# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 11:11:18 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: [(dihydroxymethanediyl)bis(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)(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
 BAH  BAH  '[(dihydroxymethanediyl)bis(1H-benzimidazole-2,6-diyl)]bis(aminomethaniminium)'  ligand  45  27  .  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_BAH
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
 BAH  C1    C  CR6   0  -0.006   5.0711   0.9332  -0.0437
 BAH  C2    C  CR16  0  -0.279   4.9008   1.3366   1.2958
 BAH  C3    C  CR16  0  -0.315   3.8308   0.8977   2.0451
 BAH  C4    C  CR56  0   0.172   2.9124   0.0439   1.4360
 BAH  C5    C  CR56  0   0.363   3.0975  -0.3489   0.0974
 BAH  C6    C  CR16  0  -0.320   4.1694   0.0779  -0.6662
 BAH  C7    C  C     0   0.589   6.2242   1.4330  -0.8048
 BAH  C8    C  CR5   0   0.423   1.3027  -1.2426   0.9492
 BAH  C9    C  CT    0   0.327   0.0287  -2.0464   1.0589
 BAH  N1    N  NH2   0  -0.767   6.7964   0.6578  -1.6958
 BAH  N2    N  NC2   1  -0.767   6.6657   2.6490  -0.5841
 BAH  N3    N  N     0  -0.470   1.7761  -0.5338   1.9343
 BAH  N4    N  NR15  0  -0.682   2.0419  -1.1741  -0.1752
 BAH  C1'   C  CR6   0  -0.015  -5.0012   0.7165  -0.5510
 BAH  C2'   C  CR16  0  -0.275  -4.1352   1.3930  -1.4329
 BAH  C3'   C  CR16  0  -0.316  -2.7857   1.1156  -1.4619
 BAH  C4'   C  CR56  0   0.164  -2.2967   0.1498  -0.5823
 BAH  C5'   C  CR56  0   0.362  -3.1754  -0.5066   0.2984
 BAH  C6'   C  CR16  0  -0.311  -4.5346  -0.2466   0.3340
 BAH  C7'   C  C     0   0.582  -6.4366   1.0356  -0.5656
 BAH  C8'   C  CR5   0   0.427  -1.1219  -1.2019   0.5486
 BAH  N1'   N  NH2   0  -0.762  -6.8175   2.2785  -0.7322
 BAH  N2'   N  NC2   1  -0.762  -7.3092   0.0692  -0.4126
 BAH  N3'   N  N     0  -0.455  -1.0216  -0.3134  -0.4003
 BAH  N4'   N  NR15  0  -0.692  -2.3808  -1.3563   1.0152
 BAH  O91   O  OH1   0  -0.636   0.1992  -3.1689   0.2726
 BAH  O92   O  OH1   0  -0.642  -0.1965  -2.4247   2.3741
 BAH  HC2   H  HCR6  0   0.279   5.6342   1.9816   1.7612
 BAH  HC3   H  HCR6  0   0.277   3.7121   1.2022   3.0759
 BAH  HC6   H  HCR6  0   0.297   4.2738  -0.2175  -1.7019
 BAH  HN11  H  HNH2  0   0.447   6.5407  -0.3131  -1.7760
 BAH  HN12  H  HNH2  0   0.439   7.5626   0.9813  -2.2677
 BAH  HN21  H  HNC2  0   0.439   7.4698   3.0199  -1.0687
 BAH  HN22  H  HNC2  0   0.447   6.1572   3.2835   0.0102
 BAH  HN4   H  HNR5  0   0.432   1.8486  -1.6442  -1.0472
 BAH  HC2'  H  HCR6  0   0.280  -4.5361   2.1200  -2.1273
