# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX
#   - file written: Thu May  7 11:32:45 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 4-[2'-(3-iodophenyl)-1H,3'H-2,5'-bibenzimidazol-6-yl]-1-methylpiperazin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[NH+]1CCN(CC1)c2ccc3nc([nH]c3c2)c4ccc5nc([nH]c5c4)c6cccc(I)c6
#
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
 IA  IA  4-[2'-(3-iodophenyl)-1H,3'H-2,5'-bibenzimidazol-6-yl]-1-methylpiperazin-1-ium  ligand  56  32  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IA
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
 IA  C     C  CR16  0  -0.228  -7.5030  -1.4088   0.0361
 IA  C1    C  CR6   0   0.024  -4.7126  -1.5520   0.0618
 IA  C2    C  CR16  0  -0.230  -6.8605  -2.5776   0.4259
 IA  C3    C  CR16  0  -0.282  -5.4793  -2.6539   0.4401
 IA  C4    C  CR6   0  -0.205  -6.7335  -0.3192  -0.3432
 IA  C5    C  CR16  0  -0.275  -5.3488  -0.3766  -0.3375
 IA  C6    C  CR5   0   0.488  -3.2551  -1.6566   0.0843
 IA  C7    C  CR56  0   0.382  -1.1428  -1.0493   0.0544
 IA  C8    C  CR56  0   0.155  -1.2781  -2.4440   0.1711
 IA  C9    C  CR16  0  -0.321  -0.1351  -3.2396   0.2467
 IA  C10   C  CR16  0  -0.312   1.0949  -2.6161   0.2095
 IA  C11   C  CR6   0  -0.005   1.2178  -1.2155   0.0981
 IA  C12   C  CR16  0  -0.364   0.0844  -0.4121   0.0183
 IA  N1    N  NR15  0  -0.735  -2.4262  -0.5815  -0.0008
 IA  N2    N  N     0  -0.475  -2.6012  -2.7866   0.1869
 IA  C13   C  CR5   0   0.485   2.5259  -0.5668   0.0615
 IA  C14   C  CR56  0   0.360   4.7172  -0.3232   0.1100
 IA  C15   C  CR56  0   0.147   4.0630   0.9073  -0.0689
 IA  C16   C  CR16  0  -0.335   4.8221   2.0657  -0.1984
 IA  C17   C  CR16  0  -0.345   6.2001   1.9609  -0.1359
 IA  C18   C  CR6   0   0.332   6.8479   0.7198   0.0305
 IA  C19   C  CR16  0  -0.391   6.0970  -0.4474   0.1499
 IA  N3    N  NR15  0  -0.748   3.7065  -1.2408   0.1877
 IA  N4    N  N     0  -0.485   2.7057   0.7195  -0.0928
 IA  N6    N  NT    0  -0.518   8.2539   0.6194   0.0590
 IA  N7    N  NT1   1  -0.517  11.0741   0.7836   0.5192
 IA  C20   C  CH2   0  -0.329   8.8295   0.1028   1.2888
 IA  C21   C  CH2   0  -0.321  10.2581  -0.3396   1.0632
 IA  C22   C  CH2   0  -0.312  10.4410   1.3339  -0.7123
 IA  C23   C  CH2   0  -0.342   9.0111   1.7461  -0.4376
 IA  C24   C  CH3   0  -0.533  12.4800   0.3812   0.2855
 IA  I     I  I     0   0.071  -7.6843   1.4559  -0.9486
 IA  H     H  HCR6  0   0.287  -8.5832  -1.3618   0.0318
 IA  H2    H  HCR6  0   0.277  -7.4504  -3.4336   0.7247
 IA  H3    H  HCR6  0   0.268  -4.9892  -3.5657   0.7518
 IA  H5    H  HCR6  0   0.270  -4.7752   0.4828  -0.6571
 IA  H9    H  HCR6  0   0.264  -0.2086  -4.3156   0.3312
 IA  H10   H  HCR6  0   0.244   1.9772  -3.2394   0.2649
 IA  H12   H  HCR6  0   0.270   0.1715   0.6625  -0.0667
 IA  HN1   H  HNR5  0   0.428  -2.6934   0.3894  -0.0420
 IA  H16   H  HCR6  0   0.256   4.3503   3.0302  -0.3350
 IA  H17   H  HCR6  0   0.268   6.7853   2.8668  -0.2107
 IA  H19   H  HCR6  0   0.270   6.5739  -1.4143   0.2500
 IA  HN3   H  HNR5  0   0.423   3.8273  -2.2326   0.3151
 IA  HN7   H  HNT1  0   0.464  11.0853   1.5281   1.2203
