# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 17:13:59 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 1-[(trans-4-aminocyclohexyl)methyl]-N-butyl-3-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCNc1ncc2c(n1)n(C[C@@H]3CC[C@@H](N)CC3)nc2c4ccc(F)cc4
#
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
 CKJ  CKJ  1-[(trans-4-aminocyclohexyl)methyl]-N-butyl-3-(4-fluorophenyl)-1H-pyrazolo[3,4-d]pyrimidin-6-amine  ligand  58  29  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CKJ
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
 CKJ  C     C  CR16  0  -0.269   3.8311  -1.9258   0.0081
 CKJ  F     F  F     0  -0.312   5.4018  -5.1370  -0.4374
 CKJ  N     N  N     0  -0.276   1.8056  -0.1168   1.0030
 CKJ  C01   C  CH1   0  -0.254   0.6660   3.0221   0.5277
 CKJ  C02   C  CH2   0  -0.233  -4.8608  -1.1871  -0.2318
 CKJ  N02   N  NR5   0  -0.384   0.6731   0.6045   1.1272
 CKJ  C03   C  CH2   0  -0.462  -6.1777  -0.4343  -0.3336
 CKJ  C04   C  CH2   0  -0.423  -7.3350  -1.3505  -0.7092
 CKJ  C05   C  CH3   0  -0.661  -8.6561  -0.6031  -0.8253
 CKJ  C06   C  CR6   0   0.048   2.5093  -2.3020   0.2563
 CKJ  C07   C  CR16  0  -0.312   2.1924  -3.6599   0.2683
 CKJ  C08   C  CR16  0  -0.395   3.1617  -4.6234   0.0339
 CKJ  C09   C  CR6   0   0.520   4.4571  -4.2120  -0.2089
 CKJ  C10   C  CR16  0  -0.399   4.8112  -2.8755  -0.2243
 CKJ  C23   C  CR16  0  -0.063  -0.9010  -2.2042  -0.2071
 CKJ  N24   N  N     0  -0.474  -2.1637  -1.8446  -0.2464
 CKJ  C25   C  CR6   0   0.600  -2.4984  -0.6119   0.2105
 CKJ  N26   N  N     0  -0.505  -1.6576   0.3065   0.6879
 CKJ  C27   C  CR56  0  -0.227   0.0772  -1.3502   0.2965
 CKJ  C28   C  CR56  0   0.611  -0.3976  -0.0951   0.7118
 CKJ  C31   C  CR5   0   0.246   1.4865  -1.2887   0.5123
 CKJ  C32   C  CH2   0  -0.286   0.6975   1.9610   1.6229
 CKJ  C33   C  CH2   0  -0.430   0.6399   4.4064   1.1750
 CKJ  C35   C  CH2   0  -0.424   1.8415   2.9065  -0.4404
 CKJ  C36   C  CH2   0  -0.432   1.8281   4.0300  -1.4712
 CKJ  C37   C  CH1   0  -0.052   1.8294   5.4020  -0.8078
 CKJ  C38   C  CH2   0  -0.433   0.6362   5.5177   0.1332
 CKJ  N39   N  NH2   0  -0.807   1.7702   6.4460  -1.8212
 CKJ  H     H  HCR6  0   0.265   4.0953  -0.8770  -0.0162
 CKJ  H01   H  HCH1  0   0.228  -0.2638   2.8979  -0.0419
 CKJ  HN01  H  HNH1  0   0.393  -4.0523   0.5970   0.5726
 CKJ  H02   H  HCH2  0   0.231  -4.6177  -1.6406  -1.1946
 CKJ  H02A  H  HCH2  0   0.223  -4.9569  -2.0075   0.4880
 CKJ  H03   H  HCH2  0   0.225  -6.3968   0.0514   0.6234
 CKJ  H03A  H  HCH2  0   0.228  -6.0825   0.3641  -1.0764
 CKJ  H04   H  HCH2  0   0.218  -7.1111  -1.8475  -1.6576
 CKJ  H04A  H  HCH2  0   0.218  -7.4267  -2.1447   0.0375
 CKJ  H05   H  HCH3  0   0.229  -9.4686  -1.2740  -1.1059
 CKJ  H05A  H  HCH3  0   0.218  -8.9282  -0.1320   0.1210
 CKJ  H05B  H  HCH3  0   0.218  -8.5986   0.1825  -1.5805
 CKJ  H07   H  HCR6  0   0.262   1.1848  -3.9864   0.4887
