# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:57:06 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-4-fluorophenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3cc(F)ccc3[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
 802  802  2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-4-fluorophenolate  ligand  31  20  .  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_802
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
 802  C1    C  CR6    0  -0.000   3.6553   0.1201   0.0002
 802  C2    C  CR16   0  -0.297   3.5500  -1.2813   0.0690
 802  C3    C  CR16   0  -0.304   2.3174  -1.9056   0.0874
 802  C4    C  CR56   0   0.360   1.1926  -1.0916   0.0464
 802  C5    C  CR56   0   0.171   1.2786   0.3186  -0.0168
 802  C6    C  CR16   0  -0.379   2.5228   0.9316  -0.0451
 802  C7    C  C      0   0.583   4.9829   0.7394  -0.0309
 802  N1    N  NH2    0  -0.770   5.1686   1.8395  -0.7241
 802  N2    N  NC2    1  -0.771   5.9740   0.1891   0.6319
 802  N3    N  NR15   0  -0.730  -0.1382  -1.3504   0.0556
 802  N4    N  N      0  -0.502   0.0291   0.8695  -0.0382
 802  C8    C  CR5    0   0.498  -0.7968  -0.1572   0.0038
 802  C1'   C  CR6    0  -0.239  -2.2407  -0.1040  -0.0019
 802  C2'   C  CR16   0  -0.451  -2.8625   1.1525  -0.0484
 802  C3'   C  CR6    0   0.469  -4.2268   1.2396  -0.0573
 802  F3'   F  F      0  -0.338  -4.8255   2.4555  -0.1013
 802  C4'   C  CR16   0  -0.379  -5.0211   0.0965  -0.0218
 802  C5'   C  CR16   0  -0.398  -4.4249  -1.1420   0.0242
 802  C6'   C  CR6    0   0.337  -3.0050  -1.3215   0.0384
 802  O6'   O  OC    -1  -0.614  -2.4814  -2.4795   0.0835
 802  HC2   H  HCR6   0   0.271   4.4422  -1.8937   0.0755
 802  HC3   H  HCR6   0   0.275   2.2419  -2.9837   0.1240
 802  HC6   H  HCR6   0   0.272   2.5978   2.0116  -0.0699
 802  HH11  H  HNH2   0   0.444   4.4552   2.1822  -1.3460
 802  HH12  H  HNH2   0   0.435   6.0511   2.3278  -0.7294
 802  HH21  H  HNC2   0   0.435   6.9159   0.5465   0.5830
 802  HH22  H  HNC2   0   0.443   5.8072  -0.5691   1.2727
 802  HN3   H  HNR5   0   0.420  -0.6818  -2.2174   0.0903
 802  HC2'  H  HCR6   0   0.259  -2.2533   2.0480  -0.0775
 802  HC4'  H  HCR6   0   0.264  -6.1012   0.1852  -0.0295
 802  HC5'  H  HCR6   0   0.237  -5.0475  -2.0286   0.0518

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
 802  C1   C2    aromatic  1.407  0.020  1.407
 802  C1   C6    aromatic  1.394  0.020  1.394
 802  C1   C7    single    1.465  0.020  1.465
 802  C2   C3    aromatic  1.382  0.020  1.382
 802  C2   HC2   single    0.930  0.020  1.080
 802  C3   C4    aromatic  1.389  0.020  1.389
 802  C3   HC3   single    0.930  0.020  1.080
 802  C4   C5    aromatic  1.414  0.020  1.414
 802  C4   N3    aromatic  1.356  0.020  1.356
 802  C5   C6    aromatic  1.387  0.020  1.387
 802  C5   N4    aromatic  1.366  0.020  1.366
 802  C6   HC6   single    0.930  0.020  1.080
 802  C7   N1    single    1.313  0.020  1.313
 802  C7   N2    double    1.313  0.020  1.313
 802  N1   HH11  single    0.860  0.020  1.020
 802  N1   HH12  single    0.860  0.020  1.020
 802  N2   HH21  single    0.860  0.020  1.020
 802  N2   HH22  single    0.860  0.020  1.020
 802  N3   C8    aromatic  1.364  0.020  1.364
