD  C7A   N1   C2   104.66  3.000
 DMD  H21   C2   N1   125.26  3.000
 DMD  H21   C2   N3   121.26  3.000
 DMD  N1    C2   N3   113.47  3.000
 DMD  C7    C7A  C3A  119.40  3.000
 DMD  C7    C7A  N1   130.45  3.000
 DMD  C3A   C7A  N1   110.16  3.000
 DMD  C4    C3A  C7A  122.17  3.000
 DMD  C4    C3A  N3   133.14  3.000
 DMD  C7A   C3A  N3   104.69  3.000
 DMD  H41   C4   C5   120.60  3.000
 DMD  H41   C4   C3A  121.36  3.000
 DMD  C5    C4   C3A  118.04  3.000
 DMD  C8    C5   C6   119.85  3.000
 DMD  C8    C5   C4   119.56  3.000
 DMD  C6    C5   C4   120.58  3.000
 DMD  C9    C6   C7   119.81  3.000
 DMD  C9    C6   C5   119.76  3.000
 DMD  C7    C6   C5   120.43  3.000
 DMD  H71   C7   C6   120.32  3.000
 DMD  H71   C7   C7A  120.31  3.000
 DMD  C6    C7   C7A  119.37  3.000
 DMD  H83   C8   H82  107.52  3.000
 DMD  H83   C8   H81  107.55  3.000
 DMD  H82   C8   H81  106.73  3.000
 DMD  H83   C8   C5   111.16  3.000
 DMD  H82   C8   C5   111.63  3.000
 DMD  H81   C8   C5   112.00  3.000
 DMD  H93   C9   H92  107.53  3.000
 DMD  H93   C9   H91  107.51  3.000
 DMD  H92   C9   H91  106.70  3.000
 DMD  H93   C9   C6   111.07  3.000
 DMD  H92   C9   C6   111.72  3.000
 DMD  H91   C9   C6   112.05  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
 DMD  CONST_01  C7A   N1   C2   N3     0.00   0.0  0
 DMD  CONST_02  N1    C7A  C3A  N3     0.00   0.0  0
 DMD  CONST_03  C7    C7A  C3A  N3   180.00   0.0  0
 DMD  CONST_04  C5    C4   C3A  N3   180.00   0.0  0
 DMD  CONST_05  C3A   N3   C2   N1     0.00   0.0  0
 DMD  CONST_06  C4    C3A  C7A  N1   180.00   0.0  0
 DMD  CONST_07  C6    C7   C7A  N1   180.00   0.0  0
 DMD  CONST_08  C7A   C3A  N3   C2     0.00   0.0  0
 DMD  CONST_09  C4    C3A  N3   C2   180.00   0.0  0
 DMD  CONST_10  C3A   C7A  N1   C2     0.00   0.0  0
 DMD  CONST_11  C7    C7A  N1   C2   180.00   0.0  0
 DMD  CONST_12  C5    C4   C3A  C7A    0.00   0.0  0
 DMD  CONST_13  C5    C6   C7   C7A    0.00   0.0  0
 DMD  CONST_14  C6    C7   C7A  C3A    0.00   0.0  0
 DMD  CONST_15  C6    C5   C4   C3A    0.00   0.0  0
 DMD  CONST_16  C7    C7A  C3A  C4     0.00   0.0  0
 DMD  CONST_17  C7    C6   C5   C4     0.00   0.0  0
 DMD  CONST_18  C9    C6   C7   C7A  180.00   0.0  0
 DMD  CONST_19  C8    C5   C4   C3A  180.00   0.0  0
 DMD  CONST_20  C9    C6   C5   C4   180.00   0.0  0
 DMD  CONST_21  C8    C5   C6   C7   180.00   0.0  0
 DMD  CONST_22  H41   C4   C3A  N3     0.00   0.0  0
 DMD  CONST_23  HN31  N3   C2   N1   180.00   0.0  0
 DMD  CONST_24  H71   C7   C7A  N1     0.00   0.0  0
 DMD  CONST_25  H21   C2   N1   C7A  180.00   0.0  0
 DMD  Var_01    H81   C8   C5   C4   121.93  30.0  2
 DMD  Var_02    H91   C9   C6   C5   -58.53  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
 DMD  plan-1  N3    0.020
 DMD  plan-1  N1    0.020
 DMD  plan-1  C2    0.020
 DMD  plan-1  C7A   0.020
 DMD  plan-1  C3A   0.020
 DMD  plan-1  C4    0.020
 DMD  plan-1  C5    0.020
 DMD  plan-1  C6    0.020
 DMD  plan-1  C7    0.020
 DMD  plan-1  C8    0.020
 DMD  plan-1  C9    0.020
 DMD  plan-1  HN31  0.020
 DMD  plan-1  H21   0.020
 DMD  plan-1  H41   0.020
 DMD  plan-1  H71   0.020

