# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 15:48:41 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (2S)-2-({6-[(3-amino-5-chlorophenyl)amino]-9-(1-methylethyl)-9H-purin-2-yl}amino)-3-methylbutan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)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
 AP9  AP9  (2S)-2-({6-[(3-amino-5-chlorophenyl)amino]-9-(1-methylethyl)-9H-purin-2-yl}amino)-3-methylbutan-1-ol  ligand  54  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AP9
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
 AP9  O1    O   OH1   0  -0.670  -0.1179   3.6926  -2.3495
 AP9  C15   C   CH2   0  -0.166  -0.8395   2.8759  -1.4581
 AP9  C12   C   CH1   0  -0.077  -0.2242   2.9890  -0.0688
 AP9  C13   C   CH1   0  -0.248  -0.1754   4.4232   0.4819
 AP9  C14   C   CH3   0  -0.671  -1.5208   5.1284   0.3449
 AP9  C16   C   CH3   0  -0.647   0.2702   4.4251   1.9418
 AP9  N2    N   NH1   0  -0.662   1.1083   2.4251  -0.0314
 AP9  C2    C   CR6   0   0.606   1.3965   1.1096   0.0445
 AP9  N3    N   N     0  -0.521   2.6852   0.7739  -0.0427
 AP9  C4    C   CR56  0   0.500   2.8742  -0.5337   0.0748
 AP9  C5    C   CR56  0  -0.073   1.8952  -1.5006   0.2633
 AP9  N7    N   N     0  -0.458   2.4496  -2.7535   0.3289
 AP9  C8    C   CR15  0   0.096   3.7251  -2.5430   0.1864
 AP9  N9    N   NR5   0  -0.501   4.0491  -1.2209   0.0324
 AP9  C9    C   CH1   0  -0.133   5.3772  -0.6594  -0.1986
 AP9  C10   C   CH3   0  -0.654   6.3383  -1.0750   0.9047
 AP9  C11   C   CH3   0  -0.646   5.8798  -1.0364  -1.5850
 AP9  C6    C   CR6   0   0.533   0.5749  -1.0267   0.3193
 AP9  N1    N   N     0  -0.548   0.3559   0.2725   0.2127
 AP9  N6    N   NH1   0  -0.778  -0.4420  -1.9120   0.4744
 AP9  C1A   C   CR6   0   0.384  -1.8200  -1.7323   0.4746
 AP9  C2A   C   CR16  0  -0.420  -2.4468  -0.4942   0.3758
 AP9  C3A   C   CR6   0   0.351  -3.8436  -0.4049   0.3694
 AP9  N10   N   NH2   0  -0.862  -4.4471   0.8184   0.2085
 AP9  C4A   C   CR16  0  -0.323  -4.6163  -1.5663   0.4738
 AP9  C5A   C   CR6   0  -0.011  -3.9642  -2.7812   0.5769
 AP9  CL1   CL  CL    0  -0.134  -4.9187  -4.2257   0.7119
 AP9  C6A   C   CR16  0  -0.372  -2.5891  -2.8995   0.5795
 AP9  HO1   H   HOH1  0   0.456  -0.4903   3.5820  -3.2284
 AP9  H151  H   HCH2  0   0.214  -0.8128   1.8220  -1.7628
 AP9  H152  H   HCH2  0   0.196  -1.8985   3.1594  -1.4061
 AP9  H12   H   HCH1  0   0.238  -0.8564   2.3994   0.6027
 AP9  H13   H   HCH1  0   0.227   0.5588   4.9888  -0.1034
 AP9  H141  H   HCH3  0   0.215  -2.3179   4.5652   0.8371
 AP9  H142  H   HCH3  0   0.234  -1.4781   6.1118   0.8151
 AP9  H143  H   HCH3  0   0.237  -1.8069   5.2781  -0.6957
 AP9  H161  H   HCH3  0   0.214  -0.4428   3.8815   2.5667
 AP9  H162  H   HCH3  0   0.230   1.2491   3.9656   2.0784
