# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 22:01:44 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: 1H-benzimidazol-2-ylmethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1[nH]c2ccccc2n1
#
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
 XIY  XIY  1H-benzimidazol-2-ylmethanol  ligand  19  11  .  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_XIY
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
 XIY  NG   N  N     0  -0.479  -0.5490   1.3670   0.0709
 XIY  CD1  C  CR5   0   0.410  -1.4071   0.3906  -0.0373
 XIY  NE1  N  NR15  0  -0.683  -0.8173  -0.8261  -0.1430
 XIY  CE2  C  CR56  0   0.334   0.5367  -0.6282  -0.0968
 XIY  CZ2  C  CR16  0  -0.308   1.6207  -1.4964  -0.1487
 XIY  CH2  C  CR16  0  -0.279   2.8792  -0.9245  -0.0717
 XIY  CZ3  C  CR16  0  -0.272   3.0486   0.4627   0.0557
 XIY  CE3  C  CR16  0  -0.336   1.9633   1.3193   0.1098
 XIY  CD2  C  CR56  0   0.134   0.6867   0.7632   0.0321
 XIY  C    C  CH2   0  -0.236  -2.8872   0.5529  -0.1064
 XIY  O    O  OH1   0  -0.668  -3.4877  -0.5825   0.4642
 XIY  HE1  H  HNR5  0   0.417  -1.2974  -1.7092  -0.2174
 XIY  HC1  H  HCH2  0   0.232  -3.1547   1.4826   0.4071
 XIY  HC2  H  HCH2  0   0.242  -3.1720   0.6775  -1.1590
 XIY  HZ2  H  HCR6  0   0.265   1.4921  -2.5667  -0.2445
 XIY  HH2  H  HCR6  0   0.254   3.7521  -1.5627  -0.1113
 XIY  HZ3  H  HCR6  0   0.251   4.0509   0.8668   0.1139
 XIY  HE3  H  HCR6  0   0.253   2.0973   2.3890   0.2086
 XIY  H    H  HOH1  0   0.468  -4.4160  -0.5898   0.2144

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
 XIY  NG   CD1  aromatic  1.304  0.020  1.304
 XIY  NG   CD2  aromatic  1.376  0.020  1.376
 XIY  CD1  NE1  aromatic  1.356  0.020  1.356
 XIY  CD1  C    single    1.490  0.020  1.490
 XIY  NE1  CE2  aromatic  1.369  0.020  1.369
 XIY  CE2  CZ2  aromatic  1.390  0.020  1.390
 XIY  CE2  CD2  aromatic  1.405  0.020  1.405
 XIY  CZ2  CH2  aromatic  1.384  0.020  1.384
 XIY  CH2  CZ3  aromatic  1.403  0.020  1.403
 XIY  CZ3  CE3  aromatic  1.384  0.020  1.384
 XIY  CE3  CD2  aromatic  1.395  0.020  1.395
 XIY  C    O    single    1.405  0.020  1.405
 XIY  NE1  HE1  single    0.860  0.020  1.020
 XIY  C    HC1  single    0.970  0.020  1.090
 XIY  C    HC2  single    0.970  0.020  1.090
 XIY  CZ2  HZ2  single    0.930  0.020  1.080
 XIY  CH2  HH2  single    0.930  0.020  1.080
 XIY  CZ3  HZ3  single    0.930  0.020  1.080
 XIY  CE3  HE3  single    0.930  0.020  1.080
 XIY  O    H    single    0.850  0.020  0.980

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
 XIY  CD2  NG   CD1  105.07  3.000
 XIY  C    CD1  NE1  121.73  3.000
 XIY  C    CD1  NG   125.14  3.000
 XIY  NE1  CD1  NG   113.07  3.000
 XIY  HE1  NE1  CE2  126.88  3.000
