# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 02:44:36 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-[amino(iminio)methyl]-2-({6-[amino(iminio)methyl]-1H-benzimidazol-2-yl}methyl)-1H-benzimidazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2nc(Cc3[nH]c4cc(ccc4[nH+]3)C(N)=[NH2+])[nH]c2c1
#
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
 BAB  BAB  6-[amino(iminio)methyl]-2-({6-[amino(iminio)methyl]-1H-benzimidazol-2-yl}methyl)-1H-benzimidazol-3-ium  ligand  44  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BAB
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
 BAB  C1    C  CR6   0  -0.014  -2.6218   -9.9262  -1.8857
 BAB  C2    C  CR16  0  -0.275  -1.3496   -9.3558  -2.0802
 BAB  C3    C  CR16  0  -0.308  -1.1803   -7.9886  -2.1405
 BAB  C4    C  CR56  0   0.217  -2.3123   -7.1879  -2.0113
 BAB  C5    C  CR56  0   0.339  -3.5743   -7.7727  -1.8183
 BAB  C6    C  CR16  0  -0.312  -3.7606   -9.1415  -1.7482
 BAB  C7    C  C     0   0.585  -2.7537  -11.3891  -1.8323
 BAB  C8    C  CR5   0   0.557  -3.7166   -5.5904  -1.8745
 BAB  C9    C  CH2   0  -0.657  -4.3619   -4.2482  -1.8333
 BAB  N1    N  NC2   1  -0.762  -2.0200  -12.1277  -2.6288
 BAB  N2    N  NH2   0  -0.762  -3.6045  -11.9265  -0.9919
 BAB  N3    N  N     0  -0.547  -2.4415   -5.8241  -2.0404
 BAB  N4    N  NR15  0  -0.708  -4.4439   -6.7187  -1.7391
 BAB  C1'   C  CR6   0  -0.006  -0.1663   -0.0450  -2.4296
 BAB  C2'   C  CR16  0  -0.265  -1.2583    0.8258  -2.2645
 BAB  C3'   C  CR16  0  -0.273  -2.5360    0.3495  -2.0590
 BAB  C4'   C  CR56  0   0.336  -2.6873   -1.0287  -2.0363
 BAB  C5'   C  CR56  0   0.348  -1.6045   -1.8915  -2.2019
 BAB  C6'   C  CR16  0  -0.299  -0.3177   -1.4237  -2.3966
 BAB  C7'   C  C     0   0.589   1.1755    0.5231  -2.6507
 BAB  C8'   C  CR5   0   0.669  -3.4219   -3.1080  -1.9442
 BAB  N1'   N  NC2   1  -0.757   1.3014    1.5678  -3.4292
 BAB  N2'   N  NH2   0  -0.757   2.2062   -0.0310  -2.0641
 BAB  N3'   N  NR15  1  -0.686  -3.7910   -1.8321  -1.8764
 BAB  N4'   N  NR15  0  -0.685  -2.1165   -3.1672  -2.1382
 BAB  H2    H  HCR6  0   0.283  -0.4804   -9.9956  -2.1547
 BAB  H3    H  HCR6  0   0.280  -0.1996   -7.5549  -2.2793
 BAB  H6    H  HCR6  0   0.300  -4.7461   -9.5712  -1.6254
 BAB  H91   H  HCH2  0   0.358  -5.0915   -4.1655  -2.6457
 BAB  H92   H  HCH2  0   0.355  -4.9319   -4.1391  -0.9058
 BAB  HN21  H  HNH2  0   0.439  -3.7777  -12.9203  -0.9653
 BAB  HN22  H  HNH2  0   0.447  -4.0601  -11.3659  -0.2898
 BAB  HN4   H  HNR5  0   0.440  -5.4427   -6.7730  -1.6052
 BAB  H2'   H  HCR6  0   0.300  -1.0985    1.8954  -2.2731
