# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 00:42:27 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 2-{4-[(6,7-difluoro-1H-benzimidazol-2-yl)amino]phenoxy}-N-methyl-3,4'-bipyridin-2'-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(ccn1)c2cccnc2Oc3ccc(Nc4[nH]c5c(F)c(F)ccc5n4)cc3
#
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
 2F4  2F4  2-{4-[(6,7-difluoro-1H-benzimidazol-2-yl)amino]phenoxy}-N-methyl-3,4'-bipyridin-2'-amine  ligand  51  33  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2F4
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
 2F4  C01  C  CH3   0  -0.529   8.1954   2.7688   1.4143
 2F4  N02  N  NH1   0  -0.654   7.8099   2.7219   0.0308
 2F4  C03  C  CR6   0   0.507   6.9176   1.8496  -0.4852
 2F4  C04  C  CR16  0  -0.464   6.2488   0.9107   0.3241
 2F4  C05  C  CR6   0   0.192   5.3398   0.0439  -0.2571
 2F4  C06  C  CR16  0  -0.401   5.1156   0.1323  -1.6345
 2F4  C07  C  CR16  0  -0.060   5.8258   1.0856  -2.3393
 2F4  N08  N  N     0  -0.467   6.6993   1.9261  -1.8015
 2F4  C09  C  CR6   0  -0.090   4.6743  -0.9711   0.5831
 2F4  C10  C  CR16  0  -0.177   5.4052  -1.7649   1.4540
 2F4  C11  C  CR16  0  -0.339   4.7702  -2.7157   2.2442
 2F4  C12  C  CR16  0  -0.059   3.3995  -2.8306   2.1344
 2F4  N13  N  N     0  -0.436   2.6726  -2.0704   1.3182
 2F4  C14  C  CR6   0   0.476   3.2859  -1.1824   0.5752
 2F4  O15  O  O2    0  -0.515   2.5523  -0.3879  -0.2300
 2F4  C16  C  CR6   0   0.350   1.1987  -0.6116  -0.3523
 2F4  C17  C  CR16  0  -0.308   0.3158   0.2887   0.2112
 2F4  C18  C  CR16  0  -0.318  -1.0550   0.1349   0.0441
 2F4  C19  C  CR6   0   0.362  -1.5485  -0.9433  -0.6891
 2F4  N20  N  NH1   0  -0.809  -2.9006  -1.1907  -0.9073
 2F4  C21  C  CR5   0   0.720  -3.9717  -0.4816  -0.4815
 2F4  N22  N  N     0  -0.532  -3.9694   0.6189   0.2228
 2F4  C23  C  CR56  0   0.197  -5.2953   0.9418   0.3923
 2F4  C24  C  CR16  0  -0.338  -5.8807   2.0109   1.0609
 2F4  C25  C  CR16  0  -0.430  -7.2650   2.0995   1.0792
 2F4  C26  C  CR6   0   0.364  -8.0422   1.1402   0.4436
 2F4  F27  F  F     0  -0.317  -9.3805   1.2412   0.4709
 2F4  C28  C  CR6   0   0.378  -7.4779   0.0702  -0.2261
 2F4  F29  F  F     0  -0.302  -8.2404  -0.8457  -0.8328
 2F4  C30  C  CR56  0   0.167  -6.1016  -0.0173  -0.2442
 2F4  N31  N  NR15  0  -0.740  -5.2299  -0.9158  -0.7954
 2F4  C32  C  CR16  0  -0.359  -0.6414  -1.8464  -1.2545
 2F4  C33  C  CR16  0  -0.293   0.7202  -1.6838  -1.0905
 2F4  H1   H  HCH3  0   0.232   7.3591   3.0275   2.0695
 2F4  H2   H  HCH3  0   0.231   8.6142   1.8205   1.7613
 2F4  H3   H  HCH3  0   0.264   8.9587   3.5324   1.5346
 2F4  H4   H  HNH1  0   0.386   8.2537   3.3486  -0.6183
 2F4  H5   H  HCR6  0   0.272   6.4315   0.8718   1.3898
 2F4  H6   H  HCR6  0   0.251   4.4308  -0.5263  -2.1483
 2F4  H7   H  HCR6  0   0.255   5.6819   1.1752  -3.4112
 2F4  H8   H  HCR6  0   0.275   6.4808  -1.6491   1.5011