 XIY  HE1  NE1  CD1  125.77  3.000
 XIY  CE2  NE1  CD1  107.33  3.000
 XIY  CD2  CE2  CZ2  122.59  3.000
 XIY  CD2  CE2  NE1  104.58  3.000
 XIY  CZ2  CE2  NE1  132.83  3.000
 XIY  HZ2  CZ2  CH2  121.44  3.000
 XIY  HZ2  CZ2  CE2  121.89  3.000
 XIY  CH2  CZ2  CE2  116.67  3.000
 XIY  HH2  CH2  CZ3  119.27  3.000
 XIY  HH2  CH2  CZ2  119.18  3.000
 XIY  CZ3  CH2  CZ2  121.55  3.000
 XIY  HZ3  CZ3  CE3  119.55  3.000
 XIY  HZ3  CZ3  CH2  119.06  3.000
 XIY  CE3  CZ3  CH2  121.39  3.000
 XIY  HE3  CE3  CD2  120.82  3.000
 XIY  HE3  CE3  CZ3  121.22  3.000
 XIY  CD2  CE3  CZ3  117.96  3.000
 XIY  CE3  CD2  CE2  119.84  3.000
 XIY  CE3  CD2  NG   130.20  3.000
 XIY  CE2  CD2  NG   109.95  3.000
 XIY  HC2  C    HC1  106.85  3.000
 XIY  HC2  C    O    111.73  3.000
 XIY  HC1  C    O    113.02  3.000
 XIY  HC2  C    CD1  108.33  3.000
 XIY  HC1  C    CD1  108.25  3.000
 XIY  O    C    CD1  108.51  3.000
 XIY  H    O    C    108.25  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
 XIY  CONST_01  CE2  NE1  CD1  NG      0.00   0.0  0
 XIY  CONST_02  NE1  CE2  CD2  NG      0.00   0.0  0
 XIY  CONST_03  CZ2  CE2  CD2  NG    180.00   0.0  0
 XIY  CONST_04  CZ3  CE3  CD2  NG    180.00   0.0  0
 XIY  CONST_05  CE2  CD2  NG   CD1     0.00   0.0  0
 XIY  CONST_06  CE3  CD2  NG   CD1   180.00   0.0  0
 XIY  CONST_07  CZ2  CE2  NE1  CD1   180.00   0.0  0
 XIY  CONST_08  CD2  CE2  NE1  CD1     0.00   0.0  0
 XIY  CONST_09  CD2  NG   CD1  NE1     0.00   0.0  0
 XIY  CONST_10  CH2  CZ2  CE2  NE1   180.00   0.0  0
 XIY  CONST_11  CE3  CD2  CE2  NE1   180.00   0.0  0
 XIY  CONST_12  CZ3  CH2  CZ2  CE2     0.00   0.0  0
 XIY  CONST_13  CZ3  CE3  CD2  CE2     0.00   0.0  0
 XIY  CONST_14  CE3  CD2  CE2  CZ2     0.00   0.0  0
 XIY  CONST_15  CE3  CZ3  CH2  CZ2     0.00   0.0  0
 XIY  CONST_16  CD2  CE2  CZ2  CH2     0.00   0.0  0
 XIY  CONST_17  CD2  CE3  CZ3  CH2     0.00   0.0  0
 XIY  CONST_18  C    CD1  NE1  CE2   180.00   0.0  0
 XIY  CONST_19  C    CD1  NG   CD2   180.00   0.0  0
 XIY  CONST_20  HE1  NE1  CD1  NG    180.00   0.0  0
 XIY  CONST_21  HE3  CE3  CD2  NG      0.00   0.0  0
 XIY  CONST_22  HZ2  CZ2  CE2  NE1     0.00   0.0  0
 XIY  CONST_23  HH2  CH2  CZ2  CE2   180.00   0.0  0
 XIY  CONST_24  HZ3  CZ3  CH2  CZ2   180.00   0.0  0
 XIY  Var_01    O    C    CD1  NG   -149.68  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
 XIY  plan-1  NG   0.020
 XIY  plan-1  CD1  0.020
 XIY  plan-1  NE1  0.020
 XIY  plan-1  CE2  0.020
 XIY  plan-1  CZ2  0.020
 XIY  plan-1  CH2  0.020
 XIY  plan-1  CZ3  0.020
 XIY  plan-1  CE3  0.020
 XIY  plan-1  CD2  0.020
 XIY  plan-1  C    0.020
 XIY  plan-1  HE1  0.020
 XIY  plan-1  HZ2  0.020
 XIY  plan-1  HH2  0.020
 XIY  plan-1  HZ3  0.020
 XIY  plan-1  HE3  0.020

