# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 02:50:01 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: amino[2-(2-hydroxyphenyl)-1H-benzimidazol-6-yl]methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2nc([nH]c2c1)c3ccccc3O
#
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
 122  122  amino[2-(2-hydroxyphenyl)-1H-benzimidazol-6-yl]methaniminium  ligand  32  19  .  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_122
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
 122  C1    C  CR6   0  -0.014   3.3120  -0.0142   0.0547
 122  C2    C  CR16  0  -0.275   3.0538   1.3634   0.1837
 122  C3    C  CR16  0  -0.316   1.7639   1.8498   0.2267
 122  C4    C  CR56  0   0.236   0.7192   0.9338   0.1282
 122  C5    C  CR56  0   0.337   0.9930  -0.4389  -0.0045
 122  C6    C  CR16  0  -0.326   2.2792  -0.9426  -0.0399
 122  C7    C  C     0   0.584   4.7022  -0.4863   0.0208
 122  N1    N  NH2   0  -0.764   5.0085  -1.6230   0.5997
 122  N2    N  NC2   1  -0.765   5.6132   0.2347  -0.5872
 122  N3    N  N     0  -0.604  -0.6313   1.1257   0.1302
 122  N4    N  NR15  0  -0.729  -0.2332  -1.0403  -0.0866
 122  C8    C  CR5   0   0.607  -1.1739  -0.0697   0.0016
 122  C1'   C  CR6   0  -0.132  -2.6067  -0.2911  -0.0414
 122  C2'   C  CR16  0  -0.301  -3.1460  -1.5741  -0.1888
 122  C3'   C  CR16  0  -0.269  -4.5090  -1.7785  -0.2300
 122  C4'   C  CR16  0  -0.238  -5.3632  -0.6825  -0.1200
 122  C5'   C  CR16  0  -0.343  -4.8582   0.5943   0.0266
 122  C6'   C  CR6   0   0.350  -3.4790   0.8132   0.0661
 122  O6'   O  OH1   0  -0.631  -3.0504   2.0669   0.2029
 122  HC2   H  HCR6  0   0.280   3.8769   2.0582   0.2831
 122  HC3   H  HCR6  0   0.278   1.5721   2.9081   0.3382
 122  HC6   H  HCR6  0   0.296   2.4659  -2.0012  -0.1654
 122  HH11  H  HNH2  0   0.438   5.9379  -2.0136   0.5580
 122  HH12  H  HNH2  0   0.447   4.3438  -2.0943   1.1913
 122  HH21  H  HNC2  0   0.446   5.3536   1.0322  -1.1443
 122  HH22  H  HNC2  0   0.438   6.5900  -0.0186  -0.5814
 122  HN4   H  HNR5  0   0.436  -0.3944  -2.0310  -0.1779
 122  HC2'  H  HCR6  0   0.254  -2.4909  -2.4322  -0.2737
 122  HC3'  H  HCR6  0   0.263  -4.9058  -2.7773  -0.3467
 122  HC4'  H  HCR6  0   0.268  -6.4353  -0.8272  -0.1492
 122  HC5'  H  HCR6  0   0.270  -5.5249   1.4429   0.1111
 122  HO6   H  HOH1  0   0.478  -2.0610   2.0732   0.2101

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
 122  C1   C2    aromatic  1.407  0.020  1.407
 122  C1   C6    aromatic  1.392  0.020  1.392
 122  C1   C7    single    1.469  0.020  1.469
 122  C2   C3    aromatic  1.379  0.020  1.379
 122  C2   HC2   single    0.930  0.020  1.080
 122  C3   C4    aromatic  1.393  0.020  1.393
 122  C3   HC3   single    0.930  0.020  1.080
 122  C4   C5    aromatic  1.406  0.020  1.406
 122  C4   N3    aromatic  1.364  0.020  1.364
 122  C5   C6    aromatic  1.382  0.020  1.382
 122  C5   N4    aromatic  1.368  0.020  1.368
 122  C6   HC6   single    0.930  0.020  1.080
 122  C7   N1    single    1.312  0.020  1.312
 122  C7   N2    double    1.311  0.020  1.311
 122  N1   HH11  single    0.860  0.020  1.020
 122  N1   HH12  single    0.860  0.020  1.020
 122  N2   HH21  single    0.860  0.020  1.020
 122  N2   HH22  single    0.860  0.020  1.020