 BAB  H3'   H  HCR6  0   0.308  -3.3717    1.0202  -1.9222
 BAB  H6'   H  HCR6  0   0.317   0.5101   -2.1042  -2.5429
 BAB  H2'1  H  HNH2  0   0.443   3.1506    0.2856  -2.2278
 BAB  H2'2  H  HNH2  0   0.451   2.0801   -0.7408  -1.3605
 BAB  HN4'  H  HNR5  0   0.469  -1.6395   -4.0727  -2.2108
 BAB  HN1   H  HNC2  0   0.443   2.1886    2.0289  -3.5680
 BAB  HN2   H  HNC2  0   0.450   0.5266    1.8971  -3.9828
 BAB  HN3   H  HNR5  0   0.465  -4.7403   -1.5138  -1.7315
 BAB  HN5   H  HNC2  0   0.439  -2.0340  -13.1360  -2.5905
 BAB  HN6   H  HNC2  0   0.447  -1.4701  -11.7077  -3.3610

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
 BAB  C1   C2    aromatic  1.408  0.020  1.408
 BAB  C1   C6    aromatic  1.390  0.020  1.390
 BAB  C1   C7    single    1.470  0.020  1.470
 BAB  C2   C3    aromatic  1.379  0.020  1.379
 BAB  C2   H2    single    0.930  0.020  1.080
 BAB  C3   C4    aromatic  1.393  0.020  1.393
 BAB  C3   H3    single    0.930  0.020  1.080
 BAB  C4   C5    aromatic  1.404  0.020  1.404
 BAB  C4   N3    aromatic  1.370  0.020  1.370
 BAB  C5   C6    aromatic  1.383  0.020  1.383
 BAB  C5   N4    aromatic  1.369  0.020  1.369
 BAB  C6   H6    single    0.930  0.020  1.080
 BAB  C7   N1    double    1.311  0.020  1.311
 BAB  C7   N2    single    1.311  0.020  1.311
 BAB  C8   C9    single    1.490  0.020  1.490
 BAB  C8   N3    aromatic  1.307  0.020  1.307
 BAB  C8   N4    aromatic  1.349  0.020  1.349
 BAB  C9   C8'   single    1.482  0.020  1.482
 BAB  C9   H91   single    0.970  0.020  1.090
 BAB  C9   H92   single    0.970  0.020  1.090
 BAB  N2   HN21  single    0.860  0.020  1.020
 BAB  N2   HN22  single    0.860  0.020  1.020
 BAB  N4   HN4   single    0.860  0.020  1.020
 BAB  C1'  C2'   aromatic  1.406  0.020  1.406
 BAB  C1'  C6'   aromatic  1.387  0.020  1.387
 BAB  C1'  C7'   single    1.474  0.020  1.474
 BAB  C2'  C3'   aromatic  1.379  0.020  1.379
 BAB  C2'  H2'   single    0.930  0.020  1.080
 BAB  C3'  C4'   aromatic  1.387  0.020  1.387
 BAB  C3'  H3'   single    0.930  0.020  1.080
 BAB  C4'  C5'   aromatic  1.394  0.020  1.394
 BAB  C4'  N3'   aromatic  1.374  0.020  1.374
 BAB  C5'  C6'   aromatic  1.383  0.020  1.383
 BAB  C5'  N4'   aromatic  1.376  0.020  1.376
 BAB  C6'  H6'   single    0.930  0.020  1.080
 BAB  C7'  N1'   double    1.309  0.020  1.309
 BAB  C7'  N2'   single    1.309  0.020  1.309
 BAB  C8'  N3'   aromatic  1.330  0.020  1.330
 BAB  C8'  N4'   aromatic  1.321  0.020  1.321
 BAB  N2'  H2'1  single    0.860  0.020  1.020
 BAB  N2'  H2'2  single    0.860  0.020  1.020
 BAB  N4'  HN4'  single    0.860  0.020  1.020
