# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:58:04 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}pyridin-3-olate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3ncccc3[O-]
#
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
 801  801  2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}pyridin-3-olate  ligand  30  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_801
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
 801  C1    C  CR6    0  -0.001   3.2878  -0.0329   0.0364
 801  C2    C  CR16   0  -0.295   3.1005  -1.4190   0.1885
 801  C3    C  CR16   0  -0.302   1.8349  -1.9706   0.2417
 801  C4    C  CR56   0   0.367   0.7599  -1.0981   0.1290
 801  C5    C  CR56   0   0.160   0.9270   0.2946  -0.0285
 801  C6    C  CR16   0  -0.379   2.2027   0.8361  -0.0715
 801  C7    C  C      0   0.582   4.6483   0.5093  -0.0006
 801  N1    N  NH2    0  -0.769   4.8888   1.6921   0.5179
 801  N2    N  NC2    1  -0.771   5.6137  -0.1907  -0.5507
 801  N3    N  NR15   0  -0.707  -0.5830  -1.2774   0.1323
 801  N4    N  N      0  -0.478  -0.2897   0.9131  -0.1199
 801  C8    C  CR5    0   0.456  -1.1784  -0.0498  -0.0175
 801  C1'   C  CR6    0  -0.083  -2.6264   0.0340  -0.0429
 801  N2'   N  N      0  -0.429  -3.2380  -1.1518   0.0840
 801  C3'   C  CR16   0  -0.155  -4.5487  -1.2294   0.0785
 801  C4'   C  CR16   0  -0.290  -5.3483  -0.0848  -0.0590
 801  C5'   C  CR16   0  -0.341  -4.7513   1.1404  -0.1894
 801  C6'   C  CR6    0   0.295  -3.3198   1.2903  -0.1886
 801  O6'   O  OC    -1  -0.570  -2.7605   2.4043  -0.3030
 801  HC2   H  HCR6   0   0.272   3.9552  -2.0728   0.3004
 801  HC3   H  HCR6   0   0.277   1.6977  -3.0352   0.3730
 801  HC6   H  HCR6   0   0.272   2.3364   1.9011  -0.2143
 801  HH11  H  HNH2   0   0.444   4.1887   2.1667   1.0637
 801  HH12  H  HNH2   0   0.435   5.7981   2.1255   0.4663
 801  HH21  H  HNC2   0   0.435   6.5742   0.1168  -0.5366
 801  HH22  H  HNC2   0   0.443   5.4114  -1.0297  -1.0687
 801  HN3   H  HNR5   0   0.412  -1.0969  -2.1397   0.2297
 801  HC3'  H  HCR6   0   0.234  -4.9923  -2.2132   0.1843
 801  HC4'  H  HCR6   0   0.249  -6.4278  -0.1786  -0.0612
 801  HC5'  H  HCR6   0   0.235  -5.3556   2.0346  -0.2977

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
 801  C1   C2    aromatic  1.407  0.020  1.407
 801  C1   C6    aromatic  1.394  0.020  1.394
 801  C1   C7    single    1.465  0.020  1.465
 801  C2   C3    aromatic  1.382  0.020  1.382
 801  C2   HC2   single    0.930  0.020  1.080
 801  C3   C4    aromatic  1.389  0.020  1.389
 801  C3   HC3   single    0.930  0.020  1.080
 801  C4   C5    aromatic  1.411  0.020  1.411
 801  C4   N3    aromatic  1.355  0.020  1.355
 801  C5   C6    aromatic  1.387  0.020  1.387
 801  C5   N4    aromatic  1.368  0.020  1.368
 801  C6   HC6   single    0.930  0.020  1.080
 801  C7   N1    single    1.314  0.020  1.314
 801  C7   N2    double    1.313  0.020  1.313
 801  N1   HH11  single    0.860  0.020  1.020
 801  N1   HH12  single    0.860  0.020  1.020
 801  N2   HH21  single    0.860  0.020  1.020
 801  N2   HH22  single    0.860  0.020  1.020
 801  N3   C8    aromatic  1.373  0.020  1.373
 801  N3   HN3   single    0.860  0.020  1.020
 801  N4   C8    aromatic  1.314  0.020  1.314
 801  C8   C1'   single    1.451  0.020  1.451
 801  C1'  N2'   aromatic  1.340  0.020  1.340
 801  C1'  C6'   aromatic  1.442  0.020  1.442
 801  N2'  C3'   aromatic  1.313  0.020  1.313
 801  C3'  C4'   aromatic  1.403  0.020  1.403
 801  C3'  HC3'  single    0.930  0.020  1.080
 801  C4'  C5'   aromatic  1.369  0.020  1.369
 801  C4'  HC4'  single    0.930  0.020  1.080
 801  C5'  C6'   aromatic  1.439  0.020  1.439
 801  C5'  HC5'  single    0.930  0.020  1.080
 801  C6'  O6'   single    1.252  0.020  1.252

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
 801  C7    C1   C6    119.35  3.000
 801  C7    C1   C2    119.40  3.000
 801  C6    C1   C2    121.25  3.000
 801  HC2   C2   C3    118.58  3.000
 801  HC2   C2   C1    120.09  3.000
 801  C3    C2   C1    121.29  3.000
 801  HC3   C3   C4    122.01  3.000
 801  HC3   C3   C2    120.92  3.000
 801  C4    C3   C2    117.06  3.000
 801  N3    C4   C5    104.37  3.000
 801  N3    C4   C3    133.13  3.000
 801  C5    C4   C3    122.49  3.000
 801  N4    C5   C6    129.77  3.000
 801  N4    C5   C4    110.38  3.000
 801  C6    C5   C4    119.85  3.000
 801  HC6   C6   C5    120.12  3.000
 801  HC6   C6   C1    121.81  3.000
 801  C5    C6   C1    118.04  3.000
 801  N2    C7   N1    120.71  3.000
 801  N2    C7   C1    119.73  3.000
 801  N1    C7   C1    119.56  3.000
 801  HH12  N1   HH11  116.88  3.000
 801  HH12  N1   C7    122.13  3.000