 CKJ  H08   H  HCR6  0   0.284   2.9120  -5.6759   0.0514
 CKJ  H10   H  HCR6  0   0.283   5.8330  -2.5804  -0.4228
 CKJ  H23   H  HCR6  0   0.267  -0.6661  -3.1908  -0.5927
 CKJ  H32   H  HCH2  0   0.260   1.5993   2.0612   2.2283
 CKJ  H32A  H  HCH2  0   0.263  -0.1573   2.0897   2.2896
 CKJ  H33   H  HCH2  0   0.234  -0.2349   4.4985   1.8248
 CKJ  H33A  H  HCH2  0   0.214   1.5175   4.5147   1.8234
 CKJ  H35   H  HCH2  0   0.211   2.7796   2.9388   0.1267
 CKJ  H35A  H  HCH2  0   0.236   1.8251   1.9409  -0.9511
 CKJ  H36   H  HCH2  0   0.228   2.6925   3.9346  -2.1357
 CKJ  H36A  H  HCH2  0   0.210   0.9363   3.9470  -2.1024
 CKJ  H37   H  HCH1  0   0.184   2.7424   5.4682  -0.1912
 CKJ  H38   H  HCH2  0   0.211  -0.2851   5.4702  -0.4581
 CKJ  H38A  H  HCH2  0   0.228   0.6420   6.4931   0.6294
 CKJ  HN39  H  HNH2  0   0.339   1.8222   7.3529  -1.3724
 CKJ  HN3A  H  HNH2  0   0.339   2.5937   6.3886  -2.4087
 CKJ  N01   N  NH1   0  -0.662  -3.7986  -0.2861   0.1597

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
 CKJ  C10  C     aromatic  1.384  0.020  1.384
 CKJ  C    C06   aromatic  1.396  0.020  1.396
 CKJ  C    H     single    0.930  0.020  1.080
 CKJ  F    C09   single    1.342  0.020  1.342
 CKJ  C31  N     aromatic  1.310  0.020  1.310
 CKJ  N    N02   aromatic  1.348  0.020  1.348
 CKJ  C32  C01   single    1.525  0.020  1.525
 CKJ  C01  C33   single    1.528  0.020  1.528
 CKJ  C01  C35   single    1.527  0.020  1.527
 CKJ  C01  H01   single    0.970  0.020  1.090
 CKJ  C25  N01   single    1.341  0.020  1.341
 CKJ  N01  C02   single    1.447  0.020  1.447
 CKJ  N01  HN01  single    0.860  0.020  1.020
 CKJ  C02  C03   single    1.520  0.020  1.520
 CKJ  C02  H02   single    0.970  0.020  1.090
 CKJ  C02  H02A  single    0.970  0.020  1.090
 CKJ  N02  C28   aromatic  1.345  0.020  1.345
 CKJ  N02  C32   single    1.444  0.020  1.444
 CKJ  C03  C04   single    1.523  0.020  1.523
 CKJ  C03  H03   single    0.970  0.020  1.090
 CKJ  C03  H03A  single    0.970  0.020  1.090
 CKJ  C05  C04   single    1.522  0.020  1.522
 CKJ  C04  H04   single    0.970  0.020  1.090
 CKJ  C04  H04A  single    0.970  0.020  1.090
 CKJ  C05  H05   single    0.970  0.020  1.090
 CKJ  C05  H05A  single    0.970  0.020  1.090
 CKJ  C05  H05B  single    0.970  0.020  1.090
 CKJ  C07  C06   aromatic  1.394  0.020  1.394
 CKJ  C06  C31   single    1.462  0.020  1.462
 CKJ  C08  C07   aromatic  1.387  0.020  1.387
 CKJ  C07  H07   single    0.930  0.020  1.080
 CKJ  C09  C08   aromatic  1.381  0.020  1.381
 CKJ  C08  H08   single    0.930  0.020  1.080
 CKJ  C09  C10   aromatic  1.383  0.020  1.383
 CKJ  C10  H10   single    0.930  0.020  1.080
 CKJ  C27  C23   aromatic  1.393  0.020  1.393
 CKJ  C23  N24   aromatic  1.313  0.020  1.313
 CKJ  C23  H23   single    0.930  0.020  1.080
 CKJ  N24  C25   aromatic  1.357  0.020  1.357
 CKJ  N26  C25   aromatic  1.334  0.020  1.334
