# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:37:08 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-4-(trifluoromethoxy)phenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3cc(OC(F)(F)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
 785  785  2-{5-[amino(iminio)methyl]-1H-benzimidazol-2-yl}-4-(trifluoromethoxy)phenolate  ligand  35  24  .  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_785
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
 785  C1    C  CR6    0   0.001   4.8124   0.4660  -0.0411
 785  C2    C  CR16   0  -0.298   4.9834  -0.9292   0.0348
 785  C3    C  CR16   0  -0.303   3.8984  -1.7776   0.1357
 785  C4    C  CR56   0   0.360   2.6376  -1.1950   0.1520
 785  C5    C  CR56   0   0.172   2.4447   0.2031   0.0745
 785  C6    C  CR16   0  -0.378   3.5444   1.0443  -0.0199
 785  C7    C  C      0   0.584   5.9929   1.3287  -0.1406
 785  N1    N  NH2    0  -0.770   5.9805   2.5141   0.4248
 785  N2    N  NC2    1  -0.771   7.0523   0.9093  -0.7938
 785  N3    N  NR15   0  -0.729   1.3844  -1.7067   0.2330
 785  N4    N  N      0  -0.502   1.1118   0.4997   0.1069
 785  C8    C  CR5    0   0.502   0.5044  -0.6656   0.2065
 785  C1'   C  CR6    0  -0.249  -0.9221  -0.8881   0.2901
 785  C2'   C  CR16   0  -0.337  -1.7715   0.2217   0.2610
 785  C3'   C  CR6    0   0.261  -3.1314   0.0592   0.3482
 785  O3'   O  O2     0  -0.528  -3.9705   1.1810   0.3793
 785  C3X   C  CT     0   1.064  -4.4244   1.6380  -0.7873
 785  FV'   F  F      0  -0.305  -5.1594   0.7409  -1.4527
 785  FW'   F  F      0  -0.284  -5.1888   2.6942  -0.5418
 785  FX'   F  F      0  -0.304  -3.4494   2.0192  -1.6182
 785  C4'   C  CR16   0  -0.273  -3.6853  -1.2162   0.4780
 785  C5'   C  CR16   0  -0.414  -2.8665  -2.3175   0.5093
 785  C6'   C  CR6    0   0.346  -1.4402  -2.2273   0.4103
 785  O6'   O  OC    -1  -0.601  -0.7065  -3.2603   0.4374
 785  HC2   H  HCR6   0   0.272   5.9789  -1.3529   0.0491
 785  HC3   H  HCR6   0   0.276   4.0341  -2.8482   0.2066
 785  HC6   H  HCR6   0   0.272   3.4050   2.1145  -0.1068
 785  HH11  H  HNH2   0   0.444   5.2330   2.7832   1.0429
 785  HH12  H  HNH2   0   0.435   6.7432   3.1653   0.3205
 785  HH21  H  HNC2   0   0.435   7.9093   1.4407  -0.8228
 785  HH22  H  HNC2   0   0.443   7.0205   0.0654  -1.3418
 785  HN3   H  HNR5   0   0.421   1.0344  -2.6627   0.3129
 785  HC2'  H  HCR6   0   0.259  -1.3412   1.2129   0.1816
 785  HC4'  H  HCR6   0   0.263  -4.7584  -1.3362   0.5668
 785  HC5'  H  HCR6   0   0.237  -3.3036  -3.3037   0.6147

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
 785  C1   C2    aromatic  1.408  0.020  1.408
 785  C1   C6    aromatic  1.394  0.020  1.394
 785  C1   C7    single    1.465  0.020  1.465
 785  C2   C3    aromatic  1.381  0.020  1.381
 785  C2   HC2   single    0.930  0.020  1.080
 785  C3   C4    aromatic  1.389  0.020  1.389
 785  C3   HC3   single    0.930  0.020  1.080
 785  C4   C5    aromatic  1.413  0.020  1.413
 785  C4   N3    aromatic  1.356  0.020  1.356
 785  C5   C6    aromatic  1.388  0.020  1.388
 785  C5   N4    aromatic  1.366  0.020  1.366
 785  C6   HC6   single    0.930  0.020  1.080
 785  C7   N1    single    1.313  0.020  1.313
 785  C7   N2    double    1.313  0.020  1.313
 785  N1   HH11  single    0.860  0.020  1.020
 785  N1   HH12  single    0.860  0.020  1.020
 785  N2   HH21  single    0.860  0.020  1.020
 785  N2   HH22  single    0.860  0.020  1.020
 785  N3   C8    aromatic  1.363  0.020  1.363
