# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:01:39 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: 2'-(4-iodophenyl)-6-(4-methylpiperazin-1-yl)-1H,3'H-2,5'-bibenzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)c2ccc3nc([nH]c3c2)c4ccc5nc([nH]c5c4)c6ccc(I)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
 58F  58F  2'-(4-iodophenyl)-6-(4-methylpiperazin-1-yl)-1H,3'H-2,5'-bibenzimidazole  ligand  55  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_58F
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
 58F  C    C  CR6   0  -0.231  -7.0581   0.0166  -0.1041
 58F  C1   C  CR6   0   0.017  -4.3135  -0.4234  -0.1089
 58F  C2   C  CR16  0  -0.204  -6.1923   1.0947  -0.2144
 58F  C3   C  CR16  0  -0.295  -4.8248   0.8688  -0.2164
 58F  C4   C  CR16  0  -0.207  -6.5710  -1.2794   0.0048
 58F  C5   C  CR16  0  -0.277  -5.2033  -1.4924   0.0012
 58F  C6   C  CR5   0   0.492  -2.8780  -0.6901  -0.1114
 58F  C7   C  CR56  0   0.381  -0.7111  -0.3153  -0.1302
 58F  C8   C  CR56  0   0.157  -0.9978  -1.6916  -0.1000
 58F  C9   C  CR16  0  -0.321   0.0520  -2.6096  -0.0867
 58F  C10  C  CR16  0  -0.315   1.3422  -2.1217  -0.1012
 58F  C11  C  CR6   0  -0.003   1.6183  -0.7384  -0.1278
 58F  C12  C  CR16  0  -0.366   0.5782   0.1862  -0.1438
 58F  N1   N  NR15  0  -0.739  -1.9360   0.2910  -0.1382
 58F  N2   N  N     0  -0.478  -2.3502  -1.8888  -0.0887
 58F  C13  C  CR5   0   0.478   2.9897  -0.2366  -0.1375
 58F  C14  C  CR56  0   0.367   5.1965  -0.2449  -0.1182
 58F  C15  C  CR56  0   0.135   4.6836   1.0612  -0.1645
 58F  C16  C  CR16  0  -0.333   5.5752   2.1285  -0.1914
 58F  C17  C  CR16  0  -0.364   6.9320   1.8606  -0.1643
 58F  C18  C  CR6   0   0.357   7.4454   0.5420  -0.1322
 58F  N3   N  NR15  0  -0.750   4.0887  -1.0473  -0.1033
 58F  N4   N  N     0  -0.485   3.3119   1.0299  -0.1746
 58F  C19  C  CR16  0  -0.421   6.5517  -0.5326  -0.1122
 58F  N5   N  NT    0  -0.517   8.8215   0.2930  -0.1461
 58F  N6   N  NT    0  -0.400  11.6696  -0.0025   0.2822
 58F  C20  C  CH2   0  -0.312   9.3326  -0.6434   0.8509
 58F  C21  C  CH2   0  -0.324  10.7389  -1.0972   0.4807
 58F  C22  C  CH2   0  -0.320  11.1177   0.9228  -0.6878
 58F  C23  C  CH2   0  -0.319   9.7137   1.4198  -0.3535
 58F  C24  C  CH3   0  -0.531  12.0914   0.6277   1.5167
 58F  I    I  I     0   0.072  -9.1313   0.3495  -0.1010
 58F  H1   H  HCR6  0   0.288  -6.5629   2.1067  -0.3008
 58F  H2   H  HCR6  0   0.259  -4.1728   1.7279  -0.3079
 58F  H3   H  HCR6  0   0.286  -7.2404  -2.1238   0.0931
 58F  H4   H  HCR6  0   0.270  -4.8225  -2.5010   0.0870
 58F  H5   H  HCR6  0   0.263  -0.1368  -3.6746  -0.0660
 58F  H6   H  HCR6  0   0.243   2.1512  -2.8397  -0.0918
 58F  H7   H  HCR6  0   0.268   0.7790   1.2487  -0.1648
 58F  H8   H  HNR5  0   0.428  -2.0964   1.2855  -0.1455
 58F  H10  H  HCR6  0   0.252   5.2213   3.1515  -0.2168
 58F  H11  H  HCR6  0   0.266   7.6105   2.7010  -0.1535
 58F  H12  H  HNR5  0   0.420   4.0966  -2.0534  -0.0706
 58F  H14  H  HCR6  0   0.267   6.8991  -1.5575  -0.1118
 58F  H16  H  HCH2  0   0.216   9.3290  -0.1842   1.8513
