# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 19:04:26 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 1-tert-butyl-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)n1nc(c2cccc3ccccc23)c4c(N)ncnc14
#
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
 0J9  0J9  1-tert-butyl-3-(naphthalen-1-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  43  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0J9
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
 0J9  N1   N  N     0  -0.479  -2.1852  -3.0191   0.9709
 0J9  C2   C  CR16  0   0.048  -3.2815  -2.2636   0.9091
 0J9  N3   N  N     0  -0.467  -3.3976  -1.0110   0.5237
 0J9  C4   C  CR56  0   0.584  -2.2292  -0.4839   0.1352
 0J9  C5   C  CR56  0  -0.262  -1.0051  -1.1560   0.1207
 0J9  C6   C  CR6   0   0.437  -1.0202  -2.4887   0.5944
 0J9  CAA  C  CH3   0  -0.646  -3.5145   2.2054   0.9614
 0J9  CAB  C  CH3   0  -0.651  -4.0642   1.4776  -1.3889
 0J9  CAC  C  CH3   0  -0.649  -2.2332   3.1142  -0.9721
 0J9  NAD  N  NH2   0  -0.817   0.0742  -3.2446   0.6843
 0J9  CAE  C  CR16  0  -0.258   4.3268   2.0127   1.2916
 0J9  CAF  C  CR16  0  -0.251   2.9638   2.2298   1.5776
 0J9  CAI  C  CR16  0  -0.340   1.7779  -1.3614  -1.4494
 0J9  CAJ  C  CR16  0  -0.310   4.6912   1.0305   0.4134
 0J9  CAK  C  CR16  0  -0.320   4.0905  -0.8043  -1.1128
 0J9  CAL  C  CR16  0  -0.331   1.9954   1.4732   0.9753
 0J9  NAO  N  N     0  -0.263  -0.6904   0.9371  -0.5861
 0J9  CAQ  C  CR6   0   0.012   1.3671  -0.3685  -0.5914
 0J9  CAR  C  CR5   0   0.250  -0.0740  -0.1964  -0.3502
 0J9  CAS  C  CR66  0   0.112   3.7145   0.2263  -0.2203
 0J9  CAT  C  CR66  0   0.106   2.3380   0.4541   0.0536
 0J9  NAW  N  NR5   0  -0.376  -1.9890   0.7725  -0.2988
 0J9  CAX  C  CT    0   0.060  -2.9510   1.8871  -0.4241
 0J9  CAG  C  CR16  0  -0.241   3.1426  -1.5845  -1.7120
 0J9  H1   H  HCR6  0   0.253  -4.1972  -2.7517   1.2265
 0J9  H2   H  HCH3  0   0.235  -2.7148   2.4928   1.6456
 0J9  H3   H  HCH3  0   0.235  -4.2129   3.0392   0.8892
 0J9  H4   H  HCH3  0   0.246  -4.0469   1.3563   1.3866
 0J9  H5   H  HCH3  0   0.235  -4.7819   2.2930  -1.4874
 0J9  H6   H  HCH3  0   0.236  -3.6602   1.2641  -2.3796
 0J9  H7   H  HCH3  0   0.248  -4.6014   0.5989  -1.0367
 0J9  H8   H  HCH3  0   0.240  -1.4273   3.4473  -0.3194
 0J9  H9   H  HCH3  0   0.238  -1.8194   2.9395  -1.9647
 0J9  H10  H  HCH3  0   0.238  -2.9596   3.9235  -1.0491
 0J9  H11  H  HNH2  0   0.406   0.0111  -4.1613   1.0944
 0J9  H12  H  HNH2  0   0.414   0.9905  -2.8746   0.5022