 CKJ  C28  N26   aromatic  1.323  0.020  1.323
 CKJ  C31  C27   aromatic  1.427  0.020  1.427
 CKJ  C27  C28   aromatic  1.405  0.020  1.405
 CKJ  C32  H32   single    0.970  0.020  1.090
 CKJ  C32  H32A  single    0.970  0.020  1.090
 CKJ  C33  C38   single    1.523  0.020  1.523
 CKJ  C33  H33   single    0.970  0.020  1.090
 CKJ  C33  H33A  single    0.970  0.020  1.090
 CKJ  C35  C36   single    1.525  0.020  1.525
 CKJ  C35  H35   single    0.970  0.020  1.090
 CKJ  C35  H35A  single    0.970  0.020  1.090
 CKJ  C36  C37   single    1.524  0.020  1.524
 CKJ  C36  H36   single    0.970  0.020  1.090
 CKJ  C36  H36A  single    0.970  0.020  1.090
 CKJ  C38  C37   single    1.524  0.020  1.524
 CKJ  C37  N39   single    1.456  0.020  1.456
 CKJ  C37  H37   single    0.970  0.020  1.090
 CKJ  C38  H38   single    0.970  0.020  1.090
 CKJ  C38  H38A  single    0.970  0.020  1.090
 CKJ  N39  HN39  single    0.890  0.020  1.040
 CKJ  N39  HN3A  single    0.890  0.020  1.040

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
 CKJ  H     C    C10   119.24  3.000
 CKJ  H     C    C06   119.75  3.000
 CKJ  C10   C    C06   121.01  3.000
 CKJ  C31   N    N02   107.96  3.000
 CKJ  H01   C01  C35   108.33  3.000
 CKJ  H01   C01  C33   107.93  3.000
 CKJ  C35   C01  C33   110.49  3.000
 CKJ  H01   C01  C32   108.15  3.000
 CKJ  C35   C01  C32   112.74  3.000
 CKJ  C33   C01  C32   109.05  3.000
 CKJ  H02A  C02  H02   106.73  3.000
 CKJ  H02A  C02  C03   109.80  3.000
 CKJ  H02   C02  C03   109.85  3.000
 CKJ  H02A  C02  N01   110.66  3.000
 CKJ  H02   C02  N01   109.51  3.000
 CKJ  C03   C02  N01   110.23  3.000
 CKJ  C32   N02  C28   127.45  3.000
 CKJ  C32   N02  N     121.32  3.000
 CKJ  C28   N02  N     111.22  3.000
 CKJ  H03A  C03  H03   106.67  3.000
 CKJ  H03A  C03  C04   109.72  3.000
 CKJ  H03   C03  C04   109.28  3.000
 CKJ  H03A  C03  C02   109.35  3.000
 CKJ  H03   C03  C02   109.53  3.000
 CKJ  C04   C03  C02   112.14  3.000
 CKJ  H04A  C04  H04   106.21  3.000
 CKJ  H04A  C04  C05   109.62  3.000
 CKJ  H04   C04  C05   109.55  3.000
 CKJ  H04A  C04  C03   109.39  3.000
 CKJ  H04   C04  C03   109.36  3.000
 CKJ  C05   C04  C03   112.51  3.000
 CKJ  H05B  C05  H05A  107.60  3.000
 CKJ  H05B  C05  H05   107.71  3.000
 CKJ  H05A  C05  H05   107.63  3.000
 CKJ  H05B  C05  C04   111.13  3.000
 CKJ  H05A  C05  C04   111.23  3.000
 CKJ  H05   C05  C04   111.35  3.000
 CKJ  C31   C06  C07   120.95  3.000
 CKJ  C31   C06  C     120.43  3.000
 CKJ  C07   C06  C     118.61  3.000
 CKJ  H07   C07  C08   118.41  3.000
 CKJ  H07   C07  C06   120.48  3.000
 CKJ  C08   C07  C06   121.08  3.000
 CKJ  H08   C08  C09   120.62  3.000
 CKJ  H08   C08  C07   120.79  3.000
 CKJ  C09   C08  C07   118.59  3.000
 CKJ  C10   C09  C08   122.02  3.000
 CKJ  C10   C09  F     118.96  3.000
 CKJ  C08   C09  F     119.02  3.000
 CKJ  H10   C10  C09   120.50  3.000
 CKJ  H10   C10  C     120.82  3.000
 CKJ  C09   C10  C     118.68  3.000