 BAH  HC3'  H  HCR6  0   0.276  -2.1295   1.6250  -2.1544
 BAH  HC6'  H  HCR6  0   0.298  -5.1885  -0.7553   1.0297
 BAH  H1'1  H  HNH2  0   0.446  -6.1489   3.0315  -0.7185
 BAH  H1'2  H  HNH2  0   0.439  -7.7907   2.5343  -0.8030
 BAH  H2'1  H  HNC2  0   0.439  -8.3006   0.2478  -0.3563
 BAH  H2'2  H  HNC2  0   0.447  -7.0198  -0.8953  -0.4259
 BAH  HN4'  H  HNR5  0   0.433  -2.6749  -1.9797   1.7527
 BAH  H91   H  HOH1  0   0.480  -0.6481  -3.6015   0.1058
 BAH  H92   H  HOH1  0   0.471   0.0557  -1.7046   2.9694

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
 BAH  C1   C2    aromatic  1.409  0.020  1.409
 BAH  C1   C6    aromatic  1.390  0.020  1.390
 BAH  C1   C7    single    1.469  0.020  1.469
 BAH  C2   C3    aromatic  1.378  0.020  1.378
 BAH  C2   HC2   single    0.930  0.020  1.080
 BAH  C3   C4    aromatic  1.394  0.020  1.394
 BAH  C3   HC3   single    0.930  0.020  1.080
 BAH  C4   C5    aromatic  1.407  0.020  1.407
 BAH  C4   N3    aromatic  1.369  0.020  1.369
 BAH  C5   C6    aromatic  1.383  0.020  1.383
 BAH  C5   N4    aromatic  1.367  0.020  1.367
 BAH  C6   HC6   single    0.930  0.020  1.080
 BAH  C7   N1    single    1.312  0.020  1.312
 BAH  C7   N2    double    1.312  0.020  1.312
 BAH  C8   C9    single    1.510  0.020  1.510
 BAH  C8   N3    aromatic  1.303  0.020  1.303
 BAH  C8   N4    aromatic  1.347  0.020  1.347
 BAH  C9   C8'   single    1.516  0.020  1.516
 BAH  C9   O91   single    1.381  0.020  1.381
 BAH  C9   O92   single    1.387  0.020  1.387
 BAH  N1   HN11  single    0.860  0.020  1.020
 BAH  N1   HN12  single    0.860  0.020  1.020
 BAH  N2   HN21  single    0.860  0.020  1.020
 BAH  N2   HN22  single    0.860  0.020  1.020
 BAH  N4   HN4   single    0.860  0.020  1.020
 BAH  C1'  C2'   aromatic  1.409  0.020  1.409
 BAH  C1'  C6'   aromatic  1.389  0.020  1.389
 BAH  C1'  C7'   single    1.471  0.020  1.471
 BAH  C2'  C3'   aromatic  1.378  0.020  1.378
 BAH  C2'  HC2'  single    0.930  0.020  1.080
 BAH  C3'  C4'   aromatic  1.395  0.020  1.395
 BAH  C3'  HC3'  single    0.930  0.020  1.080
 BAH  C4'  C5'   aromatic  1.407  0.020  1.407
 BAH  C4'  N3'   aromatic  1.369  0.020  1.369
 BAH  C5'  C6'   aromatic  1.384  0.020  1.384
 BAH  C5'  N4'   aromatic  1.366  0.020  1.366
 BAH  C6'  HC6'  single    0.930  0.020  1.080
 BAH  C7'  N1'   single    1.311  0.020  1.311
 BAH  C7'  N2'   double    1.311  0.020  1.311
 BAH  C8'  N3'   aromatic  1.304  0.020  1.304
 BAH  C8'  N4'   aromatic  1.351  0.020  1.351
 BAH  N1'  H1'1  single    0.860  0.020  1.020
 BAH  N1'  H1'2  single    0.860  0.020  1.020
