# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:36:31 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}biphenyl-2-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3cccc(c3[O-])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
 780  780  3-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}biphenyl-2-olate  ligand  41  25  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_780
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
 780  C1    C  CR6    0   0.002   4.8382   0.4496  -0.0604
 780  C2    C  CR16   0  -0.297   5.0202  -0.8380  -0.5975
 780  C3    C  CR16   0  -0.300   3.9519  -1.6927  -0.7896
 780  C4    C  CR56   0   0.359   2.6967  -1.2254  -0.4233
 780  C5    C  CR56   0   0.159   2.4913   0.0644   0.1075
 780  C6    C  CR16   0  -0.375   3.5720   0.9137   0.2929
 780  C7    C  C      0   0.585   6.0032   1.3176   0.1336
 780  N1    N  NH2    0  -0.771   5.8758   2.6177  -0.0000
 780  N2    N  NC2    1  -0.772   7.1655   0.7877   0.4395
 780  N3    N  NR15   0  -0.718   1.4562  -1.7752  -0.4587
 780  N4    N  N      0  -0.470   1.1660   0.2625   0.3764
 780  C8    C  CR5    0   0.465   0.5604  -0.8505   0.0290
 780  C1'   C  CR6    0  -0.224  -0.8510  -1.1681   0.1421
 780  C2'   C  CR16   0  -0.287  -1.2235  -2.4983   0.3616
 780  C3'   C  CR16   0  -0.316  -2.5466  -2.8736   0.4726
 780  C4'   C  CR16   0  -0.283  -3.5270  -1.8856   0.3556
 780  C5'   C  CR6    0  -0.144  -3.2174  -0.5563   0.1378
 780  C6'   C  CR6    0   0.285  -1.8390  -0.1203   0.0080
 780  O6'   O  OC    -1  -0.547  -1.5409   1.0705  -0.2362
 780  C1B   C  CR6    0   0.109  -4.3118   0.4258   0.0067
 780  C2B   C  CR16   0  -0.322  -5.4458   0.1187  -0.7516
 780  C3B   C  CR16   0  -0.243  -6.5135   1.0011  -0.8498
 780  C4B   C  CR16   0  -0.279  -6.4703   2.2231  -0.1935
 780  C5B   C  CR16   0  -0.246  -5.3484   2.5475   0.5606
 780  C6B   C  CR16   0  -0.298  -4.2818   1.6657   0.6548
 780  HC2   H  HCR6   0   0.273   6.0063  -1.1659  -0.8980
 780  HC3   H  HCR6   0   0.278   4.0981  -2.6771  -1.2126
 780  HC6   H  HCR6   0   0.272   3.4228   1.8929   0.7302
 780  HH11  H  HNH2   0   0.444   5.0281   3.0197  -0.3648
 780  HH12  H  HNH2   0   0.435   6.6315   3.2537   0.2033
 780  HH21  H  HNC2   0   0.435   8.0047   1.3427   0.5130
 780  HH22  H  HNC2   0   0.443   7.2428  -0.1875   0.6771
 780  HN3   H  HNR5   0   0.421   1.2219  -2.6769  -0.8426
 780  HC2'  H  HCR6   0   0.236  -0.4580  -3.2568   0.4860
 780  HC3'  H  HCR6   0   0.231  -2.8178  -3.9019   0.6685
 780  HC4'  H  HCR6   0   0.237  -4.5692  -2.1687   0.4629
 780  H2B   H  HCR6   0   0.241  -5.4874  -0.8238  -1.2850
 780  H3B   H  HCR6   0   0.247  -7.3760   0.7345  -1.4480
 780  H4B   H  HCR6   0   0.249  -7.2984   2.9161  -0.2684
 780  H5B   H  HCR6   0   0.246  -5.3049   3.4954   1.0829
 780  H6B   H  HCR6   0   0.237  -3.4253   1.9363   1.2556

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
 780  C1   C2    aromatic  1.407  0.020  1.407
 780  C1   C6    aromatic  1.394  0.020  1.394
 780  C1   C7    single    1.466  0.020  1.466
