# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:25:14 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: 4-[6-(4-methylpiperazin-1-yl)-1H,3'H-2,5'-bibenzimidazol-2'-yl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc3nc([nH]c3c2)c4ccc5nc([nH]c5c4)c6ccc(O)cc6
#
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
 HT  HT  4-[6-(4-methylpiperazin-1-yl)-1H,3'H-2,5'-bibenzimidazol-2'-yl]phenol  ligand  56  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HT
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
 HT  O1    O  OH1   0  -0.618  10.7955  16.2158  18.5788
 HT  C1    C  CR6   0   0.357  10.4135  16.8443  17.4565
 HT  C4    C  CR6   0  -0.013   9.4927  18.1571  15.1556
 HT  C2    C  CR16  0  -0.319   9.0489  17.0735  17.2743
 HT  C3    C  CR16  0  -0.272   8.6020  17.7185  16.1401
 HT  C6    C  CR16  0  -0.365  11.3130  17.2722  16.4819
 HT  C5    C  CR16  0  -0.288  10.8534  17.9194  15.3479
 HT  C7    C  CR5   0   0.483   8.9645  18.8374  13.9789
 HT  N1    N  NR15  0  -0.737   9.7399  19.4747  13.0574
 HT  C8    C  CR56  0   0.369   8.9057  20.0051  12.1122
 HT  C9    C  CR56  0   0.158   7.6162  19.6404  12.5326
 HT  N2    N  N     0  -0.484   7.6874  18.9168  13.6892
 HT  C10   C  CR16  0  -0.324   6.5120  20.0403  11.7786
 HT  C11   C  CR16  0  -0.300   6.7348  20.7933  10.6457
 HT  C12   C  CR6   0  -0.009   8.0340  21.1596  10.2347
 HT  C13   C  CR16  0  -0.379   9.1436  20.7594  10.9749
 HT  C14   C  CR5   0   0.465   8.1726  21.9784   9.0328
 HT  N3    N  NR15  0  -0.737   9.3656  22.2086   8.4080
 HT  C15   C  CR56  0   0.378   9.1219  23.0161   7.3323
 HT  C16   C  CR56  0   0.123   7.7401  23.2383   7.3650
 HT  N4    N  N     0  -0.483   7.1799  22.5824   8.4305
 HT  C17   C  CR16  0  -0.329   7.1675  24.0497   6.3835
 HT  C18   C  CR16  0  -0.328   7.9872  24.5983   5.4223
 HT  C19   C  CR6   0   0.344   9.3848  24.3575   5.3837
 HT  C20   C  CR16  0  -0.445   9.9617  23.5433   6.3561
 HT  N5    N  NT    0  -0.514  10.1461  24.9834   4.3918
 HT  C21   C  CH2   0  -0.306   9.7061  24.8166   3.0130
 HT  C22   C  CH2   0  -0.281  10.3729  25.8385   2.1139
 HT  N6    N  NT    0  -0.410  11.8141  25.7342   2.2022
 HT  C23   C  CH2   0  -0.274  12.2402  25.9170   3.5730
 HT  C24   C  CH2   0  -0.314  11.5879  24.9022   4.4951
 HT  C25   C  CH3   0  -0.516  12.4737  26.6581   1.3090
 HT  HO1   H  HOH1  0   0.477  11.7530  16.1012  18.5981
 HT  H2    H  HCR6  0   0.268   8.3441  16.7459  18.0279
 HT  H3    H  HCR6  0   0.258   7.5419  17.8916  16.0138
 HT  H5    H  HCR6  0   0.256  11.5872  18.2241  14.6126
 HT  H6    H  HCR6  0   0.278  12.3759  17.0976  16.6031
 HT  HN1   H  HNR5  0   0.425  10.7419  19.5810  13.0752
 HT  H10   H  HCR6  0   0.255   5.5073  19.7696  12.0763
 HT  H11   H  HCR6  0   0.251   5.8944  21.1179  10.0477
 HT  H13   H  HCR6  0   0.261  10.1552  21.0306  10.7009
 HT  HN3   H  HNR5  0   0.420  10.2664  21.8379   8.6656
 HT  H17   H  HCR6  0   0.249   6.1055  24.2604   6.3839
 HT  H18   H  HCR6  0   0.255   7.5483  25.2594   4.6867
 HT  H20   H  HCR6  0   0.272  11.0180  23.3135   6.3625
 HT  H211  H  HCH2  0   0.213   9.9423  23.8048   2.6505
