# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 18:31:22 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-{5-[amino(iminio)methyl]-6-chloro-1H-benzimidazol-2-yl}biphenyl-2-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1cc2nc([nH]c2cc1Cl)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
 762  762  3-{5-[amino(iminio)methyl]-6-chloro-1H-benzimidazol-2-yl}biphenyl-2-olate  ligand  41  26  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_762
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
 762  C1    C   CR6    0   0.035  -4.1945   0.6770   0.2566
 762  C2    C   CR6    0  -0.089  -4.4388  -0.6293  -0.2032
 762  CL2   CL  CL     0  -0.105  -6.0509  -1.1339  -0.5922
 762  C3    C   CR16   0  -0.261  -3.4132  -1.5322  -0.4156
 762  C4    C   CR56   0   0.360  -2.1283  -1.0896  -0.1429
 762  C5    C   CR56   0   0.165  -1.8484   0.2146   0.3076
 762  C6    C   CR16   0  -0.360  -2.8920   1.1062   0.5015
 762  C7    C   C      0   0.545  -5.2783   1.6469   0.4964
 762  N1    N   NH2    0  -0.739  -6.2544   1.3517   1.3163
 762  N2    N   NC2    1  -0.742  -5.2053   2.8130  -0.0956
 762  N3    N   NR15   0  -0.726  -0.9129  -1.6864  -0.2239
 762  N4    N   N      0  -0.469  -0.5053   0.3795   0.4868
 762  C8    C   CR5    0   0.470   0.0430  -0.7710   0.1624
 762  C1'   C   CR6    0  -0.222   1.4461  -1.1327   0.1999
 762  C2'   C   CR16   0  -0.289   1.7890  -2.4801   0.3686
 762  C3'   C   CR16   0  -0.313   3.1017  -2.8984   0.4060
 762  C4'   C   CR16   0  -0.283   4.1082  -1.9395   0.2590
 762  C5'   C   CR6    0  -0.144   3.8306  -0.5990   0.0803
 762  C6'   C   CR6    0   0.285   2.4623  -0.1124   0.0531
 762  O6'   O   OC    -1  -0.542   2.1985   1.1011  -0.0943
 762  C1B   C   CR6    0   0.108   4.9478   0.3567  -0.0564
 762  C2B   C   CR16   0  -0.322   6.0537   0.2745   0.7943
 762  C3B   C   CR16   0  -0.243   7.1410   1.1272   0.6535
 762  C4B   C   CR16   0  -0.279   7.1452   2.0923  -0.3435
 762  C5B   C   CR16   0  -0.246   6.0510   2.1913  -1.1954
 762  C6B   C   CR16   0  -0.296   4.9651   1.3405  -1.0512
 762  HC3   H   HCR6   0   0.298  -3.6149  -2.5289  -0.7831
 762  HC6   H   HCR6   0   0.285  -2.6991   2.1096   0.8594
 762  HH11  H   HNH2   0   0.439  -7.0283   1.9790   1.4802
 762  HH12  H   HNH2   0   0.443  -6.2490   0.4900   1.8367
 762  HH21  H   HNC2   0   0.449  -4.5014   2.9884  -0.7946
 762  HH22  H   HNC2   0   0.439  -5.8645   3.5544   0.0909
 762  HN3   H   HNR5   0   0.423  -0.7347  -2.6095  -0.5861
 762  HC2'  H   HCR6   0   0.235   1.0104  -3.2230   0.5051
 762  HC3'  H   HCR6   0   0.232   3.3475  -3.9419   0.5471
 762  HC4'  H   HCR6   0   0.238   5.1440  -2.2631   0.2721
 762  H2B   H   HCR6   0   0.242   6.0594  -0.4619   1.5890
 762  H3B   H   HCR6   0   0.248   7.9818   1.0389   1.3299
 762  H4B   H   HCR6   0   0.248   7.9898   2.7597  -0.4575
 762  H5B   H   HCR6   0   0.247   6.0443   2.9365  -1.9810
 762  H6B   H   HCR6   0   0.237   4.1296   1.4301  -1.7305

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
 762  C1   C2    aromatic  1.406  0.020  1.406