 2F4  H9   H  HCR6  0   0.272   5.3286  -3.3476   2.9196
 2F4  H10  H  HCR6  0   0.271   2.8534  -3.5576   2.7238
 2F4  H11  H  HCR6  0   0.270   0.6897   1.1288   0.7829
 2F4  H12  H  HCR6  0   0.294  -1.7280   0.8508   0.4882
 2F4  H13  H  HNH1  0   0.421  -3.1061  -2.0200  -1.4427
 2F4  H15  H  HCR6  0   0.267  -5.2756   2.7586   1.5548
 2F4  H16  H  HCR6  0   0.285  -7.7585   2.9174   1.5871
 2F4  H17  H  HNR5  0   0.428  -5.4672  -1.7401  -1.3250
 2F4  H18  H  HCR6  0   0.275  -1.0067  -2.6896  -1.8288
 2F4  H19  H  HCR6  0   0.274   1.4014  -2.3932  -1.5426

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
 2F4  C11  C10  aromatic  1.390  0.020  1.390
 2F4  C11  C12  aromatic  1.380  0.020  1.380
 2F4  C10  C09  aromatic  1.387  0.020  1.387
 2F4  C06  C07  aromatic  1.382  0.020  1.382
 2F4  C06  C05  aromatic  1.398  0.020  1.398
 2F4  C07  N08  aromatic  1.326  0.020  1.326
 2F4  C12  N13  aromatic  1.331  0.020  1.331
 2F4  C09  C05  single    1.476  0.020  1.476
 2F4  C09  C14  aromatic  1.404  0.020  1.404
 2F4  C05  C04  aromatic  1.384  0.020  1.384
 2F4  N08  C03  aromatic  1.336  0.020  1.336
 2F4  N13  C14  aromatic  1.310  0.020  1.310
 2F4  C14  O15  single    1.348  0.020  1.348
 2F4  C04  C03  aromatic  1.408  0.020  1.408
 2F4  O15  C16  single    1.377  0.020  1.377
 2F4  C03  N02  single    1.350  0.020  1.350
 2F4  C16  C17  aromatic  1.381  0.020  1.381
 2F4  C16  C33  aromatic  1.387  0.020  1.387
 2F4  N02  C01  single    1.437  0.020  1.437
 2F4  C17  C18  aromatic  1.389  0.020  1.389
 2F4  C33  C32  aromatic  1.381  0.020  1.381
 2F4  C18  C19  aromatic  1.394  0.020  1.394
 2F4  C32  C19  aromatic  1.399  0.020  1.399
 2F4  C19  N20  single    1.392  0.020  1.392
 2F4  N22  C21  aromatic  1.307  0.020  1.307
 2F4  N22  C23  aromatic  1.375  0.020  1.375
 2F4  N20  C21  single    1.353  0.020  1.353
 2F4  C24  C23  aromatic  1.390  0.020  1.390
 2F4  C24  C25  aromatic  1.387  0.020  1.387
 2F4  C21  N31  aromatic  1.368  0.020  1.368
 2F4  C23  C30  aromatic  1.405  0.020  1.405
 2F4  C25  C26  aromatic  1.389  0.020  1.389
 2F4  N31  C30  aromatic  1.368  0.020  1.368
 2F4  C30  C28  aromatic  1.379  0.020  1.379
 2F4  C26  C28  aromatic  1.383  0.020  1.383
 2F4  C26  F27  single    1.342  0.020  1.342
 2F4  C28  F29  single    1.337  0.020  1.337
 2F4  C01  H1   single    0.970  0.020  1.090
 2F4  C01  H2   single    0.970  0.020  1.090
 2F4  C01  H3   single    0.970  0.020  1.090
 2F4  N02  H4   single    0.860  0.020  1.020
 2F4  C04  H5   single    0.930  0.020  1.080
 2F4  C06  H6   single    0.930  0.020  1.080
 2F4  C07  H7   single    0.930  0.020  1.080
 2F4  C10  H8   single    0.930  0.020  1.080
 2F4  C11  H9   single    0.930  0.020  1.080
 2F4  C12  H10  single    0.930  0.020  1.080
 2F4  C17  H11  single    0.930  0.020  1.080
 2F4  C18  H12  single    0.930  0.020  1.080