 HT  H212  H  HCH2  0   0.252   8.6274  24.9411   2.9416
 HT  H221  H  HCH2  0   0.238  10.0615  25.6547   1.0826
 HT  H222  H  HCH2  0   0.192  10.0158  26.8474   2.3861
 HT  H231  H  HCH2  0   0.238  13.3244  25.7947   3.6324
 HT  H232  H  HCH2  0   0.191  12.0086  26.9325   3.9397
 HT  H241  H  HCH2  0   0.249  11.8934  25.1292   5.5177
 HT  H242  H  HCH2  0   0.209  11.9620  23.8944   4.2559
 HT  H253  H  HCH3  0   0.232  12.1669  26.4661   0.2797
 HT  H252  H  HCH3  0   0.191  12.2516  27.7129   1.5343
 HT  H251  H  HCH3  0   0.232  13.5553  26.5265   1.3657

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
 HT  O1   C1    single    1.342  0.020  1.342
 HT  O1   HO1   single    0.850  0.020  0.980
 HT  C1   C2    aromatic  1.396  0.020  1.396
 HT  C1   C6    aromatic  1.394  0.020  1.394
 HT  C2   C3    aromatic  1.379  0.020  1.379
 HT  C2   H2    single    0.930  0.020  1.080
 HT  C3   C4    aromatic  1.398  0.020  1.398
 HT  C3   H3    single    0.930  0.020  1.080
 HT  C4   C5    aromatic  1.395  0.020  1.395
 HT  C4   C7    single    1.458  0.020  1.458
 HT  C5   C6    aromatic  1.384  0.020  1.384
 HT  C5   H5    single    0.930  0.020  1.080
 HT  C6   H6    single    0.930  0.020  1.080
 HT  C7   N1    aromatic  1.363  0.020  1.363
 HT  C7   N2    aromatic  1.312  0.020  1.312
 HT  N1   C8    aromatic  1.368  0.020  1.368
 HT  N1   HN1   single    0.860  0.020  1.020
 HT  C8   C9    aromatic  1.404  0.020  1.404
 HT  C8   C13   aromatic  1.385  0.020  1.385
 HT  C9   N2    aromatic  1.366  0.020  1.366
 HT  C9   C10   aromatic  1.396  0.020  1.396
 HT  C10  C11   aromatic  1.378  0.020  1.378
 HT  C10  H10   single    0.930  0.020  1.080
 HT  C11  C12   aromatic  1.411  0.020  1.411
 HT  C11  H11   single    0.930  0.020  1.080
 HT  C12  C13   aromatic  1.393  0.020  1.393
 HT  C12  C14   single    1.461  0.020  1.461
 HT  C13  H13   single    0.930  0.020  1.080
 HT  C14  N3    aromatic  1.366  0.020  1.366
 HT  C14  N4    aromatic  1.309  0.020  1.309
 HT  N3   C15   aromatic  1.367  0.020  1.367
 HT  N3   HN3   single    0.860  0.020  1.020
 HT  C15  C16   aromatic  1.400  0.020  1.400
 HT  C15  C20   aromatic  1.391  0.020  1.391
 HT  C16  N4    aromatic  1.371  0.020  1.371
 HT  C16  C17   aromatic  1.396  0.020  1.396
 HT  C17  C18   aromatic  1.377  0.020  1.377
 HT  C17  H17   single    0.930  0.020  1.080
 HT  C18  C19   aromatic  1.419  0.020  1.419
 HT  C18  H18   single    0.930  0.020  1.080
 HT  C19  C20   aromatic  1.393  0.020  1.393
 HT  C19  N5    single    1.398  0.020  1.398
 HT  C20  H20   single    0.930  0.020  1.080
 HT  N5   C21   single    1.457  0.020  1.457
 HT  N5   C24   single    1.448  0.020  1.448
 HT  C21  C22   single    1.516  0.020  1.516
 HT  C21  H211  single    0.970  0.020  1.090
 HT  C21  H212  single    0.970  0.020  1.090
 HT  C22  N6    single    1.448  0.020  1.448
 HT  C22  H221  single    0.970  0.020  1.090
 HT  C22  H222  single    0.970  0.020  1.090
 HT  N6   C23   single    1.447  0.020  1.447
 HT  N6   C25   single    1.444  0.020  1.444
 HT  C23  C24   single    1.518  0.020  1.518
 HT  C23  H231  single    0.970  0.020  1.090
