# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:06:38 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-({[2-{[(1R)-1-(hydroxymethyl)propyl]amino}-9-(1-methylethyl)-9H-purin-6-yl]amino}methyl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](CO)Nc1nc(NCc2ccccc2O)c3ncn(C(C)C)c3n1
#
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
 CK9  CK9  2-({[2-{[(1R)-1-(hydroxymethyl)propyl]amino}-9-(1-methylethyl)-9H-purin-6-yl]amino}methyl)phenol  ligand  53  27  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CK9
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
 CK9  O27   O  OH1   0  -0.615   2.3196   0.1307  -1.2108
 CK9  C24   C  CR6   0   0.337   3.4985  -0.2135  -0.6597
 CK9  C23   C  CR16  0  -0.376   4.6048  -0.5615  -1.4292
 CK9  C22   C  CR16  0  -0.255   5.8006  -0.9080  -0.8156
 CK9  C21   C  CR16  0  -0.273   5.9028  -0.9091   0.5670
 CK9  C20   C  CR16  0  -0.297   4.7926  -0.5610   1.3268
 CK9  C19   C  CR6   0   0.007   3.5846  -0.2088   0.7383
 CK9  C18   C  CH2   0  -0.352   2.3929   0.1533   1.5847
 CK9  N17   N  NH1   0  -0.654   1.3375  -0.8303   1.4845
 CK9  C4    C  CR6   0   0.541   0.1040  -0.5863   1.0198
 CK9  C5    C  CR56  0  -0.070  -0.8050  -1.6323   0.7646
 CK9  N9    N  N     0  -0.457  -0.7250  -2.9984   0.8774
 CK9  C8    C  CR15  0   0.085  -1.8867  -3.4203   0.4722
 CK9  C6    C  CR56  0   0.488  -2.0455  -1.2483   0.2770
 CK9  N7    N  NR5   0  -0.499  -2.7310  -2.4115   0.0899
 CK9  C10   C  CH1   0  -0.130  -4.1022  -2.5447  -0.3912
 CK9  C12   C  CH3   0  -0.657  -4.1696  -3.5099  -1.5660
 CK9  C11   C  CH3   0  -0.646  -5.0333  -2.9480   0.7439
 CK9  N3    N  N     0  -0.530  -2.4590  -0.0095   0.0329
 CK9  C2    C  CR6   0   0.577  -1.5220   0.8964   0.3262
 CK9  N1    N  N     0  -0.533  -0.2935   0.6622   0.8071
 CK9  N13   N  NH1   0  -0.658  -1.8651   2.1942   0.1374
 CK9  C14   C  CH1   0  -0.094  -0.9244   3.2951   0.1598
 CK9  C25   C  CH2   0  -0.437  -1.6797   4.6055   0.3734
 CK9  C26   C  CH3   0  -0.659  -2.3947   4.6802   1.7151
 CK9  C15   C  CH2   0  -0.170  -0.0378   3.3284  -1.0789
 CK9  O16   O  OH1   0  -0.675  -0.8395   3.5253  -2.2225
 CK9  H27   H  HOH1  0   0.473   2.3797   0.1087  -2.1721
 CK9  H23   H  HCR6  0   0.268   4.5315  -0.5609  -2.5113
 CK9  H22   H  HCR6  0   0.258   6.6520  -1.1778  -1.4271
 CK9  H21   H  HCR6  0   0.251   6.8317  -1.1801   1.0503
 CK9  H20   H  HCR6  0   0.252   4.8637  -0.5609   2.4084
 CK9  H181  H  HCH2  0   0.275   1.9732   1.1143   1.2905
 CK9  H182  H  HCH2  0   0.255   2.7127   0.2479   2.6255
 CK9  H17   H  HNH1  0   0.394   1.5937  -1.7968   1.6065
 CK9  H8    H  HCR5  0   0.284  -2.1874  -4.4565   0.4264
 CK9  H10   H  HCH1  0   0.265  -4.3815  -1.5485  -0.7376