 2F4  N20  H13  single    0.860  0.020  1.020
 2F4  C24  H15  single    0.930  0.020  1.080
 2F4  C25  H16  single    0.930  0.020  1.080
 2F4  N31  H17  single    0.860  0.020  1.020
 2F4  C32  H18  single    0.930  0.020  1.080
 2F4  C33  H19  single    0.930  0.020  1.080

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
 2F4  H3   C01  H2   107.78  3.000
 2F4  H3   C01  H1   107.74  3.000
 2F4  H2   C01  H1   107.94  3.000
 2F4  H3   C01  N02  108.54  3.000
 2F4  H2   C01  N02  112.34  3.000
 2F4  H1   C01  N02  112.31  3.000
 2F4  H4   N02  C03  116.58  3.000
 2F4  H4   N02  C01  118.88  3.000
 2F4  C03  N02  C01  124.49  3.000
 2F4  N08  C03  C04  121.77  3.000
 2F4  C04  C03  N02  121.65  3.000
 2F4  N08  C03  N02  116.57  3.000
 2F4  H5   C04  C05  120.13  3.000
 2F4  H5   C04  C03  120.65  3.000
 2F4  C05  C04  C03  119.21  3.000
 2F4  C09  C05  C06  122.13  3.000
 2F4  C09  C05  C04  119.19  3.000
 2F4  C06  C05  C04  118.64  3.000
 2F4  H6   C06  C07  120.25  3.000
 2F4  H6   C06  C05  122.12  3.000
 2F4  C07  C06  C05  117.62  3.000
 2F4  H7   C07  N08  115.81  3.000
 2F4  H7   C07  C06  119.52  3.000
 2F4  N08  C07  C06  124.67  3.000
 2F4  C07  N08  C03  118.08  3.000
 2F4  C14  C09  C10  116.01  3.000
 2F4  C14  C09  C05  123.08  3.000
 2F4  C10  C09  C05  120.90  3.000
 2F4  H8   C10  C11  120.15  3.000
 2F4  H8   C10  C09  119.31  3.000
 2F4  C11  C10  C09  120.52  3.000
 2F4  H9   C11  C12  120.96  3.000
 2F4  H9   C11  C10  121.30  3.000
 2F4  C12  C11  C10  117.75  3.000
 2F4  H10  C12  N13  116.20  3.000
 2F4  H10  C12  C11  120.88  3.000
 2F4  N13  C12  C11  122.93  3.000
 2F4  C14  N13  C12  118.63  3.000
 2F4  O15  C14  N13  118.91  3.000
 2F4  O15  C14  C09  116.91  3.000
 2F4  N13  C14  C09  124.16  3.000
 2F4  C16  O15  C14  119.47  3.000
 2F4  C33  C16  C17  120.04  3.000
 2F4  C33  C16  O15  120.79  3.000
 2F4  C17  C16  O15  119.09  3.000
 2F4  H11  C17  C18  119.34  3.000
 2F4  H11  C17  C16  120.03  3.000
 2F4  C18  C17  C16  120.63  3.000
 2F4  H12  C18  C19  120.61  3.000
 2F4  H12  C18  C17  119.53  3.000
 2F4  C19  C18  C17  119.87  3.000
 2F4  C32  C19  N20  116.85  3.000
 2F4  N20  C19  C18  124.32  3.000
 2F4  C32  C19  C18  118.83  3.000
 2F4  H13  N20  C21  115.89  3.000
 2F4  H13  N20  C19  115.31  3.000
 2F4  C21  N20  C19  128.79  3.000
 2F4  N31  C21  N22  113.12  3.000
 2F4  N31  C21  N20  119.32  3.000
 2F4  N22  C21  N20  127.56  3.000
 2F4  C23  N22  C21  105.22  3.000
 2F4  C30  C23  C24  120.07  3.000
 2F4  C30  C23  N22  109.70  3.000
 2F4  C24  C23  N22  130.23  3.000
 2F4  H15  C24  C25  120.54  3.000
 2F4  H15  C24  C23  121.05  3.000
 2F4  C25  C24  C23  118.40  3.000
 2F4  H16  C25  C26  118.81  3.000
 2F4  H16  C25  C24  120.64  3.000
 2F4  C26  C25  C24  120.55  3.000
 2F4  C28  C26  F27  118.36  3.000
 2F4  F27  C26  C25  119.78  3.000
 2F4  C28  C26  C25  121.86  3.000
 2F4  C30  C28  F29  121.30  3.000