 801  HH11  N1   C7    120.74  3.000
 801  HH22  N2   HH21  116.92  3.000
 801  HH22  N2   C7    120.80  3.000
 801  HH21  N2   C7    122.11  3.000
 801  HN3   N3   C8    123.66  3.000
 801  HN3   N3   C4    128.20  3.000
 801  C8    N3   C4    108.13  3.000
 801  C8    N4   C5    105.36  3.000
 801  C1'   C8   N4    129.14  3.000
 801  C1'   C8   N3    119.11  3.000
 801  N4    C8   N3    111.75  3.000
 801  C6'   C1'  N2'   124.11  3.000
 801  C6'   C1'  C8    122.14  3.000
 801  N2'   C1'  C8    113.75  3.000
 801  C3'   N2'  C1'   120.49  3.000
 801  HC3'  C3'  C4'   121.10  3.000
 801  HC3'  C3'  N2'   117.49  3.000
 801  C4'   C3'  N2'   121.41  3.000
 801  HC4'  C4'  C5'   120.78  3.000
 801  HC4'  C4'  C3'   119.82  3.000
 801  C5'   C4'  C3'   119.40  3.000
 801  HC5'  C5'  C6'   117.93  3.000
 801  HC5'  C5'  C4'   120.28  3.000
 801  C6'   C5'  C4'   121.79  3.000
 801  O6'   C6'  C5'   122.48  3.000
 801  O6'   C6'  C1'   124.72  3.000
 801  C5'   C6'  C1'   112.80  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
 801  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 801  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 801  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 801  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 801  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 801  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 801  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 801  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 801  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 801  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 801  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 801  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 801  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 801  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 801  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 801  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 801  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 801  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 801  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 801  CONST_20  N2'   C1'  C8   N3      0.00   0.0  0
 801  CONST_21  C6'   C1'  C8   N3    180.00   0.0  0
 801  CONST_22  N2'   C1'  C8   N4    180.00   0.0  0
 801  CONST_23  C6'   C1'  C8   N4      0.00   0.0  0
 801  CONST_24  C3'   N2'  C1'  C8    180.00   0.0  0
 801  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 801  CONST_26  C4'   C3'  N2'  C1'     0.00   0.0  0
 801  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 801  CONST_28  C5'   C6'  C1'  N2'     0.00   0.0  0
 801  CONST_29  C5'   C4'  C3'  N2'     0.00   0.0  0
 801  CONST_30  C6'   C1'  N2'  C3'     0.00   0.0  0
 801  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 801  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 801  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 801  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 801  CONST_35  O6'   C6'  C1'  N2'   180.00   0.0  0
 801  CONST_36  O6'   C6'  C5'  C4'   180.00   0.0  0
 801  CONST_37  HC3   C3   C2   C1    180.00   0.0  0
 801  CONST_38  HC6   C6   C1   C2    180.00   0.0  0
 801  CONST_39  HN3   N3   C4   C3      0.00   0.0  0
 801  CONST_40  HC2   C2   C3   C4    180.00   0.0  0
 801  CONST_41  HC3'  C3'  N2'  C1'   180.00   0.0  0
 801  CONST_42  HC5'  C5'  C6'  C1'   180.00   0.0  0
 801  CONST_43  HC4'  C4'  C3'  N2'   180.00   0.0  0
 801  CONST_44  HH11  N1   C7   C1      0.00   0.0  0
 801  CONST_45  HH12  N1   C7   C1    180.00   0.0  0
 801  CONST_46  HH21  N2   C7   C1    180.00   0.0  0
 801  CONST_47  HH22  N2   C7   C1      0.00   0.0  0
 801  Var_01    N1    C7   C1   C2   -145.78  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
 801  plan-1  C8    0.020
 801  plan-1  C1'   0.020
 801  plan-1  N2'   0.020
 801  plan-1  C3'   0.020
 801  plan-1  C4'   0.020
 801  plan-1  C5'   0.020
 801  plan-1  C6'   0.020
 801  plan-1  O6'   0.020
 801  plan-1  HC3'  0.020
 801  plan-1  HC4'  0.020
 801  plan-1  HC5'  0.020
 801  plan-2  C1    0.020
 801  plan-2  C2    0.020
 801  plan-2  C3    0.020
 801  plan-2  C4    0.020
 801  plan-2  C5    0.020
 801  plan-2  C6    0.020
 801  plan-2  C7    0.020
 801  plan-2  N3    0.020
 801  plan-2  N4    0.020
 801  plan-2  C8    0.020
 801  plan-2  C1'   0.020
 801  plan-2  HC2   0.020
 801  plan-2  HC3   0.020
 801  plan-2  HC6   0.020
 801  plan-2  HN3   0.020
 801  plan-3  C1    0.020
 801  plan-3  C7    0.020
 801  plan-3  N1    0.020
 801  plan-3  N2    0.020
 801  plan-3  HH11  0.020
 801  plan-3  HH12  0.020
 801  plan-3  HH21  0.020
 801  plan-3  HH22  0.020

