# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 01:42:34 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: amino[2-(2-oxo-1,2-dihydropyridin-3-yl)-1H-benzimidazol-5-yl]methaniminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(nc2c1)C3=CC=CNC3=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
 120  120  amino[2-(2-oxo-1,2-dihydropyridin-3-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_120
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
 120  C1    C  CR6   0  -0.003   3.3448   0.0067   0.0365
 120  C2    C  CR16  0  -0.290   3.1399  -1.3729   0.2371
 120  C3    C  CR16  0  -0.296   1.8698  -1.9007   0.3417
 120  C4    C  CR56  0   0.361   0.8078  -1.0113   0.2296
 120  C5    C  CR56  0   0.176   0.9936   0.3703   0.0241
 120  C6    C  CR16  0  -0.361   2.2775   0.8917  -0.0684
 120  C7    C  C     0   0.583   4.7159   0.5208  -0.0641
 120  N1    N  NH2   0  -0.765   5.0022   1.6976   0.4414
 120  N2    N  NC2   1  -0.767   5.6356  -0.2020  -0.6587
 120  N3    N  NR15  0  -0.724  -0.5402  -1.1737   0.2707
 120  N4    N  N     0  -0.487  -0.2157   1.0005  -0.0581
 120  C8    C  CR5   0   0.520  -1.1081   0.0522   0.0946
 120  C1'   C  CR6   0  -0.269  -2.5462   0.2684   0.0750
 120  C2'   C  CR16  0  -0.147  -3.0434   1.5306  -0.1415
 120  C3'   C  CR16  0  -0.372  -4.4219   1.7880  -0.1673
 120  C4'   C  CR16  0   0.065  -5.2673   0.7396   0.0309
 120  N5'   N  NR16  0  -0.651  -4.7821  -0.4974   0.2421
 120  C6'   C  CR6   0   0.563  -3.4478  -0.8416   0.2828
 120  O6'   O  OC    0  -0.503  -3.1219  -2.0118   0.4833
 120  HC2   H  HCR6  0   0.278   3.9883  -2.0356   0.3433
 120  HC3   H  HCR6  0   0.282   1.7174  -2.9582   0.5082
 120  HC6   H  HCR6  0   0.281   2.4264   1.9490  -0.2461
 120  HH11  H  HNH2  0   0.445   4.3392   2.1824   1.0238
 120  HH12  H  HNH2  0   0.437   5.9156   2.1149   0.3445
 120  HH21  H  HNC2  0   0.437   6.6024   0.0841  -0.6946
 120  HH22  H  HNC2  0   0.445   5.3886  -1.0344  -1.1682
 120  HN3   H  HNR5  0   0.429  -1.0702  -2.0234   0.4128
 120  HC2'  H  HCR6  0   0.285  -2.3474   2.3452  -0.2956
 120  HC3'  H  HCR6  0   0.287  -4.8085   2.7801  -0.3385
 120  HC4'  H  HCR6  0   0.325  -6.3431   0.8323   0.0306
 120  HN5'  H  HNR6  0   0.434  -5.4403  -1.2528   0.3867

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
 120  C1   C2    aromatic  1.409  0.020  1.409
 120  C1   C6    aromatic  1.390  0.020  1.390
 120  C1   C7    single    1.468  0.020  1.468
 120  C2   C3    aromatic  1.379  0.020  1.379
 120  C2   HC2   single    0.930  0.020  1.080
 120  C3   C4    aromatic  1.390  0.020  1.390
 120  C3   HC3   single    0.930  0.020  1.080
 120  C4   C5    aromatic  1.409  0.020  1.409
 120  C4   N3    aromatic  1.358  0.020  1.358
 120  C5   C6    aromatic  1.389  0.020  1.389
 120  C5   N4    aromatic  1.366  0.020  1.366
 120  C6   HC6   single    0.930  0.020  1.080
 120  C7   N1    single    1.312  0.020  1.312
 120  C7   N2    double    1.312  0.020  1.312
 120  N1   HH11  single    0.860  0.020  1.020
 120  N1   HH12  single    0.860  0.020  1.020
 120  N2   HH21  single    0.860  0.020  1.020
 120  N2   HH22  single    0.860  0.020  1.020
 120  N3   C8    aromatic  1.362  0.020  1.362