 780  C2   C3    aromatic  1.382  0.020  1.382
 780  C2   HC2   single    0.930  0.020  1.080
 780  C3   C4    aromatic  1.389  0.020  1.389
 780  C3   HC3   single    0.930  0.020  1.080
 780  C4   C5    aromatic  1.410  0.020  1.410
 780  C4   N3    aromatic  1.357  0.020  1.357
 780  C5   C6    aromatic  1.387  0.020  1.387
 780  C5   N4    aromatic  1.367  0.020  1.367
 780  C6   HC6   single    0.930  0.020  1.080
 780  C7   N1    single    1.313  0.020  1.313
 780  C7   N2    double    1.313  0.020  1.313
 780  N1   HH11  single    0.860  0.020  1.020
 780  N1   HH12  single    0.860  0.020  1.020
 780  N2   HH21  single    0.860  0.020  1.020
 780  N2   HH22  single    0.860  0.020  1.020
 780  N3   C8    aromatic  1.377  0.020  1.377
 780  N3   HN3   single    0.860  0.020  1.020
 780  N4   C8    aromatic  1.314  0.020  1.314
 780  C8   C1'   single    1.451  0.020  1.451
 780  C1'  C2'   aromatic  1.399  0.020  1.399
 780  C1'  C6'   aromatic  1.446  0.020  1.446
 780  C2'  C3'   aromatic  1.380  0.020  1.380
 780  C2'  HC2'  single    0.930  0.020  1.080
 780  C3'  C4'   aromatic  1.397  0.020  1.397
 780  C3'  HC3'  single    0.930  0.020  1.080
 780  C4'  C5'   aromatic  1.382  0.020  1.382
 780  C4'  HC4'  single    0.930  0.020  1.080
 780  C5'  C6'   aromatic  1.452  0.020  1.452
 780  C5'  C1B   single    1.476  0.020  1.476
 780  C6'  O6'   single    1.252  0.020  1.252
 780  C1B  C2B   aromatic  1.398  0.020  1.398
 780  C1B  C6B   aromatic  1.399  0.020  1.399
 780  C2B  C3B   aromatic  1.389  0.020  1.389
 780  C2B  H2B   single    0.930  0.020  1.080
 780  C3B  C4B   aromatic  1.388  0.020  1.388
 780  C3B  H3B   single    0.930  0.020  1.080
 780  C4B  C5B   aromatic  1.390  0.020  1.390
 780  C4B  H4B   single    0.930  0.020  1.080
 780  C5B  C6B   aromatic  1.387  0.020  1.387
 780  C5B  H5B   single    0.930  0.020  1.080
 780  C6B  H6B   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
 780  C7    C1   C6    119.43  3.000
 780  C7    C1   C2    119.32  3.000
 780  C6    C1   C2    121.26  3.000
 780  HC2   C2   C3    118.60  3.000
 780  HC2   C2   C1    120.09  3.000
 780  C3    C2   C1    121.28  3.000
 780  HC3   C3   C4    122.13  3.000
 780  HC3   C3   C2    120.86  3.000
 780  C4    C3   C2    117.01  3.000
 780  N3    C4   C5    104.31  3.000
 780  N3    C4   C3    133.08  3.000
 780  C5    C4   C3    122.61  3.000
 780  N4    C5   C6    129.83  3.000
 780  N4    C5   C4    110.36  3.000
 780  C6    C5   C4    119.81  3.000
 780  HC6   C6   C5    120.03  3.000
 780  HC6   C6   C1    121.91  3.000
 780  C5    C6   C1    118.03  3.000
 780  N2    C7   N1    120.60  3.000
 780  N2    C7   C1    119.69  3.000
 780  N1    C7   C1    119.71  3.000
 780  HH12  N1   HH11  116.90  3.000
 780  HH12  N1   C7    122.08  3.000
 780  HH11  N1   C7    120.93  3.000
 780  HH22  N2   HH21  116.86  3.000
 780  HH22  N2   C7    120.91  3.000
 780  HH21  N2   C7    122.08  3.000
 780  HN3   N3   C8    125.78  3.000
 780  HN3   N3   C4    125.79  3.000
 780  C8    N3   C4    108.26  3.000