 58F  H17  H  HCH2  0   0.254   8.6916  -1.5213   0.9052
 58F  H18  H  HCH2  0   0.233  10.6868  -1.6790  -0.4457
 58F  H19  H  HCH2  0   0.240  11.1216  -1.7620   1.2586
 58F  H20  H  HCH2  0   0.241  11.7861   1.7806  -0.7905
 58F  H21  H  HCH2  0   0.232  11.0824   0.4199  -1.6599
 58F  H22  H  HCH2  0   0.251   9.3589   2.0129  -1.1978
 58F  H23  H  HCH2  0   0.212   9.7416   2.0885   0.5207
 58F  H24  H  HCH3  0   0.201  11.2923   1.1036   2.1004
 58F  H25  H  HCH3  0   0.233  12.5641  -0.1163   2.1600
 58F  H26  H  HCH3  0   0.233  12.8359   1.3949   1.2975

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
 58F  C24  N6   single    1.449  0.020  1.449
 58F  C21  N6   single    1.451  0.020  1.451
 58F  C21  C20  single    1.523  0.020  1.523
 58F  N6   C22  single    1.450  0.020  1.450
 58F  C20  N5   single    1.460  0.020  1.460
 58F  C22  C23  single    1.526  0.020  1.526
 58F  N5   C23  single    1.452  0.020  1.452
 58F  N5   C18  single    1.399  0.020  1.399
 58F  C17  C18  aromatic  1.415  0.020  1.415
 58F  C17  C16  aromatic  1.383  0.020  1.383
 58F  C18  C19  aromatic  1.398  0.020  1.398
 58F  C16  C15  aromatic  1.391  0.020  1.391
 58F  C19  C14  aromatic  1.385  0.020  1.385
 58F  C15  C14  aromatic  1.404  0.020  1.404
 58F  C15  N4   aromatic  1.372  0.020  1.372
 58F  C14  N3   aromatic  1.368  0.020  1.368
 58F  N4   C13  aromatic  1.307  0.020  1.307
 58F  N3   C13  aromatic  1.366  0.020  1.366
 58F  C13  C11  single    1.460  0.020  1.460
 58F  C11  C10  aromatic  1.411  0.020  1.411
 58F  C11  C12  aromatic  1.392  0.020  1.392
 58F  C10  C9   aromatic  1.379  0.020  1.379
 58F  C12  C7   aromatic  1.383  0.020  1.383
 58F  C9   C8   aromatic  1.395  0.020  1.395
 58F  C7   C8   aromatic  1.406  0.020  1.406
 58F  C7   N1   aromatic  1.367  0.020  1.367
 58F  C8   N2   aromatic  1.367  0.020  1.367
 58F  N1   C6   aromatic  1.360  0.020  1.360
 58F  N2   C6   aromatic  1.310  0.020  1.310
 58F  C6   C1   single    1.460  0.020  1.460
 58F  C1   C5   aromatic  1.395  0.020  1.395
 58F  C1   C3   aromatic  1.394  0.020  1.394
 58F  C5   C4   aromatic  1.384  0.020  1.384
 58F  C3   C2   aromatic  1.386  0.020  1.386
 58F  C4   C    aromatic  1.389  0.020  1.389
 58F  C2   C    aromatic  1.387  0.020  1.387
 58F  C    I    single    2.100  0.020  2.100
 58F  C2   H1   single    0.930  0.020  1.080
 58F  C3   H2   single    0.930  0.020  1.080
 58F  C4   H3   single    0.930  0.020  1.080
 58F  C5   H4   single    0.930  0.020  1.080
 58F  C9   H5   single    0.930  0.020  1.080
 58F  C10  H6   single    0.930  0.020  1.080
 58F  C12  H7   single    0.930  0.020  1.080
 58F  N1   H8   single    0.860  0.020  1.020
 58F  C16  H10  single    0.930  0.020  1.080
 58F  C17  H11  single    0.930  0.020  1.080
 58F  N3   H12  single    0.860  0.020  1.020
 58F  C19  H14  single    0.930  0.020  1.080
 58F  C20  H16  single    0.970  0.020  1.090
 58F  C20  H17  single    0.970  0.020  1.090
 58F  C21  H18  single    0.970  0.020  1.090
 58F  C21  H19  single    0.970  0.020  1.090
 58F  C22  H20  single    0.970  0.020  1.090