 BAB  HN1  N1'   single    0.860  0.020  1.020
 BAB  HN3  N3'   single    0.860  0.020  1.020
 BAB  HN5  N1    single    0.860  0.020  1.020
 BAB  HN6  N1    single    0.860  0.020  1.020
 BAB  HN2  N1'   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
 BAB  C7    C1   C6    119.00  3.000
 BAB  C7    C1   C2    119.30  3.000
 BAB  C6    C1   C2    121.70  3.000
 BAB  H2    C2   C3    118.99  3.000
 BAB  H2    C2   C1    119.73  3.000
 BAB  C3    C2   C1    121.25  3.000
 BAB  H3    C3   C4    121.23  3.000
 BAB  H3    C3   C2    120.98  3.000
 BAB  C4    C3   C2    117.79  3.000
 BAB  N3    C4   C5    109.43  3.000
 BAB  N3    C4   C3    130.32  3.000
 BAB  C5    C4   C3    120.25  3.000
 BAB  N4    C5   C6    132.34  3.000
 BAB  N4    C5   C4    104.97  3.000
 BAB  C6    C5   C4    122.69  3.000
 BAB  H6    C6   C5    121.43  3.000
 BAB  H6    C6   C1    122.23  3.000
 BAB  C5    C6   C1    116.32  3.000
 BAB  N2    C7   N1    121.45  3.000
 BAB  N2    C7   C1    119.31  3.000
 BAB  N1    C7   C1    119.24  3.000
 BAB  N4    C8   N3    112.90  3.000
 BAB  N4    C8   C9    121.14  3.000
 BAB  N3    C8   C9    125.96  3.000
 BAB  H92   C9   H91   105.91  3.000
 BAB  H92   C9   C8'   108.49  3.000
 BAB  H91   C9   C8'   108.00  3.000
 BAB  H92   C9   C8    109.82  3.000
 BAB  H91   C9   C8    109.64  3.000
 BAB  C8'   C9   C8    114.61  3.000
 BAB  HN6   N1   HN5   116.85  3.000
 BAB  HN6   N1   C7    120.81  3.000
 BAB  HN5   N1   C7    122.16  3.000
 BAB  HN22  N2   HN21  116.88  3.000
 BAB  HN22  N2   C7    120.80  3.000
 BAB  HN21  N2   C7    122.13  3.000
 BAB  C8    N3   C4    105.50  3.000
 BAB  HN4   N4   C8    126.29  3.000
 BAB  HN4   N4   C5    126.52  3.000
 BAB  C8    N4   C5    107.20  3.000
 BAB  C7'   C1'  C6'   119.08  3.000
 BAB  C7'   C1'  C2'   119.07  3.000
 BAB  C6'   C1'  C2'   121.85  3.000
 BAB  H2'   C2'  C3'   118.66  3.000
 BAB  H2'   C2'  C1'   119.78  3.000
 BAB  C3'   C2'  C1'   121.54  3.000
 BAB  H3'   C3'  C4'   122.04  3.000
 BAB  H3'   C3'  C2'   121.41  3.000
 BAB  C4'   C3'  C2'   116.54  3.000
 BAB  N3'   C4'  C5'   106.00  3.000
 BAB  N3'   C4'  C3'   132.11  3.000
 BAB  C5'   C4'  C3'   121.89  3.000
 BAB  N4'   C5'  C6'   131.78  3.000
 BAB  N4'   C5'  C4'   106.21  3.000
 BAB  C6'   C5'  C4'   122.00  3.000
 BAB  H6'   C6'  C5'   121.22  3.000
 BAB  H6'   C6'  C1'   122.58  3.000
 BAB  C5'   C6'  C1'   116.17  3.000
 BAB  N2'   C7'  N1'   121.91  3.000
 BAB  N2'   C7'  C1'   119.11  3.000
 BAB  N1'   C7'  C1'   118.98  3.000
 BAB  N4'   C8'  N3'   108.95  3.000
 BAB  N4'   C8'  C9    127.11  3.000
