# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 22:45:03 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: amino[2-(2-hydroxy-5-methoxyphenyl)-1H-benzimidazol-5-yl]methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(O)c(c1)c2[nH]c3ccc(cc3n2)C(N)=[NH2+]
#
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
 123  123  amino[2-(2-hydroxy-5-methoxyphenyl)-1H-benzimidazol-5-yl]methaniminium  ligand  36  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_123
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
 123  C1    C  CR6   0  -0.001  -3.9214  -0.2649  -0.0225
 123  C2    C  CR16  0  -0.290  -3.9592   1.1435  -0.0544
 123  C3    C  CR16  0  -0.294  -2.8003   1.8913  -0.0563
 123  C4    C  CR56  0   0.353  -1.6003   1.1903  -0.0357
 123  C5    C  CR56  0   0.187  -1.5433  -0.2155  -0.0060
 123  C6    C  CR16  0  -0.360  -2.7167  -0.9582   0.0051
 123  C7    C  C     0   0.585  -5.1823  -1.0157  -0.0190
 123  N1    N  NH2   0  -0.768  -6.2064  -0.5615  -0.7019
 123  N2    N  NC2   1  -0.767  -5.2689  -2.1315   0.6668
 123  N3    N  NR15  0  -0.731  -0.3012   1.5875  -0.0389
 123  N4    N  N     0  -0.483  -0.2421  -0.6308   0.0029
 123  C8    C  CR5   0   0.522   0.4760   0.4657  -0.0160
 123  C1'   C  CR6   0  -0.086   1.9384   0.4710  -0.0164
 123  C2'   C  CR16  0  -0.401   2.5886  -0.7623  -0.0169
 123  C3'   C  CR6   0   0.400   3.9728  -0.8575  -0.0219
 123  O3'   O  O2    0  -0.477   4.4905  -2.1042  -0.0247
 123  CM3   C  CH3   0  -0.437   5.8959  -2.2459  -0.0581
 123  C4'   C  CR16  0  -0.366   4.7279   0.3129  -0.0243
 123  C5'   C  CR16  0  -0.357   4.0926   1.5450  -0.0226
 123  C6'   C  CR6   0   0.333   2.7089   1.6433  -0.0200
 123  O6'   O  OH1   0  -0.650   2.0784   2.8364  -0.0197
 123  HC2   H  HCR6  0   0.279  -4.9093   1.6614  -0.0464
 123  HC3   H  HCR6  0   0.283  -2.8352   2.9718  -0.0664
 123  HC6   H  HCR6  0   0.281  -2.6773  -2.0400   0.0025
 123  HH11  H  HNH2  0   0.445  -6.1020   0.2196  -1.3287
 123  HH12  H  HNH2  0   0.437  -7.1108  -1.0082  -0.6747
 123  HH21  H  HNC2  0   0.437  -6.0997  -2.7039   0.6558
 123  HH22  H  HNC2  0   0.446  -4.5365  -2.4032   1.3023
 123  HN3   H  HNR5  0   0.433   0.0397   2.5369  -0.0595
 123  HC2'  H  HCR6  0   0.270   1.9924  -1.6656  -0.0155
 123  H3'1  H  HCH3  0   0.227   6.3745  -1.8133   0.8251
 123  H3'2  H  HCH3  0   0.260   6.0984  -3.3140  -0.0744
 123  H3'3  H  HCH3  0   0.227   6.3331  -1.7929  -0.9523
 123  HC4'  H  HCR6  0   0.290   5.8088   0.2934  -0.0286
 123  HC5'  H  HCR6  0   0.283   4.6948   2.4460  -0.0245
 123  HO6   H  HOH1  0   0.488   2.7101   3.5644  -0.0475

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
 123  C1   C2    aromatic  1.409  0.020  1.409
 123  C1   C6    aromatic  1.390  0.020  1.390
 123  C1   C7    single    1.467  0.020  1.467
 123  C2   C3    aromatic  1.379  0.020  1.379
 123  C2   HC2   single    0.930  0.020  1.080
 123  C3   C4    aromatic  1.390  0.020  1.390
 123  C3   HC3   single    0.930  0.020  1.080
 123  C4   C5    aromatic  1.407  0.020  1.407
 123  C4   N3    aromatic  1.359  0.020  1.359
 123  C5   C6    aromatic  1.389  0.020  1.389
 123  C5   N4    aromatic  1.366  0.020  1.366
 123  C6   HC6   single    0.930  0.020  1.080
 123  C7   N1    single    1.312  0.020  1.312
 123  C7   N2    double    1.313  0.020  1.313
 123  N1   HH11  single    0.860  0.020  1.020
 123  N1   HH12  single    0.860  0.020  1.020
 123  N2   HH21  single    0.860  0.020  1.020
 123  N2   HH22  single    0.860  0.020  1.020
