# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 11:10:09 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: trans-4-({9-[(3S)-tetrahydrofuran-3-yl]-8-[(2,4,6-trifluorophenyl)amino]-9H-purin-2-yl}amino)cyclohexanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CC[C@H](CC1)Nc2ncc3nc(Nc4c(F)cc(F)cc4F)n([C@H]5CCOC5)c3n2
#
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
 KBI  KBI  trans-4-({9-[(3S)-tetrahydrofuran-3-yl]-8-[(2,4,6-trifluorophenyl)amino]-9H-purin-2-yl}amino)cyclohexanol  ligand  55  32  .  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_KBI
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
 KBI  C1    C  CR6   0   0.588   2.6838   0.1772   0.1815
 KBI  F1    F  F     0  -0.289  -4.6779   0.1593  -2.0417
 KBI  N1    N  N     0  -0.482   2.5048  -1.1470   0.2362
 KBI  O1    O  OH1   0  -0.679   9.1493  -1.4778  -0.1170
 KBI  C2    C  CR56  0   0.509   0.5035   0.5843   0.1055
 KBI  F2    F  F     0  -0.301  -6.8867  -3.2960   0.1909
 KBI  N2    N  N     0  -0.501   1.7074   1.0999   0.0995
 KBI  O2    O  O     0  -0.494  -3.0350   3.4500   0.1204
 KBI  C3    C  CR56  0   0.045   0.1798  -0.7771   0.1742
 KBI  F3    F  F     0  -0.288  -3.3540  -1.0605   2.2617
 KBI  N3    N  NR5   0  -0.587  -0.6927   1.2473   0.0523
 KBI  C4    C  CR16  0  -0.089   1.2619  -1.6259   0.2355
 KBI  N4    N  N     0  -0.513  -1.1881  -0.9489   0.1581
 KBI  C5    C  CR5   0   0.710  -1.6627   0.2598   0.0876
 KBI  N5    N  NH1   0  -0.799  -2.9793   0.5763   0.0593
 KBI  C6    C  CR6   0  -0.059  -3.9624  -0.4153   0.1020
 KBI  N6    N  NH1   0  -0.678   3.9475   0.6537   0.2340
 KBI  C7    C  CH1   0  -0.037   5.1370  -0.1646   0.2784
 KBI  C8    C  CH2   0  -0.455   6.2453   0.5766   1.0200
 KBI  C9    C  CH2   0  -0.462   7.5129  -0.2664   1.1048
 KBI  C10   C  CH1   0   0.084   7.9866  -0.6897  -0.2767
 KBI  C11   C  CH2   0  -0.482   6.8808  -1.4351  -1.0161
 KBI  C12   C  CH2   0  -0.441   5.6144  -0.5903  -1.1109
 KBI  C13   C  CR15  0  -0.152  -0.8349   2.6783  -0.1487
 KBI  C14   C  CH2   0  -0.222  -1.8094   3.3541   0.8241
 KBI  C15   C  CH2   0  -0.199  -2.6798   3.8438  -1.1991
 KBI  C16   C  CH2   0  -0.504  -1.4182   3.0423  -1.5327
 KBI  C17   C  CR6   0   0.576  -4.1438  -1.2393   1.2077
 KBI  C18   C  CR16  0  -0.590  -5.1099  -2.2235   1.2601
 KBI  C19   C  CR6   0   0.562  -5.9371  -2.3589   0.1613
 KBI  C20   C  CR16  0  -0.586  -5.8269  -1.5661  -0.9641
 KBI  C21   C  CR6   0   0.552  -4.8262  -0.6145  -0.9676
 KBI  H4    H  HCR6  0   0.261   1.1481  -2.7042   0.2818
 KBI  HN5   H  HNH1  0   0.429  -3.2646   1.5518   0.0167
 KBI  HN6   H  HNH1  0   0.381   4.0562   1.6462   0.0987
 KBI  H7    H  HCH1  0   0.232   4.8899  -1.0662   0.8455
 KBI  H8    H  HCH2  0   0.221   6.4646   1.5170   0.5010
 KBI  H8A   H  HCH2  0   0.245   5.9041   0.8431   2.0227
