# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 22:56:54 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: amino[2-(3-hydroxypyridin-2-yl)-1H-benzimidazol-5-yl]methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)c3ncccc3O
#
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
 121  121  amino[2-(3-hydroxypyridin-2-yl)-1H-benzimidazol-5-yl]methaniminium  ligand  31  19  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_121
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
 121  C1    C  CR6   0  -0.002   3.2617   0.0015   0.0203
 121  C2    C  CR16  0  -0.284   3.1385   1.3912   0.2118
 121  C3    C  CR16  0  -0.292   1.9026   1.9975   0.2966
 121  C4    C  CR56  0   0.342   0.7901   1.1746   0.1735
 121  C5    C  CR56  0   0.228   0.8981  -0.2154  -0.0231
 121  C6    C  CR16  0  -0.351   2.1454  -0.8181  -0.0957
 121  C7    C  C     0   0.585   4.6022  -0.5945  -0.0570
 121  N1    N  NH2   0  -0.764   4.8127  -1.7759   0.4725
 121  N2    N  NC2   1  -0.765   5.5664   0.0640  -0.6542
 121  N3    N  NR15  0  -0.700  -0.5484   1.4262   0.1950
 121  N4    N  N     0  -0.589  -0.3546  -0.7615  -0.1198
 121  C8    C  CR5   0   0.561  -1.1855   0.2449   0.0163
 121  C1'   C  CR6   0   0.002  -2.6317   0.1207  -0.0240
 121  N2'   N  N     0  -0.423  -3.3337   1.2413   0.1320
 121  C3'   C  CR16  0  -0.099  -4.6495   1.1814   0.0985
 121  C4'   C  CR16  0  -0.296  -5.3340  -0.0178  -0.0966
 121  C5'   C  CR16  0  -0.250  -4.6185  -1.1852  -0.2599
 121  C6'   C  CR6   0   0.346  -3.2240  -1.1366  -0.2248
 121  O6'   O  OH1   0  -0.625  -2.5264  -2.2583  -0.3817
 121  HC2   H  HCR6  0   0.283   4.0245   2.0014   0.3252
 121  HC3   H  HCR6  0   0.288   1.8122   3.0627   0.4562
 121  HC6   H  HCR6  0   0.288   2.2316  -1.8832  -0.2676
 121  HH11  H  HNH2  0   0.438   5.7021  -2.2464   0.3972
 121  HH12  H  HNH2  0   0.446   4.1161  -2.2114   1.0546
 121  HH21  H  HNC2  0   0.446   5.3730   0.9026  -1.1768
 121  HH22  H  HNC2  0   0.438   6.5161  -0.2760  -0.6735
 121  HN3   H  HNR5  0   0.431  -1.0052   2.3176   0.3210
 121  HC3'  H  HCR6  0   0.268  -5.1885   2.1117   0.2301
 121  HC4'  H  HCR6  0   0.281  -6.4148  -0.0285  -0.1188
 121  HC5'  H  HCR6  0   0.287  -5.1199  -2.1318  -0.4163
 121  HO6   H  HOH1  0   0.481  -1.5629  -2.0545  -0.3309

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
 121  C1   C2    aromatic  1.408  0.020  1.408
 121  C1   C6    aromatic  1.390  0.020  1.390
 121  C1   C7    single    1.469  0.020  1.469
 121  C2   C3    aromatic  1.379  0.020  1.379
 121  C2   HC2   single    0.930  0.020  1.080
 121  C3   C4    aromatic  1.389  0.020  1.389
 121  C3   HC3   single    0.930  0.020  1.080
 121  C4   C5    aromatic  1.408  0.020  1.408
 121  C4   N3    aromatic  1.362  0.020  1.362
 121  C5   C6    aromatic  1.387  0.020  1.387
 121  C5   N4    aromatic  1.370  0.020  1.370
 121  C6   HC6   single    0.930  0.020  1.080
 121  C7   N1    single    1.312  0.020  1.312
 121  C7   N2    double    1.311  0.020  1.311
 121  N1   HH11  single    0.860  0.020  1.020
 121  N1   HH12  single    0.860  0.020  1.020
 121  N2   HH21  single    0.860  0.020  1.020
