# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 07:19:24 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: ~{N}-[[6,7-bis(fluoranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(3-fluorophenyl)-2-morpholin-4-yl-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(c1)n2cnc3c(NCc4[nH]c5c(F)c(F)ccc5n4)nc(nc23)N6CCOCC6
#
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
 K0E  K0E  ~{N}-[[6,7-bis(fluoranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(3-fluorophenyl)-2-morpholin-4-yl-purin-6-amine  ligand  54  35  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K0E
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
 K0E  C4   C  CR56  0   0.175  -5.7417   0.2318  -0.0940
 K0E  C5   C  CR6   0   0.378  -7.1062   0.4218   0.0339
 K0E  C6   C  CR5   0   0.448  -3.5607   0.3170  -0.2163
 K0E  N1   N  NR15  0  -0.696  -4.6694   1.0717  -0.0045
 K0E  C7   C  CH2   0  -0.327  -2.1951   0.9117  -0.1944
 K0E  C8   C  CR6   0   0.532   0.0963   0.1045  -0.2966
 K0E  N2   N  NH1   0  -0.677  -1.2191  -0.1331  -0.3292
 K0E  C9   C  CR6   0   0.639   1.8412   1.5986  -0.0543
 K0E  C10  C  CR56  0   0.491   2.3688  -0.5197  -0.4056
 K0E  C11  C  CR56  0  -0.054   1.0465  -0.9228  -0.4610
 K0E  C12  C  CR15  0   0.088   2.1724  -2.6854  -0.7425
 K0E  N3   N  N     0  -0.552   0.5223   1.3452  -0.1016
 K0E  C13  C  CH2   0  -0.310   3.5815   3.3156   0.0877
 K0E  C14  C  CH2   0  -0.188   3.8477   4.4241   1.0899
 K0E  C15  C  CH2   0  -0.187   1.6157   5.0544   1.1168
 K0E  N4   N  N     0  -0.522   2.8228   0.7088  -0.2074
 K0E  C    C  CR6   0   0.372  -7.9167  -0.6825  -0.1188
 K0E  C1   C  CR16  0  -0.429  -7.4002  -1.9478  -0.3923
 K0E  C2   C  CR16  0  -0.324  -6.0368  -2.1395  -0.5185
 K0E  C3   C  CR56  0   0.154  -5.2013  -1.0355  -0.3661
 K0E  N    N  N     0  -0.494  -3.8307  -0.9364  -0.4347
 K0E  N5   N  NR5   0  -0.626   3.0947  -1.6712  -0.5868
 K0E  N6   N  N     0  -0.441   0.9461  -2.2752  -0.6758
 K0E  N7   N  NT    0  -0.517   2.2004   2.8875   0.1890
 K0E  O    O  O2    0  -0.484   2.9436   5.4957   0.9440
 K0E  C16  C  CH2   0  -0.313   1.2431   3.9741   0.1187
 K0E  C17  C  CR6   0   0.360   4.4950  -1.8147  -0.5982
 K0E  F    F  F     0  -0.298  -7.6170   1.6274   0.2980
 K0E  F1   F  F     0  -0.313  -9.2419  -0.5238   0.0032
 K0E  C18  C  CR16  0  -0.289   5.2943  -0.8689  -1.2308
 K0E  C19  C  CR16  0  -0.239   6.6700  -1.0410  -1.2379
 K0E  C20  C  CR16  0  -0.410   7.2594  -2.1449  -0.6375
 K0E  C21  C  CR6   0   0.540   6.4345  -3.0645  -0.0211
 K0E  C22  C  CR16  0  -0.467   5.0619  -2.9210   0.0248
 K0E  F2   F  F     0  -0.311   6.9822  -4.1335   0.5740
 K0E  H1   H  HNR5  0   0.431  -4.6904   2.0626   0.1804
 K0E  H2   H  HCH2  0   0.279  -2.1069   1.6485  -1.0004
 K0E  H3   H  HCH2  0   0.279  -2.0548   1.4638   0.7399
 K0E  H4   H  HNH1  0   0.411  -1.5478  -1.0697  -0.5094
 K0E  H5   H  HCR5  0   0.298   2.4866  -3.7027  -0.9220
 K0E  H7   H  HCH2  0   0.269   4.2451   2.4793   0.2915
 K0E  H8   H  HCH2  0   0.205   3.7937   4.0120   2.1078
 K0E  H9   H  HCH2  0   0.241   4.8531   4.8200   0.9404