 0J9  H13  H  HCR6  0   0.260   5.0801   2.6234   1.7715
 0J9  H14  H  HCR6  0   0.260   2.6824   3.0029   2.2807
 0J9  H15  H  HCR6  0   0.269   1.0395  -1.9738  -1.9532
 0J9  H16  H  HCR6  0   0.258   5.7365   0.8518   0.1919
 0J9  H17  H  HCR6  0   0.260   5.1425  -0.9673  -1.3125
 0J9  H18  H  HCR6  0   0.254   0.9556   1.6613   1.2024
 0J9  H19  H  HCR6  0   0.264   3.4309  -2.3726  -2.3948

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
 0J9  N1   C2   aromatic  1.333  0.020  1.333
 0J9  N1   C6   aromatic  1.334  0.020  1.334
 0J9  NAD  C6   single    1.333  0.020  1.333
 0J9  C2   N3   aromatic  1.316  0.020  1.316
 0J9  C6   C5   aromatic  1.415  0.020  1.415
 0J9  N3   C4   aromatic  1.339  0.020  1.339
 0J9  C5   C4   aromatic  1.397  0.020  1.397
 0J9  C5   CAR  aromatic  1.418  0.020  1.418
 0J9  C4   NAW  aromatic  1.351  0.020  1.351
 0J9  CAI  CAG  aromatic  1.408  0.020  1.408
 0J9  CAI  CAQ  aromatic  1.375  0.020  1.375
 0J9  CAG  CAK  aromatic  1.366  0.020  1.366
 0J9  CAA  CAX  single    1.529  0.020  1.529
 0J9  CAR  CAQ  single    1.471  0.020  1.471
 0J9  CAR  NAO  aromatic  1.312  0.020  1.312
 0J9  CAK  CAS  aromatic  1.414  0.020  1.414
 0J9  CAQ  CAT  aromatic  1.427  0.020  1.427
 0J9  CAT  CAS  aromatic  1.422  0.020  1.422
 0J9  CAT  CAL  aromatic  1.416  0.020  1.416
 0J9  CAS  CAJ  aromatic  1.415  0.020  1.415
 0J9  CAL  CAF  aromatic  1.369  0.020  1.369
 0J9  CAJ  CAE  aromatic  1.367  0.020  1.367
 0J9  NAW  NAO  aromatic  1.340  0.020  1.340
 0J9  NAW  CAX  single    1.478  0.020  1.478
 0J9  CAE  CAF  aromatic  1.409  0.020  1.409
 0J9  CAX  CAC  single    1.524  0.020  1.524
 0J9  CAX  CAB  single    1.529  0.020  1.529
 0J9  C2   H1   single    0.930  0.020  1.080
 0J9  CAA  H2   single    0.970  0.020  1.090
 0J9  CAA  H3   single    0.970  0.020  1.090
 0J9  CAA  H4   single    0.970  0.020  1.090
 0J9  CAB  H5   single    0.970  0.020  1.090
 0J9  CAB  H6   single    0.970  0.020  1.090
 0J9  CAB  H7   single    0.970  0.020  1.090
 0J9  CAC  H8   single    0.970  0.020  1.090
 0J9  CAC  H9   single    0.970  0.020  1.090
 0J9  CAC  H10  single    0.970  0.020  1.090
 0J9  NAD  H11  single    0.860  0.020  1.020
 0J9  NAD  H12  single    0.860  0.020  1.020
 0J9  CAE  H13  single    0.930  0.020  1.080
 0J9  CAF  H14  single    0.930  0.020  1.080
 0J9  CAI  H15  single    0.930  0.020  1.080
 0J9  CAJ  H16  single    0.930  0.020  1.080
 0J9  CAK  H17  single    0.930  0.020  1.080
 0J9  CAL  H18  single    0.930  0.020  1.080