 AP9  H163  H   HCH3  0   0.227   0.3297   5.4461   2.3220
 AP9  HN2   H   HNH1  0   0.385   1.8828   3.0312  -0.2499
 AP9  H8    H   HCR5  0   0.289   4.4817  -3.3134   0.1872
 AP9  H9    H   HCH1  0   0.267   5.2402   0.4219  -0.1556
 AP9  H101  H   HCH3  0   0.245   7.3022  -0.5896   0.7526
 AP9  H102  H   HCH3  0   0.245   5.9637  -0.7832   1.8854
 AP9  H103  H   HCH3  0   0.230   6.5096  -2.1523   0.9065
 AP9  H111  H   HCH3  0   0.243   5.1724  -0.7280  -2.3549
 AP9  H112  H   HCH3  0   0.242   6.8308  -0.5431  -1.7845
 AP9  H113  H   HCH3  0   0.229   6.0370  -2.1127  -1.6738
 AP9  HN6   H   HNH1  0   0.418  -0.1404  -2.8731   0.5474
 AP9  H2A   H   HCR6  0   0.308  -1.8507   0.4007   0.2968
 AP9  H11   H   HNH2  0   0.375  -3.9104   1.6223   0.4903
 AP9  H12A  H   HNH2  0   0.385  -5.4093   0.8849   0.4981
 AP9  H4A   H   HCR6  0   0.275  -5.6970  -1.5124   0.4758
 AP9  H6A   H   HCR6  0   0.281  -2.1159  -3.8692   0.6594

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
 AP9  O1   C15   single    1.408  0.020  1.408
 AP9  O1   HO1   single    0.850  0.020  0.980
 AP9  C15  C12   single    1.524  0.020  1.524
 AP9  C15  H151  single    0.970  0.020  1.090
 AP9  C15  H152  single    0.970  0.020  1.090
 AP9  C12  C13   single    1.537  0.020  1.537
 AP9  C12  N2    single    1.447  0.020  1.447
 AP9  C12  H12   single    0.970  0.020  1.090
 AP9  C13  C14   single    1.525  0.020  1.525
 AP9  C13  C16   single    1.526  0.020  1.526
 AP9  C13  H13   single    0.970  0.020  1.090
 AP9  C14  H141  single    0.970  0.020  1.090
 AP9  C14  H142  single    0.970  0.020  1.090
 AP9  C14  H143  single    0.970  0.020  1.090
 AP9  C16  H161  single    0.970  0.020  1.090
 AP9  C16  H162  single    0.970  0.020  1.090
 AP9  C16  H163  single    0.970  0.020  1.090
 AP9  N2   C2    single    1.349  0.020  1.349
 AP9  N2   HN2   single    0.860  0.020  1.020
 AP9  C2   N3    aromatic  1.335  0.020  1.335
 AP9  C2   N1    aromatic  1.346  0.020  1.346
 AP9  N3   C4    aromatic  1.326  0.020  1.326
 AP9  C4   C5    aromatic  1.389  0.020  1.389
 AP9  C4   N9    aromatic  1.362  0.020  1.362
 AP9  C5   N7    aromatic  1.372  0.020  1.372
 AP9  C5   C6    aromatic  1.404  0.020  1.404
 AP9  N7   C8    aromatic  1.301  0.020  1.301
 AP9  C8   N9    aromatic  1.370  0.020  1.370
 AP9  C8   H8    single    0.930  0.020  1.080
 AP9  N9   C9    single    1.460  0.020  1.460
 AP9  C9   C10   single    1.521  0.020  1.521
 AP9  C9   C11   single    1.522  0.020  1.522
 AP9  C9   H9    single    0.970  0.020  1.090
 AP9  C10  H101  single    0.970  0.020  1.090
 AP9  C10  H102  single    0.970  0.020  1.090
 AP9  C10  H103  single    0.970  0.020  1.090
 AP9  C11  H111  single    0.970  0.020  1.090