 IA  H201  H  HCH2  0   0.247   8.7933   0.8489   2.0973
 IA  H202  H  HCH2  0   0.292   8.2743  -0.7677   1.6323
 IA  H211  H  HCH2  0   0.299  10.3111  -1.1516   0.3384
 IA  H212  H  HCH2  0   0.312  10.7180  -0.6590   1.9960
 IA  H221  H  HCH2  0   0.311  11.0326   2.1885  -1.0340
 IA  H222  H  HCH2  0   0.299  10.4916   0.5553  -1.4728
 IA  H231  H  HCH2  0   0.242   9.0053   2.6049   0.2518
 IA  H232  H  HCH2  0   0.292   8.5933   2.0887  -1.3842
 IA  H241  H  HCH3  0   0.295  13.0345   1.2399  -0.0810
 IA  H242  H  HCH3  0   0.296  12.9071   0.0369   1.2226
 IA  H243  H  HCH3  0   0.290  12.5005  -0.4179  -0.4500

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
 IA  C    C2    aromatic  1.390  0.020  1.390
 IA  C    C4    aromatic  1.387  0.020  1.387
 IA  C    H     single    0.930  0.020  1.080
 IA  C1   C3    aromatic  1.395  0.020  1.395
 IA  C1   C5    aromatic  1.395  0.020  1.395
 IA  C1   C6    single    1.461  0.020  1.461
 IA  C2   C3    aromatic  1.383  0.020  1.383
 IA  C2   H2    single    0.930  0.020  1.080
 IA  C3   H3    single    0.930  0.020  1.080
 IA  C4   C5    aromatic  1.386  0.020  1.386
 IA  C4   I     single    2.103  0.020  2.103
 IA  C5   H5    single    0.930  0.020  1.080
 IA  C6   N1    aromatic  1.360  0.020  1.360
 IA  C6   N2    aromatic  1.310  0.020  1.310
 IA  C7   C8    aromatic  1.406  0.020  1.406
 IA  C7   C12   aromatic  1.383  0.020  1.383
 IA  C7   N1    aromatic  1.367  0.020  1.367
 IA  C8   C9    aromatic  1.395  0.020  1.395
 IA  C8   N2    aromatic  1.367  0.020  1.367
 IA  C9   C10   aromatic  1.380  0.020  1.380
 IA  C9   H9    single    0.930  0.020  1.080
 IA  C10  C11   aromatic  1.410  0.020  1.410
 IA  C10  H10   single    0.930  0.020  1.080
 IA  C11  C12   aromatic  1.392  0.020  1.392
 IA  C11  C13   single    1.461  0.020  1.461
 IA  C12  H12   single    0.930  0.020  1.080
 IA  N1   HN1   single    0.860  0.020  1.020
 IA  C13  N3    aromatic  1.365  0.020  1.365
 IA  C13  N4    aromatic  1.308  0.020  1.308
 IA  C14  C15   aromatic  1.405  0.020  1.405
 IA  C14  C19   aromatic  1.386  0.020  1.386
 IA  C14  N3    aromatic  1.367  0.020  1.367
 IA  C15  C16   aromatic  1.391  0.020  1.391
 IA  C15  N4    aromatic  1.370  0.020  1.370
 IA  C16  C17   aromatic  1.383  0.020  1.383
 IA  C16  H16   single    0.930  0.020  1.080
 IA  C17  C18   aromatic  1.410  0.020  1.410
 IA  C17  H17   single    0.930  0.020  1.080
 IA  C18  C19   aromatic  1.393  0.020  1.393
 IA  C18  N6    single    1.410  0.020  1.410
 IA  C19  H19   single    0.930  0.020  1.080
 IA  N3   HN3   single    0.860  0.020  1.020
 IA  N6   C20   single    1.453  0.020  1.453
 IA  N6   C23   single    1.445  0.020  1.445
 IA  N7   C21   single    1.491  0.020  1.491
 IA  N7   C22   single    1.490  0.020  1.490
 IA  N7   C24   single    1.481  0.020  1.481
 IA  N7   HN7   single    0.890  0.020  1.040
 IA  C20  C21   single    1.513  0.020  1.513
 IA  C20  H201  single    0.970  0.020  1.090
 IA  C20  H202  single    0.970  0.020  1.090
 IA  C21  H211  single    0.970  0.020  1.090
 IA  C21  H212  single    0.970  0.020  1.090