 BAH  N2'  H2'1  single    0.860  0.020  1.020
 BAH  N2'  H2'2  single    0.860  0.020  1.020
 BAH  N4'  HN4'  single    0.860  0.020  1.020
 BAH  O91  H91   single    0.850  0.020  0.980
 BAH  O92  H92   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
 BAH  C7    C1   C6    119.10  3.000
 BAH  C7    C1   C2    119.33  3.000
 BAH  C6    C1   C2    121.56  3.000
 BAH  HC2   C2   C3    118.84  3.000
 BAH  HC2   C2   C1    119.84  3.000
 BAH  C3    C2   C1    121.30  3.000
 BAH  HC3   C3   C4    121.10  3.000
 BAH  HC3   C3   C2    120.92  3.000
 BAH  C4    C3   C2    117.97  3.000
 BAH  N3    C4   C5    109.74  3.000
 BAH  N3    C4   C3    130.27  3.000
 BAH  C5    C4   C3    119.99  3.000
 BAH  N4    C5   C6    132.40  3.000
 BAH  N4    C5   C4    104.87  3.000
 BAH  C6    C5   C4    122.74  3.000
 BAH  HC6   C6   C5    121.26  3.000
 BAH  HC6   C6   C1    122.28  3.000
 BAH  C5    C6   C1    116.44  3.000
 BAH  N2    C7   N1    120.99  3.000
 BAH  N2    C7   C1    119.48  3.000
 BAH  N1    C7   C1    119.54  3.000
 BAH  N4    C8   N3    113.83  3.000
 BAH  N4    C8   C9    123.40  3.000
 BAH  N3    C8   C9    122.76  3.000
 BAH  O92   C9   O91   109.77  3.000
 BAH  O92   C9   C8'   110.37  3.000
 BAH  O91   C9   C8'   110.79  3.000
 BAH  O92   C9   C8    110.55  3.000
 BAH  O91   C9   C8    106.68  3.000
 BAH  C8'   C9   C8    108.62  3.000
 BAH  HN12  N1   HN11  117.16  3.000
 BAH  HN12  N1   C7    121.76  3.000
 BAH  HN11  N1   C7    120.84  3.000
 BAH  HN22  N2   HN21  117.00  3.000
 BAH  HN22  N2   C7    120.88  3.000
 BAH  HN21  N2   C7    121.85  3.000
 BAH  C8    N3   C4    104.84  3.000
 BAH  HN4   N4   C8    126.32  3.000
 BAH  HN4   N4   C5    126.95  3.000
 BAH  C8    N4   C5    106.73  3.000
 BAH  C7'   C1'  C6'   118.99  3.000
 BAH  C7'   C1'  C2'   119.31  3.000
 BAH  C6'   C1'  C2'   121.69  3.000
 BAH  HC2'  C2'  C3'   118.98  3.000
 BAH  HC2'  C2'  C1'   119.76  3.000
 BAH  C3'   C2'  C1'   121.23  3.000
 BAH  HC3'  C3'  C4'   121.15  3.000
 BAH  HC3'  C3'  C2'   120.85  3.000
 BAH  C4'   C3'  C2'   118.00  3.000
 BAH  N3'   C4'  C5'   109.93  3.000
 BAH  N3'   C4'  C3'   130.14  3.000
 BAH  C5'   C4'  C3'   119.93  3.000
 BAH  N4'   C5'  C6'   132.39  3.000
 BAH  N4'   C5'  C4'   104.80  3.000
 BAH  C6'   C5'  C4'   122.81  3.000
 BAH  HC6'  C6'  C5'   121.45  3.000
 BAH  HC6'  C6'  C1'   122.20  3.000
 BAH  C5'   C6'  C1'   116.34  3.000
 BAH  N2'   C7'  N1'   121.37  3.000
 BAH  N2'   C7'  C1'   119.25  3.000
 BAH  N1'   C7'  C1'   119.38  3.000
 BAH  N4'   C8'  N3'   113.63  3.000