 AP9  C11  H112  single    0.970  0.020  1.090
 AP9  C11  H113  single    0.970  0.020  1.090
 AP9  C6   N1    aromatic  1.322  0.020  1.322
 AP9  C6   N6    single    1.357  0.020  1.357
 AP9  N6   C1A   single    1.390  0.020  1.390
 AP9  N6   HN6   single    0.860  0.020  1.020
 AP9  C1A  C2A   aromatic  1.391  0.020  1.391
 AP9  C1A  C6A   aromatic  1.402  0.020  1.402
 AP9  C2A  C3A   aromatic  1.400  0.020  1.400
 AP9  C2A  H2A   single    0.930  0.020  1.080
 AP9  C3A  N10   single    1.374  0.020  1.374
 AP9  C3A  C4A   aromatic  1.399  0.020  1.399
 AP9  N10  H11   single    0.890  0.020  1.040
 AP9  N10  H12A  single    0.890  0.020  1.040
 AP9  C4A  C5A   aromatic  1.383  0.020  1.383
 AP9  C4A  H4A   single    0.930  0.020  1.080
 AP9  C5A  CL1   single    1.737  0.020  1.737
 AP9  C5A  C6A   aromatic  1.380  0.020  1.380
 AP9  C6A  H6A   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
 AP9  HO1   O1   C15   108.28  3.000
 AP9  H152  C15  H151  106.54  3.000
 AP9  H152  C15  C12   109.11  3.000
 AP9  H151  C15  C12   108.34  3.000
 AP9  H152  C15  O1    112.00  3.000
 AP9  H151  C15  O1    111.65  3.000
 AP9  C12   C15  O1    109.10  3.000
 AP9  H12   C12  N2    107.82  3.000
 AP9  H12   C12  C13   107.52  3.000
 AP9  N2    C12  C13   108.97  3.000
 AP9  H12   C12  C15   106.63  3.000
 AP9  N2    C12  C15   111.49  3.000
 AP9  C13   C12  C15   114.13  3.000
 AP9  H13   C13  C16   108.33  3.000
 AP9  H13   C13  C14   107.72  3.000
 AP9  C16   C13  C14   110.05  3.000
 AP9  H13   C13  C12   108.14  3.000
 AP9  C16   C13  C12   110.68  3.000
 AP9  C14   C13  C12   111.79  3.000
 AP9  H143  C14  H142  107.34  3.000
 AP9  H143  C14  H141  108.02  3.000
 AP9  H142  C14  H141  107.40  3.000
 AP9  H143  C14  C13   112.39  3.000
 AP9  H142  C14  C13   110.09  3.000
 AP9  H141  C14  C13   111.38  3.000
 AP9  H163  C16  H162  107.57  3.000
 AP9  H163  C16  H161  107.56  3.000
 AP9  H162  C16  H161  107.73  3.000
 AP9  H163  C16  C13   110.51  3.000
 AP9  H162  C16  C13   112.43  3.000
 AP9  H161  C16  C13   110.84  3.000
 AP9  HN2   N2   C2    115.76  3.000
 AP9  HN2   N2   C12   117.89  3.000
 AP9  C2    N2   C12   125.32  3.000
 AP9  N1    C2   N3    126.74  3.000
 AP9  N1    C2   N2    116.64  3.000
 AP9  N3    C2   N2    116.62  3.000
 AP9  C4    N3   C2    112.32  3.000
 AP9  N9    C4   C5    105.14  3.000
 AP9  N9    C4   N3    128.14  3.000
 AP9  C5    C4   N3    126.72  3.000
 AP9  C6    C5   N7    133.36  3.000
 AP9  C6    C5   C4    115.68  3.000
 AP9  N7    C5   C4    110.95  3.000
 AP9  C8    N7   C5    104.08  3.000
 AP9  H8    C8   N9    121.53  3.000
 AP9  H8    C8   N7    124.86  3.000
 AP9  N9    C8   N7    113.61  3.000
 AP9  C9    N9   C8    127.16  3.000
 AP9  C9    N9   C4    126.55  3.000