 BAB  N3'   C8'  C9    123.94  3.000
 BAB  HN2   N1'  HN1   116.81  3.000
 BAB  HN2   N1'  C7'   120.91  3.000
 BAB  HN1   N1'  C7'   122.07  3.000
 BAB  H2'2  N2'  H2'1  116.83  3.000
 BAB  H2'2  N2'  C7'   120.84  3.000
 BAB  H2'1  N2'  C7'   122.09  3.000
 BAB  HN3   N3'  C8'   124.72  3.000
 BAB  HN3   N3'  C4'   125.89  3.000
 BAB  C8'   N3'  C4'   109.39  3.000
 BAB  HN4'  N4'  C8'   120.62  3.000
 BAB  HN4'  N4'  C5'   129.93  3.000
 BAB  C8'   N4'  C5'   109.45  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
 BAB  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 BAB  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 BAB  CONST_03  N4    C5   C6   C1    180.00   0.0  0
 BAB  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 BAB  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 BAB  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 BAB  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 BAB  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 BAB  CONST_09  N4    C5   C4   C3    180.00   0.0  0
 BAB  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 BAB  CONST_11  C8    N4   C5   C4      0.00   0.0  0
 BAB  CONST_12  N4    C8   N3   C4      0.00   0.0  0
 BAB  CONST_13  C8    N3   C4   C5      0.00   0.0  0
 BAB  CONST_14  N3    C8   N4   C5      0.00   0.0  0
 BAB  CONST_15  N3    C4   C5   C6    180.00   0.0  0
 BAB  CONST_16  C8    N4   C5   C6    180.00   0.0  0
 BAB  CONST_17  N4    C5   C4   N3      0.00   0.0  0
 BAB  CONST_18  C4'   C3'  C2'  C1'     0.00   0.0  0
 BAB  CONST_19  C4'   C5'  C6'  C1'     0.00   0.0  0
 BAB  CONST_20  N4'   C5'  C6'  C1'   180.00   0.0  0
 BAB  CONST_21  C5'   C6'  C1'  C2'     0.00   0.0  0
 BAB  CONST_22  C5'   C4'  C3'  C2'     0.00   0.0  0
 BAB  CONST_23  N3'   C4'  C3'  C2'   180.00   0.0  0
 BAB  CONST_24  C6'   C1'  C2'  C3'     0.00   0.0  0
 BAB  CONST_25  C6'   C5'  C4'  C3'     0.00   0.0  0
 BAB  CONST_26  N4'   C5'  C4'  C3'   180.00   0.0  0
 BAB  CONST_27  C8'   N3'  C4'  C3'   180.00   0.0  0
 BAB  CONST_28  C8'   N4'  C5'  C4'     0.00   0.0  0
 BAB  CONST_29  N4'   C8'  N3'  C4'     0.00   0.0  0
 BAB  CONST_30  C8'   N3'  C4'  C5'     0.00   0.0  0
 BAB  CONST_31  N3'   C8'  N4'  C5'     0.00   0.0  0
 BAB  CONST_32  N3'   C4'  C5'  C6'   180.00   0.0  0
 BAB  CONST_33  C8'   N4'  C5'  C6'   180.00   0.0  0
 BAB  CONST_34  N4'   C5'  C4'  N3'     0.00   0.0  0
 BAB  CONST_35  C7    C1   C2   C3    180.00   0.0  0
 BAB  CONST_36  C9    C8   N3   C4    180.00   0.0  0
 BAB  CONST_37  C7    C1   C6   C5    180.00   0.0  0
 BAB  CONST_38  C9    C8   N4   C5    180.00   0.0  0