 762  C1   C6    aromatic  1.393  0.020  1.393
 762  C1   C7    single    1.474  0.020  1.474
 762  C2   CL2   single    1.733  0.020  1.733
 762  C2   C3    aromatic  1.383  0.020  1.383
 762  C3   C4    aromatic  1.386  0.020  1.386
 762  C3   HC3   single    0.930  0.020  1.080
 762  C4   C5    aromatic  1.408  0.020  1.408
 762  C4   N3    aromatic  1.356  0.020  1.356
 762  C5   C6    aromatic  1.386  0.020  1.386
 762  C5   N4    aromatic  1.365  0.020  1.365
 762  C6   HC6   single    0.930  0.020  1.080
 762  C7   N1    single    1.309  0.020  1.309
 762  C7   N2    double    1.310  0.020  1.310
 762  N1   HH11  single    0.860  0.020  1.020
 762  N1   HH12  single    0.860  0.020  1.020
 762  N2   HH21  single    0.860  0.020  1.020
 762  N2   HH22  single    0.860  0.020  1.020
 762  N3   C8    aromatic  1.379  0.020  1.379
 762  N3   HN3   single    0.860  0.020  1.020
 762  N4   C8    aromatic  1.315  0.020  1.315
 762  C8   C1'   single    1.449  0.020  1.449
 762  C1'  C2'   aromatic  1.401  0.020  1.401
 762  C1'  C6'   aromatic  1.448  0.020  1.448
 762  C2'  C3'   aromatic  1.378  0.020  1.378
 762  C2'  HC2'  single    0.930  0.020  1.080
 762  C3'  C4'   aromatic  1.398  0.020  1.398
 762  C3'  HC3'  single    0.930  0.020  1.080
 762  C4'  C5'   aromatic  1.381  0.020  1.381
 762  C4'  HC4'  single    0.930  0.020  1.080
 762  C5'  C6'   aromatic  1.453  0.020  1.453
 762  C5'  C1B   single    1.477  0.020  1.477
 762  C6'  O6'   single    1.251  0.020  1.251
 762  C1B  C2B   aromatic  1.398  0.020  1.398
 762  C1B  C6B   aromatic  1.399  0.020  1.399
 762  C2B  C3B   aromatic  1.389  0.020  1.389
 762  C2B  H2B   single    0.930  0.020  1.080
 762  C3B  C4B   aromatic  1.388  0.020  1.388
 762  C3B  H3B   single    0.930  0.020  1.080
 762  C4B  C5B   aromatic  1.390  0.020  1.390
 762  C4B  H4B   single    0.930  0.020  1.080
 762  C5B  C6B   aromatic  1.387  0.020  1.387
 762  C5B  H5B   single    0.930  0.020  1.080
 762  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
 762  C7    C1   C6    117.13  3.000
 762  C7    C1   C2    122.46  3.000
 762  C6    C1   C2    120.41  3.000
 762  C3    C2   CL2   117.72  3.000
 762  C3    C2   C1    121.87  3.000
 762  CL2   C2   C1    120.35  3.000
 762  HC3   C3   C4    122.28  3.000
 762  HC3   C3   C2    121.05  3.000
 762  C4    C3   C2    116.67  3.000
 762  N3    C4   C5    104.39  3.000
 762  N3    C4   C3    132.72  3.000
 762  C5    C4   C3    122.89  3.000
 762  N4    C5   C6    130.14  3.000
 762  N4    C5   C4    110.46  3.000
 762  C6    C5   C4    119.40  3.000
 762  HC6   C6   C5    120.54  3.000
 762  HC6   C6   C1    120.68  3.000
 762  C5    C6   C1    118.76  3.000
 762  N2    C7   N1    121.71  3.000
 762  N2    C7   C1    118.12  3.000
 762  N1    C7   C1    120.13  3.000
 762  HH12  N1   HH11  116.88  3.000
 762  HH12  N1   C7    120.87  3.000
 762  HH11  N1   C7    122.23  3.000
 762  HH22  N2   HH21  117.17  3.000
 762  HH22  N2   C7    122.28  3.000
 762  HH21  N2   C7    120.50  3.000
 762  HN3   N3   C8    125.91  3.000
 762  HN3   N3   C4    125.66  3.000