 802  N3   HN3   single    0.860  0.020  1.020
 802  N4   C8    aromatic  1.318  0.020  1.318
 802  C8   C1'   single    1.445  0.020  1.445
 802  C1'  C2'   aromatic  1.403  0.020  1.403
 802  C1'  C6'   aromatic  1.438  0.020  1.438
 802  C2'  C3'   aromatic  1.367  0.020  1.367
 802  C2'  HC2'  single    0.930  0.020  1.080
 802  C3'  F3'   single    1.356  0.020  1.356
 802  C3'  C4'   aromatic  1.392  0.020  1.392
 802  C4'  C5'   aromatic  1.375  0.020  1.375
 802  C4'  HC4'  single    0.930  0.020  1.080
 802  C5'  C6'   aromatic  1.431  0.020  1.431
 802  C5'  HC5'  single    0.930  0.020  1.080
 802  C6'  O6'   single    1.272  0.020  1.272

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
 802  C7    C1   C6    119.30  3.000
 802  C7    C1   C2    119.33  3.000
 802  C6    C1   C2    121.37  3.000
 802  HC2   C2   C3    118.67  3.000
 802  HC2   C2   C1    120.15  3.000
 802  C3    C2   C1    121.16  3.000
 802  HC3   C3   C4    121.91  3.000
 802  HC3   C3   C2    120.87  3.000
 802  C4    C3   C2    117.21  3.000
 802  N3    C4   C5    104.50  3.000
 802  N3    C4   C3    133.07  3.000
 802  C5    C4   C3    122.44  3.000
 802  N4    C5   C6    129.94  3.000
 802  N4    C5   C4    110.32  3.000
 802  C6    C5   C4    119.74  3.000
 802  HC6   C6   C5    120.22  3.000
 802  HC6   C6   C1    121.67  3.000
 802  C5    C6   C1    118.08  3.000
 802  N2    C7   N1    120.71  3.000
 802  N2    C7   C1    119.74  3.000
 802  N1    C7   C1    119.55  3.000
 802  HH12  N1   HH11  116.87  3.000
 802  HH12  N1   C7    122.14  3.000
 802  HH11  N1   C7    120.74  3.000
 802  HH22  N2   HH21  116.91  3.000
 802  HH22  N2   C7    120.78  3.000
 802  HH21  N2   C7    122.13  3.000
 802  HN3   N3   C8    119.06  3.000
 802  HN3   N3   C4    133.08  3.000
 802  C8    N3   C4    107.86  3.000
 802  C8    N4   C5    104.98  3.000
 802  C1'   C8   N4    126.67  3.000
 802  C1'   C8   N3    120.99  3.000
 802  N4    C8   N3    112.34  3.000
 802  C6'   C1'  C2'   121.58  3.000
 802  C6'   C1'  C8    119.99  3.000
 802  C2'   C1'  C8    118.43  3.000
 802  HC2'  C2'  C3'   120.55  3.000
 802  HC2'  C2'  C1'   119.47  3.000
 802  C3'   C2'  C1'   119.98  3.000
 802  C4'   C3'  F3'   119.02  3.000
 802  C4'   C3'  C2'   121.12  3.000
 802  F3'   C3'  C2'   119.87  3.000
 802  HC4'  C4'  C5'   120.39  3.000
 802  HC4'  C4'  C3'   120.08  3.000
 802  C5'   C4'  C3'   119.52  3.000
 802  HC5'  C5'  C6'   117.85  3.000
 802  HC5'  C5'  C4'   119.24  3.000
 802  C6'   C5'  C4'   122.91  3.000
 802  O6'   C6'  C5'   121.53  3.000
 802  O6'   C6'  C1'   123.58  3.000
 802  C5'   C6'  C1'   114.89  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
 802  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 802  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 802  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 802  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 802  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 802  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 802  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 802  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 802  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 