 IA  C22  C23   single    1.513  0.020  1.513
 IA  C22  H221  single    0.970  0.020  1.090
 IA  C22  H222  single    0.970  0.020  1.090
 IA  C23  H231  single    0.970  0.020  1.090
 IA  C23  H232  single    0.970  0.020  1.090
 IA  C24  H241  single    0.970  0.020  1.090
 IA  C24  H242  single    0.970  0.020  1.090
 IA  C24  H243  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
 IA  H     C    C4    121.27  3.000
 IA  H     C    C2    119.97  3.000
 IA  C4    C    C2    118.75  3.000
 IA  C6    C1   C5    121.31  3.000
 IA  C6    C1   C3    119.18  3.000
 IA  C5    C1   C3    119.51  3.000
 IA  H2    C2   C3    119.87  3.000
 IA  H2    C2   C     119.41  3.000
 IA  C3    C2   C     120.72  3.000
 IA  H3    C3   C2    120.14  3.000
 IA  H3    C3   C1    119.69  3.000
 IA  C2    C3   C1    120.17  3.000
 IA  I     C4   C5    119.21  3.000
 IA  I     C4   C     119.41  3.000
 IA  C5    C4   C     121.38  3.000
 IA  H5    C5   C4    119.72  3.000
 IA  H5    C5   C1    120.81  3.000
 IA  C4    C5   C1    119.46  3.000
 IA  N2    C6   N1    112.50  3.000
 IA  N2    C6   C1    124.12  3.000
 IA  N1    C6   C1    123.38  3.000
 IA  N1    C7   C12   132.39  3.000
 IA  N1    C7   C8    104.62  3.000
 IA  C12   C7   C8    122.99  3.000
 IA  N2    C8   C9    130.51  3.000
 IA  N2    C8   C7    110.05  3.000
 IA  C9    C8   C7    119.44  3.000
 IA  H9    C9   C10   120.82  3.000
 IA  H9    C9   C8    121.06  3.000
 IA  C10   C9   C8    118.12  3.000
 IA  H10   C10  C11   120.34  3.000
 IA  H10   C10  C9    117.74  3.000
 IA  C11   C10  C9    121.92  3.000
 IA  C13   C11  C12   118.14  3.000
 IA  C13   C11  C10   121.41  3.000
 IA  C12   C11  C10   120.45  3.000
 IA  H12   C12  C11   120.84  3.000
 IA  H12   C12  C7    122.09  3.000
 IA  C11   C12  C7    117.08  3.000
 IA  HN1   N1   C7    125.47  3.000
 IA  HN1   N1   C6    127.04  3.000
 IA  C7    N1   C6    107.40  3.000
 IA  C8    N2   C6    105.43  3.000
 IA  N4    C13  N3    112.19  3.000
 IA  N4    C13  C11   124.25  3.000
 IA  N3    C13  C11   123.56  3.000
 IA  N3    C14  C19   132.38  3.000
 IA  N3    C14  C15   104.52  3.000
 IA  C19   C14  C15   123.08  3.000
 IA  N4    C15  C16   130.77  3.000
 IA  N4    C15  C14   110.08  3.000
 IA  C16   C15  C14   119.15  3.000
 IA  H16   C16  C17   120.49  3.000
 IA  H16   C16  C15   121.06  3.000
 IA  C17   C16  C15   118.45  3.000
 IA  H17   C17  C18   119.81  3.000
 IA  H17   C17  C16   118.21  3.000
 IA  C18   C17  C16   121.98  3.000
 IA  N6    C18  C19   118.43  3.000
 IA  N6    C18  C17   121.55  3.000
 IA  C19   C18  C17   120.01  3.000
 IA  H19   C19  C18   121.25  3.000
 IA  H19   C19  C14   121.41  3.000
 IA  C18   C19  C14   117.32  3.000
 IA  HN3   N3   C14   125.41  3.000
 IA  HN3   N3   C13   126.98  3.000
 IA  C14   N3   C13   107.61  3.000
 IA  C15   N4   C13   105.60  3.000
 IA  C23   N6   C20   111.13  3.000
 IA  C23   N6   C18   117.39  3.000
 IA  C20   N6   C18   115.94  3.000
 IA  HN7   N7   C24   107.19  3.000
 IA  HN7   N7   C22   107.60  3.000
 IA  C24   N7   C22   111.92  3.000
 IA  HN7   N7   C21   107.71  3.000
 IA  C24   N7   C21   111.86  3.000
 IA  C22   N7   C21   110.32  3.000
