# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 08:31:34 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: [carbonylbis(1H-benzimidazole-2,6-diyl)]bis(aminomethaniminium)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2nc([nH]c2c1)C(=O)c3[nH]c4cc(ccc4n3)C(N)=[NH2+]
#
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
 BAK  BAK  '[carbonylbis(1H-benzimidazole-2,6-diyl)]bis(aminomethaniminium)'  ligand  42  26  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BAK
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
 BAK  C1    C  CR6   0  -0.014   5.5593   0.5094  -0.0159
 BAK  C2    C  CR16  0  -0.272   4.9436   1.7722  -0.1643
 BAK  C3    C  CR16  0  -0.309   3.5758   1.8948  -0.2228
 BAK  C4    C  CR56  0   0.160   2.8117   0.7269  -0.1427
 BAK  C5    C  CR56  0   0.374   3.4442  -0.5238  -0.0001
 BAK  C6    C  CR16  0  -0.304   4.8242  -0.6608   0.0736
 BAK  C7    C  C     0   0.583   7.0281   0.4325   0.0353
 BAK  C8    C  CR5   0   0.391   1.2738  -0.7249  -0.0767
 BAK  C9    C  C     0   0.257  -0.0054  -1.4588  -0.0934
 BAK  N1    N  NC2   1  -0.759   7.5963  -0.3956   0.8769
 BAK  N2    N  NH2   0  -0.759   7.7337   1.1927  -0.7652
 BAK  N3    N  N     0  -0.433   1.4603   0.5644  -0.1840
 BAK  N4    N  NR15  0  -0.690   2.4309  -1.4267   0.0326
 BAK  C1'   C  CR6   0  -0.012  -5.5738   0.4967   0.0324
 BAK  C2'   C  CR16  0  -0.273  -4.9569   1.7517   0.2335
 BAK  C3'   C  CR16  0  -0.309  -3.5885   1.8753   0.2701
 BAK  C4'   C  CR56  0   0.160  -2.8240   0.7156   0.1130
 BAK  C5'   C  CR56  0   0.374  -3.4571  -0.5273  -0.0850
 BAK  C6'   C  CR16  0  -0.305  -4.8381  -0.6645  -0.1363
 BAK  C7'   C  C     0   0.584  -7.0434   0.4190   0.0160
 BAK  C8'   C  CR5   0   0.391  -1.2854  -0.7270  -0.0556
 BAK  N1'   N  NC2   1  -0.760  -7.7287   1.1478   0.8623
 BAK  N2'   N  NH2   0  -0.760  -7.6342  -0.3777  -0.8402
 BAK  N3'   N  N     0  -0.433  -1.4719   0.5545   0.1236
 BAK  N4'   N  NR15  0  -0.690  -2.4431  -1.4245  -0.1839
 BAK  O9    O  O     0  -0.350  -0.0048  -2.6701  -0.1336
 BAK  H2    H  HCR6  0   0.285   5.5559   2.6632  -0.2036
 BAK  H3    H  HCR6  0   0.280   3.1059   2.8635  -0.3232
 BAK  H6    H  HCR6  0   0.303   5.2921  -1.6323   0.1638
 BAK  HH11  H  HNC2  0   0.448   7.0521  -0.8677   1.5811
 BAK  HH12  H  HNC2  0   0.440   8.5963  -0.5277   0.9074
 BAK  HH21  H  HNH2  0   0.440   8.7422   1.2160  -0.7343
 BAK  HH22  H  HNH2  0   0.448   7.2880   1.7248  -1.4956
 BAK  HN4   H  HNR5  0   0.437   2.5139  -2.4295   0.1191
 BAK  H2'   H  HCR6  0   0.285  -5.5695   2.6376   0.3339
 BAK  H3'   H  HCR6  0   0.280  -3.1187   2.8385   0.4137
 BAK  H6'   H  HCR6  0   0.302  -5.3054  -1.6318  -0.2660
 BAK  H1'1  H  HNC2  0   0.448  -7.2653   1.6548   1.5994
 BAK  H1'2  H  HNC2  0   0.440  -8.7377   1.1698   0.8580
 BAK  H2'1  H  HNH2  0   0.440  -8.6347  -0.5090  -0.8484
 BAK  H2'2  H  HNH2  0   0.448  -7.1100  -0.8275  -1.5733
 BAK  HN4'  H  HNR5  0   0.437  -2.5258  -2.4215  -0.3217

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
 BAK  C1   C2    aromatic  1.413  0.020  1.413
 BAK  C1   C6    aromatic  1.385  0.020  1.385
