# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 11:20:24 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: 1-methylbenzimidazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(N)nc2ccccc12
#
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
 ES7  ES7  1-methylbenzimidazol-2-amine  ligand  20  11  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ES7
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
 ES7  C10   C  CR5   0   0.621  -1.6556   0.5394  -0.1247
 ES7  C01   C  CH3   0  -0.554  -1.8207  -1.9570  -0.0693
 ES7  N02   N  NR5   0  -0.553  -1.1024  -0.7060  -0.0645
 ES7  C03   C  CR56  0   0.346   0.2626  -0.5222  -0.0031
 ES7  C04   C  CR16  0  -0.322   1.3214  -1.4103   0.0794
 ES7  C05   C  CR16  0  -0.284   2.5999  -0.8651   0.1203
 ES7  C06   C  CR16  0  -0.276   2.7997   0.5173   0.0812
 ES7  C07   C  CR16  0  -0.345   1.7296   1.3992  -0.0002
 ES7  C08   C  CR56  0   0.153   0.4427   0.8724  -0.0423
 ES7  N09   N  N     0  -0.526  -0.7733   1.5084  -0.1149
 ES7  N11   N  NH2   0  -0.857  -2.9957   0.7062  -0.2504
 ES7  H01   H  HCH3  0   0.264  -2.4855  -2.0185  -0.9302
 ES7  H01A  H  HCH3  0   0.273  -1.1123  -2.7777  -0.1334
 ES7  H01B  H  HCH3  0   0.261  -2.4047  -2.0843   0.8425
 ES7  H04   H  HCR6  0   0.260   1.1754  -2.4827   0.1120
 ES7  H05   H  HCR6  0   0.248   3.4538  -1.5266   0.1850
 ES7  H06   H  HCR6  0   0.245   3.8090   0.9072   0.1160
 ES7  H07   H  HCR6  0   0.245   1.8890   2.4698  -0.0291
 ES7  HN11  H  HNH2  0   0.403  -3.5985   0.0043   0.1488
 ES7  HN1A  H  HNH2  0   0.399  -3.3207   1.6445  -0.0811

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
 ES7  C10  N02   aromatic  1.364  0.020  1.364
 ES7  C10  N09   aromatic  1.310  0.020  1.310
 ES7  C10  N11   single    1.356  0.020  1.356
 ES7  C01  N02   single    1.443  0.020  1.443
 ES7  N02  C03   aromatic  1.379  0.020  1.379
 ES7  C03  C04   aromatic  1.384  0.020  1.384
 ES7  C03  C08   aromatic  1.407  0.020  1.407
 ES7  C04  C05   aromatic  1.391  0.020  1.391
 ES7  C05  C06   aromatic  1.397  0.020  1.397
 ES7  C06  C07   aromatic  1.389  0.020  1.389
 ES7  C07  C08   aromatic  1.391  0.020  1.391
 ES7  C08  N09   aromatic  1.374  0.020  1.374
 ES7  C01  H01   single    0.970  0.020  1.090
 ES7  C01  H01A  single    0.970  0.020  1.090
 ES7  C01  H01B  single    0.970  0.020  1.090
 ES7  C04  H04   single    0.930  0.020  1.080
 ES7  C05  H05   single    0.930  0.020  1.080
 ES7  C06  H06   single    0.930  0.020  1.080
 ES7  C07  H07   single    0.930  0.020  1.080
 ES7  N11  HN11  single    0.890  0.020  1.040
 ES7  N11  HN1A  single    0.890  0.020  1.040

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
 ES7  N11   C10  N09   125.10  3.000
 ES7  N11   C10  N02   121.13  3.000
 ES7  N09   C10  N02   113.69  3.000
 ES7  H01B  C01  H01A  108.10  3.000
 ES7  H01B  C01  H01   109.11  3.000
 ES7  H01A  C01  H01   107.98  3.000
 ES7  H01B  C01  N02   111.42  3.000
 ES7  H01A  C01  N02   109.31  3.000
 ES7  H01   C01  N02   110.82  3.000