 IA  H202  C20  H201  107.07  3.000
 IA  H202  C20  C21   107.15  3.000
 IA  H201  C20  C21   109.80  3.000
 IA  H202  C20  N6    110.46  3.000
 IA  H201  C20  N6    111.58  3.000
 IA  C21   C20  N6    110.61  3.000
 IA  H212  C21  H211  109.33  3.000
 IA  H212  C21  C20   110.93  3.000
 IA  H211  C21  C20   111.29  3.000
 IA  H212  C21  N7    107.62  3.000
 IA  H211  C21  N7    106.98  3.000
 IA  C20   C21  N7    110.54  3.000
 IA  H222  C22  H221  109.24  3.000
 IA  H222  C22  C23   111.43  3.000
 IA  H221  C22  C23   110.70  3.000
 IA  H222  C22  N7    107.06  3.000
 IA  H221  C22  N7    107.66  3.000
 IA  C23   C22  N7    110.61  3.000
 IA  H232  C23  H231  107.25  3.000
 IA  H232  C23  C22   106.86  3.000
 IA  H231  C23  C22   109.34  3.000
 IA  H232  C23  N6    110.03  3.000
 IA  H231  C23  N6    112.95  3.000
 IA  C22   C23  N6    110.18  3.000
 IA  H243  C24  H242  110.10  3.000
 IA  H243  C24  H241  110.10  3.000
 IA  H242  C24  H241  109.95  3.000
 IA  H243  C24  N7    108.95  3.000
 IA  H242  C24  N7    108.86  3.000
 IA  H241  C24  N7    108.85  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
 IA  CONST_01  C1   C3   C2   C       0.00   0.0  0
 IA  CONST_02  C1   C5   C4   C       0.00   0.0  0
 IA  CONST_03  C7   N1   C6   C1    180.00   0.0  0
 IA  CONST_04  C8   N2   C6   C1    180.00   0.0  0
 IA  CONST_05  C5   C4   C    C2      0.00   0.0  0
 IA  CONST_06  C5   C1   C3   C2      0.00   0.0  0
 IA  CONST_07  C6   C1   C3   C2    180.00   0.0  0
 IA  CONST_08  C4   C5   C1   C3      0.00   0.0  0
 IA  CONST_09  N1   C6   C1   C3    180.00   0.0  0
 IA  CONST_10  N2   C6   C1   C3      0.00   0.0  0
 IA  CONST_11  C4   C    C2   C3      0.00   0.0  0
 IA  CONST_12  C6   C1   C5   C4    180.00   0.0  0
 IA  CONST_13  N1   C6   C1   C5      0.00   0.0  0
 IA  CONST_14  N2   C6   C1   C5    180.00   0.0  0
 IA  CONST_15  C8   C7   N1   C6      0.00   0.0  0
 IA  CONST_16  C12  C7   N1   C6    180.00   0.0  0
 IA  CONST_17  C7   C8   N2   C6      0.00   0.0  0
 IA  CONST_18  C9   C8   N2   C6    180.00   0.0  0
 IA  CONST_19  C10  C9   C8   C7      0.00   0.0  0
 IA  CONST_20  C10  C11  C12  C7      0.00   0.0  0
 IA  CONST_21  C13  C11  C12  C7    180.00   0.0  0
 IA  CONST_22  N2   C6   N1   C7      0.00   0.0  0
 IA  CONST_23  C11  C12  C7   C8      0.00   0.0  0
 IA  CONST_24  C11  C10  C9   C8      0.00   0.0  0
 IA  CONST_25  N1   C6   N2   C8      0.00   0.0  0
 IA  CONST_26  C12  C7   C8   C9      0.00   0.0  0
 IA  CONST_27  N1   C7   C8   C9    180.00   0.0  0
 IA  CONST_28  C12  C11  C10  C9      0.00   0.0  0
 IA  CONST_29  C13  C11  C10  C9    180.00   0.0  0
 IA  CONST_30  N2   C8   C9   C10   180.00   0.0  0
 IA  CONST_31  N3   C13  C11  C10     0.00   0.0  0
 IA  CONST_32  N4   C13  C11  C10   180.00   0.0  0
 IA  CONST_33  N1   C7   C12  C11   180.00   0.0  0
 IA  CONST_34  C14  N3   C13  C11   180.00   0.0  0
 IA  CONST_35  C15  N4   C13  C11   180.00   0.0  0
 IA  CONST_36  N2   C8   C7   C12   180.00   0.0  0
 IA  CONST_37  N3   C13  C11  C12   180.00   0.0  0
 IA  CONST_38  N4   C13  C11  C12     0.00   0.0  0
 IA  CONST_39  N2   C8   C7   N1      0.00   0.0  0