 HT  C23  H232  single    0.970  0.020  1.090
 HT  C24  H241  single    0.970  0.020  1.090
 HT  C24  H242  single    0.970  0.020  1.090
 HT  C25  H253  single    0.970  0.020  1.090
 HT  C25  H252  single    0.970  0.020  1.090
 HT  C25  H251  single    0.970  0.020  1.090

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
 HT  HO1   O1   C1    110.80  3.000
 HT  C6    C1   C2    119.30  3.000
 HT  C6    C1   O1    123.03  3.000
 HT  C2    C1   O1    117.67  3.000
 HT  C7    C4   C5    122.97  3.000
 HT  C7    C4   C3    118.94  3.000
 HT  C5    C4   C3    118.10  3.000
 HT  H2    C2   C3    120.20  3.000
 HT  H2    C2   C1    119.73  3.000
 HT  C3    C2   C1    120.06  3.000
 HT  H3    C3   C2    119.24  3.000
 HT  H3    C3   C4    119.47  3.000
 HT  C2    C3   C4    121.29  3.000
 HT  H6    C6   C5    119.51  3.000
 HT  H6    C6   C1    120.34  3.000
 HT  C5    C6   C1    120.15  3.000
 HT  H5    C5   C6    117.58  3.000
 HT  H5    C5   C4    121.32  3.000
 HT  C6    C5   C4    121.10  3.000
 HT  N2    C7   N1    112.11  3.000
 HT  N2    C7   C4    123.99  3.000
 HT  N1    C7   C4    123.90  3.000
 HT  HN1   N1   C8    125.29  3.000
 HT  HN1   N1   C7    127.10  3.000
 HT  C8    N1   C7    107.56  3.000
 HT  C13   C8   C9    123.02  3.000
 HT  C13   C8   N1    132.36  3.000
 HT  C9    C8   N1    104.62  3.000
 HT  C10   C9   N2    130.57  3.000
 HT  C10   C9   C8    119.36  3.000
 HT  N2    C9   C8    110.07  3.000
 HT  C9    N2   C7    105.65  3.000
 HT  H10   C10  C11   120.85  3.000
 HT  H10   C10  C9    120.94  3.000
 HT  C11   C10  C9    118.21  3.000
 HT  H11   C11  C12   118.46  3.000
 HT  H11   C11  C10   119.53  3.000
 HT  C12   C11  C10   122.01  3.000
 HT  C14   C12  C13   121.52  3.000
 HT  C14   C12  C11   118.20  3.000
 HT  C13   C12  C11   120.28  3.000
 HT  H13   C13  C12   122.55  3.000
 HT  H13   C13  C8    120.31  3.000
 HT  C12   C13  C8    117.13  3.000
 HT  N4    C14  N3    111.96  3.000
 HT  N4    C14  C12   124.42  3.000
 HT  N3    C14  C12   123.61  3.000
 HT  HN3   N3   C15   125.31  3.000
 HT  HN3   N3   C14   126.99  3.000
 HT  C15   N3   C14   107.68  3.000
 HT  C20   C15  C16   123.50  3.000
 HT  C20   C15  N3    131.93  3.000
 HT  C16   C15  N3    104.56  3.000
 HT  C17   C16  N4    131.05  3.000
 HT  C17   C16  C15   118.73  3.000
 HT  N4    C16  C15   110.21  3.000
 HT  C16   N4   C14   105.58  3.000
 HT  H17   C17  C18   120.44  3.000
 HT  H17   C17  C16   121.00  3.000
 HT  C18   C17  C16   118.55  3.000
 HT  H18   C18  C19   119.00  3.000
 HT  H18   C18  C17   118.45  3.000
 HT  C19   C18  C17   122.53  3.000
 HT  N5    C19  C20   122.08  3.000
 HT  N5    C19  C18   118.66  3.000
 HT  C20   C19  C18   119.22  3.000
 HT  H20   C20  C19   122.20  3.000
 HT  H20   C20  C15   120.34  3.000
 HT  C19   C20  C15   117.46  3.000
 HT  C24   N5   C21   111.22  3.000
 HT  C24   N5   C19   117.81  3.000
 HT  C21   N5   C19   117.11  3.000
 HT  H212  C21  H211  107.24  3.000
 HT  H212  C21  C22   108.66  3.000
 HT  H211  C21  C22   109.27  3.000
 HT  H212  C21  N5    110.39  3.000
 HT  H211  C21  N5    110.63  3.000
 HT  C22   C21  N5    110.57  3.000
 HT  H222  C22  H221  107.11  3.000