 58F  C22  H21  single    0.970  0.020  1.090
 58F  C23  H22  single    0.970  0.020  1.090
 58F  C23  H23  single    0.970  0.020  1.090
 58F  C24  H24  single    0.970  0.020  1.090
 58F  C24  H25  single    0.970  0.020  1.090
 58F  C24  H26  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
 58F  I    C    C4   119.61  3.000
 58F  I    C    C2   119.55  3.000
 58F  C4   C    C2   120.84  3.000
 58F  C6   C1   C5   119.15  3.000
 58F  C5   C1   C3   118.85  3.000
 58F  C6   C1   C3   122.00  3.000
 58F  H1   C2   C3   119.38  3.000
 58F  H1   C2   C    121.33  3.000
 58F  C3   C2   C    119.29  3.000
 58F  H2   C3   C2   117.72  3.000
 58F  H2   C3   C1   121.42  3.000
 58F  C2   C3   C1   120.86  3.000
 58F  H3   C4   C5   119.46  3.000
 58F  H3   C4   C    121.20  3.000
 58F  C5   C4   C    119.33  3.000
 58F  H4   C5   C4   119.42  3.000
 58F  H4   C5   C1   119.75  3.000
 58F  C4   C5   C1   120.83  3.000
 58F  N2   C6   N1   112.41  3.000
 58F  N2   C6   C1   124.29  3.000
 58F  N1   C6   C1   123.31  3.000
 58F  N1   C7   C12  132.40  3.000
 58F  N1   C7   C8   104.57  3.000
 58F  C12  C7   C8   123.02  3.000
 58F  N2   C8   C9   130.53  3.000
 58F  N2   C8   C7   110.07  3.000
 58F  C9   C8   C7   119.40  3.000
 58F  H5   C9   C10  120.77  3.000
 58F  H5   C9   C8   121.12  3.000
 58F  C10  C9   C8   118.11  3.000
 58F  H6   C10  C11  120.31  3.000
 58F  H6   C10  C9   117.69  3.000
 58F  C11  C10  C9   122.00  3.000
 58F  C13  C11  C12  118.26  3.000
 58F  C12  C11  C10  120.35  3.000
 58F  C13  C11  C10  121.39  3.000
 58F  H7   C12  C11  120.93  3.000
 58F  H7   C12  C7   121.96  3.000
 58F  C11  C12  C7   117.10  3.000
 58F  H8   N1   C7   125.50  3.000
 58F  H8   N1   C6   127.00  3.000
 58F  C7   N1   C6   107.49  3.000
 58F  C8   N2   C6   105.46  3.000
 58F  N4   C13  N3   112.17  3.000
 58F  N3   C13  C11  123.46  3.000
 58F  N4   C13  C11  124.37  3.000
 58F  C19  C14  N3   132.09  3.000
 58F  N3   C14  C15  104.49  3.000
 58F  C19  C14  C15  123.41  3.000
 58F  N4   C15  C16  131.16  3.000
 58F  N4   C15  C14  110.13  3.000
 58F  C16  C15  C14  118.70  3.000
 58F  H10  C16  C17  120.27  3.000
 58F  H10  C16  C15  121.05  3.000
 58F  C17  C16  C15  118.67  3.000
 58F  H11  C17  C18  119.78  3.000
 58F  H11  C17  C16  117.75  3.000
 58F  C18  C17  C16  122.46  3.000
 58F  N5   C18  C19  119.50  3.000
 58F  C19  C18  C17  118.99  3.000
 58F  N5   C18  C17  121.51  3.000
 58F  H12  N3   C14  125.47  3.000
 58F  H12  N3   C13  126.88  3.000
 58F  C14  N3   C13  107.65  3.000
 58F  C15  N4   C13  105.56  3.000
 58F  H14  C19  C18  121.52  3.000
 58F  H14  C19  C14  120.71  3.000
 58F  C18  C19  C14  117.75  3.000
 58F  C23  N5   C20  112.34  3.000
 58F  C23  N5   C18  117.89  3.000
 58F  C20  N5   C18  116.86  3.000
 58F  C24  N6   C22  113.79  3.000
 58F  C22  N6   C21  109.21  3.000
 58F  C24  N6   C21  113.48  3.000
 58F  H17  C20  H16  106.81  3.000
 58F  H17  C20  C21  108.39  3.000
 58F  H16  C20  C21  110.38  3.000
 58F  H17  C20  N5   110.19  3.000
 58F  H16  C20  N5   110.60  3.000
 58F  C21  C20  N5   110.38  3.000