 KBI  H9    H  HCH2  0   0.240   8.2983   0.2982   1.6135
 KBI  H9A   H  HCH2  0   0.220   7.3200  -1.1599   1.7090
 KBI  H10   H  HCH1  0   0.186   8.2217   0.2229  -0.8485
 KBI  H11   H  HCH2  0   0.235   7.2223  -1.7136  -2.0177
 KBI  H11A  H  HCH2  0   0.218   6.6625  -2.3682  -0.4845
 KBI  H12   H  HCH2  0   0.239   4.8254  -1.1503  -1.6173
 KBI  H12A  H  HCH2  0   0.215   5.8054   0.3042  -1.7143
 KBI  H13   H  HCR5  0   0.300   0.1672   3.0820  -0.0162
 KBI  H14   H  HCH2  0   0.261  -1.4333   4.3530   1.0724
 KBI  H14A  H  HCH2  0   0.271  -1.9650   2.8048   1.7528
 KBI  H15   H  HCH2  0   0.254  -3.5182   3.6309  -1.8613
 KBI  H15A  H  HCH2  0   0.238  -2.4816   4.9213  -1.2266
 KBI  H16   H  HCH2  0   0.280  -0.7120   3.6209  -2.1252
 KBI  H16A  H  HCH2  0   0.267  -1.6602   2.1417  -2.0982
 KBI  H18   H  HCR6  0   0.312  -5.2221  -2.8503   2.1346
 KBI  H20   H  HCR6  0   0.313  -6.4853  -1.6912  -1.8133
 KBI  HO1   H  HOH1  0   0.446   9.4673  -1.7233  -0.9917

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
 KBI  N1   C1    aromatic  1.337  0.020  1.337
 KBI  C1   N2    aromatic  1.346  0.020  1.346
 KBI  C1   N6    single    1.352  0.020  1.352
 KBI  C21  F1    single    1.332  0.020  1.332
 KBI  C4   N1    aromatic  1.332  0.020  1.332
 KBI  C10  O1    single    1.414  0.020  1.414
 KBI  O1   HO1   single    0.850  0.020  0.980
 KBI  C3   C2    aromatic  1.401  0.020  1.401
 KBI  N3   C2    aromatic  1.369  0.020  1.369
 KBI  C2   N2    aromatic  1.310  0.020  1.310
 KBI  F2   C19   single    1.335  0.020  1.335
 KBI  C15  O2    single    1.422  0.020  1.422
 KBI  C14  O2    single    1.417  0.020  1.417
 KBI  N4   C3    aromatic  1.379  0.020  1.379
 KBI  C4   C3    aromatic  1.377  0.020  1.377
 KBI  F3   C17   single    1.329  0.020  1.329
 KBI  C5   N3    aromatic  1.385  0.020  1.385
 KBI  N3   C13   single    1.452  0.020  1.452
 KBI  C4   H4    single    0.930  0.020  1.080
 KBI  N4   C5    aromatic  1.300  0.020  1.300
 KBI  N5   C5    single    1.354  0.020  1.354
 KBI  C6   N5    single    1.397  0.020  1.397
 KBI  N5   HN5   single    0.860  0.020  1.020
 KBI  C17  C6    aromatic  1.391  0.020  1.391
 KBI  C6   C21   aromatic  1.389  0.020  1.389
 KBI  N6   C7    single    1.444  0.020  1.444
 KBI  N6   HN6   single    0.860  0.020  1.020
 KBI  C12  C7    single    1.530  0.020  1.530
 KBI  C7   C8    single    1.526  0.020  1.526
 KBI  C7   H7    single    0.970  0.020  1.090
 KBI  C8   C9    single    1.525  0.020  1.525
 KBI  C8   H8    single    0.970  0.020  1.090
 KBI  C8   H8A   single    0.970  0.020  1.090
 KBI  C10  C9    single    1.521  0.020  1.521
 KBI  C9   H9    single    0.970  0.020  1.090
 KBI  C9   H9A   single    0.970  0.020  1.090
 KBI  C11  C10   single    1.525  0.020  1.525
 KBI  C10  H10   single    0.970  0.020  1.090
 KBI  C12  C11   single    1.525  0.020  1.525