 BAK  C1   C7    single    1.472  0.020  1.472
 BAK  C2   C3    aromatic  1.375  0.020  1.375
 BAK  C2   H2    single    0.930  0.020  1.080
 BAK  C3   C4    aromatic  1.398  0.020  1.398
 BAK  C3   H3    single    0.930  0.020  1.080
 BAK  C4   C5    aromatic  1.409  0.020  1.409
 BAK  C4   N3    aromatic  1.362  0.020  1.362
 BAK  C5   C6    aromatic  1.389  0.020  1.389
 BAK  C5   N4    aromatic  1.358  0.020  1.358
 BAK  C6   H6    single    0.930  0.020  1.080
 BAK  C7   N1    double    1.310  0.020  1.310
 BAK  C7   N2    single    1.310  0.020  1.310
 BAK  C8   C9    single    1.475  0.020  1.475
 BAK  C8   N3    aromatic  1.307  0.020  1.307
 BAK  C8   N4    aromatic  1.358  0.020  1.358
 BAK  C9   C8'   single    1.475  0.020  1.475
 BAK  C9   O9    double    1.212  0.020  1.212
 BAK  N1   HH11  single    0.860  0.020  1.020
 BAK  N1   HH12  single    0.860  0.020  1.020
 BAK  N2   HH21  single    0.860  0.020  1.020
 BAK  N2   HH22  single    0.860  0.020  1.020
 BAK  N4   HN4   single    0.860  0.020  1.020
 BAK  C1'  C2'   aromatic  1.413  0.020  1.413
 BAK  C1'  C6'   aromatic  1.385  0.020  1.385
 BAK  C1'  C7'   single    1.472  0.020  1.472
 BAK  C2'  C3'   aromatic  1.374  0.020  1.374
 BAK  C2'  H2'   single    0.930  0.020  1.080
 BAK  C3'  C4'   aromatic  1.398  0.020  1.398
 BAK  C3'  H3'   single    0.930  0.020  1.080
 BAK  C4'  C5'   aromatic  1.409  0.020  1.409
 BAK  C4'  N3'   aromatic  1.362  0.020  1.362
 BAK  C5'  C6'   aromatic  1.389  0.020  1.389
 BAK  C5'  N4'   aromatic  1.358  0.020  1.358
 BAK  C6'  H6'   single    0.930  0.020  1.080
 BAK  C7'  N1'   double    1.310  0.020  1.310
 BAK  C7'  N2'   single    1.310  0.020  1.310
 BAK  C8'  N3'   aromatic  1.307  0.020  1.307
 BAK  C8'  N4'   aromatic  1.358  0.020  1.358
 BAK  N1'  H1'1  single    0.860  0.020  1.020
 BAK  N1'  H1'2  single    0.860  0.020  1.020
 BAK  N2'  H2'1  single    0.860  0.020  1.020
 BAK  N2'  H2'2  single    0.860  0.020  1.020
 BAK  N4'  HN4'  single    0.860  0.020  1.020

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
 BAK  C7    C1   C6    118.91  3.000
 BAK  C7    C1   C2    119.03  3.000
 BAK  C6    C1   C2    122.06  3.000
 BAK  H2    C2   C3    119.22  3.000
 BAK  H2    C2   C1    119.56  3.000
 BAK  C3    C2   C1    121.19  3.000
 BAK  H3    C3   C4    121.08  3.000
 BAK  H3    C3   C2    121.08  3.000
 BAK  C4    C3   C2    117.84  3.000
 BAK  N3    C4   C5    110.04  3.000
 BAK  N3    C4   C3    129.82  3.000
 BAK  C5    C4   C3    120.14  3.000
 BAK  N4    C5   C6    132.44  3.000
 BAK  N4    C5   C4    104.94  3.000
 BAK  C6    C5   C4    122.62  3.000
 BAK  H6    C6   C5    121.51  3.000
 BAK  H6    C6   C1    122.31  3.000
 BAK  C5    C6   C1    116.15  3.000
 BAK  N2    C7   N1    121.71  3.000
 BAK  N2    C7   C1    119.07  3.000
 BAK  N1    C7   C1    119.22  3.000
 BAK  N4    C8   N3    113.26  3.000
 BAK  N4    C8   C9    118.87  3.000
 BAK  N3    C8   C9    127.85  3.000
 BAK  O9    C9   C8'   119.81  3.000
 BAK  O9    C9   C8    119.82  3.000
 BAK  C8'   C9   C8    120.36  3.000
 BAK  HH12  N1   HH11  116.92  3.000
 BAK  HH12  N1   C7    122.13  3.000