 CKJ  H23   C23  C27   122.27  3.000
 CKJ  H23   C23  N24   116.52  3.000
 CKJ  C27   C23  N24   121.21  3.000
 CKJ  C25   N24  C23   118.42  3.000
 CKJ  N26   C25  N24   126.21  3.000
 CKJ  N26   C25  N01   117.22  3.000
 CKJ  N24   C25  N01   116.56  3.000
 CKJ  C28   N26  C25   113.45  3.000
 CKJ  C31   C27  C28   104.51  3.000
 CKJ  C28   C27  C23   114.67  3.000
 CKJ  C31   C27  C23   140.78  3.000
 CKJ  C27   C28  N26   126.01  3.000
 CKJ  C27   C28  N02   106.68  3.000
 CKJ  N26   C28  N02   127.30  3.000
 CKJ  C27   C31  C06   129.37  3.000
 CKJ  C27   C31  N     109.62  3.000
 CKJ  C06   C31  N     121.00  3.000
 CKJ  H32A  C32  H32   107.31  3.000
 CKJ  H32A  C32  N02   107.88  3.000
 CKJ  H32   C32  N02   106.90  3.000
 CKJ  H32A  C32  C01   109.90  3.000
 CKJ  H32   C32  C01   110.59  3.000
 CKJ  N02   C32  C01   113.99  3.000
 CKJ  H33A  C33  H33   106.29  3.000
 CKJ  H33A  C33  C38   109.53  3.000
 CKJ  H33   C33  C38   110.06  3.000
 CKJ  H33A  C33  C01   109.04  3.000
 CKJ  H33   C33  C01   109.97  3.000
 CKJ  C38   C33  C01   111.79  3.000
 CKJ  H35A  C35  H35   106.30  3.000
 CKJ  H35A  C35  C36   109.58  3.000
 CKJ  H35   C35  C36   109.60  3.000
 CKJ  H35A  C35  C01   110.59  3.000
 CKJ  H35   C35  C01   109.17  3.000
 CKJ  C36   C35  C01   111.47  3.000
 CKJ  H36A  C36  H36   106.64  3.000
 CKJ  H36A  C36  C37   108.64  3.000
 CKJ  H36   C36  C37   110.00  3.000
 CKJ  H36A  C36  C35   109.93  3.000
 CKJ  H36   C36  C35   109.84  3.000
 CKJ  C37   C36  C35   111.66  3.000
 CKJ  H37   C37  N39   112.30  3.000
 CKJ  H37   C37  C38   107.35  3.000
 CKJ  N39   C37  C38   110.09  3.000
 CKJ  H37   C37  C36   107.33  3.000
 CKJ  N39   C37  C36   110.03  3.000
 CKJ  C38   C37  C36   109.66  3.000
 CKJ  H38A  C38  H38   106.72  3.000
 CKJ  H38A  C38  C37   110.09  3.000
 CKJ  H38   C38  C37   108.77  3.000
 CKJ  H38A  C38  C33   109.89  3.000
 CKJ  H38   C38  C33   109.84  3.000
 CKJ  C37   C38  C33   111.41  3.000
 CKJ  HN3A  N39  HN39  105.42  3.000
 CKJ  HN3A  N39  C37   109.26  3.000
 CKJ  HN39  N39  C37   109.35  3.000
 CKJ  HN01  N01  C25   116.20  3.000
 CKJ  HN01  N01  C02   118.17  3.000
 CKJ  C25   N01  C02   124.79  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
 CKJ  CONST_01  C08   C09  C10  C       0.00   0.0  0
 CKJ  CONST_02  C08   C07  C06  C       0.00   0.0  0
 CKJ  CONST_06  C23   C27  C31  N     180.00   0.0  0
 CKJ  CONST_07  C28   C27  C31  N       0.00   0.0  0
 CKJ  CONST_08  N26   C28  N02  N     180.00   0.0  0
 CKJ  CONST_09  C27   C28  N02  N       0.00   0.0  0
 CKJ  CONST_10  C06   C31  N    N02   180.00   0.0  0
 CKJ  CONST_11  C27   C31  N    N02     0.00   0.0  0
 CKJ  CONST_12  C25   N26  C28  N02   180.00   0.0  0
 CKJ  CONST_13  C23   C27  C28  N02   180.00   0.0  0
 CKJ  CONST_14  C31   C27  C28  N02     0.00   0.0  0
 CKJ  CONST_15  C09   C10  C    C06     0.00   0.0  0
 CKJ  CONST_16  C09   C08  C07  C06     0.00   0.0  0