 CK9  H121  H  HCH3  0   0.245  -5.1827  -3.5316  -1.9667
 CK9  H122  H  HCH3  0   0.245  -3.4967  -3.2052  -2.3674
 CK9  H123  H  HCH3  0   0.230  -3.9120  -4.5273  -1.2670
 CK9  H111  H  HCH3  0   0.242  -4.9936  -2.2288   1.5618
 CK9  H112  H  HCH3  0   0.239  -6.0612  -2.9928   0.3841
 CK9  H113  H  HCH3  0   0.228  -4.7748  -3.9317   1.1395
 CK9  H13   H  HNH1  0   0.376  -2.7216   2.3361  -0.3743
 CK9  H14   H  HCH1  0   0.241  -0.2533   3.1432   1.0089
 CK9  H251  H  HCH2  0   0.224  -2.3966   4.7599  -0.4384
 CK9  H252  H  HCH2  0   0.228  -0.9581   5.4233   0.2996
 CK9  H261  H  HCH3  0   0.228  -2.8869   5.6453   1.8392
 CK9  H262  H  HCH3  0   0.222  -3.1573   3.9070   1.8107
 CK9  H263  H  HCH3  0   0.217  -1.6933   4.5582   2.5425
 CK9  H151  H  HCH2  0   0.190   0.6961   4.1366  -0.9522
 CK9  H152  H  HCH2  0   0.220   0.5235   2.3886  -1.1337
 CK9  H16   H  HOH1  0   0.454  -0.2800   3.4404  -2.9987

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
 CK9  O27  C24   single    1.346  0.020  1.346
 CK9  O27  H27   single    0.850  0.020  0.980
 CK9  C24  C23   aromatic  1.392  0.020  1.392
 CK9  C24  C19   aromatic  1.401  0.020  1.401
 CK9  C23  C22   aromatic  1.388  0.020  1.388
 CK9  C23  H23   single    0.930  0.020  1.080
 CK9  C22  C21   aromatic  1.386  0.020  1.386
 CK9  C22  H22   single    0.930  0.020  1.080
 CK9  C21  C20   aromatic  1.390  0.020  1.390
 CK9  C21  H21   single    0.930  0.020  1.080
 CK9  C20  C19   aromatic  1.389  0.020  1.389
 CK9  C20  H20   single    0.930  0.020  1.080
 CK9  C19  C18   single    1.506  0.020  1.506
 CK9  C18  N17   single    1.446  0.020  1.446
 CK9  C18  H181  single    0.970  0.020  1.090
 CK9  C18  H182  single    0.970  0.020  1.090
 CK9  N17  C4    single    1.341  0.020  1.341
 CK9  N17  H17   single    0.860  0.020  1.020
 CK9  C4   C5    aromatic  1.409  0.020  1.409
 CK9  C4   N1    aromatic  1.327  0.020  1.327
 CK9  C5   N9    aromatic  1.373  0.020  1.373
 CK9  C5   C6    aromatic  1.387  0.020  1.387
 CK9  N9   C8    aromatic  1.301  0.020  1.301
 CK9  C8   N7    aromatic  1.370  0.020  1.370
 CK9  C8   H8    single    0.930  0.020  1.080
 CK9  C6   N7    aromatic  1.363  0.020  1.363
 CK9  C6   N3    aromatic  1.329  0.020  1.329
 CK9  N7   C10   single    1.459  0.020  1.459
 CK9  C10  C12   single    1.522  0.020  1.522
 CK9  C10  C11   single    1.522  0.020  1.522
 CK9  C10  H10   single    0.970  0.020  1.090
 CK9  C12  H121  single    0.970  0.020  1.090
 CK9  C12  H122  single    0.970  0.020  1.090
 CK9  C12  H123  single    0.970  0.020  1.090
 CK9  C11  H111  single    0.970  0.020  1.090
 CK9  C11  H112  single    0.970  0.020  1.090
 CK9  C11  H113  single    0.970  0.020  1.090
 CK9  N3   C2    aromatic  1.336  0.020  1.336
