# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 23:54:11 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: amino[2-(2-hydroxyphenyl)-1H-benzimidazol-5-yl]methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)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
 BMZ  BMZ  amino[2-(2-hydroxyphenyl)-1H-benzimidazol-5-yl]methaniminium  ligand  32  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BMZ
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
 BMZ  C1    C  CR6   0  -0.008   3.2520  -0.0063  -0.0341
 BMZ  C2    C  CR16  0  -0.260   3.1487  -1.3966  -0.2173
 BMZ  C3    C  CR16  0  -0.265   1.9192  -2.0183  -0.2851
 BMZ  C4    C  CR56  0   0.348   0.7998  -1.2091  -0.1521
 BMZ  C5    C  CR56  0   0.249   0.8889   0.1805   0.0402
 BMZ  C6    C  CR16  0  -0.321   2.1272   0.8003   0.0938
 BMZ  C7    C  C     0   0.609   4.5803   0.6076   0.0201
 BMZ  N1    N  NH2   0  -0.732   4.7745   1.7634  -0.5691
 BMZ  N2    N  NC2   1  -0.732   5.5464  -0.0113   0.6547
 BMZ  N3    N  NR15  0  -0.722  -0.5368  -1.4776  -0.1576
 BMZ  N4    N  N     0  -0.601  -0.3691   0.7054   0.1514
 BMZ  C8    C  CR5   0   0.614  -1.2010  -0.3040   0.0269
 BMZ  C1'   C  CR6   0  -0.123  -2.6424  -0.1640   0.0904
 BMZ  C2'   C  CR16  0  -0.267  -3.4993  -1.2540  -0.0965
 BMZ  C3'   C  CR16  0  -0.246  -4.8680  -1.1125  -0.0211
 BMZ  C4'   C  CR16  0  -0.218  -5.4061   0.1442   0.2476
 BMZ  C5'   C  CR16  0  -0.325  -4.5855   1.2380   0.4317
 BMZ  C6'   C  CR6   0   0.357  -3.1971   1.1069   0.3537
 BMZ  O6'   O  OH1   0  -0.622  -2.4575   2.1975   0.5361
 BMZ  HC2   H  HCR6  0   0.261   4.0403  -1.9946  -0.3458
 BMZ  HC3   H  HCR6  0   0.261   1.8452  -3.0847  -0.4406
 BMZ  HC6   H  HCR6  0   0.263   2.1988   1.8659   0.2654
 BMZ  HH11  H  HNH2  0   0.426   4.0919   2.1324  -1.2087
 BMZ  HH12  H  HNH2  0   0.404   5.6419   2.2693  -0.5108
 BMZ  HH21  H  HNC2  0   0.406   6.4976   0.3158   0.6612
 BMZ  HH22  H  HNC2  0   0.425   5.3491  -0.8018   1.2440
 BMZ  HN3   H  HNR5  0   0.400  -0.9443  -2.3892  -0.2718
 BMZ  HC2'  H  HCR6  0   0.206  -3.0991  -2.2360  -0.3122
 BMZ  HC3'  H  HCR6  0   0.241  -5.5123  -1.9663  -0.1715
 BMZ  HC4'  H  HCR6  0   0.246  -6.4784   0.2694   0.3118
 BMZ  HC5'  H  HCR6  0   0.252  -5.0059   2.2134   0.6388
 BMZ  HO6   H  HOH1  0   0.472  -1.5028   1.9606   0.4411

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
 BMZ  C1   C2    aromatic  1.406  0.020  1.406
 BMZ  C1   C6    aromatic  1.390  0.020  1.390
 BMZ  C1   C7    single    1.464  0.020  1.464
 BMZ  C2   C3    aromatic  1.379  0.020  1.379
 BMZ  C2   HC2   single    0.930  0.020  1.080
 BMZ  C3   C4    aromatic  1.388  0.020  1.388
 BMZ  C3   HC3   single    0.930  0.020  1.080
 BMZ  C4   C5    aromatic  1.406  0.020  1.406
 BMZ  C4   N3    aromatic  1.363  0.020  1.363
 BMZ  C5   C6    aromatic  1.386  0.020  1.386
 BMZ  C5   N4    aromatic  1.368  0.020  1.368
 BMZ  C6   HC6   single    0.930  0.020  1.080
 BMZ  C7   N1    single    1.312  0.020  1.312
 BMZ  C7   N2    double    1.311  0.020  1.311
 BMZ  N1   HH11  single    0.860  0.020  1.020
 BMZ  N1   HH12  single    0.860  0.020  1.020
 BMZ  N2   HH21  single    0.860  0.020  1.020
 BMZ  N2   HH22  single    0.860  0.020  1.020