 2F4  F29  C28  C26  121.14  3.000
 2F4  C30  C28  C26  117.57  3.000
 2F4  N31  C30  C28  133.07  3.000
 2F4  C28  C30  C23  121.55  3.000
 2F4  N31  C30  C23  105.38  3.000
 2F4  H17  N31  C30  126.79  3.000
 2F4  H17  N31  C21  126.64  3.000
 2F4  C30  N31  C21  106.57  3.000
 2F4  H18  C32  C33  119.13  3.000
 2F4  H18  C32  C19  119.86  3.000
 2F4  C33  C32  C19  121.01  3.000
 2F4  H19  C33  C32  119.58  3.000
 2F4  H19  C33  C16  120.79  3.000
 2F4  C32  C33  C16  119.63  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
 2F4  CONST_01  C06  C07  N08  C03    0.00   0.0  0
 2F4  CONST_02  C06  C05  C04  C03    0.00   0.0  0
 2F4  CONST_03  C09  C05  C04  C03  180.00   0.0  0
 2F4  CONST_04  C07  C06  C05  C04    0.00   0.0  0
 2F4  CONST_07  C07  N08  C03  C04    0.00   0.0  0
 2F4  CONST_08  N08  C07  C06  C05    0.00   0.0  0
 2F4  CONST_09  C11  C10  C09  C05  180.00   0.0  0
 2F4  CONST_10  N13  C14  C09  C05  180.00   0.0  0
 2F4  CONST_11  N08  C03  C04  C05    0.00   0.0  0
 2F4  CONST_14  C09  C05  C06  C07  180.00   0.0  0
 2F4  CONST_15  C12  C11  C10  C09    0.00   0.0  0
 2F4  CONST_16  C12  N13  C14  C09    0.00   0.0  0
 2F4  CONST_17  N13  C12  C11  C10    0.00   0.0  0
 2F4  CONST_18  N13  C14  C09  C10    0.00   0.0  0
 2F4  CONST_19  C14  C09  C10  C11    0.00   0.0  0
 2F4  CONST_20  C14  N13  C12  C11    0.00   0.0  0
 2F4  CONST_21  C19  C18  C17  C16    0.00   0.0  0
 2F4  CONST_22  C19  C32  C33  C16    0.00   0.0  0
 2F4  CONST_23  C32  C33  C16  C17    0.00   0.0  0
 2F4  CONST_24  C32  C19  C18  C17    0.00   0.0  0
 2F4  CONST_25  C33  C16  C17  C18    0.00   0.0  0
 2F4  CONST_26  C33  C32  C19  C18    0.00   0.0  0
 2F4  CONST_27  C24  C23  N22  C21  180.00   0.0  0
 2F4  CONST_28  C30  C23  N22  C21    0.00   0.0  0
 2F4  CONST_29  C23  C30  N31  C21    0.00   0.0  0
 2F4  CONST_30  C28  C30  N31  C21  180.00   0.0  0
 2F4  CONST_31  C30  N31  C21  N22    0.00   0.0  0
 2F4  CONST_32  C25  C24  C23  N22  180.00   0.0  0
 2F4  CONST_33  N31  C30  C23  N22    0.00   0.0  0
 2F4  CONST_34  C28  C30  C23  N22  180.00   0.0  0
 2F4  CONST_35  N31  C21  N22  C23    0.00   0.0  0
 2F4  CONST_36  C26  C25  C24  C23    0.00   0.0  0
 2F4  CONST_37  C26  C28  C30  C23    0.00   0.0  0
 2F4  CONST_38  N31  C30  C23  C24  180.00   0.0  0
 2F4  CONST_39  C28  C30  C23  C24    0.00   0.0  0
 2F4  CONST_40  C28  C26  C25  C24    0.00   0.0  0
 2F4  CONST_41  C30  C23  C24  C25    0.00   0.0  0
 2F4  CONST_42  C30  C28  C26  C25    0.00   0.0  0
 2F4  CONST_43  N31  C30  C28  C26  180.00   0.0  0
 2F4  CONST_44  C07  N08  C03  N02  180.00   0.0  0
 2F4  CONST_45  C05  C04  C03  N02  180.00   0.0  0
 2F4  CONST_46  O15  C14  C09  C05    0.00   0.0  0
 2F4  CONST_47  O15  C14  C09  C10  180.00   0.0  0
 2F4  CONST_48  O15  C14  N13  C12  180.00   0.0  0
 2F4  CONST_49  C18  C17  C16  O15  180.00   0.0  0