 785  N3   HN3   single    0.860  0.020  1.020
 785  N4   C8    aromatic  1.318  0.020  1.318
 785  C8   C1'   single    1.446  0.020  1.446
 785  C1'  C2'   aromatic  1.398  0.020  1.398
 785  C1'  C6'   aromatic  1.441  0.020  1.441
 785  C2'  C3'   aromatic  1.372  0.020  1.372
 785  C2'  HC2'  single    0.930  0.020  1.080
 785  C3'  O3'   single    1.401  0.020  1.401
 785  C3'  C4'   aromatic  1.397  0.020  1.397
 785  O3'  C3X   single    1.333  0.020  1.333
 785  C3X  FV'   single    1.337  0.020  1.337
 785  C3X  FW'   single    1.327  0.020  1.327
 785  C3X  FX'   single    1.337  0.020  1.337
 785  C4'  C5'   aromatic  1.373  0.020  1.373
 785  C4'  HC4'  single    0.930  0.020  1.080
 785  C5'  C6'   aromatic  1.433  0.020  1.433
 785  C5'  HC5'  single    0.930  0.020  1.080
 785  C6'  O6'   single    1.267  0.020  1.267

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
 785  C7    C1   C6    119.31  3.000
 785  C7    C1   C2    119.29  3.000
 785  C6    C1   C2    121.40  3.000
 785  HC2   C2   C3    118.77  3.000
 785  HC2   C2   C1    120.04  3.000
 785  C3    C2   C1    121.16  3.000
 785  HC3   C3   C4    121.90  3.000
 785  HC3   C3   C2    120.96  3.000
 785  C4    C3   C2    117.15  3.000
 785  N3    C4   C5    104.51  3.000
 785  N3    C4   C3    132.94  3.000
 785  C5    C4   C3    122.56  3.000
 785  N4    C5   C6    130.04  3.000
 785  N4    C5   C4    110.28  3.000
 785  C6    C5   C4    119.68  3.000
 785  HC6   C6   C5    120.17  3.000
 785  HC6   C6   C1    121.74  3.000
 785  C5    C6   C1    118.06  3.000
 785  N2    C7   N1    120.66  3.000
 785  N2    C7   C1    119.71  3.000
 785  N1    C7   C1    119.63  3.000
 785  HH12  N1   HH11  116.91  3.000
 785  HH12  N1   C7    122.09  3.000
 785  HH11  N1   C7    120.84  3.000
 785  HH22  N2   HH21  116.92  3.000
 785  HH22  N2   C7    120.86  3.000
 785  HH21  N2   C7    122.10  3.000
 785  HN3   N3   C8    119.68  3.000
 785  HN3   N3   C4    132.43  3.000
 785  C8    N3   C4    107.89  3.000
 785  C8    N4   C5    105.04  3.000
 785  C1'   C8   N4    126.52  3.000
 785  C1'   C8   N3    121.20  3.000
 785  N4    C8   N3    112.28  3.000
 785  C6'   C1'  C2'   121.40  3.000
 785  C6'   C1'  C8    120.17  3.000
 785  C2'   C1'  C8    118.43  3.000
 785  HC2'  C2'  C3'   120.43  3.000
 785  HC2'  C2'  C1'   119.11  3.000
 785  C3'   C2'  C1'   120.46  3.000
 785  C4'   C3'  O3'   119.44  3.000
 785  C4'   C3'  C2'   120.47  3.000
 785  O3'   C3'  C2'   120.00  3.000
 785  C3X   O3'  C3'   117.33  3.000
 785  FX'   C3X  FW'   107.95  3.000
 785  FX'   C3X  FV'   106.44  3.000
 785  FW'   C3X  FV'   108.03  3.000
 785  FX'   C3X  O3'   113.18  3.000
 785  FW'   C3X  O3'   107.89  3.000
 785  FV'   C3X  O3'   113.13  3.000
 785  HC4'  C4'  C5'   120.00  3.000
 785  HC4'  C4'  C3'   120.11  3.000
 785  C5'   C4'  C3'   119.89  3.000
 785  HC5'  C5'  C6'   117.74  3.000
 785  HC5'  C5'  C4'   119.46  3.000
 785  C6'   C5'  C4'   122.80  3.000
 785  O6'   C6'  C5'   121.57  3.000
 785  O6'   C6'  C1'   123.45  3.000
 785  C5'   C6'  C1'   114.98  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