 762  C8    N3   C4    108.20  3.000
 762  C8    N4   C5    105.80  3.000
 762  C1'   C8   N4    127.99  3.000
 762  C1'   C8   N3    120.84  3.000
 762  N4    C8   N3    111.16  3.000
 762  C6'   C1'  C2'   121.23  3.000
 762  C6'   C1'  C8    120.07  3.000
 762  C2'   C1'  C8    118.70  3.000
 762  HC2'  C2'  C3'   118.19  3.000
 762  HC2'  C2'  C1'   119.89  3.000
 762  C3'   C2'  C1'   121.90  3.000
 762  HC3'  C3'  C4'   120.80  3.000
 762  HC3'  C3'  C2'   120.86  3.000
 762  C4'   C3'  C2'   118.34  3.000
 762  HC4'  C4'  C5'   118.88  3.000
 762  HC4'  C4'  C3'   118.78  3.000
 762  C5'   C4'  C3'   122.34  3.000
 762  C1B   C5'  C6'   119.62  3.000
 762  C1B   C5'  C4'   119.23  3.000
 762  C6'   C5'  C4'   121.14  3.000
 762  O6'   C6'  C5'   121.73  3.000
 762  O6'   C6'  C1'   123.22  3.000
 762  C5'   C6'  C1'   115.04  3.000
 762  C6B   C1B  C2B   117.66  3.000
 762  C6B   C1B  C5'   122.02  3.000
 762  C2B   C1B  C5'   120.28  3.000
 762  H2B   C2B  C3B   119.17  3.000
 762  H2B   C2B  C1B   119.38  3.000
 762  C3B   C2B  C1B   121.44  3.000
 762  H3B   C3B  C4B   120.21  3.000
 762  H3B   C3B  C2B   119.64  3.000
 762  C4B   C3B  C2B   120.15  3.000
 762  H4B   C4B  C5B   120.37  3.000
 762  H4B   C4B  C3B   120.46  3.000
 762  C5B   C4B  C3B   119.17  3.000
 762  H5B   C5B  C6B   119.52  3.000
 762  H5B   C5B  C4B   119.90  3.000
 762  C6B   C5B  C4B   120.58  3.000
 762  H6B   C6B  C5B   119.29  3.000
 762  H6B   C6B  C1B   119.71  3.000
 762  C5B   C6B  C1B   120.99  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
 762  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 762  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 762  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 762  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 762  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 762  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 762  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 762  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 762  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 762  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 762  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 762  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 762  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 762  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 762  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 762  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 762  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 762  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 762  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 762  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 762  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 762  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 762  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 762  CONST_28  C1B   C5'  C6'  C1'  180.00   0.0  0
 762  CONST_29  C5'   C6'  C1'  C2'    0.00   0.0  0
 762  CONST_30  C5'   C4'  C3'  C2'    0.00   0.0  0