 CKJ  CONST_17  C23   C27  C31  C06     0.00   0.0  0
 CKJ  CONST_18  C28   C27  C31  C06   180.00   0.0  0
 CKJ  CONST_19  C10   C    C06  C07     0.00   0.0  0
 CKJ  CONST_21  C10   C09  C08  C07     0.00   0.0  0
 CKJ  CONST_22  C31   C06  C07  C08   180.00   0.0  0
 CKJ  CONST_23  C31   C06  C    C10   180.00   0.0  0
 CKJ  CONST_24  N26   C28  C27  C23     0.00   0.0  0
 CKJ  CONST_25  N26   C25  N24  C23     0.00   0.0  0
 CKJ  CONST_26  C31   C27  C23  N24   180.00   0.0  0
 CKJ  CONST_27  C28   C27  C23  N24     0.00   0.0  0
 CKJ  CONST_28  C28   N26  C25  N24     0.00   0.0  0
 CKJ  CONST_29  C27   C23  N24  C25     0.00   0.0  0
 CKJ  CONST_30  C27   C28  N26  C25     0.00   0.0  0
 CKJ  CONST_31  C31   C27  C28  N26   180.00   0.0  0
 CKJ  CONST_32  C31   N    N02  C28     0.00   0.0  0
 CKJ  CONST_33  F     C09  C10  C     180.00   0.0  0
 CKJ  CONST_34  C07   C08  C09  F     180.00   0.0  0
 CKJ  CONST_35  C23   N24  C25  N01   180.00   0.0  0
 CKJ  CONST_36  C28   N26  C25  N01   180.00   0.0  0
 CKJ  CONST_37  C32   N02  C28  N26     0.00   0.0  0
 CKJ  CONST_38  C32   N02  C28  C27   180.00   0.0  0
 CKJ  CONST_39  C32   N02  N    C31   180.00   0.0  0
 CKJ  CONST_40  H07   C07  C06  C     180.00   0.0  0
 CKJ  CONST_41  H10   C10  C    C06   180.00   0.0  0
 CKJ  CONST_42  H08   C08  C07  C06   180.00   0.0  0
 CKJ  CONST_43  H     C    C06  C07   180.00   0.0  0
 CKJ  CONST_44  H23   C23  N24  C25   180.00   0.0  0
 CKJ  CONST_45  N24   C25  N01  C02     0.00   0.0  0
 CKJ  CONST_46  N26   C25  N01  C02   180.00   0.0  0
 CKJ  CONST_47  HN01  N01  C25  N24   180.00   0.0  0
 CKJ  Var_01    C37   C38  C33  C01   -56.34  30.0  1
 CKJ  Var_02    C37   C36  C35  C01    56.41  30.0  1
 CKJ  Var_03    C01   C32  N02  N      98.25  30.0  2
 CKJ  Var_04    C25   N01  C02  C03  -173.21  30.0  1
 CKJ  Var_05    C04   C03  C02  N01  -178.53  30.0  3
 CKJ  Var_06    C05   C04  C03  C02  -179.51  30.0  3
 CKJ  Var_07    H05   C05  C04  C03   179.34  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
 CKJ  chir_01  C01  C32  C33  C35  negativ
 CKJ  chir_02  C37  N39  C36  C38  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
 CKJ  plan-1  C     0.020
 CKJ  plan-1  F     0.020
 CKJ  plan-1  C06   0.020
 CKJ  plan-1  C07   0.020
 CKJ  plan-1  C08   0.020
 CKJ  plan-1  C09   0.020
 CKJ  plan-1  C10   0.020
 CKJ  plan-1  C31   0.020
 CKJ  plan-1  H     0.020
 CKJ  plan-1  H07   0.020
 CKJ  plan-1  H08   0.020
 CKJ  plan-1  H10   0.020
 CKJ  plan-2  N     0.020
 CKJ  plan-2  N02   0.020
 CKJ  plan-2  C06   0.020
 CKJ  plan-2  C23   0.020
 CKJ  plan-2  N24   0.020
 CKJ  plan-2  C25   0.020
 CKJ  plan-2  N26   0.020
 CKJ  plan-2  C27   0.020
 CKJ  plan-2  C28   0.020
 CKJ  plan-2  C31   0.020
 CKJ  plan-2  C32   0.020
 CKJ  plan-2  H23   0.020
 CKJ  plan-2  N01   0.020
 CKJ  plan-3  C02   0.020
 CKJ  plan-3  C25   0.020
 CKJ  plan-3  HN01  0.020
 CKJ  plan-3  N01   0.020