 K0E  H10  H  HCH2  0   0.205   1.4668   4.6732   2.1372
 K0E  H11  H  HCH2  0   0.241   0.9622   5.9175   0.9820
 K0E  H12  H  HCR6  0   0.290  -8.0882  -2.7753  -0.5032
 K0E  H13  H  HCR6  0   0.273  -5.6338  -3.1201  -0.7302
 K0E  H15  H  HCH2  0   0.272   0.2465   3.6040   0.3429
 K0E  H16  H  HCH2  0   0.227   1.2212   4.3954  -0.8952
 K0E  H17  H  HCR6  0   0.279   4.8508  -0.0112  -1.7138
 K0E  H18  H  HCR6  0   0.278   7.2940  -0.3073  -1.7297
 K0E  H19  H  HCR6  0   0.286   8.3317  -2.2862  -0.6491
 K0E  H20  H  HCR6  0   0.300   4.4550  -3.6493   0.5470
 K0E  H6   H  HCH2  0   0.228   3.7976   3.6687  -0.9292

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
 K0E  C19  C18  aromatic  1.386  0.020  1.386
 K0E  C19  C20  aromatic  1.388  0.020  1.388
 K0E  C18  C17  aromatic  1.391  0.020  1.391
 K0E  C20  C21  aromatic  1.381  0.020  1.381
 K0E  C12  N6   aromatic  1.295  0.020  1.295
 K0E  C12  N5   aromatic  1.380  0.020  1.380
 K0E  C17  N5   single    1.408  0.020  1.408
 K0E  C17  C22  aromatic  1.390  0.020  1.390
 K0E  N6   C11  aromatic  1.373  0.020  1.373
 K0E  N5   C10  aromatic  1.373  0.020  1.373
 K0E  C21  C22  aromatic  1.381  0.020  1.381
 K0E  C21  F2   single    1.340  0.020  1.340
 K0E  C11  C10  aromatic  1.384  0.020  1.384
 K0E  C11  C8   aromatic  1.409  0.020  1.409
 K0E  C10  N4   aromatic  1.325  0.020  1.325
 K0E  N2   C8   single    1.337  0.020  1.337
 K0E  N2   C7   single    1.436  0.020  1.436
 K0E  C8   N3   aromatic  1.326  0.020  1.326
 K0E  N4   C9   aromatic  1.334  0.020  1.334
 K0E  C7   C6   single    1.490  0.020  1.490
 K0E  N3   C9   aromatic  1.344  0.020  1.344
 K0E  C9   N7   single    1.360  0.020  1.360
 K0E  N7   C16  single    1.450  0.020  1.450
 K0E  N7   C13  single    1.449  0.020  1.449
 K0E  C6   N    aromatic  1.301  0.020  1.301
 K0E  C6   N1   aromatic  1.358  0.020  1.358
 K0E  C16  C15  single    1.517  0.020  1.517
 K0E  N    C3   aromatic  1.376  0.020  1.376
 K0E  C13  C14  single    1.518  0.020  1.518
 K0E  N1   C4   aromatic  1.365  0.020  1.365
 K0E  C15  O    single    1.410  0.020  1.410
 K0E  C3   C4   aromatic  1.404  0.020  1.404
 K0E  C3   C2   aromatic  1.393  0.020  1.393
 K0E  C4   C5   aromatic  1.384  0.020  1.384
 K0E  C14  O    single    1.410  0.020  1.410
 K0E  C2   C1   aromatic  1.383  0.020  1.383
 K0E  C5   F    single    1.336  0.020  1.336
 K0E  C5   C    aromatic  1.378  0.020  1.378
 K0E  C1   C    aromatic  1.394  0.020  1.394
 K0E  C    F1   single    1.340  0.020  1.340
 K0E  N1   H1   single    0.860  0.020  1.020
 K0E  C7   H2   single    0.970  0.020  1.090
 K0E  C7   H3   single    0.970  0.020  1.090
 K0E  N2   H4   single    0.860  0.020  1.020
 K0E  C12  H5   single    0.930  0.020  1.080
 K0E  C13  H6   single    0.970  0.020  1.090
 K0E  C13  H7   single    0.970  0.020  1.090
 K0E  C14  H8   single    0.970  0.020  1.090
 K0E  C14  H9   single    0.970  0.020  1.090
 K0E  C15  H10  single    0.970  0.020  1.090
 K0E  C15  H11  single    0.970  0.020  1.090
 K0E  C1   H12  single    0.930  0.020  1.080