 CK9  C2   N1    aromatic  1.340  0.020  1.340
 CK9  C2   N13   single    1.356  0.020  1.356
 CK9  N13  C14   single    1.448  0.020  1.448
 CK9  N13  H13   single    0.890  0.020  1.040
 CK9  C14  C25   single    1.527  0.020  1.527
 CK9  C14  C15   single    1.524  0.020  1.524
 CK9  C14  H14   single    0.970  0.020  1.090
 CK9  C25  C26   single    1.522  0.020  1.522
 CK9  C25  H251  single    0.970  0.020  1.090
 CK9  C25  H252  single    0.970  0.020  1.090
 CK9  C26  H261  single    0.970  0.020  1.090
 CK9  C26  H262  single    0.970  0.020  1.090
 CK9  C26  H263  single    0.970  0.020  1.090
 CK9  C15  O16   single    1.411  0.020  1.411
 CK9  C15  H151  single    0.970  0.020  1.090
 CK9  C15  H152  single    0.970  0.020  1.090
 CK9  O16  H16   single    0.850  0.020  0.980

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
 CK9  H27   O27  C24   110.36  3.000
 CK9  C19   C24  C23   120.25  3.000
 CK9  C19   C24  O27   117.49  3.000
 CK9  C23   C24  O27   122.26  3.000
 CK9  H23   C23  C22   119.96  3.000
 CK9  H23   C23  C24   119.85  3.000
 CK9  C22   C23  C24   120.19  3.000
 CK9  H22   C22  C21   120.35  3.000
 CK9  H22   C22  C23   119.35  3.000
 CK9  C21   C22  C23   120.30  3.000
 CK9  H21   C21  C20   120.30  3.000
 CK9  H21   C21  C22   120.61  3.000
 CK9  C20   C21  C22   119.09  3.000
 CK9  H20   C20  C19   118.67  3.000
 CK9  H20   C20  C21   119.55  3.000
 CK9  C19   C20  C21   121.78  3.000
 CK9  C18   C19  C20   120.73  3.000
 CK9  C18   C19  C24   120.88  3.000
 CK9  C20   C19  C24   118.39  3.000
 CK9  H182  C18  H181  107.07  3.000
 CK9  H182  C18  N17   109.78  3.000
 CK9  H181  C18  N17   107.47  3.000
 CK9  H182  C18  C19   108.94  3.000
 CK9  H181  C18  C19   111.42  3.000
 CK9  N17   C18  C19   112.03  3.000
 CK9  H17   N17  C4    116.79  3.000
 CK9  H17   N17  C18   117.29  3.000
 CK9  C4    N17  C18   124.88  3.000
 CK9  N1    C4   C5    118.43  3.000
 CK9  N1    C4   N17   120.15  3.000
 CK9  C5    C4   N17   121.42  3.000
 CK9  C6    C5   N9    110.88  3.000
 CK9  C6    C5   C4    115.79  3.000
 CK9  N9    C5   C4    133.32  3.000
 CK9  C8    N9   C5    104.19  3.000
 CK9  H8    C8   N7    121.54  3.000
 CK9  H8    C8   N9    124.97  3.000
 CK9  N7    C8   N9    113.49  3.000
 CK9  N3    C6   N7    127.88  3.000
 CK9  N3    C6   C5    126.94  3.000
 CK9  N7    C6   C5    105.17  3.000
 CK9  C10   N7   C6    126.56  3.000
 CK9  C10   N7   C8    127.16  3.000
 CK9  C6    N7   C8    106.27  3.000
 CK9  H10   C10  C11   108.79  3.000
 CK9  H10   C10  C12   108.82  3.000
 CK9  C11   C10  C12   112.36  3.000
 CK9  H10   C10  N7    105.18  3.000
 CK9  C11   C10  N7    110.67  3.000
 CK9  C12   C10  N7    110.73  3.000