 58F  H19  C21  H18  107.20  3.000
 58F  H19  C21  C20  109.37  3.000
 58F  H18  C21  C20  108.66  3.000
 58F  H19  C21  N6   109.38  3.000
 58F  H18  C21  N6   108.40  3.000
 58F  C20  C21  N6   113.62  3.000
 58F  H21  C22  H20  107.28  3.000
 58F  H21  C22  C23  108.32  3.000
 58F  H20  C22  C23  109.14  3.000
 58F  H21  C22  N6   108.24  3.000
 58F  H20  C22  N6   109.34  3.000
 58F  C23  C22  N6   114.29  3.000
 58F  H23  C23  H22  107.01  3.000
 58F  H23  C23  C22  110.38  3.000
 58F  H22  C23  C22  107.85  3.000
 58F  H23  C23  N5   111.93  3.000
 58F  H22  C23  N5   109.43  3.000
 58F  C22  C23  N5   110.11  3.000
 58F  H26  C24  H25  107.59  3.000
 58F  H26  C24  H24  107.37  3.000
 58F  H25  C24  H24  107.30  3.000
 58F  H26  C24  N6   109.47  3.000
 58F  H25  C24  N6   109.38  3.000
 58F  H24  C24  N6   115.44  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
 58F  CONST_01  C1   C5   C4   C       0.00   0.0  0
 58F  CONST_02  C1   C3   C2   C       0.00   0.0  0
 58F  CONST_03  C7   N1   C6   C1    180.00   0.0  0
 58F  CONST_04  C8   N2   C6   C1    180.00   0.0  0
 58F  CONST_05  C6   C1   C3   C2    180.00   0.0  0
 58F  CONST_06  C5   C1   C3   C2      0.00   0.0  0
 58F  CONST_07  C5   C4   C    C2      0.00   0.0  0
 58F  CONST_08  N1   C6   C1   C3      0.00   0.0  0
 58F  CONST_09  N2   C6   C1   C3    180.00   0.0  0
 58F  CONST_10  C4   C5   C1   C3      0.00   0.0  0
 58F  CONST_11  C4   C    C2   C3      0.00   0.0  0
 58F  CONST_12  C6   C1   C5   C4    180.00   0.0  0
 58F  CONST_13  N1   C6   C1   C5    180.00   0.0  0
 58F  CONST_14  N2   C6   C1   C5      0.00   0.0  0
 58F  CONST_15  C12  C7   N1   C6    180.00   0.0  0
 58F  CONST_16  C8   C7   N1   C6      0.00   0.0  0
 58F  CONST_17  C9   C8   N2   C6    180.00   0.0  0
 58F  CONST_18  C7   C8   N2   C6      0.00   0.0  0
 58F  CONST_19  C13  C11  C12  C7    180.00   0.0  0
 58F  CONST_20  C10  C11  C12  C7      0.00   0.0  0
 58F  CONST_21  C10  C9   C8   C7      0.00   0.0  0
 58F  CONST_22  N2   C6   N1   C7      0.00   0.0  0
 58F  CONST_23  C11  C10  C9   C8      0.00   0.0  0
 58F  CONST_24  C11  C12  C7   C8      0.00   0.0  0
 58F  CONST_25  N1   C6   N2   C8      0.00   0.0  0
 58F  CONST_26  C13  C11  C10  C9    180.00   0.0  0
 58F  CONST_27  C12  C11  C10  C9      0.00   0.0  0
 58F  CONST_28  C12  C7   C8   C9      0.00   0.0  0
 58F  CONST_29  N1   C7   C8   C9    180.00   0.0  0
 58F  CONST_30  N4   C13  C11  C10   180.00   0.0  0
 58F  CONST_31  N3   C13  C11  C10     0.00   0.0  0
 58F  CONST_32  N2   C8   C9   C10   180.00   0.0  0
 58F  CONST_33  C15  N4   C13  C11   180.00   0.0  0
 58F  CONST_34  C14  N3   C13  C11   180.00   0.0  0
 58F  CONST_35  N1   C7   C12  C11   180.00   0.0  0
 58F  CONST_36  N4   C13  C11  C12     0.00   0.0  0
 58F  CONST_37  N3   C13  C11  C12   180.00   0.0  0
 58F  CONST_38  N2   C8   C7   C12   180.00   0.0  0
 58F  CONST_39  N2   C8   C7   N1      0.00   0.0  0
 58F  CONST_40  C16  C15  N4   C13   180.00   0.0  0
 58F  CONST_41  C14  C15  N4   C13     0.00   0.0  0
 58F  CONST_42  C19  C14  N3   C13   180.00   0.0  0