 BAB  CONST_39  C4'   N3'  C8'  C9    180.00   0.0  0
 BAB  CONST_40  C5'   N4'  C8'  C9    180.00   0.0  0
 BAB  CONST_41  C7'   C1'  C2'  C3'   180.00   0.0  0
 BAB  CONST_42  C7'   C1'  C6'  C5'   180.00   0.0  0
 BAB  CONST_43  H3    C3   C2   C1    180.00   0.0  0
 BAB  CONST_44  H6    C6   C1   C2    180.00   0.0  0
 BAB  CONST_45  H2    C2   C3   C4    180.00   0.0  0
 BAB  CONST_46  HN4   N4   C5   C4    180.00   0.0  0
 BAB  CONST_47  H3'   C3'  C2'  C1'   180.00   0.0  0
 BAB  CONST_48  H6'   C6'  C1'  C2'   180.00   0.0  0
 BAB  CONST_49  HN3   N3'  C4'  C3'     0.00   0.0  0
 BAB  CONST_50  H2'   C2'  C3'  C4'   180.00   0.0  0
 BAB  CONST_51  HN4'  N4'  C5'  C4'   180.00   0.0  0
 BAB  CONST_52  HN5   N1   C7   C1    180.00   0.0  0
 BAB  CONST_53  HN6   N1   C7   C1      0.00   0.0  0
 BAB  CONST_54  HN21  N2   C7   C1    180.00   0.0  0
 BAB  CONST_55  HN22  N2   C7   C1      0.00   0.0  0
 BAB  CONST_56  HN1   N1'  C7'  C1'   180.00   0.0  0
 BAB  CONST_57  HN2   N1'  C7'  C1'     0.00   0.0  0
 BAB  CONST_58  H2'1  N2'  C7'  C1'   180.00   0.0  0
 BAB  CONST_59  H2'2  N2'  C7'  C1'     0.00   0.0  0
 BAB  Var_01    N3'   C8'  C9   C8   -177.28  30.0  2
 BAB  Var_02    C8'   C9   C8   N3     -2.40  30.0  2
 BAB  Var_03    N1    C7   C1   C2    -37.89  30.0  2
 BAB  Var_04    N1'   C7'  C1'  C2'   -40.08  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
 BAB  plan-1  C1    0.020
 BAB  plan-1  C2    0.020
 BAB  plan-1  C3    0.020
 BAB  plan-1  C4    0.020
 BAB  plan-1  C5    0.020
 BAB  plan-1  C6    0.020
 BAB  plan-1  C7    0.020
 BAB  plan-1  C8    0.020
 BAB  plan-1  C9    0.020
 BAB  plan-1  N3    0.020
 BAB  plan-1  N4    0.020
 BAB  plan-1  H2    0.020
 BAB  plan-1  H3    0.020
 BAB  plan-1  H6    0.020
 BAB  plan-1  HN4   0.020
 BAB  plan-2  C9    0.020
 BAB  plan-2  C1'   0.020
 BAB  plan-2  C2'   0.020
 BAB  plan-2  C3'   0.020
 BAB  plan-2  C4'   0.020
 BAB  plan-2  C5'   0.020
 BAB  plan-2  C6'   0.020
 BAB  plan-2  C7'   0.020
 BAB  plan-2  C8'   0.020
 BAB  plan-2  N3'   0.020
 BAB  plan-2  N4'   0.020
 BAB  plan-2  H2'   0.020
 BAB  plan-2  H3'   0.020
 BAB  plan-2  H6'   0.020
 BAB  plan-2  HN4'  0.020
 BAB  plan-2  HN3   0.020
 BAB  plan-3  C1    0.020
 BAB  plan-3  C7    0.020
 BAB  plan-3  N1    0.020
 BAB  plan-3  N2    0.020
 BAB  plan-3  HN21  0.020
 BAB  plan-3  HN22  0.020
 BAB  plan-3  HN5   0.020
 BAB  plan-3  HN6   0.020
 BAB  plan-4  C1'   0.020
 BAB  plan-4  C7'   0.020
 BAB  plan-4  N1'   0.020
 BAB  plan-4  N2'   0.020
 BAB  plan-4  H2'1  0.020
 BAB  plan-4  H2'2  0.020
 BAB  plan-4  HN1   0.020
 BAB  plan-4  HN2   0.020

