# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 08:53:13 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 2-amino-1H-benzimidazol-5-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]c2ccc(O)cc2n1
#
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
 172  172  2-amino-1H-benzimidazol-5-ol  ligand  18  11  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_172
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
 172  C1    C  CR6   0   0.335   0.2699   0.0219  -2.1754
 172  C2    C  CR16  0  -0.470   1.1358  -0.0195  -1.0909
 172  C3    C  CR56  0   0.215   0.5870  -0.0431   0.1868
 172  C4    C  CR56  0   0.146  -0.8088  -0.0204   0.3450
 172  C5    C  CR16  0  -0.232  -1.6770   0.0290  -0.7291
 172  C6    C  CR16  0  -0.433  -1.1154   0.0532  -1.9997
 172  N10   N  N     0  -0.570   1.2087  -0.0792   1.4125
 172  C11   C  CR5   0   0.544   0.2329  -0.0864   2.2844
 172  N12   N  NR15  0  -0.546  -1.0006  -0.0443   1.7104
 172  N14   N  NH2   0  -0.795   0.3934  -0.1805   3.6282
 172  O17   O  OH1   0  -0.547   0.7835   0.0028  -3.4478
 172  HC2   H  HCR6  0   0.231   2.2079  -0.0386  -1.2401
 172  HC5   H  HCR6  0   0.249  -2.7505   0.0474  -0.5975
 172  HC6   H  HCR6  0   0.216  -1.7592   0.0811  -2.8688
 172  H12   H  HNR5  0   0.418  -1.8824  -0.1267   2.1849
 172  H141  H  HNH2  0   0.359   1.3253   0.0111   3.9529
 172  H142  H  HNH2  0   0.391  -0.3143   0.2223   4.2173
 172  H17   H  HOH1  0   0.489   0.8204   0.9035  -3.7813

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
 172  C1   C2    aromatic  1.388  0.020  1.388
 172  C1   C6    aromatic  1.397  0.020  1.397
 172  C1   O17   single    1.372  0.020  1.372
 172  C2   C3    aromatic  1.391  0.020  1.391
 172  C2   HC2   single    0.930  0.020  1.080
 172  C3   C4    aromatic  1.405  0.020  1.405
 172  C3   N10   aromatic  1.375  0.020  1.375
 172  C4   C5    aromatic  1.382  0.020  1.382
 172  C4   N12   aromatic  1.379  0.020  1.379
 172  C5   C6    aromatic  1.389  0.020  1.389
 172  C5   HC5   single    0.930  0.020  1.080
 172  C6   HC6   single    0.930  0.020  1.080
 172  N10  C11   aromatic  1.309  0.020  1.309
 172  C11  N12   aromatic  1.361  0.020  1.361
 172  C11  N14   single    1.357  0.020  1.357
 172  N12  H12   single    0.860  0.020  1.020
 172  N14  H141  single    0.890  0.020  1.040
 172  N14  H142  single    0.890  0.020  1.040
 172  O17  H17   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
 172  O17   C1   C6    119.22  3.000
 172  O17   C1   C2    119.37  3.000
 172  C6    C1   C2    121.40  3.000
 172  HC2   C2   C3    121.14  3.000
 172  HC2   C2   C1    120.70  3.000
 172  C3    C2   C1    118.17  3.000
 172  N10   C3   C4    110.44  3.000
 172  N10   C3   C2    129.87  3.000
 172  C4    C3   C2    119.68  3.000
 172  N12   C4   C5    133.06  3.000
 172  N12   C4   C3    104.44  3.000
 172  C5    C4   C3    122.50  3.000
 172  HC5   C5   C6    120.81  3.000
 172  HC5   C5   C4    121.97  3.000
 172  C6    C5   C4    117.22  3.000
 172  HC6   C6   C5    119.64  3.000
 172  HC6   C6   C1    119.32  3.000
 172  C5    C6   C1    121.03  3.000
 172  C11   N10  C3    104.89  3.000
 172  N14   C11  N12   121.81  3.000
 172  N14   C11  N10   124.90  3.000
 172  N12   C11  N10   113.24  3.000
 172  H12   N12  C11   126.42  3.000
 172  H12   N12  C4    126.23  3.000
 172  C11   N12  C4    106.98  3.000
 172  H142  N14  H141  112.77  3.000
 172  H142  N14  C11   118.00  3.000
 172  H141  N14  C11   114.61  3.000
 172  H17   O17  C1    108.85  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
 172  CONST_01  C4   C3   C2   C1     0.00  0.0  0
 172  CONST_02  N10  C3   C2   C1   180.00  0.0  0
 172  CONST_03  C4   C5   C6   C1     0.00  0.0  0
 172  CONST_04  C5   C6   C1   C2     0.00  0.0  0
 172  CONST_05  C5   C4   C3   C2     0.00  0.0  0
 172  CONST_06  N12  C4   C3   C2   180.00  0.0  0
 172  CONST_07  C11  N10  C3   C2   180.00  0.0  0
 172  CONST_08  C6   C1   C2   C3     0.00  0.0  0
 172  CONST_09  C6   C5   C4   C3     0.00  0.0  0
 172  CONST_10  C11  N12  C4   C3     0.00  0.0  0
 172  CONST_11  N12  C11  N10  C3     0.00  0.0  0
 172  CONST_12  C11  N10  C3   C4     0.00  0.0  0
 172  CONST_13  N10  C11  N12  C4     0.00  0.0  0
 172  CONST_14  N10  C3   C4   C5   180.00  0.0  0
 172  CONST_15  C11  N12  C4   C5   180.00  0.0  0
 172  CONST_16  N12  C4   C5   C6   180.00  0.0  0
 172  CONST_17  N12  C4   C3   N10    0.00  0.0  0
 172  CONST_18  O17  C1   C2   C3   180.00  0.0  0
 172  CONST_19  N14  C11  N10  C3   180.00  0.0  0
 172  CONST_20  N14  C11  N12  C4   180.00  0.0  0
 172  CONST_21  O17  C1   C6   C5   180.00  0.0  0
 172  CONST_22  HC5  C5   C6   C1   180.00  0.0  0
 172  CONST_23  HC6  C6   C1   C2   180.00  0.0  0
 172  CONST_24  H12  N12  C4   C3   180.00  0.0  0
 172  CONST_25  HC2  C2   C3   C4   180.00  0.0  0

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
 172  plan-1  C1    0.020
 172  plan-1  C2    0.020
 172  plan-1  C3    0.020
 172  plan-1  C4    0.020
 172  plan-1  C5    0.020
 172  plan-1  C6    0.020
 172  plan-1  N10   0.020
 172  plan-1  C11   0.020
 172  plan-1  N12   0.020
 172  plan-1  N14   0.020
 172  plan-1  O17   0.020
 172  plan-1  HC2   0.020
 172  plan-1  HC5   0.020
 172  plan-1  HC6   0.020
 172  plan-1  H12   0.020
 172  plan-2  C11   0.020
 172  plan-2  N14   0.020
 172  plan-2  H141  0.020
 172  plan-2  H142  0.020