 BMZ  N3   C8    aromatic  1.361  0.020  1.361
 BMZ  N3   HN3   single    0.860  0.020  1.020
 BMZ  N4   C8    aromatic  1.314  0.020  1.314
 BMZ  C8   C1'   single    1.450  0.020  1.450
 BMZ  C1'  C2'   aromatic  1.399  0.020  1.399
 BMZ  C1'  C6'   aromatic  1.411  0.020  1.411
 BMZ  C2'  C3'   aromatic  1.378  0.020  1.378
 BMZ  C2'  HC2'  single    0.930  0.020  1.080
 BMZ  C3'  C4'   aromatic  1.393  0.020  1.393
 BMZ  C3'  HC3'  single    0.930  0.020  1.080
 BMZ  C4'  C5'   aromatic  1.380  0.020  1.380
 BMZ  C4'  HC4'  single    0.930  0.020  1.080
 BMZ  C5'  C6'   aromatic  1.397  0.020  1.397
 BMZ  C5'  HC5'  single    0.930  0.020  1.080
 BMZ  C6'  O6'   single    1.330  0.020  1.330
 BMZ  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
 BMZ  C7    C1   C6    119.17  3.000
 BMZ  C7    C1   C2    119.07  3.000
 BMZ  C6    C1   C2    121.76  3.000
 BMZ  HC2   C2   C3    118.68  3.000
 BMZ  HC2   C2   C1    120.12  3.000
 BMZ  C3    C2   C1    121.16  3.000
 BMZ  HC3   C3   C4    122.29  3.000
 BMZ  HC3   C3   C2    120.87  3.000
 BMZ  C4    C3   C2    116.84  3.000
 BMZ  N3    C4   C5    104.91  3.000
 BMZ  N3    C4   C3    132.51  3.000
 BMZ  C5    C4   C3    122.58  3.000
 BMZ  N4    C5   C6    130.32  3.000
 BMZ  N4    C5   C4    109.41  3.000
 BMZ  C6    C5   C4    120.27  3.000
 BMZ  HC6   C6   C5    120.39  3.000
 BMZ  HC6   C6   C1    122.18  3.000
 BMZ  C5    C6   C1    117.38  3.000
 BMZ  N2    C7   N1    121.62  3.000
 BMZ  N2    C7   C1    119.24  3.000
 BMZ  N1    C7   C1    119.15  3.000
 BMZ  HH12  N1   HH11  115.96  3.000
 BMZ  HH12  N1   C7    123.01  3.000
 BMZ  HH11  N1   C7    120.56  3.000
 BMZ  HH22  N2   HH21  115.94  3.000
 BMZ  HH22  N2   C7    120.68  3.000
 BMZ  HH21  N2   C7    123.12  3.000
 BMZ  HN3   N3   C8    126.84  3.000
 BMZ  HN3   N3   C4    125.21  3.000
 BMZ  C8    N3   C4    107.94  3.000
 BMZ  C8    N4   C5    106.25  3.000
 BMZ  C1'   C8   N4    123.45  3.000
 BMZ  C1'   C8   N3    125.06  3.000
 BMZ  N4    C8   N3    111.49  3.000
 BMZ  C6'   C1'  C2'   119.06  3.000
 BMZ  C6'   C1'  C8    119.07  3.000
 BMZ  C2'   C1'  C8    121.87  3.000
 BMZ  HC2'  C2'  C3'   118.12  3.000
 BMZ  HC2'  C2'  C1'   120.47  3.000
 BMZ  C3'   C2'  C1'   121.40  3.000
 BMZ  HC3'  C3'  C4'   120.63  3.000
 BMZ  HC3'  C3'  C2'   120.25  3.000
 BMZ  C4'   C3'  C2'   119.13  3.000
 BMZ  HC4'  C4'  C5'   119.34  3.000
 BMZ  HC4'  C4'  C3'   119.92  3.000
 BMZ  C5'   C4'  C3'   120.74  3.000
 BMZ  HC5'  C5'  C6'   118.78  3.000
 BMZ  HC5'  C5'  C4'   120.60  3.000
 BMZ  C6'   C5'  C4'   120.61  3.000
 BMZ  O6'   C6'  C5'   117.91  3.000
 BMZ  O6'   C6'  C1'   123.04  3.000
 BMZ  C5'   C6'  C1'   119.05  3.000
 BMZ  HO6   O6'  C6'   109.11  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