 2F4  CONST_50  C32  C33  C16  O15  180.00   0.0  0
 2F4  CONST_51  N20  C19  C18  C17  180.00   0.0  0
 2F4  CONST_52  C33  C32  C19  N20  180.00   0.0  0
 2F4  CONST_53  C23  N22  C21  N20  180.00   0.0  0
 2F4  CONST_54  C30  N31  C21  N20  180.00   0.0  0
 2F4  CONST_55  F29  C28  C30  C23  180.00   0.0  0
 2F4  CONST_56  F27  C26  C25  C24  180.00   0.0  0
 2F4  CONST_57  F29  C28  C26  C25  180.00   0.0  0
 2F4  CONST_58  C30  C28  C26  F27  180.00   0.0  0
 2F4  CONST_59  N31  C30  C28  F29    0.00   0.0  0
 2F4  CONST_60  H7   C07  N08  C03  180.00   0.0  0
 2F4  CONST_61  H6   C06  C05  C04  180.00   0.0  0
 2F4  CONST_62  H8   C10  C09  C05    0.00   0.0  0
 2F4  CONST_63  H5   C04  C05  C06  180.00   0.0  0
 2F4  CONST_64  H9   C11  C10  C09  180.00   0.0  0
 2F4  CONST_65  H10  C12  C11  C10  180.00   0.0  0
 2F4  CONST_66  H12  C18  C17  C16  180.00   0.0  0
 2F4  CONST_67  H18  C32  C33  C16  180.00   0.0  0
 2F4  CONST_68  H19  C33  C16  C17  180.00   0.0  0
 2F4  CONST_69  H11  C17  C18  C19  180.00   0.0  0
 2F4  CONST_70  H17  N31  C21  N22  180.00   0.0  0
 2F4  CONST_71  H15  C24  C23  N22    0.00   0.0  0
 2F4  CONST_72  H16  C25  C24  C23  180.00   0.0  0
 2F4  CONST_73  N08  C03  N02  C01  180.00   0.0  0
 2F4  CONST_74  C04  C03  N02  C01    0.00   0.0  0
 2F4  CONST_75  H4   N02  C03  C04  180.00   0.0  0
 2F4  Var_01    C17  C16  O15  C14  109.11  30.0  2
 2F4  Var_02    C21  N20  C19  C18    0.01  30.0  2
 2F4  Var_03    N22  C21  N20  C19    1.09  30.0  2
 2F4  Var_04    H1   C01  N02  C03  -63.66  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
 2F4  plan-1  N02  0.020
 2F4  plan-1  C03  0.020
 2F4  plan-1  C04  0.020
 2F4  plan-1  C05  0.020
 2F4  plan-1  C06  0.020
 2F4  plan-1  C07  0.020
 2F4  plan-1  N08  0.020
 2F4  plan-1  C09  0.020
 2F4  plan-1  H5   0.020
 2F4  plan-1  H6   0.020
 2F4  plan-1  H7   0.020
 2F4  plan-2  C05  0.020
 2F4  plan-2  C09  0.020
 2F4  plan-2  C10  0.020
 2F4  plan-2  C11  0.020
 2F4  plan-2  C12  0.020
 2F4  plan-2  N13  0.020
 2F4  plan-2  C14  0.020
 2F4  plan-2  O15  0.020
 2F4  plan-2  H8   0.020
 2F4  plan-2  H9   0.020
 2F4  plan-2  H10  0.020
 2F4  plan-3  O15  0.020
 2F4  plan-3  C16  0.020
 2F4  plan-3  C17  0.020
 2F4  plan-3  C18  0.020
 2F4  plan-3  C19  0.020
 2F4  plan-3  N20  0.020
 2F4  plan-3  C32  0.020
 2F4  plan-3  C33  0.020
 2F4  plan-3  H11  0.020
 2F4  plan-3  H12  0.020
 2F4  plan-3  H18  0.020
 2F4  plan-3  H19  0.020
 2F4  plan-4  N20  0.020
 2F4  plan-4  C21  0.020
 2F4  plan-4  N22  0.020
 2F4  plan-4  C23  0.020
 2F4  plan-4  C24  0.020
 2F4  plan-4  C25  0.020
 2F4  plan-4  C26  0.020
 2F4  plan-4  F27  0.020
 2F4  plan-4  C28  0.020
 2F4  plan-4  F29  0.020
 2F4  plan-4  C30  0.020
 2F4  plan-4  N31  0.020
 2F4  plan-4  H15  0.020
 2F4  plan-4  H16  0.020
 2F4  plan-4  H17  0.020
 2F4  plan-5  C01  0.020
 2F4  plan-5  N02  0.020
 2F4  plan-5  C03  0.020
 2F4  plan-5  H4   0.020