 KBI  C11  H11   single    0.970  0.020  1.090
 KBI  C11  H11A  single    0.970  0.020  1.090
 KBI  C12  H12   single    0.970  0.020  1.090
 KBI  C12  H12A  single    0.970  0.020  1.090
 KBI  C16  C13   single    1.545  0.020  1.545
 KBI  C13  C14   single    1.534  0.020  1.534
 KBI  C13  H13   single    0.970  0.020  1.090
 KBI  C14  H14   single    0.970  0.020  1.090
 KBI  C14  H14A  single    0.970  0.020  1.090
 KBI  C16  C15   single    1.531  0.020  1.531
 KBI  C15  H15   single    0.970  0.020  1.090
 KBI  C15  H15A  single    0.970  0.020  1.090
 KBI  C16  H16   single    0.970  0.020  1.090
 KBI  C16  H16A  single    0.970  0.020  1.090
 KBI  C18  C17   aromatic  1.380  0.020  1.380
 KBI  C18  C19   aromatic  1.382  0.020  1.382
 KBI  C18  H18   single    0.930  0.020  1.080
 KBI  C19  C20   aromatic  1.381  0.020  1.381
 KBI  C20  C21   aromatic  1.381  0.020  1.381
 KBI  C20  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
 KBI  N6    C1   N2   116.04  3.000
 KBI  N6    C1   N1   118.21  3.000
 KBI  N2    C1   N1   125.75  3.000
 KBI  C4    N1   C1   118.74  3.000
 KBI  HO1   O1   C10  108.13  3.000
 KBI  N3    C2   C3   105.70  3.000
 KBI  N3    C2   N2   127.78  3.000
 KBI  C3    C2   N2   126.52  3.000
 KBI  C2    N2   C1   113.38  3.000
 KBI  C15   O2   C14  105.28  3.000
 KBI  N4    C3   C4   134.71  3.000
 KBI  C4    C3   C2   114.82  3.000
 KBI  N4    C3   C2   110.47  3.000
 KBI  C13   N3   C5   129.63  3.000
 KBI  C13   N3   C2   124.63  3.000
 KBI  C5    N3   C2   105.42  3.000
 KBI  H4    C4   C3   122.15  3.000
 KBI  H4    C4   N1   117.07  3.000
 KBI  C3    C4   N1   120.78  3.000
 KBI  C5    N4   C3   104.29  3.000
 KBI  N5    C5   N4   124.97  3.000
 KBI  N5    C5   N3   120.91  3.000
 KBI  N4    C5   N3   114.12  3.000
 KBI  HN5   N5   C6   118.98  3.000
 KBI  HN5   N5   C5   119.84  3.000
 KBI  C6    N5   C5   121.17  3.000
 KBI  C21   C6   C17  116.49  3.000
 KBI  C21   C6   N5   121.06  3.000
 KBI  C17   C6   N5   122.45  3.000
 KBI  HN6   N6   C7   118.25  3.000
 KBI  HN6   N6   C1   116.29  3.000
 KBI  C7    N6   C1   124.85  3.000
 KBI  H7    C7   C12  108.19  3.000
 KBI  H7    C7   C8   108.22  3.000
 KBI  C12   C7   C8   110.49  3.000
 KBI  H7    C7   N6   107.27  3.000
 KBI  C8    C7   N6   109.75  3.000
 KBI  C12   C7   N6   112.76  3.000
 KBI  H8A   C8   H8   106.72  3.000
 KBI  H8A   C8   C9   110.09  3.000
 KBI  H8    C8   C9   109.53  3.000
 KBI  H8A   C8   C7   109.75  3.000
 KBI  H8    C8   C7   109.39  3.000
 KBI  C9    C8   C7   111.25  3.000
 KBI  H9A   C9   H9   106.93  3.000
 KBI  H9A   C9   C10  109.19  3.000
 KBI  H9    C9   C10  110.05  3.000
 KBI  H9A   C9   C8   109.58  3.000
 KBI  H9    C9   C8   109.74  3.000
 KBI  C10   C9   C8   111.25  3.000
 KBI  H10   C10  C11  107.93  3.000
 KBI  H10   C10  C9   107.89  3.000
 KBI  C11   C10  C9   110.53  3.000