 AP9  C8    N9   C4    106.22  3.000
 AP9  H9    C9   C11   108.83  3.000
 AP9  H9    C9   C10   108.76  3.000
 AP9  C11   C9   C10   112.60  3.000
 AP9  H9    C9   N9    105.11  3.000
 AP9  C11   C9   N9    110.43  3.000
 AP9  C10   C9   N9    110.79  3.000
 AP9  H103  C10  H102  108.47  3.000
 AP9  H103  C10  H101  107.53  3.000
 AP9  H102  C10  H101  108.09  3.000
 AP9  H103  C10  C9    111.73  3.000
 AP9  H102  C10  C9    111.25  3.000
 AP9  H101  C10  C9    109.63  3.000
 AP9  H113  C11  H112  107.81  3.000
 AP9  H113  C11  H111  108.36  3.000
 AP9  H112  C11  H111  108.00  3.000
 AP9  H113  C11  C9    111.46  3.000
 AP9  H112  C11  C9    110.05  3.000
 AP9  H111  C11  C9    111.04  3.000
 AP9  N6    C6   N1    121.75  3.000
 AP9  N6    C6   C5    119.27  3.000
 AP9  N1    C6   C5    118.98  3.000
 AP9  C6    N1   C2    119.55  3.000
 AP9  HN6   N6   C1A   114.78  3.000
 AP9  HN6   N6   C6    113.91  3.000
 AP9  C1A   N6   C6    131.19  3.000
 AP9  C6A   C1A  C2A   119.94  3.000
 AP9  C6A   C1A  N6    115.87  3.000
 AP9  C2A   C1A  N6    124.18  3.000
 AP9  H2A   C2A  C3A   119.90  3.000
 AP9  H2A   C2A  C1A   119.65  3.000
 AP9  C3A   C2A  C1A   120.45  3.000
 AP9  C4A   C3A  N10   120.36  3.000
 AP9  C4A   C3A  C2A   119.87  3.000
 AP9  N10   C3A  C2A   119.73  3.000
 AP9  H12A  N10  H11   112.10  3.000
 AP9  H12A  N10  C3A   116.42  3.000
 AP9  H11   N10  C3A   116.37  3.000
 AP9  H4A   C4A  C5A   120.97  3.000
 AP9  H4A   C4A  C3A   120.70  3.000
 AP9  C5A   C4A  C3A   118.33  3.000
 AP9  C6A   C5A  CL1   118.44  3.000
 AP9  C6A   C5A  C4A   123.04  3.000
 AP9  CL1   C5A  C4A   118.52  3.000
 AP9  H6A   C6A  C5A   120.84  3.000
 AP9  H6A   C6A  C1A   120.79  3.000
 AP9  C5A   C6A  C1A   118.37  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
 AP9  CONST_01  C5    C4   N3   C2      0.00   0.0  0
 AP9  CONST_02  N9    C4   N3   C2    180.00   0.0  0
 AP9  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 AP9  CONST_04  C6    N1   C2   N3      0.00   0.0  0
 AP9  CONST_05  N7    C5   C4   N3    180.00   0.0  0
 AP9  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 AP9  CONST_07  C8    N9   C4   N3    180.00   0.0  0
 AP9  CONST_08  N1    C2   N3   C4      0.00   0.0  0
 AP9  CONST_09  C8    N7   C5   C4      0.00   0.0  0
 AP9  CONST_10  N1    C6   C5   C4      0.00   0.0  0
 AP9  CONST_11  N7    C8   N9   C4      0.00   0.0  0
 AP9  CONST_12  C8    N9   C4   C5      0.00   0.0  0
 AP9  CONST_13  N9    C8   N7   C5      0.00   0.0  0
 AP9  CONST_14  N9    C4   C5   N7      0.00   0.0  0
 AP9  CONST_15  N1    C6   C5   N7    180.00   0.0  0
 AP9  CONST_16  C6    C5   N7   C8    180.00   0.0  0
 AP9  CONST_17  C6    C5   C4   N9    180.00   0.0  0
 AP9  CONST_18  C4A   C3A  C2A  C1A     0.00   0.0  0