 K0E  C2   H13  single    0.930  0.020  1.080
 K0E  C16  H15  single    0.970  0.020  1.090
 K0E  C16  H16  single    0.970  0.020  1.090
 K0E  C18  H17  single    0.930  0.020  1.080
 K0E  C19  H18  single    0.930  0.020  1.080
 K0E  C20  H19  single    0.930  0.020  1.080
 K0E  C22  H20  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
 K0E  C3   C4   N1   105.40  3.000
 K0E  C3   C4   C5   121.42  3.000
 K0E  N1   C4   C5   133.17  3.000
 K0E  F    C5   C    121.35  3.000
 K0E  C    C5   C4   117.37  3.000
 K0E  F    C5   C4   121.29  3.000
 K0E  N    C6   C7   125.28  3.000
 K0E  N    C6   N1   113.10  3.000
 K0E  C7   C6   N1   121.63  3.000
 K0E  H1   N1   C6   126.29  3.000
 K0E  H1   N1   C4   126.90  3.000
 K0E  C6   N1   C4   106.81  3.000
 K0E  H3   C7   H2   106.17  3.000
 K0E  H3   C7   N2   111.11  3.000
 K0E  H2   C7   N2   111.44  3.000
 K0E  H3   C7   C6   109.36  3.000
 K0E  H2   C7   C6   109.36  3.000
 K0E  N2   C7   C6   109.34  3.000
 K0E  N3   C8   C11  118.86  3.000
 K0E  N3   C8   N2   119.07  3.000
 K0E  C11  C8   N2   122.07  3.000
 K0E  H4   N2   C8   119.33  3.000
 K0E  H4   N2   C7   118.09  3.000
 K0E  C8   N2   C7   122.48  3.000
 K0E  N7   C9   N4   117.29  3.000
 K0E  N7   C9   N3   116.37  3.000
 K0E  N4   C9   N3   126.33  3.000
 K0E  N5   C10  N4   128.05  3.000
 K0E  N4   C10  C11  127.15  3.000
 K0E  N5   C10  C11  104.81  3.000
 K0E  N6   C11  C10  111.30  3.000
 K0E  C10  C11  C8   115.30  3.000
 K0E  N6   C11  C8   133.40  3.000
 K0E  H5   C12  N6   125.64  3.000
 K0E  H5   C12  N5   121.12  3.000
 K0E  N6   C12  N5   113.23  3.000
 K0E  C9   N3   C8   119.79  3.000
 K0E  H7   C13  H6   107.51  3.000
 K0E  H7   C13  N7   109.96  3.000
 K0E  H6   C13  N7   110.32  3.000
 K0E  H7   C13  C14  109.33  3.000
 K0E  H6   C13  C14  110.01  3.000
 K0E  N7   C13  C14  109.67  3.000
 K0E  H9   C14  H8   107.95  3.000
 K0E  H9   C14  O    107.52  3.000
 K0E  H8   C14  O    110.45  3.000
 K0E  H9   C14  C13  109.64  3.000
 K0E  H8   C14  C13  109.20  3.000
 K0E  O    C14  C13  111.98  3.000
 K0E  H11  C15  H10  107.93  3.000
 K0E  H11  C15  C16  109.56  3.000
 K0E  H10  C15  C16  109.29  3.000
 K0E  H11  C15  O    107.55  3.000
 K0E  H10  C15  O    110.48  3.000
 K0E  C16  C15  O    111.93  3.000
 K0E  C10  N4   C9   112.56  3.000
 K0E  F1   C    C1   119.46  3.000
 K0E  F1   C    C5   118.45  3.000
 K0E  C1   C    C5   122.09  3.000
 K0E  H12  C1   C2   120.78  3.000
 K0E  H12  C1   C    118.61  3.000
 K0E  C2   C1   C    120.61  3.000
 K0E  H13  C2   C3   121.11  3.000
 K0E  H13  C2   C1   120.74  3.000
 K0E  C3   C2   C1   118.14  3.000
 K0E  N    C3   C2   130.48  3.000
 K0E  C2   C3   C4   120.37  3.000
 K0E  N    C3   C4   109.15  3.000
 K0E  C3   N    C6   105.54  3.000
 K0E  C17  N5   C12  126.09  3.000
 K0E  C17  N5   C10  127.76  3.000
 K0E  C12  N5   C10  106.14  3.000
 K0E  C12  N6   C11  104.53  3.000
 K0E  C16  N7   C13  113.85  3.000
 K0E  C13  N7   C9   121.27  3.000
 K0E  C16  N7   C9   121.82  3.000
 K0E  C15  O    C14  110.70  3.000
 K0E  H16  C16  H15  107.63  3.000
 K0E  H16  C16  N7   110.21  3.000