 KBI  H10   C10  O1   110.17  3.000
 KBI  C11   C10  O1   112.25  3.000
 KBI  C9    C10  O1   107.99  3.000
 KBI  H11A  C11  H11  106.83  3.000
 KBI  H11A  C11  C12  109.66  3.000
 KBI  H11   C11  C12  110.07  3.000
 KBI  H11A  C11  C10  108.99  3.000
 KBI  H11   C11  C10  109.99  3.000
 KBI  C12   C11  C10  111.19  3.000
 KBI  H12A  C12  H12  106.81  3.000
 KBI  H12A  C12  C11  109.98  3.000
 KBI  H12   C12  C11  110.16  3.000
 KBI  H12A  C12  C7   109.11  3.000
 KBI  H12   C12  C7   109.78  3.000
 KBI  C11   C12  C7   110.91  3.000
 KBI  H13   C13  C16  111.66  3.000
 KBI  H13   C13  C14  110.14  3.000
 KBI  C16   C13  C14  102.96  3.000
 KBI  H13   C13  N3   104.99  3.000
 KBI  C14   C13  N3   114.12  3.000
 KBI  C16   C13  N3   113.14  3.000
 KBI  H14A  C14  H14  108.38  3.000
 KBI  H14A  C14  C13  114.14  3.000
 KBI  H14   C14  C13  109.11  3.000
 KBI  H14A  C14  O2   109.50  3.000
 KBI  H14   C14  O2   110.35  3.000
 KBI  C13   C14  O2   105.34  3.000
 KBI  H15A  C15  H15  108.43  3.000
 KBI  H15A  C15  C16  111.11  3.000
 KBI  H15   C15  C16  113.53  3.000
 KBI  H15A  C15  O2   109.92  3.000
 KBI  H15   C15  O2   108.52  3.000
 KBI  C16   C15  O2   105.24  3.000
 KBI  H16A  C16  H16  107.49  3.000
 KBI  H16A  C16  C15  111.25  3.000
 KBI  H16   C16  C15  112.02  3.000
 KBI  H16A  C16  C13  110.71  3.000
 KBI  H16   C16  C13  111.58  3.000
 KBI  C15   C16  C13  103.84  3.000
 KBI  C18   C17  C6   122.95  3.000
 KBI  C18   C17  F3   118.80  3.000
 KBI  C6    C17  F3   118.25  3.000
 KBI  H18   C18  C19  121.59  3.000
 KBI  H18   C18  C17  121.10  3.000
 KBI  C19   C18  C17  117.31  3.000
 KBI  C20   C19  C18  122.95  3.000
 KBI  C20   C19  F2   118.55  3.000
 KBI  C18   C19  F2   118.50  3.000
 KBI  H20   C20  C21  121.25  3.000
 KBI  H20   C20  C19  121.65  3.000
 KBI  C21   C20  C19  117.09  3.000
 KBI  C20   C21  C6   123.19  3.000
 KBI  C20   C21  F1   118.88  3.000
 KBI  C6    C21  F1   117.92  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
 KBI  CONST_01  C3   C4   N1   C1      0.00   0.0  0
 KBI  CONST_02  C3   C2   N2   C1      0.00   0.0  0
 KBI  CONST_03  N3   C2   N2   C1    180.00   0.0  0
 KBI  CONST_04  C2   N2   C1   N1      0.00   0.0  0
 KBI  CONST_05  C2   C3   C4   N1      0.00   0.0  0
 KBI  CONST_06  N4   C3   C4   N1    180.00   0.0  0
 KBI  CONST_07  C5   N4   C3   C2      0.00   0.0  0
 KBI  CONST_08  N4   C5   N3   C2      0.00   0.0  0
 KBI  CONST_09  C4   N1   C1   N2      0.00   0.0  0
 KBI  CONST_10  N4   C3   C2   N2    180.00   0.0  0
 KBI  CONST_11  C4   C3   C2   N2      0.00   0.0  0
 KBI  CONST_12  C5   N3   C2   N2    180.00   0.0  0
 KBI  CONST_13  C5   N3   C2   C3      0.00   0.0  0
 KBI  CONST_14  N3   C5   N4   C3      0.00   0.0  0
 KBI  CONST_15  N4   C3   C2   N3      0.00   0.0  0
 KBI  CONST_16  C4   C3   C2   N3    180.00   0.0  0
