# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 07:41:14 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2-(2-hydroxybiphenyl-3-yl)-1H-benzimidazole-5-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2[nH]c(nc2c1)c3cccc(c3O)c4ccccc4
#
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
 130  130  2-(2-hydroxybiphenyl-3-yl)-1H-benzimidazole-5-carboximidamide  ligand  41  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_130
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
 130  C1    C  CR6   0  -0.007   0.5636   0.0206   4.6982
 130  C2    C  CR16  0  -0.299  -0.8066   0.0212   5.0223
 130  C3    C  CR16  0  -0.297  -1.7892   0.0219   4.0497
 130  C4    C  CR56  0   0.313  -1.3631   0.0112   2.7289
 130  C5    C  CR56  0   0.239  -0.0030   0.0037   2.3834
 130  C6    C  CR16  0  -0.381   0.9735   0.0118   3.3717
 130  C7    C  C     0   0.332   1.5939   0.0536   5.7745
 130  N1    N  NH2   0  -0.804   1.2548  -0.6084   6.9182
 130  N2    N  N     0  -0.643   2.7083   0.6747   5.6935
 130  N3    N  NR15  0  -0.731  -2.0339   0.0029   1.5369
 130  N4    N  N     0  -0.613   0.1158  -0.0127   1.0180
 130  C8    C  CR5   0   0.594  -1.1105  -0.0109   0.5422
 130  C1'   C  CR6   0  -0.112  -1.4192  -0.0198  -0.8778
 130  C2'   C  CR16  0  -0.314  -2.7386  -0.0043  -1.3363
 130  C3'   C  CR16  0  -0.259  -3.0185   0.0028  -2.6866
 130  C4'   C  CR16  0  -0.283  -1.9682  -0.0110  -3.5977
 130  C5'   C  CR6   0  -0.057  -0.6431  -0.0353  -3.1848
 130  C6'   C  CR6   0   0.321  -0.3587  -0.0320  -1.8087
 130  O6'   O  OH1   0  -0.623   0.9171  -0.0222  -1.4321
 130  C1B   C  CR6   0   0.092   0.4445  -0.0361  -4.1885
 130  C2B   C  CR16  0  -0.301   0.4668   0.9384  -5.1857
 130  C3B   C  CR16  0  -0.241   1.4537   0.9343  -6.1626
 130  C4B   C  CR16  0  -0.267   2.4348  -0.0471  -6.1566
 130  C5B   C  CR16  0  -0.243   2.4203  -1.0244  -5.1688
 130  C6B   C  CR16  0  -0.287   1.4362  -1.0182  -4.1916
 130  HC2   H  HCR6  0   0.265  -1.1061   0.0435   6.0617
 130  HC3   H  HCR6  0   0.275  -2.8382   0.0350   4.3127
 130  HC6   H  HCR6  0   0.268   2.0227  -0.0118   3.1049
 130  HH11  H  HNH2  0   0.383   1.9869  -0.7055   7.6043
 130  HH12  H  HNH2  0   0.391   0.6580  -1.4152   6.8400
 130  HH21  H  H     0   0.332   2.7599   1.2068   4.8326
 130  HN3   H  HNR5  0   0.432  -3.0355   0.0050   1.4291
 130  HC'2  H  HCR6  0   0.253  -3.5613   0.0038  -0.6327
 130  HC'3  H  HCR6  0   0.261  -4.0427   0.0133  -3.0321
 130  HC'4  H  HCR6  0   0.262  -2.1821  -0.0180  -4.6595
 130  HO6   H  HOH1  0   0.477   0.9628  -0.0193  -0.4399
 130  H2'   H  HCR6  0   0.253  -0.2881   1.7151  -5.1924
 130  H3'   H  HCR6  0   0.257   1.4565   1.7021  -6.9252
 130  H4'   H  HCR6  0   0.257   3.2049  -0.0527  -6.9168
 130  H5'   H  HCR6  0   0.256   3.1774  -1.7978  -5.1605
 130  H6'   H  HCR6  0   0.249   1.4308  -1.7948  -3.4382

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
 130  C1   C2    aromatic  1.408  0.020  1.408
 130  C1   C6    aromatic  1.388  0.020  1.388
 130  C1   C7    single    1.490  0.020  1.490