 BMZ  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 BMZ  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 BMZ  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 BMZ  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 BMZ  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 BMZ  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 BMZ  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 BMZ  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 BMZ  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 BMZ  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 BMZ  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 BMZ  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 BMZ  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 BMZ  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 BMZ  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 BMZ  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 BMZ  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 BMZ  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 BMZ  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 BMZ  CONST_20  C2'   C1'  C8   N3     0.00   0.0  0
 BMZ  CONST_21  C6'   C1'  C8   N3   180.00   0.0  0
 BMZ  CONST_22  C2'   C1'  C8   N4   180.00   0.0  0
 BMZ  CONST_23  C6'   C1'  C8   N4     0.00   0.0  0
 BMZ  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 BMZ  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 BMZ  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 BMZ  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 BMZ  CONST_28  C5'   C6'  C1'  C2'    0.00   0.0  0
 BMZ  CONST_29  C5'   C4'  C3'  C2'    0.00   0.0  0
 BMZ  CONST_30  C6'   C1'  C2'  C3'    0.00   0.0  0
 BMZ  CONST_31  C6'   C5'  C4'  C3'    0.00   0.0  0
 BMZ  CONST_32  C7    C1   C2   C3   180.00   0.0  0
 BMZ  CONST_33  C7    C1   C6   C5   180.00   0.0  0
 BMZ  CONST_34  O6'   C6'  C1'  C8     0.00   0.0  0
 BMZ  CONST_35  O6'   C6'  C1'  C2'  180.00   0.0  0
 BMZ  CONST_36  O6'   C6'  C5'  C4'  180.00   0.0  0
 BMZ  CONST_37  HC3   C3   C2   C1   180.00   0.0  0
 BMZ  CONST_38  HC6   C6   C1   C2   180.00   0.0  0
 BMZ  CONST_39  HN3   N3   C4   C3     0.00   0.0  0
 BMZ  CONST_40  HC2   C2   C3   C4   180.00   0.0  0
 BMZ  CONST_41  HC2'  C2'  C1'  C8     0.00   0.0  0
 BMZ  CONST_42  HC3'  C3'  C2'  C1'  180.00   0.0  0
 BMZ  CONST_43  HC5'  C5'  C6'  C1'  180.00   0.0  0
 BMZ  CONST_44  HC4'  C4'  C3'  C2'  180.00   0.0  0
 BMZ  CONST_45  HH11  N1   C7   C1     0.00   0.0  0
 BMZ  CONST_46  HH12  N1   C7   C1   180.00   0.0  0
 BMZ  CONST_47  HH21  N2   C7   C1   180.00   0.0  0
 BMZ  CONST_48  HH22  N2   C7   C1     0.00   0.0  0
 BMZ  Var_01    N1    C7   C1   C2   140.25  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
 BMZ  plan-1  C8    0.020
 BMZ  plan-1  C1'   0.020
 BMZ  plan-1  C2'   0.020
 BMZ  plan-1  C3'   0.020
 BMZ  plan-1  C4'   0.020
 BMZ  plan-1  C5'   0.020
 BMZ  plan-1  C6'   0.020
 BMZ  plan-1  O6'   0.020
 BMZ  plan-1  HC2'  0.020
 BMZ  plan-1  HC3'  0.020
 BMZ  plan-1  HC4'  0.020
 BMZ  plan-1  HC5'  0.020
 BMZ  plan-2  C1    0.020
 BMZ  plan-2  C2    0.020
 BMZ  plan-2  C3    0.020
 BMZ  plan-2  C4    0.020
 BMZ  plan-2  C5    0.020
 BMZ  plan-2  C6    0.020
 BMZ  plan-2  C7    0.020
 BMZ  plan-2  N3    0.020
 BMZ  plan-2  N4    0.020
 BMZ  plan-2  C8    0.020
 BMZ  plan-2  C1'   0.020
 BMZ  plan-2  HC2   0.020
 BMZ  plan-2  HC3   0.020
 BMZ  plan-2  HC6   0.020
 BMZ  plan-2  HN3   0.020
 BMZ  plan-3  C1    0.020
 BMZ  plan-3  C7    0.020
 BMZ  plan-3  N1    0.020
 BMZ  plan-3  N2    0.020
 BMZ  plan-3  HH11  0.020
 BMZ  plan-3  HH12  0.020
 BMZ  plan-3  HH21  0.020
 BMZ  plan-3  HH22  0.020