 BAH  N4'   C8'  C9    121.82  3.000
 BAH  N3'   C8'  C9    124.49  3.000
 BAH  H1'2  N1'  H1'1  116.86  3.000
 BAH  H1'2  N1'  C7'   121.99  3.000
 BAH  H1'1  N1'  C7'   120.96  3.000
 BAH  H2'2  N2'  H2'1  116.91  3.000
 BAH  H2'2  N2'  C7'   120.88  3.000
 BAH  H2'1  N2'  C7'   122.01  3.000
 BAH  C8'   N3'  C4'   104.81  3.000
 BAH  HN4'  N4'  C8'   126.46  3.000
 BAH  HN4'  N4'  C5'   126.72  3.000
 BAH  C8'   N4'  C5'   106.83  3.000
 BAH  H91   O91  C9    110.73  3.000
 BAH  H92   O92  C9    109.75  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
 BAH  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 BAH  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 BAH  CONST_03  N4    C5   C6   C1   180.00   0.0  0
 BAH  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 BAH  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 BAH  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 BAH  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 BAH  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 BAH  CONST_09  N4    C5   C4   C3   180.00   0.0  0
 BAH  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 BAH  CONST_11  C8    N4   C5   C4     0.00   0.0  0
 BAH  CONST_12  N4    C8   N3   C4     0.00   0.0  0
 BAH  CONST_13  C8    N3   C4   C5     0.00   0.0  0
 BAH  CONST_14  N3    C8   N4   C5     0.00   0.0  0
 BAH  CONST_15  N3    C4   C5   C6   180.00   0.0  0
 BAH  CONST_16  C8    N4   C5   C6   180.00   0.0  0
 BAH  CONST_17  N4    C5   C4   N3     0.00   0.0  0
 BAH  CONST_18  C4'   C3'  C2'  C1'    0.00   0.0  0
 BAH  CONST_19  C4'   C5'  C6'  C1'    0.00   0.0  0
 BAH  CONST_20  N4'   C5'  C6'  C1'  180.00   0.0  0
 BAH  CONST_21  C5'   C6'  C1'  C2'    0.00   0.0  0
 BAH  CONST_22  C5'   C4'  C3'  C2'    0.00   0.0  0
 BAH  CONST_23  N3'   C4'  C3'  C2'  180.00   0.0  0
 BAH  CONST_24  C6'   C1'  C2'  C3'    0.00   0.0  0
 BAH  CONST_25  C6'   C5'  C4'  C3'    0.00   0.0  0
 BAH  CONST_26  N4'   C5'  C4'  C3'  180.00   0.0  0
 BAH  CONST_27  C8'   N3'  C4'  C3'  180.00   0.0  0
 BAH  CONST_28  C8'   N4'  C5'  C4'    0.00   0.0  0
 BAH  CONST_29  N4'   C8'  N3'  C4'    0.00   0.0  0
 BAH  CONST_30  C8'   N3'  C4'  C5'    0.00   0.0  0
 BAH  CONST_31  N3'   C8'  N4'  C5'    0.00   0.0  0
 BAH  CONST_32  N3'   C4'  C5'  C6'  180.00   0.0  0
 BAH  CONST_33  C8'   N4'  C5'  C6'  180.00   0.0  0
 BAH  CONST_34  N4'   C5'  C4'  N3'    0.00   0.0  0
 BAH  CONST_35  C7    C1   C2   C3   180.00   0.0  0
 BAH  CONST_36  C9    C8   N3   C4   180.00   0.0  0
 BAH  CONST_37  C7    C1   C6   C5   180.00   0.0  0