 K0E  H15  C16  N7   109.90  3.000
 K0E  H16  C16  C15  109.82  3.000
 K0E  H15  C16  C15  109.39  3.000
 K0E  N7   C16  C15  109.85  3.000
 K0E  C22  C17  C18  120.70  3.000
 K0E  C22  C17  N5   118.89  3.000
 K0E  C18  C17  N5   120.41  3.000
 K0E  H17  C18  C19  120.25  3.000
 K0E  H17  C18  C17  120.52  3.000
 K0E  C19  C18  C17  119.23  3.000
 K0E  H18  C19  C20  119.43  3.000
 K0E  H18  C19  C18  119.38  3.000
 K0E  C20  C19  C18  121.19  3.000
 K0E  H19  C20  C21  120.67  3.000
 K0E  H19  C20  C19  121.35  3.000
 K0E  C21  C20  C19  117.98  3.000
 K0E  F2   C21  C22  118.32  3.000
 K0E  F2   C21  C20  119.03  3.000
 K0E  C22  C21  C20  122.65  3.000
 K0E  H20  C22  C21  120.23  3.000
 K0E  H20  C22  C17  121.53  3.000
 K0E  C21  C22  C17  118.24  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
 K0E  CONST_01  N    C6   N1   C4      0.00   0.0  0
 K0E  CONST_02  C6   N    C3   C4      0.00   0.0  0
 K0E  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 K0E  CONST_04  C1   C    C5   C4      0.00   0.0  0
 K0E  CONST_05  C6   N1   C4   C5    180.00   0.0  0
 K0E  CONST_06  N    C3   C4   C5    180.00   0.0  0
 K0E  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 K0E  CONST_08  C2   C1   C    C5      0.00   0.0  0
 K0E  CONST_09  C2   C3   N    C6    180.00   0.0  0
 K0E  CONST_10  C3   C4   N1   C6      0.00   0.0  0
 K0E  CONST_11  C3   N    C6   N1      0.00   0.0  0
 K0E  CONST_12  N    C3   C4   N1      0.00   0.0  0
 K0E  CONST_13  C2   C3   C4   N1    180.00   0.0  0
 K0E  CONST_14  C    C5   C4   N1    180.00   0.0  0
 K0E  CONST_15  C12  N6   C11  C8    180.00   0.0  0
 K0E  CONST_16  N5   C10  C11  C8    180.00   0.0  0
 K0E  CONST_17  N4   C10  C11  C8      0.00   0.0  0
 K0E  CONST_18  N4   C9   N3   C8      0.00   0.0  0
 K0E  CONST_19  N5   C10  N4   C9    180.00   0.0  0
 K0E  CONST_20  C11  C10  N4   C9      0.00   0.0  0
 K0E  CONST_21  C11  C8   N3   C9      0.00   0.0  0
 K0E  CONST_22  N6   C12  N5   C10     0.00   0.0  0
 K0E  CONST_25  C12  N6   C11  C10     0.00   0.0  0
 K0E  CONST_26  N3   C8   C11  C10     0.00   0.0  0
 K0E  CONST_27  N3   C9   N4   C10     0.00   0.0  0
 K0E  CONST_28  N5   C12  N6   C11     0.00   0.0  0
 K0E  CONST_29  C12  N5   C10  C11     0.00   0.0  0
 K0E  CONST_30  C17  N5   C10  C11   180.00   0.0  0
 K0E  CONST_33  N4   C10  N5   C12   180.00   0.0  0
 K0E  CONST_34  N6   C11  C8   N3    180.00   0.0  0
 K0E  CONST_35  C17  N5   C10  N4      0.00   0.0  0
 K0E  CONST_36  N6   C11  C10  N4    180.00   0.0  0
 K0E  CONST_37  C3   C4   C5   C       0.00   0.0  0
 K0E  CONST_38  C3   C2   C1   C       0.00   0.0  0
 K0E  CONST_39  N    C3   C2   C1    180.00   0.0  0
 K0E  CONST_40  C19  C18  C17  N5    180.00   0.0  0
 K0E  CONST_41  C21  C22  C17  N5    180.00   0.0  0
 K0E  CONST_42  N6   C11  C10  N5      0.00   0.0  0
 K0E  CONST_43  C17  N5   C12  N6    180.00   0.0  0
 K0E  CONST_44  C20  C19  C18  C17     0.00   0.0  0
 K0E  CONST_45  C20  C21  C22  C17     0.00   0.0  0
 K0E  CONST_46  C21  C20  C19  C18     0.00   0.0  0