 BAK  HH11  N1   C7    120.73  3.000
 BAK  HH22  N2   HH21  116.87  3.000
 BAK  HH22  N2   C7    120.74  3.000
 BAK  HH21  N2   C7    122.20  3.000
 BAK  C8    N3   C4    104.88  3.000
 BAK  HN4   N4   C8    126.17  3.000
 BAK  HN4   N4   C5    126.95  3.000
 BAK  C8    N4   C5    106.88  3.000
 BAK  C7'   C1'  C6'   119.00  3.000
 BAK  C7'   C1'  C2'   118.98  3.000
 BAK  C6'   C1'  C2'   122.02  3.000
 BAK  H2'   C2'  C3'   119.19  3.000
 BAK  H2'   C2'  C1'   119.57  3.000
 BAK  C3'   C2'  C1'   121.22  3.000
 BAK  H3'   C3'  C4'   121.09  3.000
 BAK  H3'   C3'  C2'   121.08  3.000
 BAK  C4'   C3'  C2'   117.83  3.000
 BAK  N3'   C4'  C5'   110.05  3.000
 BAK  N3'   C4'  C3'   129.82  3.000
 BAK  C5'   C4'  C3'   120.13  3.000
 BAK  N4'   C5'  C6'   132.44  3.000
 BAK  N4'   C5'  C4'   104.93  3.000
 BAK  C6'   C5'  C4'   122.63  3.000
 BAK  H6'   C6'  C5'   121.48  3.000
 BAK  H6'   C6'  C1'   122.32  3.000
 BAK  C5'   C6'  C1'   116.16  3.000
 BAK  N2'   C7'  N1'   121.62  3.000
 BAK  N2'   C7'  C1'   119.32  3.000
 BAK  N1'   C7'  C1'   119.06  3.000
 BAK  N4'   C8'  N3'   113.26  3.000
 BAK  N4'   C8'  C9    118.86  3.000
 BAK  N3'   C8'  C9    127.86  3.000
 BAK  H1'2  N1'  H1'1  116.87  3.000
 BAK  H1'2  N1'  C7'   122.16  3.000
 BAK  H1'1  N1'  C7'   120.78  3.000
 BAK  H2'2  N2'  H2'1  116.87  3.000
 BAK  H2'2  N2'  C7'   120.83  3.000
 BAK  H2'1  N2'  C7'   122.11  3.000
 BAK  C8'   N3'  C4'   104.87  3.000
 BAK  HN4'  N4'  C8'   126.15  3.000
 BAK  HN4'  N4'  C5'   126.96  3.000
 BAK  C8'   N4'  C5'   106.89  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
 BAK  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 BAK  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 BAK  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 BAK  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 BAK  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 BAK  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 BAK  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 BAK  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 BAK  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 BAK  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 BAK  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 BAK  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 BAK  CONST_13  C8    N3   C4   C5     0.00   0.0  0
 BAK  CONST_14  N3    C8   N4   C5     0.00   0.0  0
 BAK  CONST_15  N3    C4   C5   C6   180.00   0.0  0
 BAK  CONST_16  C8    N4   C5   C6   180.00   0.0  0
 BAK  CONST_17  N4    C5   C4   N3     0.00   0.0  0
 BAK  CONST_18  C4'   C3'  C2'  C1'    0.00   0.0  0
 BAK  CONST_19  C4'   C5'  C6'  C1'    0.00   0.0  0
 BAK  CONST_20  N4'   C5'  C6'  C1'  180.00   0.0  0
 BAK  CONST_21  C5'   C6'  C1'  C2'    0.00   0.0  0
 BAK  CONST_22  C5'   C4'  C3'  C2'    0.00   0.0  0
 BAK  CONST_23  N3'   C4'  C3'  C2'  180.00   0.0  0
 BAK  CONST_24  C6'   C1'  C2'  C3'    0.00   0.0  0
 BAK  CONST_25  C6'   C5'  C4'  C3'    0.00   0.0  0
 BAK  CONST_26  N4'   C5'  C4'  C3'  180.00   0.0  0
 BAK  CONST_27  C8'   N3'  C4'  C3'  180.00   0.0  0
 BAK  CONST_28  C8'   N4'  C5'  C4'    0.00   0.0  0