 123  N3   C8    aromatic  1.365  0.020  1.365
 123  N3   HN3   single    0.860  0.020  1.020
 123  N4   C8    aromatic  1.311  0.020  1.311
 123  C8   C1'   single    1.462  0.020  1.462
 123  C1'  C2'   aromatic  1.394  0.020  1.394
 123  C1'  C6'   aromatic  1.403  0.020  1.403
 123  C2'  C3'   aromatic  1.387  0.020  1.387
 123  C2'  HC2'  single    0.930  0.020  1.080
 123  C3'  O3'   single    1.350  0.020  1.350
 123  C3'  C4'   aromatic  1.393  0.020  1.393
 123  O3'  CM3   single    1.413  0.020  1.413
 123  CM3  H3'1  single    0.970  0.020  1.090
 123  CM3  H3'2  single    0.970  0.020  1.090
 123  CM3  H3'3  single    0.970  0.020  1.090
 123  C4'  C5'   aromatic  1.386  0.020  1.386
 123  C4'  HC4'  single    0.930  0.020  1.080
 123  C5'  C6'   aromatic  1.387  0.020  1.387
 123  C5'  HC5'  single    0.930  0.020  1.080
 123  C6'  O6'   single    1.350  0.020  1.350
 123  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
 123  C7    C1   C6    119.30  3.000
 123  C7    C1   C2    119.23  3.000
 123  C6    C1   C2    121.47  3.000
 123  HC2   C2   C3    118.57  3.000
 123  HC2   C2   C1    120.11  3.000
 123  C3    C2   C1    121.29  3.000
 123  HC3   C3   C4    122.14  3.000
 123  HC3   C3   C2    120.98  3.000
 123  C4    C3   C2    116.87  3.000
 123  N3    C4   C5    104.68  3.000
 123  N3    C4   C3    132.70  3.000
 123  C5    C4   C3    122.63  3.000
 123  N4    C5   C6    129.96  3.000
 123  N4    C5   C4    110.03  3.000
 123  C6    C5   C4    120.01  3.000
 123  HC6   C6   C5    120.24  3.000
 123  HC6   C6   C1    121.99  3.000
 123  C5    C6   C1    117.73  3.000
 123  N2    C7   N1    120.98  3.000
 123  N2    C7   C1    119.53  3.000
 123  N1    C7   C1    119.49  3.000
 123  HH12  N1   HH11  116.95  3.000
 123  HH12  N1   C7    122.16  3.000
 123  HH11  N1   C7    120.77  3.000
 123  HH22  N2   HH21  116.91  3.000
 123  HH22  N2   C7    120.74  3.000
 123  HH21  N2   C7    122.07  3.000
 123  HN3   N3   C8    125.55  3.000
 123  HN3   N3   C4    126.75  3.000
 123  C8    N3   C4    107.71  3.000
 123  C8    N4   C5    105.51  3.000
 123  C1'   C8   N4    123.43  3.000
 123  C1'   C8   N3    124.50  3.000
 123  N4    C8   N3    112.07  3.000
 123  C6'   C1'  C2'   118.89  3.000
 123  C6'   C1'  C8    123.52  3.000
 123  C2'   C1'  C8    117.59  3.000
 123  HC2'  C2'  C3'   119.49  3.000
 123  HC2'  C2'  C1'   118.77  3.000
 123  C3'   C2'  C1'   121.73  3.000
 123  C4'   C3'  O3'   124.62  3.000
 123  C4'   C3'  C2'   118.90  3.000
 123  O3'   C3'  C2'   116.49  3.000
 123  CM3   O3'  C3'   118.31  3.000
 123  H3'3  CM3  H3'2  108.67  3.000
 123  H3'3  CM3  H3'1  108.75  3.000
 123  H3'2  CM3  H3'1  108.62  3.000
 123  H3'3  CM3  O3'   112.05  3.000
 123  H3'2  CM3  O3'   106.51  3.000
 123  H3'1  CM3  O3'   112.12  3.000
 123  HC4'  C4'  C5'   118.31  3.000
 123  HC4'  C4'  C3'   121.80  3.000
 123  C5'   C4'  C3'   119.89  3.000
 123  HC5'  C5'  C6'   119.69  3.000
 123  HC5'  C5'  C4'   118.97  3.000
 123  C6'   C5'  C4'   121.34  3.000
 123  O6'   C6'  C5'   121.92  3.000
 123  O6'   C6'  C1'   118.83  3.000
 123  C5'   C6'  C1'   119.25  3.000
 123  HO6   O6'  C6'   111.19  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