802  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 802  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 802  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 802  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 802  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 802  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 802  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 802  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 802  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 802  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 802  CONST_20  C2'   C1'  C8   N3   180.00   0.0  0
 802  CONST_21  C6'   C1'  C8   N3     0.00   0.0  0
 802  CONST_22  C2'   C1'  C8   N4     0.00   0.0  0
 802  CONST_23  C6'   C1'  C8   N4   180.00   0.0  0
 802  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 802  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 802  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 802  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 802  CONST_28  C5'   C6'  C1'  C2'    0.00   0.0  0
 802  CONST_29  C5'   C4'  C3'  C2'    0.00   0.0  0
 802  CONST_30  C6'   C1'  C2'  C3'    0.00   0.0  0
 802  CONST_31  C6'   C5'  C4'  C3'    0.00   0.0  0
 802  CONST_32  C7    C1   C2   C3   180.00   0.0  0
 802  CONST_33  C7    C1   C6   C5   180.00   0.0  0
 802  CONST_34  O6'   C6'  C1'  C8     0.00   0.0  0
 802  CONST_35  F3'   C3'  C2'  C1'  180.00   0.0  0
 802  CONST_36  O6'   C6'  C1'  C2'  180.00   0.0  0
 802  CONST_37  C5'   C4'  C3'  F3'  180.00   0.0  0
 802  CONST_38  O6'   C6'  C5'  C4'  180.00   0.0  0
 802  CONST_39  HC3   C3   C2   C1   180.00   0.0  0
 802  CONST_40  HC6   C6   C1   C2   180.00   0.0  0
 802  CONST_41  HN3   N3   C4   C3     0.00   0.0  0
 802  CONST_42  HC2   C2   C3   C4   180.00   0.0  0
 802  CONST_43  HC2'  C2'  C1'  C8     0.00   0.0  0
 802  CONST_44  HC5'  C5'  C6'  C1'  180.00   0.0  0
 802  CONST_45  HC4'  C4'  C3'  C2'  180.00   0.0  0
 802  CONST_46  HH11  N1   C7   C1     0.00   0.0  0
 802  CONST_47  HH12  N1   C7   C1   180.00   0.0  0
 802  CONST_48  HH21  N2   C7   C1   180.00   0.0  0
 802  CONST_49  HH22  N2   C7   C1     0.00   0.0  0
 802  Var_01    N1    C7   C1   C2   146.04  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
 802  plan-1  C8    0.020
 802  plan-1  C1'   0.020
 802  plan-1  C2'   0.020
 802  plan-1  C3'   0.020
 802  plan-1  F3'   0.020
 802  plan-1  C4'   0.020
 802  plan-1  C5'   0.020
 802  plan-1  C6'   0.020
 802  plan-1  O6'   0.020
 802  plan-1  HC2'  0.020
 802  plan-1  HC4'  0.020
 802  plan-1  HC5'  0.020
 802  plan-2  C1    0.020
 802  plan-2  C2    0.020
 802  plan-2  C3    0.020
 802  plan-2  C4    0.020
 802  plan-2  C5    0.020
 802  plan-2  C6    0.020
 802  plan-2  C7    0.020
 802  plan-2  N3    0.020
 802  plan-2  N4    0.020
 802  plan-2  C8    0.020
 802  plan-2  C1'   0.020
 802  plan-2  HC2   0.020
 802  plan-2  HC3   0.020
 802  plan-2  HC6   0.020
 802  plan-2  HN3   0.020
 802  plan-3  C1    0.020
 802  plan-3  C7    0.020
 802  plan-3  N1    0.020
 802  plan-3  N2    0.020
 802  plan-3  HH11  0.020
 802  plan-3  HH12  0.020
 802  plan-3  HH21  0.020
 802  plan-3  HH22  0.020