 CK9  H123  C12  H122  108.44  3.000
 CK9  H123  C12  H121  107.56  3.000
 CK9  H122  C12  H121  108.01  3.000
 CK9  H123  C12  C10   111.68  3.000
 CK9  H122  C12  C10   111.28  3.000
 CK9  H121  C12  C10   109.73  3.000
 CK9  H113  C11  H112  107.82  3.000
 CK9  H113  C11  H111  108.31  3.000
 CK9  H112  C11  H111  108.01  3.000
 CK9  H113  C11  C10   111.36  3.000
 CK9  H112  C11  C10   109.97  3.000
 CK9  H111  C11  C10   111.25  3.000
 CK9  C2    N3   C6    111.94  3.000
 CK9  N13   C2   N1    116.71  3.000
 CK9  N13   C2   N3    116.17  3.000
 CK9  N1    C2   N3    127.11  3.000
 CK9  C2    N1   C4    119.77  3.000
 CK9  H13   N13  C14   116.93  3.000
 CK9  H13   N13  C2    114.88  3.000
 CK9  C14   N13  C2    124.14  3.000
 CK9  H14   C14  C15   106.10  3.000
 CK9  H14   C14  C25   108.31  3.000
 CK9  C15   C14  C25   112.50  3.000
 CK9  H14   C14  N13   107.77  3.000
 CK9  C15   C14  N13   112.46  3.000
 CK9  C25   C14  N13   109.46  3.000
 CK9  H252  C25  H251  106.07  3.000
 CK9  H252  C25  C26   109.45  3.000
 CK9  H251  C25  C26   109.84  3.000
 CK9  H252  C25  C14   107.82  3.000
 CK9  H251  C25  C14   109.96  3.000
 CK9  C26   C25  C14   113.43  3.000
 CK9  H263  C26  H262  107.69  3.000
 CK9  H263  C26  H261  107.62  3.000
 CK9  H262  C26  H261  107.58  3.000
 CK9  H263  C26  C25   111.15  3.000
 CK9  H262  C26  C25   111.78  3.000
 CK9  H261  C26  C25   110.84  3.000
 CK9  H152  C15  H151  107.12  3.000
 CK9  H152  C15  O16   111.73  3.000
 CK9  H151  C15  O16   111.74  3.000
 CK9  H152  C15  C14   108.66  3.000
 CK9  H151  C15  C14   108.12  3.000
 CK9  O16   C15  C14   109.36  3.000
 CK9  H16   O16  C15   108.16  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
 CK9  CONST_01  C21   C22  C23  C24     0.00   0.0  0
 CK9  CONST_02  C21   C20  C19  C24     0.00   0.0  0
 CK9  CONST_03  C20   C19  C24  C23     0.00   0.0  0
 CK9  CONST_04  C20   C21  C22  C23     0.00   0.0  0
 CK9  CONST_05  C19   C24  C23  C22     0.00   0.0  0
 CK9  CONST_06  C19   C20  C21  C22     0.00   0.0  0
 CK9  CONST_07  C8    N9   C5   C4    180.00   0.0  0
 CK9  CONST_08  N7    C6   C5   C4    180.00   0.0  0
 CK9  CONST_09  N3    C6   C5   C4      0.00   0.0  0
 CK9  CONST_10  N3    C2   N1   C4      0.00   0.0  0
 CK9  CONST_11  C2    N1   C4   C5      0.00   0.0  0
 CK9  CONST_12  N7    C8   N9   C5      0.00   0.0  0
 CK9  CONST_13  C8    N7   C6   C5      0.00   0.0  0
 CK9  CONST_14  C2    N3   C6   C5      0.00   0.0  0
 CK9  CONST_15  N1    C4   C5   N9    180.00   0.0  0
 CK9  CONST_16  N7    C6   C5   N9      0.00   0.0  0
 CK9  CONST_17  N3    C6   C5   N9    180.00   0.0  0
 CK9  CONST_18  C6    N7   C8   N9      0.00   0.0  0
 CK9  CONST_19  C6    C5   N9   C8      0.00   0.0  0