 780  C8    N4   C5    105.79  3.000
 780  C1'   C8   N4    127.82  3.000
 780  C1'   C8   N3    120.90  3.000
 780  N4    C8   N3    111.27  3.000
 780  C6'   C1'  C2'   121.44  3.000
 780  C6'   C1'  C8    119.91  3.000
 780  C2'   C1'  C8    118.65  3.000
 780  HC2'  C2'  C3'   118.51  3.000
 780  HC2'  C2'  C1'   119.67  3.000
 780  C3'   C2'  C1'   121.78  3.000
 780  HC3'  C3'  C4'   120.79  3.000
 780  HC3'  C3'  C2'   120.91  3.000
 780  C4'   C3'  C2'   118.29  3.000
 780  HC4'  C4'  C5'   118.79  3.000
 780  HC4'  C4'  C3'   118.77  3.000
 780  C5'   C4'  C3'   122.43  3.000
 780  C1B   C5'  C6'   119.75  3.000
 780  C1B   C5'  C4'   119.19  3.000
 780  C6'   C5'  C4'   121.05  3.000
 780  O6'   C6'  C5'   121.97  3.000
 780  O6'   C6'  C1'   123.00  3.000
 780  C5'   C6'  C1'   115.01  3.000
 780  C6B   C1B  C2B   117.59  3.000
 780  C6B   C1B  C5'   122.17  3.000
 780  C2B   C1B  C5'   120.22  3.000
 780  H2B   C2B  C3B   119.23  3.000
 780  H2B   C2B  C1B   119.28  3.000
 780  C3B   C2B  C1B   121.49  3.000
 780  H3B   C3B  C4B   120.19  3.000
 780  H3B   C3B  C2B   119.67  3.000
 780  C4B   C3B  C2B   120.14  3.000
 780  H4B   C4B  C5B   120.37  3.000
 780  H4B   C4B  C3B   120.48  3.000
 780  C5B   C4B  C3B   119.15  3.000
 780  H5B   C5B  C6B   119.52  3.000
 780  H5B   C5B  C4B   119.88  3.000
 780  C6B   C5B  C4B   120.60  3.000
 780  H6B   C6B  C5B   119.22  3.000
 780  H6B   C6B  C1B   119.75  3.000
 780  C5B   C6B  C1B   121.02  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
 780  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 780  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 780  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 780  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 780  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 780  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 780  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 780  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 780  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 780  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 780  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 780  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 780  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 780  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 780  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 780  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 780  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 780  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 780  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 780  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 780  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 780  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 780  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 780  CONST_28  C1B   C5'  C6'  C1'  180.00   0.0  0
 780  CONST_29  C5'   C6'  C1'  C2'    0.00   0.0  0
 780  CONST_30  C5'   C4'  C3'  C2'    0.00   0.0  0