 AP9  CONST_19  C4A   C5A  C6A  C1A     0.00   0.0  0
 AP9  CONST_20  C5A   C6A  C1A  C2A     0.00   0.0  0
 AP9  CONST_21  C5A   C4A  C3A  C2A     0.00   0.0  0
 AP9  CONST_22  C6A   C1A  C2A  C3A     0.00   0.0  0
 AP9  CONST_23  C6A   C5A  C4A  C3A     0.00   0.0  0
 AP9  CONST_24  C4    N3   C2   N2    180.00   0.0  0
 AP9  CONST_25  C6    N1   C2   N2    180.00   0.0  0
 AP9  CONST_26  N6    C6   N1   C2    180.00   0.0  0
 AP9  CONST_27  C9    N9   C4   N3      0.00   0.0  0
 AP9  CONST_28  N6    C6   C5   C4    180.00   0.0  0
 AP9  CONST_29  C9    N9   C4   C5    180.00   0.0  0
 AP9  CONST_30  N6    C6   C5   N7      0.00   0.0  0
 AP9  CONST_31  C9    N9   C8   N7    180.00   0.0  0
 AP9  CONST_32  C3A   C2A  C1A  N6    180.00   0.0  0
 AP9  CONST_33  C5A   C6A  C1A  N6    180.00   0.0  0
 AP9  CONST_34  N10   C3A  C2A  C1A   180.00   0.0  0
 AP9  CONST_35  CL1   C5A  C6A  C1A   180.00   0.0  0
 AP9  CONST_36  CL1   C5A  C4A  C3A   180.00   0.0  0
 AP9  CONST_37  C5A   C4A  C3A  N10   180.00   0.0  0
 AP9  CONST_38  H8    C8   N9   C4    180.00   0.0  0
 AP9  CONST_39  H6A   C6A  C1A  C2A   180.00   0.0  0
 AP9  CONST_40  H4A   C4A  C3A  C2A   180.00   0.0  0
 AP9  CONST_41  H2A   C2A  C3A  C4A   180.00   0.0  0
 AP9  CONST_42  N3    C2   N2   C12   180.00   0.0  0
 AP9  CONST_43  N1    C2   N2   C12     0.00   0.0  0
 AP9  CONST_44  HN2   N2   C2   N3      0.00   0.0  0
 AP9  Var_01    C1A   N6   C6   C5   -175.29  30.0  2
 AP9  Var_02    C2A   C1A  N6   C6     -3.80  30.0  2
 AP9  Var_03    C10   C9   N9   C4    126.73  30.0  2
 AP9  Var_04    H101  C10  C9   N9   -176.01  30.0  3
 AP9  Var_05    H111  C11  C9   N9     55.53  30.0  3
 AP9  Var_06    H141  C14  C13  C12    56.45  30.0  3
 AP9  Var_07    H161  C16  C13  C12   -62.37  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
 AP9  chir_01  C12  C15  C13  N2  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
 AP9  plan-1  N6    0.020
 AP9  plan-1  C1A   0.020
 AP9  plan-1  C2A   0.020
 AP9  plan-1  C3A   0.020
 AP9  plan-1  N10   0.020
 AP9  plan-1  C4A   0.020
 AP9  plan-1  C5A   0.020
 AP9  plan-1  CL1   0.020
 AP9  plan-1  C6A   0.020
 AP9  plan-1  H2A   0.020
 AP9  plan-1  H4A   0.020
 AP9  plan-1  H6A   0.020
 AP9  plan-2  N2    0.020
 AP9  plan-2  C2    0.020
 AP9  plan-2  N3    0.020
 AP9  plan-2  C4    0.020
 AP9  plan-2  C5    0.020
 AP9  plan-2  N7    0.020
 AP9  plan-2  C8    0.020
 AP9  plan-2  N9    0.020
 AP9  plan-2  C9    0.020
 AP9  plan-2  C6    0.020
 AP9  plan-2  N1    0.020
 AP9  plan-2  N6    0.020
 AP9  plan-2  H8    0.020
 AP9  plan-3  C12   0.020
 AP9  plan-3  N2    0.020
 AP9  plan-3  C2    0.020
 AP9  plan-3  HN2   0.020
 AP9  plan-4  C3A   0.020
 AP9  plan-4  N10   0.020
 AP9  plan-4  H11   0.020
 AP9  plan-4  H12A  0.020