 HT  H222  C22  N6    111.88  3.000
 HT  H221  C22  N6    109.22  3.000
 HT  H222  C22  C21   109.12  3.000
 HT  H221  C22  C21   108.73  3.000
 HT  N6    C22  C21   110.68  3.000
 HT  C25   N6   C23   111.75  3.000
 HT  C25   N6   C22   111.76  3.000
 HT  C23   N6   C22   109.99  3.000
 HT  H232  C23  H231  107.04  3.000
 HT  H232  C23  C24   108.84  3.000
 HT  H231  C23  C24   108.57  3.000
 HT  H232  C23  N6    111.65  3.000
 HT  H231  C23  N6    109.24  3.000
 HT  C24   C23  N6    111.37  3.000
 HT  H242  C24  H241  107.39  3.000
 HT  H242  C24  C23   109.49  3.000
 HT  H241  C24  C23   108.05  3.000
 HT  H242  C24  N5    111.97  3.000
 HT  H241  C24  N5    109.52  3.000
 HT  C23   C24  N5    110.30  3.000
 HT  H251  C25  H252  107.75  3.000
 HT  H251  C25  H253  107.85  3.000
 HT  H252  C25  H253  107.76  3.000
 HT  H251  C25  N6    110.08  3.000
 HT  H252  C25  N6    113.21  3.000
 HT  H253  C25  N6    110.02  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
 HT  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 HT  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 HT  CONST_03  C8    N1   C7   C4    180.00   0.0  0
 HT  CONST_04  C9    N2   C7   C4    180.00   0.0  0
 HT  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 HT  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 HT  CONST_07  C7    C4   C3   C2    180.00   0.0  0
 HT  CONST_08  C6    C1   C2   C3      0.00   0.0  0
 HT  CONST_09  C6    C5   C4   C3      0.00   0.0  0
 HT  CONST_10  N1    C7   C4   C3    180.00   0.0  0
 HT  CONST_11  N2    C7   C4   C3      0.00   0.0  0
 HT  CONST_12  C7    C4   C5   C6    180.00   0.0  0
 HT  CONST_13  N1    C7   C4   C5      0.00   0.0  0
 HT  CONST_14  N2    C7   C4   C5    180.00   0.0  0
 HT  CONST_15  C9    C8   N1   C7      0.00   0.0  0
 HT  CONST_16  C13   C8   N1   C7    180.00   0.0  0
 HT  CONST_17  C8    C9   N2   C7      0.00   0.0  0
 HT  CONST_18  C10   C9   N2   C7    180.00   0.0  0
 HT  CONST_19  C9    N2   C7   N1      0.00   0.0  0
 HT  CONST_20  N2    C9   C8   N1      0.00   0.0  0
 HT  CONST_21  C10   C9   C8   N1    180.00   0.0  0
 HT  CONST_22  C12   C13  C8   N1    180.00   0.0  0
 HT  CONST_23  N2    C7   N1   C8      0.00   0.0  0
 HT  CONST_24  C11   C10  C9   C8      0.00   0.0  0
 HT  CONST_25  C11   C12  C13  C8      0.00   0.0  0
 HT  CONST_26  C14   C12  C13  C8    180.00   0.0  0
 HT  CONST_27  C12   C13  C8   C9      0.00   0.0  0
 HT  CONST_28  C12   C11  C10  C9      0.00   0.0  0
 HT  CONST_29  C13   C8   C9   N2    180.00   0.0  0
 HT  CONST_30  C11   C10  C9   N2    180.00   0.0  0
 HT  CONST_31  C13   C8   C9   C10     0.00   0.0  0
 HT  CONST_32  C13   C12  C11  C10     0.00   0.0  0
 HT  CONST_33  C14   C12  C11  C10   180.00   0.0  0
 HT  CONST_34  N3    C14  C12  C11   180.00   0.0  0
 HT  CONST_35  N4    C14  C12  C11     0.00   0.0  0
 HT  CONST_36  C15   N3   C14  C12   180.00   0.0  0
 HT  CONST_37  C16   N4   C14  C12   180.00   0.0  0
 HT  CONST_38  N3    C14  C12  C13     0.00   0.0  0
 HT  CONST_39  N4    C14  C12  C13   180.00   0.0  0
 HT  CONST_40  C16   C15  N3   C14     0.00   0.0  0