 762  CONST_31  C6'   C1'  C2'  C3'    0.00   0.0  0
 762  CONST_32  C6'   C5'  C4'  C3'    0.00   0.0  0
 762  CONST_33  C1B   C5'  C4'  C3'  180.00   0.0  0
 762  CONST_36  C3B   C2B  C1B  C5'  180.00   0.0  0
 762  CONST_37  C5B   C6B  C1B  C5'  180.00   0.0  0
 762  CONST_40  C4B   C3B  C2B  C1B    0.00   0.0  0
 762  CONST_41  C4B   C5B  C6B  C1B    0.00   0.0  0
 762  CONST_42  C5B   C6B  C1B  C2B    0.00   0.0  0
 762  CONST_43  C5B   C4B  C3B  C2B    0.00   0.0  0
 762  CONST_44  C6B   C1B  C2B  C3B    0.00   0.0  0
 762  CONST_45  C6B   C5B  C4B  C3B    0.00   0.0  0
 762  CONST_46  C6    C1   C2   CL2  180.00   0.0  0
 762  CONST_47  C4    C3   C2   CL2  180.00   0.0  0
 762  CONST_48  C7    C1   C2   C3   180.00   0.0  0
 762  CONST_49  C7    C1   C6   C5   180.00   0.0  0
 762  CONST_50  O6'   C6'  C1'  C8     0.00   0.0  0
 762  CONST_51  O6'   C6'  C1'  C2'  180.00   0.0  0
 762  CONST_52  O6'   C6'  C5'  C4'  180.00   0.0  0
 762  CONST_53  C1B   C5'  C6'  O6'    0.00   0.0  0
 762  CONST_54  HC3   C3   C2   C1   180.00   0.0  0
 762  CONST_55  HC6   C6   C1   C2   180.00   0.0  0
 762  CONST_56  HN3   N3   C4   C3     0.00   0.0  0
 762  CONST_57  HC2'  C2'  C1'  C8     0.00   0.0  0
 762  CONST_58  HC3'  C3'  C2'  C1'  180.00   0.0  0
 762  CONST_59  HC4'  C4'  C3'  C2'  180.00   0.0  0
 762  CONST_60  H2B   C2B  C1B  C5'    0.00   0.0  0
 762  CONST_61  H6B   C6B  C1B  C5'    0.00   0.0  0
 762  CONST_62  H3B   C3B  C2B  C1B  180.00   0.0  0
 762  CONST_63  H5B   C5B  C6B  C1B  180.00   0.0  0
 762  CONST_64  H4B   C4B  C3B  C2B  180.00   0.0  0
 762  CONST_65  HH11  N1   C7   C1   180.00   0.0  0
 762  CONST_66  HH12  N1   C7   C1     0.00   0.0  0
 762  CONST_67  HH21  N2   C7   C1     0.00   0.0  0
 762  CONST_68  HH22  N2   C7   C1   180.00   0.0  0
 762  Var_01    N1    C7   C1   C2    56.41  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
 762  plan-1  C8    0.020
 762  plan-1  C1'   0.020
 762  plan-1  C2'   0.020
 762  plan-1  C3'   0.020
 762  plan-1  C4'   0.020
 762  plan-1  C5'   0.020
 762  plan-1  C6'   0.020
 762  plan-1  O6'   0.020
 762  plan-1  C1B   0.020
 762  plan-1  HC2'  0.020
 762  plan-1  HC3'  0.020
 762  plan-1  HC4'  0.020
 762  plan-2  C5'   0.020
 762  plan-2  C1B   0.020
 762  plan-2  C2B   0.020
 762  plan-2  C3B   0.020
 762  plan-2  C4B   0.020
 762  plan-2  C5B   0.020
 762  plan-2  C6B   0.020
 762  plan-2  H2B   0.020
 762  plan-2  H3B   0.020
 762  plan-2  H4B   0.020
 762  plan-2  H5B   0.020
 762  plan-2  H6B   0.020
 762  plan-3  C1    0.020
 762  plan-3  C2    0.020
 762  plan-3  CL2   0.020
 762  plan-3  C3    0.020
 762  plan-3  C4    0.020
 762  plan-3  C5    0.020
 762  plan-3  C6    0.020
 762  plan-3  C7    0.020
 762  plan-3  N3    0.020
 762  plan-3  N4    0.020
 762  plan-3  C8    0.020
 762  plan-3  C1'   0.020
 762  plan-3  HC3   0.020
 762  plan-3  HC6   0.020
 762  plan-3  HN3   0.020
 762  plan-4  C1    0.020
 762  plan-4  C7    0.020
 762  plan-4  N1    0.020
 762  plan-4  N2    0.020
 762  plan-4  HH11  0.020
 762  plan-4  HH12  0.020
 762  plan-4  HH21  0.020
 762  plan-4  HH22  0.020