 120  N3   HN3   single    0.860  0.020  1.020
 120  N4   C8    aromatic  1.311  0.020  1.311
 120  C8   C1'   single    1.454  0.020  1.454
 120  C1'  C2'   aromatic  1.374  0.020  1.374
 120  C1'  C6'   aromatic  1.445  0.020  1.445
 120  C2'  C3'   aromatic  1.403  0.020  1.403
 120  C2'  HC2'  single    0.930  0.020  1.080
 120  C3'  C4'   aromatic  1.361  0.020  1.361
 120  C3'  HC3'  single    0.930  0.020  1.080
 120  C4'  N5'   aromatic  1.346  0.020  1.346
 120  C4'  HC4'  single    0.930  0.020  1.080
 120  N5'  C6'   aromatic  1.379  0.020  1.379
 120  N5'  HN5'  single    0.860  0.020  1.020
 120  C6'  O6'   double    1.231  0.020  1.231

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
 120  C7    C1   C6    119.27  3.000
 120  C7    C1   C2    119.25  3.000
 120  C6    C1   C2    121.49  3.000
 120  HC2   C2   C3    118.70  3.000
 120  HC2   C2   C1    119.98  3.000
 120  C3    C2   C1    121.29  3.000
 120  HC3   C3   C4    122.05  3.000
 120  HC3   C3   C2    121.04  3.000
 120  C4    C3   C2    116.91  3.000
 120  N3    C4   C5    104.62  3.000
 120  N3    C4   C3    132.79  3.000
 120  C5    C4   C3    122.58  3.000
 120  N4    C5   C6    129.88  3.000
 120  N4    C5   C4    110.14  3.000
 120  C6    C5   C4    119.98  3.000
 120  HC6   C6   C5    120.31  3.000
 120  HC6   C6   C1    121.91  3.000
 120  C5    C6   C1    117.75  3.000
 120  N2    C7   N1    121.04  3.000
 120  N2    C7   C1    119.53  3.000
 120  N1    C7   C1    119.44  3.000
 120  HH12  N1   HH11  116.91  3.000
 120  HH12  N1   C7    122.10  3.000
 120  HH11  N1   C7    120.73  3.000
 120  HH22  N2   HH21  116.85  3.000
 120  HH22  N2   C7    120.85  3.000
 120  HH21  N2   C7    122.11  3.000
 120  HN3   N3   C8    123.76  3.000
 120  HN3   N3   C4    128.65  3.000
 120  C8    N3   C4    107.59  3.000
 120  C8    N4   C5    105.18  3.000
 120  C1'   C8   N4    124.33  3.000
 120  C1'   C8   N3    123.20  3.000
 120  N4    C8   N3    112.46  3.000
 120  C6'   C1'  C2'   120.17  3.000
 120  C6'   C1'  C8    120.06  3.000
 120  C2'   C1'  C8    119.77  3.000
 120  HC2'  C2'  C3'   119.42  3.000
 120  HC2'  C2'  C1'   118.76  3.000
 120  C3'   C2'  C1'   121.82  3.000
 120  HC3'  C3'  C4'   120.60  3.000
 120  HC3'  C3'  C2'   121.60  3.000
 120  C4'   C3'  C2'   117.80  3.000
 120  HC4'  C4'  N5'   115.99  3.000
 120  HC4'  C4'  C3'   123.55  3.000
 120  N5'   C4'  C3'   120.46  3.000
 120  HN5'  N5'  C6'   116.03  3.000
 120  HN5'  N5'  C4'   118.29  3.000
 120  C6'   N5'  C4'   125.68  3.000
 120  O6'   C6'  N5'   119.89  3.000
 120  O6'   C6'  C1'   126.04  3.000
 120  N5'   C6'  C1'   114.07  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
 120  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 120  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 120  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 120  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 120  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 120  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 120  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 120  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 120  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 120  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 120  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 120  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 120  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 120  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 120  CONST_15  N3    C8   N4   C5      0.00   0.0  0