 BAK  CONST_29  N4'   C8'  N3'  C4'    0.00   0.0  0
 BAK  CONST_30  C8'   N3'  C4'  C5'    0.00   0.0  0
 BAK  CONST_31  N3'   C8'  N4'  C5'    0.00   0.0  0
 BAK  CONST_32  N3'   C4'  C5'  C6'  180.00   0.0  0
 BAK  CONST_33  C8'   N4'  C5'  C6'  180.00   0.0  0
 BAK  CONST_34  N4'   C5'  C4'  N3'    0.00   0.0  0
 BAK  CONST_35  C7    C1   C2   C3   180.00   0.0  0
 BAK  CONST_36  C9    C8   N3   C4   180.00   0.0  0
 BAK  CONST_37  C7    C1   C6   C5   180.00   0.0  0
 BAK  CONST_38  C9    C8   N4   C5   180.00   0.0  0
 BAK  CONST_39  C4'   N3'  C8'  C9   180.00   0.0  0
 BAK  CONST_40  C5'   N4'  C8'  C9   180.00   0.0  0
 BAK  CONST_41  C7'   C1'  C2'  C3'  180.00   0.0  0
 BAK  CONST_42  C7'   C1'  C6'  C5'  180.00   0.0  0
 BAK  CONST_43  H3    C3   C2   C1   180.00   0.0  0
 BAK  CONST_44  H6    C6   C1   C2   180.00   0.0  0
 BAK  CONST_45  H2    C2   C3   C4   180.00   0.0  0
 BAK  CONST_46  HN4   N4   C5   C4   180.00   0.0  0
 BAK  CONST_47  H3'   C3'  C2'  C1'  180.00   0.0  0
 BAK  CONST_48  H6'   C6'  C1'  C2'  180.00   0.0  0
 BAK  CONST_49  H2'   C2'  C3'  C4'  180.00   0.0  0
 BAK  CONST_50  HN4'  N4'  C5'  C4'  180.00   0.0  0
 BAK  CONST_51  HH11  N1   C7   C1     0.00   0.0  0
 BAK  CONST_52  HH12  N1   C7   C1   180.00   0.0  0
 BAK  CONST_53  HH21  N2   C7   C1   180.00   0.0  0
 BAK  CONST_54  HH22  N2   C7   C1     0.00   0.0  0
 BAK  CONST_55  H1'1  N1'  C7'  C1'    0.00   0.0  0
 BAK  CONST_56  H1'2  N1'  C7'  C1'  180.00   0.0  0
 BAK  CONST_57  H2'1  N2'  C7'  C1'  180.00   0.0  0
 BAK  CONST_58  H2'2  N2'  C7'  C1'    0.00   0.0  0
 BAK  Var_01    N3'   C8'  C9   C8    -7.23  30.0  2
 BAK  Var_02    C8'   C9   C8   N3    -8.56  30.0  2
 BAK  Var_03    N1    C7   C1   C2   139.99  30.0  2
 BAK  Var_04    N1'   C7'  C1'  C2'  -39.15  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
 BAK  plan-1  C1    0.020
 BAK  plan-1  C2    0.020
 BAK  plan-1  C3    0.020
 BAK  plan-1  C4    0.020
 BAK  plan-1  C5    0.020
 BAK  plan-1  C6    0.020
 BAK  plan-1  C7    0.020
 BAK  plan-1  C8    0.020
 BAK  plan-1  C9    0.020
 BAK  plan-1  N3    0.020
 BAK  plan-1  N4    0.020
 BAK  plan-1  H2    0.020
 BAK  plan-1  H3    0.020
 BAK  plan-1  H6    0.020
 BAK  plan-1  HN4   0.020
 BAK  plan-2  C9    0.020
 BAK  plan-2  C1'   0.020
 BAK  plan-2  C2'   0.020
 BAK  plan-2  C3'   0.020
 BAK  plan-2  C4'   0.020
 BAK  plan-2  C5'   0.020
 BAK  plan-2  C6'   0.020
 BAK  plan-2  C7'   0.020
 BAK  plan-2  C8'   0.020
 BAK  plan-2  N3'   0.020
 BAK  plan-2  N4'   0.020
 BAK  plan-2  H2'   0.020
 BAK  plan-2  H3'   0.020
 BAK  plan-2  H6'   0.020
 BAK  plan-2  HN4'  0.020
 BAK  plan-3  C8    0.020
 BAK  plan-3  C9    0.020
 BAK  plan-3  C8'   0.020
 BAK  plan-3  O9    0.020
 BAK  plan-4  C1    0.020
 BAK  plan-4  C7    0.020
 BAK  plan-4  N1    0.020
 BAK  plan-4  N2    0.020
 BAK  plan-4  HH11  0.020
 BAK  plan-4  HH12  0.020
 BAK  plan-4  HH21  0.020
 BAK  plan-4  HH22  0.020
 BAK  plan-5  C1'   0.020
 BAK  plan-5  C7'   0.020
 BAK  plan-5  N1'   0.020
 BAK  plan-5  N2'   0.020
 BAK  plan-5  H1'1  0.020
 BAK  plan-5  H1'2  0.020
 BAK  plan-5  H2'1  0.020
 BAK  plan-5  H2'2  0.020