 780  CONST_31  C6'   C1'  C2'  C3'    0.00   0.0  0
 780  CONST_32  C6'   C5'  C4'  C3'    0.00   0.0  0
 780  CONST_33  C1B   C5'  C4'  C3'  180.00   0.0  0
 780  CONST_36  C3B   C2B  C1B  C5'  180.00   0.0  0
 780  CONST_37  C5B   C6B  C1B  C5'  180.00   0.0  0
 780  CONST_40  C4B   C3B  C2B  C1B    0.00   0.0  0
 780  CONST_41  C4B   C5B  C6B  C1B    0.00   0.0  0
 780  CONST_42  C5B   C6B  C1B  C2B    0.00   0.0  0
 780  CONST_43  C5B   C4B  C3B  C2B    0.00   0.0  0
 780  CONST_44  C6B   C1B  C2B  C3B    0.00   0.0  0
 780  CONST_45  C6B   C5B  C4B  C3B    0.00   0.0  0
 780  CONST_46  C7    C1   C2   C3   180.00   0.0  0
 780  CONST_47  C7    C1   C6   C5   180.00   0.0  0
 780  CONST_48  O6'   C6'  C1'  C8     0.00   0.0  0
 780  CONST_49  O6'   C6'  C1'  C2'  180.00   0.0  0
 780  CONST_50  O6'   C6'  C5'  C4'  180.00   0.0  0
 780  CONST_51  C1B   C5'  C6'  O6'    0.00   0.0  0
 780  CONST_52  HC3   C3   C2   C1   180.00   0.0  0
 780  CONST_53  HC6   C6   C1   C2   180.00   0.0  0
 780  CONST_54  HN3   N3   C4   C3     0.00   0.0  0
 780  CONST_55  HC2   C2   C3   C4   180.00   0.0  0
 780  CONST_56  HC2'  C2'  C1'  C8     0.00   0.0  0
 780  CONST_57  HC3'  C3'  C2'  C1'  180.00   0.0  0
 780  CONST_58  HC4'  C4'  C3'  C2'  180.00   0.0  0
 780  CONST_59  H2B   C2B  C1B  C5'    0.00   0.0  0
 780  CONST_60  H6B   C6B  C1B  C5'    0.00   0.0  0
 780  CONST_61  H3B   C3B  C2B  C1B  180.00   0.0  0
 780  CONST_62  H5B   C5B  C6B  C1B  180.00   0.0  0
 780  CONST_63  H4B   C4B  C3B  C2B  180.00   0.0  0
 780  CONST_64  HH11  N1   C7   C1     0.00   0.0  0
 780  CONST_65  HH12  N1   C7   C1   180.00   0.0  0
 780  CONST_66  HH21  N2   C7   C1   180.00   0.0  0
 780  CONST_67  HH22  N2   C7   C1     0.00   0.0  0
 780  Var_01    N1    C7   C1   C2   147.27  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
 780  plan-1  C8    0.020
 780  plan-1  C1'   0.020
 780  plan-1  C2'   0.020
 780  plan-1  C3'   0.020
 780  plan-1  C4'   0.020
 780  plan-1  C5'   0.020
 780  plan-1  C6'   0.020
 780  plan-1  O6'   0.020
 780  plan-1  C1B   0.020
 780  plan-1  HC2'  0.020
 780  plan-1  HC3'  0.020
 780  plan-1  HC4'  0.020
 780  plan-2  C5'   0.020
 780  plan-2  C1B   0.020
 780  plan-2  C2B   0.020
 780  plan-2  C3B   0.020
 780  plan-2  C4B   0.020
 780  plan-2  C5B   0.020
 780  plan-2  C6B   0.020
 780  plan-2  H2B   0.020
 780  plan-2  H3B   0.020
 780  plan-2  H4B   0.020
 780  plan-2  H5B   0.020
 780  plan-2  H6B   0.020
 780  plan-3  C1    0.020
 780  plan-3  C2    0.020
 780  plan-3  C3    0.020
 780  plan-3  C4    0.020
 780  plan-3  C5    0.020
 780  plan-3  C6    0.020
 780  plan-3  C7    0.020
 780  plan-3  N3    0.020
 780  plan-3  N4    0.020
 780  plan-3  C8    0.020
 780  plan-3  C1'   0.020
 780  plan-3  HC2   0.020
 780  plan-3  HC3   0.020
 780  plan-3  HC6   0.020
 780  plan-3  HN3   0.020
 780  plan-4  C1    0.020
 780  plan-4  C7    0.020
 780  plan-4  N1    0.020
 780  plan-4  N2    0.020
 780  plan-4  HH11  0.020
 780  plan-4  HH12  0.020
 780  plan-4  HH21  0.020
 780  plan-4  HH22  0.020

