# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 06:50:18 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: amino(1H-benzimidazol-6-yl)methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2nc[nH]c2c1
#
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
 ABI  ABI  amino(1H-benzimidazol-6-yl)methaniminium  ligand  21  12  .  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_ABI
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
 ABI  C1    C  CR6   0  -0.013  -1.1313   0.0870  -0.0551
 ABI  C2    C  CR16  0  -0.280  -0.7142   1.4091  -0.3057
 ABI  C3    C  CR16  0  -0.308   0.6231   1.7385  -0.3584
 ABI  C4    C  CR56  0   0.152   1.5589   0.7260  -0.1478
 ABI  C5    C  CR56  0   0.358   1.1227  -0.5895   0.1020
 ABI  C6    C  CR16  0  -0.310  -0.2153  -0.9385   0.1510
 ABI  C7    C  C     0   0.585  -2.5670  -0.2182  -0.0091
 ABI  C8    C  CR15  0   0.120   3.3025  -0.4482   0.1110
 ABI  N1    N  NH2   0  -0.765  -2.9964  -1.3656  -0.4784
 ABI  N2    N  NC2   1  -0.766  -3.3981   0.6602   0.4992
 ABI  N3    N  N     0  -0.455   2.9271   0.7774  -0.1364
 ABI  N4    N  NR15  0  -0.659   2.2728  -1.3089   0.2659
 ABI  HC2   H  HCR6  0   0.277  -1.4514   2.1783  -0.4935
 ABI  HC3   H  HCR6  0   0.273   0.9367   2.7529  -0.5643
 ABI  HC6   H  HCR6  0   0.295  -0.5258  -1.9517   0.3708
 ABI  HC8   H  HCR5  0   0.297   4.3265  -0.7804   0.1907
 ABI  HH11  H  HNH2  0   0.438  -3.9644  -1.6430  -0.4159
 ABI  HH12  H  HNH2  0   0.446  -2.3811  -1.9764  -0.9905
 ABI  HH21  H  HNC2  0   0.446  -3.0579   1.4743   0.9843
 ABI  HH22  H  HNC2  0   0.438  -4.3965   0.5144   0.5010
 ABI  HN4   H  HNR5  0   0.431   2.3519  -2.2963   0.4540

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
 ABI  C1  C2    aromatic  1.409  0.020  1.409
 ABI  C1  C6    aromatic  1.390  0.020  1.390
 ABI  C1  C7    single    1.468  0.020  1.468
 ABI  C2  C3    aromatic  1.378  0.020  1.378
 ABI  C2  HC2   single    0.930  0.020  1.080
 ABI  C3  C4    aromatic  1.395  0.020  1.395
 ABI  C3  HC3   single    0.930  0.020  1.080
 ABI  C4  C5    aromatic  1.408  0.020  1.408
 ABI  C4  N3    aromatic  1.369  0.020  1.369
 ABI  C5  C6    aromatic  1.384  0.020  1.384
 ABI  C5  N4    aromatic  1.366  0.020  1.366
 ABI  C6  HC6   single    0.930  0.020  1.080
 ABI  C7  N1    single    1.312  0.020  1.312
 ABI  C7  N2    double    1.312  0.020  1.312
 ABI  C8  N3    aromatic  1.305  0.020  1.305
 ABI  C8  N4    aromatic  1.351  0.020  1.351
 ABI  C8  HC8   single    0.930  0.020  1.080
 ABI  N1  HH11  single    0.860  0.020  1.020
 ABI  N1  HH12  single    0.860  0.020  1.020
 ABI  N2  HH21  single    0.860  0.020  1.020
 ABI  N2  HH22  single    0.860  0.020  1.020
 ABI  N4  HN4   single    0.860  0.020  1.020

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
 ABI  C7    C1  C6    119.09  3.000
 ABI  C7    C1  C2    119.34  3.000
 ABI  C6    C1  C2    121.57  3.000
 ABI  HC2   C2  C3    118.99  3.000
 ABI  HC2   C2  C1    119.76  3.000
 ABI  C3    C2  C1    121.22  3.000
 ABI  HC3   C3  C4    121.00  3.000
 ABI  HC3   C3  C2    120.85  3.000