 122  N3   C8    aromatic  1.319  0.020  1.319
 122  N4   C8    aromatic  1.354  0.020  1.354
 122  N4   HN4   single    0.860  0.020  1.020
 122  C8   C1'   single    1.450  0.020  1.450
 122  C1'  C2'   aromatic  1.400  0.020  1.400
 122  C1'  C6'   aromatic  1.411  0.020  1.411
 122  C2'  C3'   aromatic  1.379  0.020  1.379
 122  C2'  HC2'  single    0.930  0.020  1.080
 122  C3'  C4'   aromatic  1.394  0.020  1.394
 122  C3'  HC3'  single    0.930  0.020  1.080
 122  C4'  C5'   aromatic  1.381  0.020  1.381
 122  C4'  HC4'  single    0.930  0.020  1.080
 122  C5'  C6'   aromatic  1.397  0.020  1.397
 122  C5'  HC5'  single    0.930  0.020  1.080
 122  C6'  O6'   single    1.332  0.020  1.332
 122  O6'  HO6   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
 122  C7    C1   C6    119.10  3.000
 122  C7    C1   C2    119.37  3.000
 122  C6    C1   C2    121.53  3.000
 122  HC2   C2   C3    118.83  3.000
 122  HC2   C2   C1    119.83  3.000
 122  C3    C2   C1    121.31  3.000
 122  HC3   C3   C4    121.19  3.000
 122  HC3   C3   C2    120.96  3.000
 122  C4    C3   C2    117.86  3.000
 122  N3    C4   C5    109.29  3.000
 122  N3    C4   C3    130.53  3.000
 122  C5    C4   C3    120.18  3.000
 122  N4    C5   C6    132.26  3.000
 122  N4    C5   C4    105.09  3.000
 122  C6    C5   C4    122.65  3.000
 122  HC6   C6   C5    121.34  3.000
 122  HC6   C6   C1    122.17  3.000
 122  C5    C6   C1    116.47  3.000
 122  N2    C7   N1    121.25  3.000
 122  N2    C7   C1    119.45  3.000
 122  N1    C7   C1    119.30  3.000
 122  HH12  N1   HH11  116.81  3.000
 122  HH12  N1   C7    120.71  3.000
 122  HH11  N1   C7    122.16  3.000
 122  HH22  N2   HH21  116.85  3.000
 122  HH22  N2   C7    122.13  3.000
 122  HH21  N2   C7    120.86  3.000
 122  C8    N3   C4    106.24  3.000
 122  HN4   N4   C8    126.82  3.000
 122  HN4   N4   C5    125.50  3.000
 122  C8    N4   C5    107.67  3.000
 122  C1'   C8   N4    125.07  3.000
 122  C1'   C8   N3    123.20  3.000
 122  N4    C8   N3    111.72  3.000
 122  C6'   C1'  C2'   119.15  3.000
 122  C6'   C1'  C8    119.26  3.000
 122  C2'   C1'  C8    121.59  3.000
 122  HC2'  C2'  C3'   118.57  3.000
 122  HC2'  C2'  C1'   120.10  3.000
 122  C3'   C2'  C1'   121.33  3.000
 122  HC3'  C3'  C4'   120.67  3.000
 122  HC3'  C3'  C2'   120.20  3.000
 122  C4'   C3'  C2'   119.13  3.000
 122  HC4'  C4'  C5'   119.26  3.000
 122  HC4'  C4'  C3'   119.99  3.000
 122  C5'   C4'  C3'   120.75  3.000
 122  HC5'  C5'  C6'   118.88  3.000
 122  HC5'  C5'  C4'   120.53  3.000
 122  C6'   C5'  C4'   120.60  3.000
 122  O6'   C6'  C5'   117.91  3.000
 122  O6'   C6'  C1'   123.05  3.000
 122  C5'   C6'  C1'   119.04  3.000
 122  HO6   O6'  C6'   109.18  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