 785  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 785  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 785  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 785  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 785  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 785  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 785  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 785  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 785  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 785  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 785  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 785  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 785  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 785  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 785  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 785  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 785  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 785  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 785  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 785  CONST_20  C2'   C1'  C8   N3    180.00   0.0  0
 785  CONST_21  C6'   C1'  C8   N3      0.00   0.0  0
 785  CONST_22  C2'   C1'  C8   N4      0.00   0.0  0
 785  CONST_23  C6'   C1'  C8   N4    180.00   0.0  0
 785  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 785  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 785  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 785  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 785  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 785  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 785  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 785  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 785  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 785  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 785  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 785  CONST_35  O3'   C3'  C2'  C1'   180.00   0.0  0
 785  CONST_36  O6'   C6'  C1'  C2'   180.00   0.0  0
 785  CONST_37  C5'   C4'  C3'  O3'   180.00   0.0  0
 785  CONST_38  O6'   C6'  C5'  C4'   180.00   0.0  0
 785  CONST_39  HC3   C3   C2   C1    180.00   0.0  0
 785  CONST_40  HC6   C6   C1   C2    180.00   0.0  0
 785  CONST_41  HN3   N3   C4   C3      0.00   0.0  0
 785  CONST_42  HC2   C2   C3   C4    180.00   0.0  0
 785  CONST_43  HC2'  C2'  C1'  C8      0.00   0.0  0
 785  CONST_44  HC5'  C5'  C6'  C1'   180.00   0.0  0
 785  CONST_45  HC4'  C4'  C3'  C2'   180.00   0.0  0
 785  CONST_46  HH11  N1   C7   C1      0.00   0.0  0
 785  CONST_47  HH12  N1   C7   C1    180.00   0.0  0
 785  CONST_48  HH21  N2   C7   C1    180.00   0.0  0
 785  CONST_49  HH22  N2   C7   C1      0.00   0.0  0
 785  Var_01    N1    C7   C1   C2   -146.29  30.0  2
 785  Var_02    C4'   C3'  O3'  C3X   -92.50  30.0  2
 785  Var_03    FV'   C3X  O3'  C3'    60.74  30.0  3

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
 785  plan-1  C8    0.020
 785  plan-1  C1'   0.020
 785  plan-1  C2'   0.020
 785  plan-1  C3'   0.020
 785  plan-1  O3'   0.020
 785  plan-1  C4'   0.020
 785  plan-1  C5'   0.020
 785  plan-1  C6'   0.020
 785  plan-1  O6'   0.020
 785  plan-1  HC2'  0.020
 785  plan-1  HC4'  0.020
 785  plan-1  HC5'  0.020
 785  plan-2  C1    0.020
 785  plan-2  C2    0.020
 785  plan-2  C3    0.020
 785  plan-2  C4    0.020
 785  plan-2  C5    0.020
 785  plan-2  C6    0.020
 785  plan-2  C7    0.020
 785  plan-2  N3    0.020
 785  plan-2  N4    0.020
 785  plan-2  C8    0.020
 785  plan-2  C1'   0.020
 785  plan-2  HC2   0.020
 785  plan-2  HC3   0.020
 785  plan-2  HC6   0.020
 785  plan-2  HN3   0.020
 785  plan-3  C1    0.020
 785  plan-3  C7    0.020
 785  plan-3  N1    0.020
 785  plan-3  N2    0.020
 785  plan-3  HH11  0.020
 785  plan-3  HH12  0.020
 785  plan-3  HH21  0.020
 785  plan-3  HH22  0.020