 130  C2   C3    aromatic  1.383  0.020  1.383
 130  C2   HC2   single    0.930  0.020  1.080
 130  C3   C4    aromatic  1.388  0.020  1.388
 130  C3   HC3   single    0.930  0.020  1.080
 130  C4   C5    aromatic  1.403  0.020  1.403
 130  C4   N3    aromatic  1.368  0.020  1.368
 130  C5   C6    aromatic  1.389  0.020  1.389
 130  C5   N4    aromatic  1.371  0.020  1.371
 130  C6   HC6   single    0.930  0.020  1.080
 130  C7   N1    single    1.364  0.020  1.364
 130  C7   N2    double    1.278  0.020  1.278
 130  N1   HH11  single    0.890  0.020  1.040
 130  N1   HH12  single    0.890  0.020  1.040
 130  N2   HH21  single    0.890  0.020  1.040
 130  N3   C8    aromatic  1.357  0.020  1.357
 130  N3   HN3   single    0.860  0.020  1.020
 130  N4   C8    aromatic  1.315  0.020  1.315
 130  C8   C1'   single    1.453  0.020  1.453
 130  C1'  C2'   aromatic  1.397  0.020  1.397
 130  C1'  C6'   aromatic  1.411  0.020  1.411
 130  C2'  C3'   aromatic  1.379  0.020  1.379
 130  C2'  HC'2  single    0.930  0.020  1.080
 130  C3'  C4'   aromatic  1.390  0.020  1.390
 130  C3'  HC'3  single    0.930  0.020  1.080
 130  C4'  C5'   aromatic  1.388  0.020  1.388
 130  C4'  HC'4  single    0.930  0.020  1.080
 130  C5'  C6'   aromatic  1.405  0.020  1.405
 130  C5'  C1B   single    1.480  0.020  1.480
 130  C6'  O6'   single    1.330  0.020  1.330
 130  O6'  HO6   single    0.850  0.020  0.980
 130  C1B  C2B   aromatic  1.394  0.020  1.394
 130  C1B  C6B   aromatic  1.396  0.020  1.396
 130  C2B  C3B   aromatic  1.389  0.020  1.389
 130  C2B  H2'   single    0.930  0.020  1.080
 130  C3B  C4B   aromatic  1.388  0.020  1.388
 130  C3B  H3'   single    0.930  0.020  1.080
 130  C4B  C5B   aromatic  1.390  0.020  1.390
 130  C4B  H4'   single    0.930  0.020  1.080
 130  C5B  C6B   aromatic  1.387  0.020  1.387
 130  C5B  H5'   single    0.930  0.020  1.080
 130  C6B  H6'   single    0.930  0.020  1.080

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
 130  C7    C1   C6    119.08  3.000
 130  C7    C1   C2    120.44  3.000
 130  C6    C1   C2    120.48  3.000
 130  HC2   C2   C3    118.63  3.000
 130  HC2   C2   C1    119.37  3.000
 130  C3    C2   C1    121.99  3.000
 130  HC3   C3   C4    121.96  3.000
 130  HC3   C3   C2    121.21  3.000
 130  C4    C3   C2    116.82  3.000
 130  N3    C4   C5    105.12  3.000
 130  N3    C4   C3    132.75  3.000
 130  C5    C4   C3    122.13  3.000
 130  N4    C5   C6    130.37  3.000
 130  N4    C5   C4    109.23  3.000
 130  C6    C5   C4    120.40  3.000
 130  HC6   C6   C5    120.37  3.000
 130  HC6   C6   C1    121.44  3.000
 130  C5    C6   C1    118.17  3.000
 130  N2    C7   N1    120.37  3.000
 130  N2    C7   C1    124.59  3.000
 130  N1    C7   C1    115.01  3.000
 130  HH12  N1   HH11  113.97  3.000
 130  HH12  N1   C7    118.11  3.000
 130  HH11  N1   C7    115.90  3.000
 130  HH21  N2   C7    110.69  3.000
 130  HN3   N3   C8    126.73  3.000
 130  HN3   N3   C4    125.51  3.000
 130  C8    N3   C4    107.76  3.000
 130  C8    N4   C5    106.23  3.000
 130  C1'   C8   N4    123.47  3.000