 120  CONST_16  C1'   C8   N4   C5    180.00   0.0  0
 120  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 120  CONST_18  C8    N4   C5   C6    180.00   0.0  0
 120  CONST_19  N4    C5   C4   N3      0.00   0.0  0
 120  CONST_20  C2'   C1'  C8   N3    180.00   0.0  0
 120  CONST_21  C6'   C1'  C8   N3      0.00   0.0  0
 120  CONST_22  C2'   C1'  C8   N4      0.00   0.0  0
 120  CONST_23  C6'   C1'  C8   N4    180.00   0.0  0
 120  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 120  CONST_25  N5'   C6'  C1'  C8    180.00   0.0  0
 120  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 120  CONST_27  C4'   N5'  C6'  C1'     0.00   0.0  0
 120  CONST_28  N5'   C6'  C1'  C2'     0.00   0.0  0
 120  CONST_29  N5'   C4'  C3'  C2'     0.00   0.0  0
 120  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 120  CONST_31  C6'   N5'  C4'  C3'     0.00   0.0  0
 120  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 120  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 120  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 120  CONST_35  O6'   C6'  C1'  C2'   180.00   0.0  0
 120  CONST_36  O6'   C6'  N5'  C4'   180.00   0.0  0
 120  CONST_37  HC3   C3   C2   C1    180.00   0.0  0
 120  CONST_38  HC6   C6   C1   C2    180.00   0.0  0
 120  CONST_39  HN3   N3   C4   C3      0.00   0.0  0
 120  CONST_40  HC2   C2   C3   C4    180.00   0.0  0
 120  CONST_41  HC2'  C2'  C1'  C8      0.00   0.0  0
 120  CONST_42  HC3'  C3'  C2'  C1'   180.00   0.0  0
 120  CONST_43  HN5'  N5'  C6'  C1'   180.00   0.0  0
 120  CONST_44  HC4'  C4'  C3'  C2'   180.00   0.0  0
 120  CONST_45  HH11  N1   C7   C1      0.00   0.0  0
 120  CONST_46  HH12  N1   C7   C1    180.00   0.0  0
 120  CONST_47  HH21  N2   C7   C1    180.00   0.0  0
 120  CONST_48  HH22  N2   C7   C1      0.00   0.0  0
 120  Var_01    N1    C7   C1   C2   -144.00  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
 120  plan-1  C8    0.020
 120  plan-1  C1'   0.020
 120  plan-1  C2'   0.020
 120  plan-1  C3'   0.020
 120  plan-1  C4'   0.020
 120  plan-1  N5'   0.020
 120  plan-1  C6'   0.020
 120  plan-1  O6'   0.020
 120  plan-1  HC2'  0.020
 120  plan-1  HC3'  0.020
 120  plan-1  HC4'  0.020
 120  plan-1  HN5'  0.020
 120  plan-2  C1    0.020
 120  plan-2  C2    0.020
 120  plan-2  C3    0.020
 120  plan-2  C4    0.020
 120  plan-2  C5    0.020
 120  plan-2  C6    0.020
 120  plan-2  C7    0.020
 120  plan-2  N3    0.020
 120  plan-2  N4    0.020
 120  plan-2  C8    0.020
 120  plan-2  C1'   0.020
 120  plan-2  HC2   0.020
 120  plan-2  HC3   0.020
 120  plan-2  HC6   0.020
 120  plan-2  HN3   0.020
 120  plan-3  C1    0.020
 120  plan-3  C7    0.020
 120  plan-3  N1    0.020
 120  plan-3  N2    0.020
 120  plan-3  HH11  0.020
 120  plan-3  HH12  0.020
 120  plan-3  HH21  0.020
 120  plan-3  HH22  0.020

