# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 12:04:54 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 6-methoxy-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2nc[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
 5OB  5OB  6-methoxy-1H-benzimidazole  ligand  19  11  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5OB
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
 5OB  N3    N  NR15  0  -0.667  -1.2290   0.0286  -2.1717
 5OB  N1    N  N     0  -0.460   0.9574   0.0186  -2.5761
 5OB  C2    C  CR15  0   0.097  -0.2340   0.0309  -3.0963
 5OB  C7A   C  CR56  0   0.113   0.7435   0.0072  -1.2139
 5OB  C3A   C  CR56  0   0.352  -0.6351   0.0138  -0.9401
 5OB  C4    C  CR16  0  -0.407  -1.1518   0.0048   0.3473
 5OB  C5    C  CR6   0   0.373  -0.2348  -0.0119   1.3924
 5OB  C6    C  CR16  0  -0.395   1.1507  -0.0196   1.1402
 5OB  C7    C  CR16  0  -0.312   1.6428  -0.0098  -0.1538
 5OB  O10   O  O2    0  -0.478  -0.7628  -0.0215   2.6362
 5OB  C11   C  CH3   0  -0.434   0.1083  -0.0323   3.7477
 5OB  H31N  H  HNR5  0   0.420  -2.2164   0.0367  -2.3711
 5OB  H21   H  HCR5  0   0.284  -0.4548   0.0410  -4.1533
 5OB  H41   H  HCR6  0   0.270  -2.2168   0.0096   0.5417
 5OB  H61   H  HCR6  0   0.276   1.8580  -0.0324   1.9573
 5OB  H71   H  HCR6  0   0.259   2.7110  -0.0143  -0.3290
 5OB  H111  H  HCH3  0   0.258  -0.5224  -0.0327   4.6335
 5OB  H112  H  HCH3  0   0.226   0.7383  -0.9255   3.7689
 5OB  H113  H  HCH3  0   0.226   0.7494   0.8527   3.7773

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
 5OB  N3   C2    aromatic  1.358  0.020  1.358
 5OB  N3   C3A   aromatic  1.367  0.020  1.367
 5OB  N3   H31N  single    0.860  0.020  1.020
 5OB  N1   C2    aromatic  1.300  0.020  1.300
 5OB  N1   C7A   aromatic  1.379  0.020  1.379
 5OB  C2   H21   single    0.930  0.020  1.080
 5OB  C7A  C3A   aromatic  1.406  0.020  1.406
 5OB  C7A  C7    aromatic  1.390  0.020  1.390
 5OB  C3A  C4    aromatic  1.387  0.020  1.387
 5OB  C4   C5    aromatic  1.391  0.020  1.391
 5OB  C4   H41   single    0.930  0.020  1.080
 5OB  C5   C6    aromatic  1.408  0.020  1.408
 5OB  C5   O10   single    1.351  0.020  1.351
 5OB  C6   C7    aromatic  1.384  0.020  1.384
 5OB  C6   H61   single    0.930  0.020  1.080
 5OB  C7   H71   single    0.930  0.020  1.080
 5OB  O10  C11   single    1.412  0.020  1.412
 5OB  C11  H111  single    0.970  0.020  1.090
 5OB  C11  H112  single    0.970  0.020  1.090
 5OB  C11  H113  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
 5OB  H31N  N3   C3A   127.16  3.000
 5OB  H31N  N3   C2    125.68  3.000
 5OB  C3A   N3   C2    107.16  3.000
 5OB  C7A   N1   C2    104.67  3.000
 5OB  H21   C2   N1    125.39  3.000
 5OB  H21   C2   N3    121.11  3.000