 130  C1'   C8   N3    124.86  3.000
 130  N4    C8   N3    111.67  3.000
 130  C6'   C1'  C2'   119.56  3.000
 130  C6'   C1'  C8    119.01  3.000
 130  C2'   C1'  C8    121.42  3.000
 130  HC'2  C2'  C3'   118.83  3.000
 130  HC'2  C2'  C1'   120.29  3.000
 130  C3'   C2'  C1'   120.88  3.000
 130  HC'3  C3'  C4'   120.42  3.000
 130  HC'3  C3'  C2'   120.35  3.000
 130  C4'   C3'  C2'   119.23  3.000
 130  HC'4  C4'  C5'   118.68  3.000
 130  HC'4  C4'  C3'   119.56  3.000
 130  C5'   C4'  C3'   121.75  3.000
 130  C1B   C5'  C6'   121.02  3.000
 130  C1B   C5'  C4'   119.99  3.000
 130  C6'   C5'  C4'   118.98  3.000
 130  O6'   C6'  C5'   118.12  3.000
 130  O6'   C6'  C1'   122.27  3.000
 130  C5'   C6'  C1'   119.60  3.000
 130  HO6   O6'  C6'   109.08  3.000
 130  C6B   C1B  C2B   118.61  3.000
 130  C6B   C1B  C5'   121.61  3.000
 130  C2B   C1B  C5'   119.76  3.000
 130  H2'   C2B  C3B   119.54  3.000
 130  H2'   C2B  C1B   119.63  3.000
 130  C3B   C2B  C1B   120.82  3.000
 130  H3'   C3B  C4B   120.19  3.000
 130  H3'   C3B  C2B   119.71  3.000
 130  C4B   C3B  C2B   120.10  3.000
 130  H4'   C4B  C5B   120.21  3.000
 130  H4'   C4B  C3B   120.25  3.000
 130  C5B   C4B  C3B   119.54  3.000
 130  H5'   C5B  C6B   119.61  3.000
 130  H5'   C5B  C4B   120.05  3.000
 130  C6B   C5B  C4B   120.34  3.000
 130  H6'   C6B  C5B   119.40  3.000
 130  H6'   C6B  C1B   120.00  3.000
 130  C5B   C6B  C1B   120.59  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
 130  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 130  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 130  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 130  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 130  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 130  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 130  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 130  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 130  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 130  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 130  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 130  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 130  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 130  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 130  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 130  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 130  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 130  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 130  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 130  CONST_20  C2'   C1'  C8   N3     0.00   0.0  0
 130  CONST_21  C6'   C1'  C8   N3   180.00   0.0  0
 130  CONST_22  C2'   C1'  C8   N4   180.00   0.0  0
 130  CONST_23  C6'   C1'  C8   N4     0.00   0.0  0
 130  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 130  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 130  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 130  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 130  CONST_28  C1B   C5'  C6'  C1'  180.00   0.0  0