 CK9  CONST_20  N3    C6   N7   C8    180.00   0.0  0
 CK9  CONST_21  N1    C4   C5   C6      0.00   0.0  0
 CK9  CONST_22  N1    C2   N3   C6      0.00   0.0  0
 CK9  CONST_23  C2    N3   C6   N7    180.00   0.0  0
 CK9  CONST_24  C22   C23  C24  O27   180.00   0.0  0
 CK9  CONST_25  C20   C19  C24  O27   180.00   0.0  0
 CK9  CONST_26  C18   C19  C24  C23   180.00   0.0  0
 CK9  CONST_27  C18   C19  C20  C21   180.00   0.0  0
 CK9  CONST_28  N9    C5   C4   N17     0.00   0.0  0
 CK9  CONST_29  C6    C5   C4   N17   180.00   0.0  0
 CK9  CONST_30  C2    N1   C4   N17   180.00   0.0  0
 CK9  CONST_31  N13   C2   N1   C4    180.00   0.0  0
 CK9  CONST_32  C10   N7   C6   C5    180.00   0.0  0
 CK9  CONST_33  C10   N7   C8   N9    180.00   0.0  0
 CK9  CONST_34  N13   C2   N3   C6    180.00   0.0  0
 CK9  CONST_35  N3    C6   N7   C10     0.00   0.0  0
 CK9  CONST_36  H22   C22  C23  C24   180.00   0.0  0
 CK9  CONST_37  H20   C20  C19  C24   180.00   0.0  0
 CK9  CONST_38  H21   C21  C22  C23   180.00   0.0  0
 CK9  CONST_39  H23   C23  C22  C21   180.00   0.0  0
 CK9  CONST_40  H8    C8   N9   C5    180.00   0.0  0
 CK9  CONST_41  C5    C4   N17  C18   180.00   0.0  0
 CK9  CONST_42  N1    C4   N17  C18     0.00   0.0  0
 CK9  CONST_43  C14   N13  C2   N3    180.00   0.0  0
 CK9  CONST_44  C14   N13  C2   N1      0.00   0.0  0
 CK9  CONST_45  H17   N17  C4   C5      0.00   0.0  0
 CK9  CONST_46  H13   N13  C2   N3      0.00   0.0  0
 CK9  Var_01    N17   C18  C19  C24    67.16  30.0  2
 CK9  Var_02    C4    N17  C18  C19  -118.48  30.0  3
 CK9  Var_03    C12   C10  N7   C8    -54.01  30.0  2
 CK9  Var_04    H121  C12  C10  N7   -175.14  30.0  3
 CK9  Var_05    H111  C11  C10  N7     57.40  30.0  3
 CK9  Var_06    H261  C26  C25  C14   177.83  30.0  3

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
 CK9  chir_01  C14  N13  C25  C15  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
 CK9  plan-1  O27  0.020
 CK9  plan-1  C24  0.020
 CK9  plan-1  C23  0.020
 CK9  plan-1  C22  0.020
 CK9  plan-1  C21  0.020
 CK9  plan-1  C20  0.020
 CK9  plan-1  C19  0.020
 CK9  plan-1  C18  0.020
 CK9  plan-1  H23  0.020
 CK9  plan-1  H22  0.020
 CK9  plan-1  H21  0.020
 CK9  plan-1  H20  0.020
 CK9  plan-2  N17  0.020
 CK9  plan-2  C4   0.020
 CK9  plan-2  C5   0.020
 CK9  plan-2  N9   0.020
 CK9  plan-2  C8   0.020
 CK9  plan-2  C6   0.020
 CK9  plan-2  N7   0.020
 CK9  plan-2  C10  0.020
 CK9  plan-2  N3   0.020
 CK9  plan-2  C2   0.020
 CK9  plan-2  N1   0.020
 CK9  plan-2  N13  0.020
 CK9  plan-2  H8   0.020
 CK9  plan-3  C18  0.020
 CK9  plan-3  N17  0.020
 CK9  plan-3  C4   0.020
 CK9  plan-3  H17  0.020
 CK9  plan-4  C2   0.020
 CK9  plan-4  N13  0.020
 CK9  plan-4  C14  0.020
 CK9  plan-4  H13  0.020