 121  N2   HH22  single    0.860  0.020  1.020
 121  N3   C8    aromatic  1.354  0.020  1.354
 121  N3   HN3   single    0.860  0.020  1.020
 121  N4   C8    aromatic  1.312  0.020  1.312
 121  C8   C1'   single    1.452  0.020  1.452
 121  C1'  N2'   aromatic  1.332  0.020  1.332
 121  C1'  C6'   aromatic  1.404  0.020  1.404
 121  N2'  C3'   aromatic  1.318  0.020  1.318
 121  C3'  C4'   aromatic  1.395  0.020  1.395
 121  C3'  HC3'  single    0.930  0.020  1.080
 121  C4'  C5'   aromatic  1.379  0.020  1.379
 121  C4'  HC4'  single    0.930  0.020  1.080
 121  C5'  C6'   aromatic  1.396  0.020  1.396
 121  C5'  HC5'  single    0.930  0.020  1.080
 121  C6'  O6'   single    1.330  0.020  1.330
 121  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
 121  C7    C1   C6    119.29  3.000
 121  C7    C1   C2    119.17  3.000
 121  C6    C1   C2    121.54  3.000
 121  HC2   C2   C3    118.66  3.000
 121  HC2   C2   C1    119.94  3.000
 121  C3    C2   C1    121.37  3.000
 121  HC3   C3   C4    122.00  3.000
 121  HC3   C3   C2    121.14  3.000
 121  C4    C3   C2    116.86  3.000
 121  N3    C4   C5    105.07  3.000
 121  N3    C4   C3    132.54  3.000
 121  C5    C4   C3    122.39  3.000
 121  N4    C5   C6    130.19  3.000
 121  N4    C5   C4    109.46  3.000
 121  C6    C5   C4    120.35  3.000
 121  HC6   C6   C5    120.49  3.000
 121  HC6   C6   C1    121.99  3.000
 121  C5    C6   C1    117.49  3.000
 121  N2    C7   N1    121.20  3.000
 121  N2    C7   C1    119.41  3.000
 121  N1    C7   C1    119.38  3.000
 121  HH12  N1   HH11  116.83  3.000
 121  HH12  N1   C7    120.79  3.000
 121  HH11  N1   C7    122.10  3.000
 121  HH22  N2   HH21  116.85  3.000
 121  HH22  N2   C7    122.11  3.000
 121  HH21  N2   C7    120.88  3.000
 121  HN3   N3   C8    125.02  3.000
 121  HN3   N3   C4    127.58  3.000
 121  C8    N3   C4    107.40  3.000
 121  C8    N4   C5    105.42  3.000
 121  C1'   C8   N4    124.21  3.000
 121  C1'   C8   N3    123.16  3.000
 121  N4    C8   N3    112.64  3.000
 121  C6'   C1'  N2'   123.22  3.000
 121  C6'   C1'  C8    120.04  3.000
 121  N2'   C1'  C8    116.74  3.000
 121  C3'   N2'  C1'   119.03  3.000
 121  HC3'  C3'  C4'   120.75  3.000
 121  HC3'  C3'  N2'   117.06  3.000
 121  C4'   C3'  N2'   122.20  3.000
 121  HC4'  C4'  C5'   120.53  3.000
 121  HC4'  C4'  C3'   120.14  3.000
 121  C5'   C4'  C3'   119.33  3.000
 121  HC5'  C5'  C6'   119.79  3.000
 121  HC5'  C5'  C4'   121.13  3.000
 121  C6'   C5'  C4'   119.08  3.000
 121  O6'   C6'  C5'   119.45  3.000
 121  O6'   C6'  C1'   123.41  3.000
 121  C5'   C6'  C1'   117.14  3.000
 121  HO6   O6'  C6'   109.39  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