 HT  CONST_41  C20   C15  N3   C14   180.00   0.0  0
 HT  CONST_42  C15   C16  N4   C14     0.00   0.0  0
 HT  CONST_43  C17   C16  N4   C14   180.00   0.0  0
 HT  CONST_44  C16   N4   C14  N3      0.00   0.0  0
 HT  CONST_45  N4    C16  C15  N3      0.00   0.0  0
 HT  CONST_46  C17   C16  C15  N3    180.00   0.0  0
 HT  CONST_47  C19   C20  C15  N3    180.00   0.0  0
 HT  CONST_48  N4    C14  N3   C15     0.00   0.0  0
 HT  CONST_49  C18   C17  C16  C15     0.00   0.0  0
 HT  CONST_50  C18   C19  C20  C15     0.00   0.0  0
 HT  CONST_51  C19   C20  C15  C16     0.00   0.0  0
 HT  CONST_52  C19   C18  C17  C16     0.00   0.0  0
 HT  CONST_53  C20   C15  C16  N4    180.00   0.0  0
 HT  CONST_54  C18   C17  C16  N4    180.00   0.0  0
 HT  CONST_55  C20   C15  C16  C17     0.00   0.0  0
 HT  CONST_56  C20   C19  C18  C17     0.00   0.0  0
 HT  CONST_57  N5    C19  C20  C15   180.00   0.0  0
 HT  CONST_58  N5    C19  C18  C17   180.00   0.0  0
 HT  CONST_59  C3    C2   C1   O1    180.00   0.0  0
 HT  CONST_60  C5    C6   C1   O1    180.00   0.0  0
 HT  CONST_61  H3    C3   C2   C1    180.00   0.0  0
 HT  CONST_62  H5    C5   C6   C1    180.00   0.0  0
 HT  CONST_63  H2    C2   C3   C4    180.00   0.0  0
 HT  CONST_64  H6    C6   C5   C4    180.00   0.0  0
 HT  CONST_65  HN1   N1   C7   C4      0.00   0.0  0
 HT  CONST_66  H13   C13  C8   N1      0.00   0.0  0
 HT  CONST_67  H10   C10  C9   C8    180.00   0.0  0
 HT  CONST_68  H11   C11  C10  C9    180.00   0.0  0
 HT  CONST_69  HN3   N3   C14  C12     0.00   0.0  0
 HT  CONST_70  H20   C20  C15  N3      0.00   0.0  0
 HT  CONST_71  H17   C17  C16  C15   180.00   0.0  0
 HT  CONST_72  H18   C18  C17  C16   180.00   0.0  0
 HT  Var_01    C21   N5   C19  C18   -52.92  30.0  2
 HT  Var_02    C22   C21  N5   C19   164.22  30.0  1
 HT  Var_03    C23   C24  N5   C19  -165.18  30.0  1
 HT  Var_04    N6    C22  C21  N5     57.22  30.0  1
 HT  Var_05    N6    C23  C24  N5    -56.64  30.0  1
 HT  Var_06    C23   N6   C22  C21   -57.84  30.0  1
 HT  Var_07    C24   C23  N6   C22    57.75  30.0  1
 HT  Var_08    H253  C25  N6   C22   -58.82  30.0  3

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
 HT  plan-1  O1   0.020
 HT  plan-1  C1   0.020
 HT  plan-1  C4   0.020
 HT  plan-1  C2   0.020
 HT  plan-1  C3   0.020
 HT  plan-1  C6   0.020
 HT  plan-1  C5   0.020
 HT  plan-1  C7   0.020
 HT  plan-1  H2   0.020
 HT  plan-1  H3   0.020
 HT  plan-1  H5   0.020
 HT  plan-1  H6   0.020
 HT  plan-2  C4   0.020
 HT  plan-2  C7   0.020
 HT  plan-2  N1   0.020
 HT  plan-2  C8   0.020
 HT  plan-2  C9   0.020
 HT  plan-2  N2   0.020
 HT  plan-2  C10  0.020
 HT  plan-2  C11  0.020
 HT  plan-2  C12  0.020
 HT  plan-2  C13  0.020
 HT  plan-2  C14  0.020
 HT  plan-2  HN1  0.020
 HT  plan-2  H10  0.020
 HT  plan-2  H11  0.020
 HT  plan-2  H13  0.020
 HT  plan-3  C12  0.020
 HT  plan-3  C14  0.020
 HT  plan-3  N3   0.020
 HT  plan-3  C15  0.020
 HT  plan-3  C16  0.020
 HT  plan-3  N4   0.020
 HT  plan-3  C17  0.020
 HT  plan-3  C18  0.020
 HT  plan-3  C19  0.020
 HT  plan-3  C20  0.020
 HT  plan-3  N5   0.020
 HT  plan-3  HN3  0.020
 HT  plan-3  H17  0.020
 HT  plan-3  H18  0.020
 HT  plan-3  H20  0.020