 122  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 122  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 122  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 122  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 122  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 122  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 122  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 122  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 122  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 122  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 122  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 122  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 122  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 122  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 122  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 122  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 122  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 122  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 122  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 122  CONST_20  C2'   C1'  C8   N3   180.00   0.0  0
 122  CONST_21  C6'   C1'  C8   N3     0.00   0.0  0
 122  CONST_22  C2'   C1'  C8   N4     0.00   0.0  0
 122  CONST_23  C6'   C1'  C8   N4   180.00   0.0  0
 122  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 122  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 122  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 122  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 122  CONST_28  C5'   C6'  C1'  C2'    0.00   0.0  0
 122  CONST_29  C5'   C4'  C3'  C2'    0.00   0.0  0
 122  CONST_30  C6'   C1'  C2'  C3'    0.00   0.0  0
 122  CONST_31  C6'   C5'  C4'  C3'    0.00   0.0  0
 122  CONST_32  C7    C1   C2   C3   180.00   0.0  0
 122  CONST_33  C7    C1   C6   C5   180.00   0.0  0
 122  CONST_34  O6'   C6'  C1'  C8     0.00   0.0  0
 122  CONST_35  O6'   C6'  C1'  C2'  180.00   0.0  0
 122  CONST_36  O6'   C6'  C5'  C4'  180.00   0.0  0
 122  CONST_37  HC3   C3   C2   C1   180.00   0.0  0
 122  CONST_38  HC6   C6   C1   C2   180.00   0.0  0
 122  CONST_39  HC2   C2   C3   C4   180.00   0.0  0
 122  CONST_40  HN4   N4   C5   C4   180.00   0.0  0
 122  CONST_41  HC2'  C2'  C1'  C8     0.00   0.0  0
 122  CONST_42  HC3'  C3'  C2'  C1'  180.00   0.0  0
 122  CONST_43  HC5'  C5'  C6'  C1'  180.00   0.0  0
 122  CONST_44  HC4'  C4'  C3'  C2'  180.00   0.0  0
 122  CONST_45  HH11  N1   C7   C1   180.00   0.0  0
 122  CONST_46  HH12  N1   C7   C1     0.00   0.0  0
 122  CONST_47  HH21  N2   C7   C1     0.00   0.0  0
 122  CONST_48  HH22  N2   C7   C1   180.00   0.0  0
 122  Var_01    N1    C7   C1   C2   143.44  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
 122  plan-1  C8    0.020
 122  plan-1  C1'   0.020
 122  plan-1  C2'   0.020
 122  plan-1  C3'   0.020
 122  plan-1  C4'   0.020
 122  plan-1  C5'   0.020
 122  plan-1  C6'   0.020
 122  plan-1  O6'   0.020
 122  plan-1  HC2'  0.020
 122  plan-1  HC3'  0.020
 122  plan-1  HC4'  0.020
 122  plan-1  HC5'  0.020
 122  plan-2  C1    0.020
 122  plan-2  C2    0.020
 122  plan-2  C3    0.020
 122  plan-2  C4    0.020
 122  plan-2  C5    0.020
 122  plan-2  C6    0.020
 122  plan-2  C7    0.020
 122  plan-2  N3    0.020
 122  plan-2  N4    0.020
 122  plan-2  C8    0.020
 122  plan-2  C1'   0.020
 122  plan-2  HC2   0.020
 122  plan-2  HC3   0.020
 122  plan-2  HC6   0.020
 122  plan-2  HN4   0.020
 122  plan-3  C1    0.020
 122  plan-3  C7    0.020
 122  plan-3  N1    0.020
 122  plan-3  N2    0.020
 122  plan-3  HH11  0.020
 122  plan-3  HH12  0.020
 122  plan-3  HH21  0.020
 122  plan-3  HH22  0.020