 ABI  C4    C3  C2    118.15  3.000
 ABI  N3    C4  C5    110.07  3.000
 ABI  N3    C4  C3    130.13  3.000
 ABI  C5    C4  C3    119.80  3.000
 ABI  N4    C5  C6    132.60  3.000
 ABI  N4    C5  C4    104.62  3.000
 ABI  C6    C5  C4    122.78  3.000
 ABI  HC6   C6  C5    121.38  3.000
 ABI  HC6   C6  C1    122.11  3.000
 ABI  C5    C6  C1    116.47  3.000
 ABI  N2    C7  N1    121.12  3.000
 ABI  N2    C7  C1    119.50  3.000
 ABI  N1    C7  C1    119.38  3.000
 ABI  HC8   C8  N4    121.23  3.000
 ABI  HC8   C8  N3    125.15  3.000
 ABI  N4    C8  N3    113.62  3.000
 ABI  HH12  N1  HH11  116.81  3.000
 ABI  HH12  N1  C7    120.82  3.000
 ABI  HH11  N1  C7    122.17  3.000
 ABI  HH22  N2  HH21  116.76  3.000
 ABI  HH22  N2  C7    122.07  3.000
 ABI  HH21  N2  C7    120.93  3.000
 ABI  C8    N3  C4    104.70  3.000
 ABI  HN4   N4  C8    125.84  3.000
 ABI  HN4   N4  C5    127.16  3.000
 ABI  C8    N4  C5    107.00  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
 ABI  CONST_01  C4    C3  C2  C1    0.00   0.0  0
 ABI  CONST_02  C4    C5  C6  C1    0.00   0.0  0
 ABI  CONST_03  N4    C5  C6  C1  180.00   0.0  0
 ABI  CONST_04  C5    C6  C1  C2    0.00   0.0  0
 ABI  CONST_05  C5    C4  C3  C2    0.00   0.0  0
 ABI  CONST_06  N3    C4  C3  C2  180.00   0.0  0
 ABI  CONST_07  C6    C1  C2  C3    0.00   0.0  0
 ABI  CONST_08  C6    C5  C4  C3    0.00   0.0  0
 ABI  CONST_09  N4    C5  C4  C3  180.00   0.0  0
 ABI  CONST_10  C8    N3  C4  C3  180.00   0.0  0
 ABI  CONST_11  C8    N4  C5  C4    0.00   0.0  0
 ABI  CONST_12  N4    C8  N3  C4    0.00   0.0  0
 ABI  CONST_13  C8    N3  C4  C5    0.00   0.0  0
 ABI  CONST_14  N3    C8  N4  C5    0.00   0.0  0
 ABI  CONST_15  N3    C4  C5  C6  180.00   0.0  0
 ABI  CONST_16  C8    N4  C5  C6  180.00   0.0  0
 ABI  CONST_17  N4    C5  C4  N3    0.00   0.0  0
 ABI  CONST_18  C7    C1  C2  C3  180.00   0.0  0
 ABI  CONST_19  C7    C1  C6  C5  180.00   0.0  0
 ABI  CONST_20  HC3   C3  C2  C1  180.00   0.0  0
 ABI  CONST_21  HC6   C6  C1  C2  180.00   0.0  0
 ABI  CONST_22  HC2   C2  C3  C4  180.00   0.0  0
 ABI  CONST_23  HN4   N4  C5  C4  180.00   0.0  0
 ABI  CONST_24  HC8   C8  N3  C4  180.00   0.0  0
 ABI  CONST_25  HH11  N1  C7  C1  180.00   0.0  0
 ABI  CONST_26  HH12  N1  C7  C1    0.00   0.0  0
 ABI  CONST_27  HH21  N2  C7  C1    0.00   0.0  0
 ABI  CONST_28  HH22  N2  C7  C1  180.00   0.0  0
 ABI  Var_01    N1    C7  C1  C2  143.89  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
 ABI  plan-1  C1    0.020
 ABI  plan-1  C2    0.020
 ABI  plan-1  C3    0.020
 ABI  plan-1  C4    0.020
 ABI  plan-1  C5    0.020
 ABI  plan-1  C6    0.020
 ABI  plan-1  C7    0.020
 ABI  plan-1  C8    0.020
 ABI  plan-1  N3    0.020
 ABI  plan-1  N4    0.020
 ABI  plan-1  HC2   0.020
 ABI  plan-1  HC3   0.020
 ABI  plan-1  HC6   0.020
 ABI  plan-1  HC8   0.020
 ABI  plan-1  HN4   0.020
 ABI  plan-2  C1    0.020
 ABI  plan-2  C7    0.020
 ABI  plan-2  N1    0.020
 ABI  plan-2  N2    0.020
 ABI  plan-2  HH11  0.020
 ABI  plan-2  HH12  0.020
 ABI  plan-2  HH21  0.020
 ABI  plan-2  HH22  0.020