 ES7  C03   N02  C01   127.50  3.000
 ES7  C03   N02  C10   106.36  3.000
 ES7  C01   N02  C10   126.14  3.000
 ES7  C08   C03  C04   122.66  3.000
 ES7  C08   C03  N02   104.93  3.000
 ES7  C04   C03  N02   132.40  3.000
 ES7  H04   C04  C05   120.76  3.000
 ES7  H04   C04  C03   122.27  3.000
 ES7  C05   C04  C03   116.97  3.000
 ES7  H05   C05  C06   119.58  3.000
 ES7  H05   C05  C04   119.18  3.000
 ES7  C06   C05  C04   121.23  3.000
 ES7  H06   C06  C07   119.44  3.000
 ES7  H06   C06  C05   119.25  3.000
 ES7  C07   C06  C05   121.31  3.000
 ES7  H07   C07  C08   120.65  3.000
 ES7  H07   C07  C06   121.06  3.000
 ES7  C08   C07  C06   118.29  3.000
 ES7  N09   C08  C07   130.16  3.000
 ES7  N09   C08  C03   110.30  3.000
 ES7  C07   C08  C03   119.53  3.000
 ES7  C08   N09  C10   104.71  3.000
 ES7  HN1A  N11  HN11  112.91  3.000
 ES7  HN1A  N11  C10   114.69  3.000
 ES7  HN11  N11  C10   117.95  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
 ES7  CONST_01  C04   C03  N02  C10  180.00   0.0  0
 ES7  CONST_02  C08   C03  N02  C10    0.00   0.0  0
 ES7  CONST_03  C03   C08  N09  C10    0.00   0.0  0
 ES7  CONST_04  C07   C08  N09  C10  180.00   0.0  0
 ES7  CONST_05  C08   N09  C10  N02    0.00   0.0  0
 ES7  CONST_06  C05   C04  C03  N02  180.00   0.0  0
 ES7  CONST_07  C07   C08  C03  N02  180.00   0.0  0
 ES7  CONST_08  N09   C08  C03  N02    0.00   0.0  0
 ES7  CONST_09  N09   C10  N02  C03    0.00   0.0  0
 ES7  CONST_10  C06   C05  C04  C03    0.00   0.0  0
 ES7  CONST_11  C06   C07  C08  C03    0.00   0.0  0
 ES7  CONST_12  C07   C08  C03  C04    0.00   0.0  0
 ES7  CONST_13  N09   C08  C03  C04  180.00   0.0  0
 ES7  CONST_14  C07   C06  C05  C04    0.00   0.0  0
 ES7  CONST_15  C08   C03  C04  C05    0.00   0.0  0
 ES7  CONST_16  C08   C07  C06  C05    0.00   0.0  0
 ES7  CONST_17  N09   C08  C07  C06  180.00   0.0  0
 ES7  CONST_18  N09   C10  N02  C01  180.00   0.0  0
 ES7  CONST_19  C04   C03  N02  C01    0.00   0.0  0
 ES7  CONST_20  C08   C03  N02  C01  180.00   0.0  0
 ES7  CONST_21  N11   C10  N02  C03  180.00   0.0  0
 ES7  CONST_22  N11   C10  N09  C08  180.00   0.0  0
 ES7  CONST_23  H04   C04  C03  N02    0.00   0.0  0
 ES7  CONST_24  H05   C05  C04  C03  180.00   0.0  0
 ES7  CONST_25  H07   C07  C08  C03  180.00   0.0  0
 ES7  CONST_26  H06   C06  C05  C04  180.00   0.0  0
 ES7  CONST_28  HN1A  N11  C10  N02  180.00   0.0  0
 ES7  Var_01    H01   C01  N02  C10   54.31  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
 ES7  plan-1  C10   0.020
 ES7  plan-1  C01   0.020
 ES7  plan-1  N02   0.020
 ES7  plan-1  C03   0.020
 ES7  plan-1  C04   0.020
 ES7  plan-1  C05   0.020
 ES7  plan-1  C06   0.020
 ES7  plan-1  C07   0.020
 ES7  plan-1  C08   0.020
 ES7  plan-1  N09   0.020
 ES7  plan-1  N11   0.020
 ES7  plan-1  H04   0.020
 ES7  plan-1  H05   0.020
 ES7  plan-1  H06   0.020
 ES7  plan-1  H07   0.020
 ES7  plan-2  C10   0.020
 ES7  plan-2  N11   0.020
 ES7  plan-2  HN11  0.020
 ES7  plan-2  HN1A  0.020