 5OB  N1    C2   N3    113.50  3.000
 5OB  C7    C7A  C3A   119.07  3.000
 5OB  C7    C7A  N1    130.77  3.000
 5OB  C3A   C7A  N1    110.16  3.000
 5OB  C4    C3A  C7A   123.10  3.000
 5OB  C4    C3A  N3    132.39  3.000
 5OB  C7A   C3A  N3    104.51  3.000
 5OB  H41   C4   C5    120.92  3.000
 5OB  H41   C4   C3A   122.21  3.000
 5OB  C5    C4   C3A   116.87  3.000
 5OB  O10   C5   C6    123.32  3.000
 5OB  O10   C5   C4    115.73  3.000
 5OB  C6    C5   C4    120.94  3.000
 5OB  H61   C6   C7    118.30  3.000
 5OB  H61   C6   C5    120.56  3.000
 5OB  C7    C6   C5    121.14  3.000
 5OB  H71   C7   C6    120.14  3.000
 5OB  H71   C7   C7A   120.99  3.000
 5OB  C6    C7   C7A   118.87  3.000
 5OB  C11   O10  C5    118.91  3.000
 5OB  H113  C11  H112  108.84  3.000
 5OB  H113  C11  H111  108.56  3.000
 5OB  H112  C11  H111  108.55  3.000
 5OB  H113  C11  O10   112.14  3.000
 5OB  H112  C11  O10   112.15  3.000
 5OB  H111  C11  O10   106.46  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
 5OB  CONST_01  C7A   N1   C2   N3     0.00   0.0  0
 5OB  CONST_02  N1    C7A  C3A  N3     0.00   0.0  0
 5OB  CONST_03  C7    C7A  C3A  N3   180.00   0.0  0
 5OB  CONST_04  C5    C4   C3A  N3   180.00   0.0  0
 5OB  CONST_05  C3A   N3   C2   N1     0.00   0.0  0
 5OB  CONST_06  C4    C3A  C7A  N1   180.00   0.0  0
 5OB  CONST_07  C6    C7   C7A  N1   180.00   0.0  0
 5OB  CONST_08  C7A   C3A  N3   C2     0.00   0.0  0
 5OB  CONST_09  C4    C3A  N3   C2   180.00   0.0  0
 5OB  CONST_10  C3A   C7A  N1   C2     0.00   0.0  0
 5OB  CONST_11  C7    C7A  N1   C2   180.00   0.0  0
 5OB  CONST_12  C5    C4   C3A  C7A    0.00   0.0  0
 5OB  CONST_13  C5    C6   C7   C7A    0.00   0.0  0
 5OB  CONST_14  C6    C7   C7A  C3A    0.00   0.0  0
 5OB  CONST_15  C6    C5   C4   C3A    0.00   0.0  0
 5OB  CONST_16  C7    C7A  C3A  C4     0.00   0.0  0
 5OB  CONST_17  C7    C6   C5   C4     0.00   0.0  0
 5OB  CONST_18  O10   C5   C4   C3A  180.00   0.0  0
 5OB  CONST_19  O10   C5   C6   C7   180.00   0.0  0
 5OB  CONST_20  H41   C4   C3A  N3     0.00   0.0  0
 5OB  CONST_21  H31N  N3   C2   N1   180.00   0.0  0
 5OB  CONST_22  H71   C7   C7A  N1     0.00   0.0  0
 5OB  CONST_23  H21   C2   N1   C7A  180.00   0.0  0
 5OB  CONST_24  H61   C6   C7   C7A  180.00   0.0  0
 5OB  Var_01    H111  C11  O10  C5   179.66  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
 5OB  plan-1  N3    0.020
 5OB  plan-1  N1    0.020
 5OB  plan-1  C2    0.020
 5OB  plan-1  C7A   0.020
 5OB  plan-1  C3A   0.020
 5OB  plan-1  C4    0.020
 5OB  plan-1  C5    0.020
 5OB  plan-1  C6    0.020
 5OB  plan-1  C7    0.020
 5OB  plan-1  O10   0.020
 5OB  plan-1  H31N  0.020
 5OB  plan-1  H21   0.020
 5OB  plan-1  H41   0.020
 5OB  plan-1  H61   0.020
 5OB  plan-1  H71   0.020