 121  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 121  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 121  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 121  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 121  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 121  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 121  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 121  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 121  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 121  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 121  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 121  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 121  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 121  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 121  CONST_15  N3    C8   N4   C5     0.00   0.0  0
 121  CONST_16  C1'   C8   N4   C5   180.00   0.0  0
 121  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 121  CONST_18  C8    N4   C5   C6   180.00   0.0  0
 121  CONST_19  N4    C5   C4   N3     0.00   0.0  0
 121  CONST_20  N2'   C1'  C8   N3     0.00   0.0  0
 121  CONST_21  C6'   C1'  C8   N3   180.00   0.0  0
 121  CONST_22  N2'   C1'  C8   N4   180.00   0.0  0
 121  CONST_23  C6'   C1'  C8   N4     0.00   0.0  0
 121  CONST_24  C3'   N2'  C1'  C8   180.00   0.0  0
 121  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 121  CONST_26  C4'   C3'  N2'  C1'    0.00   0.0  0
 121  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 121  CONST_28  C5'   C6'  C1'  N2'    0.00   0.0  0
 121  CONST_29  C5'   C4'  C3'  N2'    0.00   0.0  0
 121  CONST_30  C6'   C1'  N2'  C3'    0.00   0.0  0
 121  CONST_31  C6'   C5'  C4'  C3'    0.00   0.0  0
 121  CONST_32  C7    C1   C2   C3   180.00   0.0  0
 121  CONST_33  C7    C1   C6   C5   180.00   0.0  0
 121  CONST_34  O6'   C6'  C1'  C8     0.00   0.0  0
 121  CONST_35  O6'   C6'  C1'  N2'  180.00   0.0  0
 121  CONST_36  O6'   C6'  C5'  C4'  180.00   0.0  0
 121  CONST_37  HC3   C3   C2   C1   180.00   0.0  0
 121  CONST_38  HC6   C6   C1   C2   180.00   0.0  0
 121  CONST_39  HN3   N3   C4   C3     0.00   0.0  0
 121  CONST_40  HC2   C2   C3   C4   180.00   0.0  0
 121  CONST_41  HC3'  C3'  N2'  C1'  180.00   0.0  0
 121  CONST_42  HC5'  C5'  C6'  C1'  180.00   0.0  0
 121  CONST_43  HC4'  C4'  C3'  N2'  180.00   0.0  0
 121  CONST_44  HH11  N1   C7   C1   180.00   0.0  0
 121  CONST_45  HH12  N1   C7   C1     0.00   0.0  0
 121  CONST_46  HH21  N2   C7   C1     0.00   0.0  0
 121  CONST_47  HH22  N2   C7   C1   180.00   0.0  0
 121  Var_01    N1    C7   C1   C2   143.15  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
 121  plan-1  C8    0.020
 121  plan-1  C1'   0.020
 121  plan-1  N2'   0.020
 121  plan-1  C3'   0.020
 121  plan-1  C4'   0.020
 121  plan-1  C5'   0.020
 121  plan-1  C6'   0.020
 121  plan-1  O6'   0.020
 121  plan-1  HC3'  0.020
 121  plan-1  HC4'  0.020
 121  plan-1  HC5'  0.020
 121  plan-2  C1    0.020
 121  plan-2  C2    0.020
 121  plan-2  C3    0.020
 121  plan-2  C4    0.020
 121  plan-2  C5    0.020
 121  plan-2  C6    0.020
 121  plan-2  C7    0.020
 121  plan-2  N3    0.020
 121  plan-2  N4    0.020
 121  plan-2  C8    0.020
 121  plan-2  C1'   0.020
 121  plan-2  HC2   0.020
 121  plan-2  HC3   0.020
 121  plan-2  HC6   0.020
 121  plan-2  HN3   0.020
 121  plan-3  C1    0.020
 121  plan-3  C7    0.020
 121  plan-3  N1    0.020
 121  plan-3  N2    0.020
 121  plan-3  HH11  0.020
 121  plan-3  HH12  0.020
 121  plan-3  HH21  0.020
 121  plan-3  HH22  0.020