 K0E  CONST_47  C21  C22  C17  C18     0.00   0.0  0
 K0E  CONST_48  C22  C17  C18  C19     0.00   0.0  0
 K0E  CONST_49  C22  C21  C20  C19     0.00   0.0  0
 K0E  CONST_50  N7   C9   N3   C8    180.00   0.0  0
 K0E  CONST_51  N7   C9   N4   C10   180.00   0.0  0
 K0E  CONST_52  C7   C6   N1   C4    180.00   0.0  0
 K0E  CONST_53  F1   C    C5   C4    180.00   0.0  0
 K0E  CONST_54  F    C5   C4   N1      0.00   0.0  0
 K0E  CONST_55  C3   N    C6   C7    180.00   0.0  0
 K0E  CONST_56  N6   C11  C8   N2      0.00   0.0  0
 K0E  CONST_57  C10  C11  C8   N2    180.00   0.0  0
 K0E  CONST_58  C9   N3   C8   N2    180.00   0.0  0
 K0E  CONST_59  F    C5   C    C1    180.00   0.0  0
 K0E  CONST_60  F1   C    C1   C2    180.00   0.0  0
 K0E  CONST_61  F    C5   C4   C3    180.00   0.0  0
 K0E  CONST_62  F2   C21  C22  C17   180.00   0.0  0
 K0E  CONST_63  F2   C21  C20  C19   180.00   0.0  0
 K0E  CONST_64  H13  C2   C3   C4    180.00   0.0  0
 K0E  CONST_65  H1   N1   C4   C5      0.00   0.0  0
 K0E  CONST_66  H12  C1   C    C5    180.00   0.0  0
 K0E  CONST_67  H5   C12  N5   C10   180.00   0.0  0
 K0E  CONST_68  H17  C18  C17  N5      0.00   0.0  0
 K0E  CONST_69  H20  C22  C17  N5      0.00   0.0  0
 K0E  CONST_70  H18  C19  C18  C17   180.00   0.0  0
 K0E  CONST_71  H19  C20  C19  C18   180.00   0.0  0
 K0E  CONST_72  C11  C8   N2   C7    180.00   0.0  0
 K0E  CONST_73  N3   C8   N2   C7      0.00   0.0  0
 K0E  CONST_74  H4   N2   C8   C11     0.00   0.0  0
 K0E  Var_01    C15  C16  N7   C9    148.07  30.0  1
 K0E  Var_02    C14  C13  N7   C9   -147.90  30.0  1
 K0E  Var_03    C16  N7   C9   N3    -12.72  30.0  2
 K0E  Var_04    C16  C15  O    C14   -58.95  30.0  1
 K0E  Var_05    O    C15  C16  N7     54.38  30.0  1
 K0E  Var_06    O    C14  C13  N7    -54.64  30.0  1
 K0E  Var_07    H8   C14  O    C15   -62.81  30.0  1
 K0E  Var_08    C8   N2   C7   C6   -177.68  30.0  1
 K0E  Var_09    N2   C7   C6   N1    174.93  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
 K0E  plan-1  N5   0.020
 K0E  plan-1  C17  0.020
 K0E  plan-1  C18  0.020
 K0E  plan-1  C19  0.020
 K0E  plan-1  C20  0.020
 K0E  plan-1  C21  0.020
 K0E  plan-1  C22  0.020
 K0E  plan-1  F2   0.020
 K0E  plan-1  H17  0.020
 K0E  plan-1  H18  0.020
 K0E  plan-1  H19  0.020
 K0E  plan-1  H20  0.020
 K0E  plan-2  C4   0.020
 K0E  plan-2  C5   0.020
 K0E  plan-2  C6   0.020
 K0E  plan-2  N1   0.020
 K0E  plan-2  C7   0.020
 K0E  plan-2  C    0.020
 K0E  plan-2  C1   0.020
 K0E  plan-2  C2   0.020
 K0E  plan-2  C3   0.020
 K0E  plan-2  N    0.020
 K0E  plan-2  F    0.020
 K0E  plan-2  F1   0.020
 K0E  plan-2  H1   0.020
 K0E  plan-2  H12  0.020
 K0E  plan-2  H13  0.020
 K0E  plan-3  C8   0.020
 K0E  plan-3  N2   0.020
 K0E  plan-3  C9   0.020
 K0E  plan-3  C10  0.020
 K0E  plan-3  C11  0.020
 K0E  plan-3  C12  0.020
 K0E  plan-3  N3   0.020
 K0E  plan-3  N4   0.020
 K0E  plan-3  N5   0.020
 K0E  plan-3  N6   0.020
 K0E  plan-3  N7   0.020
 K0E  plan-3  C17  0.020
 K0E  plan-3  H5   0.020
 K0E  plan-4  C7   0.020
 K0E  plan-4  C8   0.020
 K0E  plan-4  N2   0.020
 K0E  plan-4  H4   0.020