 BAH  CONST_38  C9    C8   N4   C5   180.00   0.0  0
 BAH  CONST_39  C4'   N3'  C8'  C9   180.00   0.0  0
 BAH  CONST_40  C5'   N4'  C8'  C9   180.00   0.0  0
 BAH  CONST_41  C7'   C1'  C2'  C3'  180.00   0.0  0
 BAH  CONST_42  C7'   C1'  C6'  C5'  180.00   0.0  0
 BAH  CONST_43  HC3   C3   C2   C1   180.00   0.0  0
 BAH  CONST_44  HC6   C6   C1   C2   180.00   0.0  0
 BAH  CONST_45  HC2   C2   C3   C4   180.00   0.0  0
 BAH  CONST_46  HN4   N4   C5   C4   180.00   0.0  0
 BAH  CONST_47  HC3'  C3'  C2'  C1'  180.00   0.0  0
 BAH  CONST_48  HC6'  C6'  C1'  C2'  180.00   0.0  0
 BAH  CONST_49  HC2'  C2'  C3'  C4'  180.00   0.0  0
 BAH  CONST_50  HN4'  N4'  C5'  C4'  180.00   0.0  0
 BAH  CONST_51  HN11  N1   C7   C1     0.00   0.0  0
 BAH  CONST_52  HN12  N1   C7   C1   180.00   0.0  0
 BAH  CONST_53  HN21  N2   C7   C1   180.00   0.0  0
 BAH  CONST_54  HN22  N2   C7   C1     0.00   0.0  0
 BAH  CONST_55  H1'1  N1'  C7'  C1'    0.00   0.0  0
 BAH  CONST_56  H1'2  N1'  C7'  C1'  180.00   0.0  0
 BAH  CONST_57  H2'1  N2'  C7'  C1'  180.00   0.0  0
 BAH  CONST_58  H2'2  N2'  C7'  C1'    0.00   0.0  0
 BAH  Var_01    N3'   C8'  C9   C8    32.15  30.0  2
 BAH  Var_02    C8'   C9   C8   N3    93.92  30.0  2
 BAH  Var_03    N1    C7   C1   C2   145.57  30.0  2
 BAH  Var_04    N1'   C7'  C1'  C2'  -38.26  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
 BAH  plan-1  C1    0.020
 BAH  plan-1  C2    0.020
 BAH  plan-1  C3    0.020
 BAH  plan-1  C4    0.020
 BAH  plan-1  C5    0.020
 BAH  plan-1  C6    0.020
 BAH  plan-1  C7    0.020
 BAH  plan-1  C8    0.020
 BAH  plan-1  C9    0.020
 BAH  plan-1  N3    0.020
 BAH  plan-1  N4    0.020
 BAH  plan-1  HC2   0.020
 BAH  plan-1  HC3   0.020
 BAH  plan-1  HC6   0.020
 BAH  plan-1  HN4   0.020
 BAH  plan-2  C9    0.020
 BAH  plan-2  C1'   0.020
 BAH  plan-2  C2'   0.020
 BAH  plan-2  C3'   0.020
 BAH  plan-2  C4'   0.020
 BAH  plan-2  C5'   0.020
 BAH  plan-2  C6'   0.020
 BAH  plan-2  C7'   0.020
 BAH  plan-2  C8'   0.020
 BAH  plan-2  N3'   0.020
 BAH  plan-2  N4'   0.020
 BAH  plan-2  HC2'  0.020
 BAH  plan-2  HC3'  0.020
 BAH  plan-2  HC6'  0.020
 BAH  plan-2  HN4'  0.020
 BAH  plan-3  C1    0.020
 BAH  plan-3  C7    0.020
 BAH  plan-3  N1    0.020
 BAH  plan-3  N2    0.020
 BAH  plan-3  HN11  0.020
 BAH  plan-3  HN12  0.020
 BAH  plan-3  HN21  0.020
 BAH  plan-3  HN22  0.020
 BAH  plan-4  C1'   0.020
 BAH  plan-4  C7'   0.020
 BAH  plan-4  N1'   0.020
 BAH  plan-4  N2'   0.020
 BAH  plan-4  H1'1  0.020
 BAH  plan-4  H1'2  0.020
 BAH  plan-4  H2'1  0.020
 BAH  plan-4  H2'2  0.020