 130  CONST_29  C5'   C6'  C1'  C2'    0.00   0.0  0
 130  CONST_30  C5'   C4'  C3'  C2'    0.00   0.0  0
 130  CONST_31  C6'   C1'  C2'  C3'    0.00   0.0  0
 130  CONST_32  C6'   C5'  C4'  C3'    0.00   0.0  0
 130  CONST_33  C1B   C5'  C4'  C3'  180.00   0.0  0
 130  CONST_36  C3B   C2B  C1B  C5'  180.00   0.0  0
 130  CONST_37  C5B   C6B  C1B  C5'  180.00   0.0  0
 130  CONST_40  C4B   C3B  C2B  C1B    0.00   0.0  0
 130  CONST_41  C4B   C5B  C6B  C1B    0.00   0.0  0
 130  CONST_42  C5B   C6B  C1B  C2B    0.00   0.0  0
 130  CONST_43  C5B   C4B  C3B  C2B    0.00   0.0  0
 130  CONST_44  C6B   C1B  C2B  C3B    0.00   0.0  0
 130  CONST_45  C6B   C5B  C4B  C3B    0.00   0.0  0
 130  CONST_46  C7    C1   C2   C3   180.00   0.0  0
 130  CONST_47  C7    C1   C6   C5   180.00   0.0  0
 130  CONST_48  O6'   C6'  C1'  C8     0.00   0.0  0
 130  CONST_49  O6'   C6'  C1'  C2'  180.00   0.0  0
 130  CONST_50  O6'   C6'  C5'  C4'  180.00   0.0  0
 130  CONST_51  C1B   C5'  C6'  O6'    0.00   0.0  0
 130  CONST_52  HC3   C3   C2   C1   180.00   0.0  0
 130  CONST_53  HC6   C6   C1   C2   180.00   0.0  0
 130  CONST_54  HN3   N3   C4   C3     0.00   0.0  0
 130  CONST_55  HC2   C2   C3   C4   180.00   0.0  0
 130  CONST_56  HC'2  C2'  C1'  C8     0.00   0.0  0
 130  CONST_57  HC'3  C3'  C2'  C1'  180.00   0.0  0
 130  CONST_58  HC'4  C4'  C3'  C2'  180.00   0.0  0
 130  CONST_59  H2'   C2B  C1B  C5'    0.00   0.0  0
 130  CONST_60  H6'   C6B  C1B  C5'    0.00   0.0  0
 130  CONST_61  H3'   C3B  C2B  C1B  180.00   0.0  0
 130  CONST_62  H5'   C5B  C6B  C1B  180.00   0.0  0
 130  CONST_63  H4'   C4B  C3B  C2B  180.00   0.0  0
 130  CONST_64  HH11  N1   C7   C1   180.00   0.0  0
 130  CONST_66  HH21  N2   C7   C1     0.00   0.0  0
 130  Var_01    N1    C7   C1   C2    33.86  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
 130  plan-1  C8    0.020
 130  plan-1  C1'   0.020
 130  plan-1  C2'   0.020
 130  plan-1  C3'   0.020
 130  plan-1  C4'   0.020
 130  plan-1  C5'   0.020
 130  plan-1  C6'   0.020
 130  plan-1  O6'   0.020
 130  plan-1  C1B   0.020
 130  plan-1  HC'2  0.020
 130  plan-1  HC'3  0.020
 130  plan-1  HC'4  0.020
 130  plan-2  C5'   0.020
 130  plan-2  C1B   0.020
 130  plan-2  C2B   0.020
 130  plan-2  C3B   0.020
 130  plan-2  C4B   0.020
 130  plan-2  C5B   0.020
 130  plan-2  C6B   0.020
 130  plan-2  H2'   0.020
 130  plan-2  H3'   0.020
 130  plan-2  H4'   0.020
 130  plan-2  H5'   0.020
 130  plan-2  H6'   0.020
 130  plan-3  C1    0.020
 130  plan-3  C2    0.020
 130  plan-3  C3    0.020
 130  plan-3  C4    0.020
 130  plan-3  C5    0.020
 130  plan-3  C6    0.020
 130  plan-3  C7    0.020
 130  plan-3  N3    0.020
 130  plan-3  N4    0.020
 130  plan-3  C8    0.020
 130  plan-3  C1'   0.020
 130  plan-3  HC2   0.020
 130  plan-3  HC3   0.020
 130  plan-3  HC6   0.020
 130  plan-3  HN3   0.020
 130  plan-4  C1    0.020
 130  plan-4  C7    0.020
 130  plan-4  N1    0.020
 130  plan-4  N2    0.020
 130  plan-4  HH11  0.020
 130  plan-4  HH12  0.020
 130  plan-4  HH21  0.020