 IA  CONST_40  C15  C14  N3   C13     0.00   0.0  0
 IA  CONST_41  C19  C14  N3   C13   180.00   0.0  0
 IA  CONST_42  C14  C15  N4   C13     0.00   0.0  0
 IA  CONST_43  C16  C15  N4   C13   180.00   0.0  0
 IA  CONST_44  C17  C16  C15  C14     0.00   0.0  0
 IA  CONST_45  C17  C18  C19  C14     0.00   0.0  0
 IA  CONST_46  N4   C13  N3   C14     0.00   0.0  0
 IA  CONST_47  C18  C19  C14  C15     0.00   0.0  0
 IA  CONST_48  C18  C17  C16  C15     0.00   0.0  0
 IA  CONST_49  N3   C13  N4   C15     0.00   0.0  0
 IA  CONST_50  C19  C14  C15  C16     0.00   0.0  0
 IA  CONST_51  N3   C14  C15  C16   180.00   0.0  0
 IA  CONST_52  C19  C18  C17  C16     0.00   0.0  0
 IA  CONST_53  N4   C15  C16  C17   180.00   0.0  0
 IA  CONST_54  N3   C14  C19  C18   180.00   0.0  0
 IA  CONST_55  N4   C15  C14  C19   180.00   0.0  0
 IA  CONST_56  N4   C15  C14  N3      0.00   0.0  0
 IA  CONST_57  N6   C18  C19  C14   180.00   0.0  0
 IA  CONST_58  N6   C18  C17  C16   180.00   0.0  0
 IA  CONST_59  I    C4   C5   C1    180.00   0.0  0
 IA  CONST_60  I    C4   C    C2    180.00   0.0  0
 IA  CONST_61  H3   C3   C2   C     180.00   0.0  0
 IA  CONST_62  H5   C5   C4   C     180.00   0.0  0
 IA  CONST_63  H2   C2   C3   C1    180.00   0.0  0
 IA  CONST_64  HN1  N1   C6   C1      0.00   0.0  0
 IA  CONST_65  H    C    C2   C3    180.00   0.0  0
 IA  CONST_66  H9   C9   C8   C7    180.00   0.0  0
 IA  CONST_67  H12  C12  C7   C8    180.00   0.0  0
 IA  CONST_68  H10  C10  C9   C8    180.00   0.0  0
 IA  CONST_69  HN3  N3   C13  C11     0.00   0.0  0
 IA  CONST_70  H16  C16  C15  C14   180.00   0.0  0
 IA  CONST_71  H19  C19  C14  C15   180.00   0.0  0
 IA  CONST_72  H17  C17  C16  C15   180.00   0.0  0
 IA  Var_01    C20  N6   C18  C17   118.54  30.0  2
 IA  Var_02    C21  C20  N6   C18   163.21  30.0  1
 IA  Var_03    C22  C23  N6   C18  -163.56  30.0  1
 IA  Var_04    N7   C21  C20  N6     56.53  30.0  1
 IA  Var_05    N7   C22  C23  N6    -57.61  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 IA  chir_01  N7  C21  C22  C24  positiv

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
 IA  plan-1  C    0.020
 IA  plan-1  C1   0.020
 IA  plan-1  C2   0.020
 IA  plan-1  C3   0.020
 IA  plan-1  C4   0.020
 IA  plan-1  C5   0.020
 IA  plan-1  C6   0.020
 IA  plan-1  I    0.020
 IA  plan-1  H    0.020
 IA  plan-1  H2   0.020
 IA  plan-1  H3   0.020
 IA  plan-1  H5   0.020
 IA  plan-2  C1   0.020
 IA  plan-2  C6   0.020
 IA  plan-2  C7   0.020
 IA  plan-2  C8   0.020
 IA  plan-2  C9   0.020
 IA  plan-2  C10  0.020
 IA  plan-2  C11  0.020
 IA  plan-2  C12  0.020
 IA  plan-2  N1   0.020
 IA  plan-2  N2   0.020
 IA  plan-2  C13  0.020
 IA  plan-2  H9   0.020
 IA  plan-2  H10  0.020
 IA  plan-2  H12  0.020
 IA  plan-2  HN1  0.020
 IA  plan-3  C11  0.020
 IA  plan-3  C13  0.020
 IA  plan-3  C14  0.020
 IA  plan-3  C15  0.020
 IA  plan-3  C16  0.020
 IA  plan-3  C17  0.020
 IA  plan-3  C18  0.020
 IA  plan-3  C19  0.020
 IA  plan-3  N3   0.020
 IA  plan-3  N4   0.020
 IA  plan-3  N6   0.020
 IA  plan-3  H16  0.020
 IA  plan-3  H17  0.020
 IA  plan-3  H19  0.020
 IA  plan-3  HN3  0.020