 123  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 123  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 123  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 123  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 123  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 123  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 123  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 123  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 123  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 123  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 123  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 123  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 123  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 123  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 123  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 123  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 123  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 123  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 123  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 123  CONST_20  C2'   C1'  C8   N3   180.00   0.0  0
 123  CONST_21  C6'   C1'  C8   N3     0.00   0.0  0
 123  CONST_22  C2'   C1'  C8   N4     0.00   0.0  0
 123  CONST_23  C6'   C1'  C8   N4   180.00   0.0  0
 123  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 123  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 123  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 123  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 123  CONST_28  C5'   C6'  C1'  C2'    0.00   0.0  0
 123  CONST_29  C5'   C4'  C3'  C2'    0.00   0.0  0
 123  CONST_30  C6'   C1'  C2'  C3'    0.00   0.0  0
 123  CONST_31  C6'   C5'  C4'  C3'    0.00   0.0  0
 123  CONST_32  C7    C1   C2   C3   180.00   0.0  0
 123  CONST_33  C7    C1   C6   C5   180.00   0.0  0
 123  CONST_34  O6'   C6'  C1'  C8     0.00   0.0  0
 123  CONST_35  O3'   C3'  C2'  C1'  180.00   0.0  0
 123  CONST_36  O6'   C6'  C1'  C2'  180.00   0.0  0
 123  CONST_37  C5'   C4'  C3'  O3'  180.00   0.0  0
 123  CONST_38  O6'   C6'  C5'  C4'  180.00   0.0  0
 123  CONST_39  HC3   C3   C2   C1   180.00   0.0  0
 123  CONST_40  HC6   C6   C1   C2   180.00   0.0  0
 123  CONST_41  HN3   N3   C4   C3     0.00   0.0  0
 123  CONST_42  HC2   C2   C3   C4   180.00   0.0  0
 123  CONST_43  HC2'  C2'  C1'  C8     0.00   0.0  0
 123  CONST_44  HC5'  C5'  C6'  C1'  180.00   0.0  0
 123  CONST_45  HC4'  C4'  C3'  C2'  180.00   0.0  0
 123  CONST_46  HH11  N1   C7   C1     0.00   0.0  0
 123  CONST_47  HH12  N1   C7   C1   180.00   0.0  0
 123  CONST_48  HH21  N2   C7   C1   180.00   0.0  0
 123  CONST_49  HH22  N2   C7   C1     0.00   0.0  0
 123  Var_01    N1    C7   C1   C2    35.41  30.0  2
 123  Var_02    C4'   C3'  O3'  CM3   -1.26  30.0  2
 123  Var_03    H3'1  CM3  O3'  C3'   62.41  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
 123  plan-1  C8    0.020
 123  plan-1  C1'   0.020
 123  plan-1  C2'   0.020
 123  plan-1  C3'   0.020
 123  plan-1  O3'   0.020
 123  plan-1  C4'   0.020
 123  plan-1  C5'   0.020
 123  plan-1  C6'   0.020
 123  plan-1  O6'   0.020
 123  plan-1  HC2'  0.020
 123  plan-1  HC4'  0.020
 123  plan-1  HC5'  0.020
 123  plan-2  C1    0.020
 123  plan-2  C2    0.020
 123  plan-2  C3    0.020
 123  plan-2  C4    0.020
 123  plan-2  C5    0.020
 123  plan-2  C6    0.020
 123  plan-2  C7    0.020
 123  plan-2  N3    0.020
 123  plan-2  N4    0.020
 123  plan-2  C8    0.020
 123  plan-2  C1'   0.020
 123  plan-2  HC2   0.020
 123  plan-2  HC3   0.020
 123  plan-2  HC6   0.020
 123  plan-2  HN3   0.020
 123  plan-3  C1    0.020
 123  plan-3  C7    0.020
 123  plan-3  N1    0.020
 123  plan-3  N2    0.020
 123  plan-3  HH11  0.020
 123  plan-3  HH12  0.020
 123  plan-3  HH21  0.020
 123  plan-3  HH22  0.020