 KBI  CONST_17  C5   N4   C3   C4    180.00   0.0  0
 KBI  CONST_18  C19  C18  C17  C6      0.00   0.0  0
 KBI  CONST_19  C19  C20  C21  C6      0.00   0.0  0
 KBI  CONST_20  C20  C21  C6   C17     0.00   0.0  0
 KBI  CONST_21  C20  C19  C18  C17     0.00   0.0  0
 KBI  CONST_22  C21  C6   C17  C18     0.00   0.0  0
 KBI  CONST_23  C21  C20  C19  C18     0.00   0.0  0
 KBI  CONST_24  C13  N3   C2   N2      0.00   0.0  0
 KBI  CONST_25  C13  N3   C2   C3    180.00   0.0  0
 KBI  CONST_26  C13  N3   C5   N4    180.00   0.0  0
 KBI  CONST_27  C17  C6   C21  F1    180.00   0.0  0
 KBI  CONST_28  C19  C20  C21  F1    180.00   0.0  0
 KBI  CONST_29  N5   C5   N3   C2    180.00   0.0  0
 KBI  CONST_30  N6   C1   N2   C2    180.00   0.0  0
 KBI  CONST_31  C17  C18  C19  F2    180.00   0.0  0
 KBI  CONST_32  C21  C20  C19  F2    180.00   0.0  0
 KBI  CONST_33  N5   C5   N4   C3    180.00   0.0  0
 KBI  CONST_34  C21  C6   C17  F3    180.00   0.0  0
 KBI  CONST_35  C19  C18  C17  F3    180.00   0.0  0
 KBI  CONST_36  N6   C1   N1   C4    180.00   0.0  0
 KBI  CONST_37  C13  N3   C5   N5      0.00   0.0  0
 KBI  CONST_38  C18  C17  C6   N5    180.00   0.0  0
 KBI  CONST_39  C20  C21  C6   N5    180.00   0.0  0
 KBI  CONST_40  C7   N6   C1   N1      0.00   0.0  0
 KBI  CONST_41  C7   N6   C1   N2    180.00   0.0  0
 KBI  CONST_42  H4   C4   N1   C1    180.00   0.0  0
 KBI  CONST_43  H18  C18  C17  C6    180.00   0.0  0
 KBI  CONST_44  H20  C20  C21  C6    180.00   0.0  0
 KBI  CONST_45  HN6  N6   C1   N1    180.00   0.0  0
 KBI  Var_01    C13  C16  C15  O2    -22.62  30.0  1
 KBI  Var_02    C10  C11  C12  C7    -56.63  30.0  1
 KBI  Var_03    C10  C9   C8   C7     56.31  30.0  1
 KBI  Var_04    C16  C15  O2   C14    40.35  30.0  1
 KBI  Var_05    C6   N5   C5   N3   -179.65  30.0  2
 KBI  Var_06    C17  C6   N5   C5     64.92  30.0  1
 KBI  Var_07    H14  C14  O2   C15    75.95  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
 KBI  chir_01  C7   N6  C12  C8   negativ
 KBI  chir_02  C10  O1  C9   C11  positiv
 KBI  chir_03  C13  N3  C16  C14  negativ

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
 KBI  plan-1  C1   0.020
 KBI  plan-1  N6   0.020
 KBI  plan-1  C7   0.020
 KBI  plan-1  HN6  0.020
 KBI  plan-2  F1   0.020
 KBI  plan-2  F2   0.020
 KBI  plan-2  F3   0.020
 KBI  plan-2  N5   0.020
 KBI  plan-2  C6   0.020
 KBI  plan-2  C17  0.020
 KBI  plan-2  C18  0.020
 KBI  plan-2  C19  0.020
 KBI  plan-2  C20  0.020
 KBI  plan-2  C21  0.020
 KBI  plan-2  H18  0.020
 KBI  plan-2  H20  0.020
 KBI  plan-3  C1   0.020
 KBI  plan-3  N1   0.020
 KBI  plan-3  C2   0.020
 KBI  plan-3  N2   0.020
 KBI  plan-3  C3   0.020
 KBI  plan-3  N3   0.020
 KBI  plan-3  C4   0.020
 KBI  plan-3  N4   0.020
 KBI  plan-3  C5   0.020
 KBI  plan-3  N5   0.020
 KBI  plan-3  N6   0.020
 KBI  plan-3  C13  0.020
 KBI  plan-3  H4   0.020