 58F  CONST_43  C15  C14  N3   C13     0.00   0.0  0
 58F  CONST_44  C17  C18  C19  C14     0.00   0.0  0
 58F  CONST_45  C17  C16  C15  C14     0.00   0.0  0
 58F  CONST_46  N4   C13  N3   C14     0.00   0.0  0
 58F  CONST_47  C18  C17  C16  C15     0.00   0.0  0
 58F  CONST_48  C18  C19  C14  C15     0.00   0.0  0
 58F  CONST_49  N3   C13  N4   C15     0.00   0.0  0
 58F  CONST_50  C19  C18  C17  C16     0.00   0.0  0
 58F  CONST_51  C19  C14  C15  C16     0.00   0.0  0
 58F  CONST_52  N3   C14  C15  C16   180.00   0.0  0
 58F  CONST_53  N4   C15  C16  C17   180.00   0.0  0
 58F  CONST_54  N3   C14  C19  C18   180.00   0.0  0
 58F  CONST_55  N4   C15  C14  N3      0.00   0.0  0
 58F  CONST_56  C19  C14  C15  N4    180.00   0.0  0
 58F  CONST_57  N5   C18  C19  C14   180.00   0.0  0
 58F  CONST_58  N5   C18  C17  C16   180.00   0.0  0
 58F  CONST_59  I    C    C2   C3    180.00   0.0  0
 58F  CONST_60  I    C    C4   C5    180.00   0.0  0
 58F  CONST_61  H4   C5   C4   C     180.00   0.0  0
 58F  CONST_62  H2   C3   C2   C     180.00   0.0  0
 58F  CONST_63  H8   N1   C6   C1      0.00   0.0  0
 58F  CONST_64  H3   C4   C5   C1    180.00   0.0  0
 58F  CONST_65  H1   C2   C3   C1    180.00   0.0  0
 58F  CONST_66  H5   C9   C8   C7    180.00   0.0  0
 58F  CONST_67  H6   C10  C9   C8    180.00   0.0  0
 58F  CONST_68  H7   C12  C7   C8    180.00   0.0  0
 58F  CONST_69  H12  N3   C13  C11     0.00   0.0  0
 58F  CONST_70  H10  C16  C15  C14   180.00   0.0  0
 58F  CONST_71  H11  C17  C16  C15   180.00   0.0  0
 58F  CONST_72  H14  C19  C14  C15   180.00   0.0  0
 58F  Var_01    C20  N5   C18  C17   131.48  30.0  2
 58F  Var_02    C21  C20  N5   C18   164.65  30.0  1
 58F  Var_03    C22  C23  N5   C18  -165.74  30.0  1
 58F  Var_04    N6   C21  C20  N5     55.02  30.0  1
 58F  Var_05    N6   C22  C23  N5    -54.38  30.0  1
 58F  Var_06    C22  N6   C21  C20   -53.81  30.0  1
 58F  Var_07    C23  C22  N6   C21    53.68  30.0  1
 58F  Var_08    H24  C24  N6   C21   -62.39  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
 58F  plan-1  C    0.020
 58F  plan-1  C1   0.020
 58F  plan-1  C2   0.020
 58F  plan-1  C3   0.020
 58F  plan-1  C4   0.020
 58F  plan-1  C5   0.020
 58F  plan-1  C6   0.020
 58F  plan-1  I    0.020
 58F  plan-1  H1   0.020
 58F  plan-1  H2   0.020
 58F  plan-1  H3   0.020
 58F  plan-1  H4   0.020
 58F  plan-2  C1   0.020
 58F  plan-2  C6   0.020
 58F  plan-2  C7   0.020
 58F  plan-2  C8   0.020
 58F  plan-2  C9   0.020
 58F  plan-2  C10  0.020
 58F  plan-2  C11  0.020
 58F  plan-2  C12  0.020
 58F  plan-2  N1   0.020
 58F  plan-2  N2   0.020
 58F  plan-2  C13  0.020
 58F  plan-2  H5   0.020
 58F  plan-2  H6   0.020
 58F  plan-2  H7   0.020
 58F  plan-2  H8   0.020
 58F  plan-3  C11  0.020
 58F  plan-3  C13  0.020
 58F  plan-3  C14  0.020
 58F  plan-3  C15  0.020
 58F  plan-3  C16  0.020
 58F  plan-3  C17  0.020
 58F  plan-3  C18  0.020
 58F  plan-3  N3   0.020
 58F  plan-3  N4   0.020
 58F  plan-3  C19  0.020
 58F  plan-3  N5   0.020
 58F  plan-3  H10  0.020
 58F  plan-3  H11  0.020
 58F  plan-3  H12  0.020
 58F  plan-3  H14  0.020