 0J9  CAG  H19  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
 0J9  C6   N1   C2   118.67  3.000
 0J9  H1   C2   N3   116.06  3.000
 0J9  H1   C2   N1   115.19  3.000
 0J9  N3   C2   N1   128.75  3.000
 0J9  C4   N3   C2   112.49  3.000
 0J9  NAW  C4   C5   106.76  3.000
 0J9  NAW  C4   N3   127.91  3.000
 0J9  C5   C4   N3   125.33  3.000
 0J9  CAR  C5   C6   139.12  3.000
 0J9  CAR  C5   C4   104.68  3.000
 0J9  C6   C5   C4   116.14  3.000
 0J9  NAD  C6   C5   123.24  3.000
 0J9  C5   C6   N1   118.58  3.000
 0J9  NAD  C6   N1   118.19  3.000
 0J9  H4   CAA  H3   108.01  3.000
 0J9  H4   CAA  H2   108.60  3.000
 0J9  H3   CAA  H2   108.03  3.000
 0J9  H4   CAA  CAX  111.82  3.000
 0J9  H3   CAA  CAX  109.59  3.000
 0J9  H2   CAA  CAX  110.67  3.000
 0J9  H7   CAB  H6   108.58  3.000
 0J9  H7   CAB  H5   107.93  3.000
 0J9  H6   CAB  H5   107.94  3.000
 0J9  H7   CAB  CAX  111.80  3.000
 0J9  H6   CAB  CAX  110.84  3.000
 0J9  H5   CAB  CAX  109.62  3.000
 0J9  H10  CAC  H9   107.93  3.000
 0J9  H10  CAC  H8   107.95  3.000
 0J9  H9   CAC  H8   108.30  3.000
 0J9  H10  CAC  CAX  108.02  3.000
 0J9  H9   CAC  CAX  112.17  3.000
 0J9  H8   CAC  CAX  112.29  3.000
 0J9  H12  NAD  H11  117.81  3.000
 0J9  H12  NAD  C6   121.84  3.000
 0J9  H11  NAD  C6   119.51  3.000
 0J9  H13  CAE  CAJ  120.32  3.000
 0J9  H13  CAE  CAF  119.76  3.000
 0J9  CAJ  CAE  CAF  119.92  3.000
 0J9  H14  CAF  CAL  119.79  3.000
 0J9  H14  CAF  CAE  119.56  3.000
 0J9  CAL  CAF  CAE  120.65  3.000
 0J9  H15  CAI  CAG  118.97  3.000
 0J9  H15  CAI  CAQ  119.65  3.000
 0J9  CAG  CAI  CAQ  121.36  3.000
 0J9  H16  CAJ  CAS  118.73  3.000
 0J9  H16  CAJ  CAE  120.47  3.000
 0J9  CAS  CAJ  CAE  120.80  3.000
 0J9  H17  CAK  CAG  120.47  3.000
 0J9  H17  CAK  CAS  118.96  3.000
 0J9  CAG  CAK  CAS  120.57  3.000
 0J9  H18  CAL  CAT  119.65  3.000
 0J9  H18  CAL  CAF  119.48  3.000
 0J9  CAT  CAL  CAF  120.87  3.000
 0J9  NAW  NAO  CAR  108.10  3.000
 0J9  CAT  CAQ  CAR  121.67  3.000
 0J9  CAT  CAQ  CAI  119.68  3.000
 0J9  CAR  CAQ  CAI  118.64  3.000
 0J9  CAQ  CAR  NAO  122.14  3.000
 0J9  NAO  CAR  C5   109.63  3.000
 0J9  CAQ  CAR  C5   128.22  3.000
 0J9  CAT  CAS  CAK  119.71  3.000
 0J9  CAT  CAS  CAJ  119.40  3.000
 0J9  CAK  CAS  CAJ  120.89  3.000
 0J9  CAS  CAT  CAQ  118.65  3.000
 0J9  CAS  CAT  CAL  118.35  3.000
 0J9  CAQ  CAT  CAL  122.99  3.000
 0J9  CAX  NAW  NAO  121.33  3.000
 0J9  CAX  NAW  C4   127.81  3.000
 0J9  NAO  NAW  C4   110.82  3.000
 0J9  NAW  CAX  CAC  109.35  3.000
 0J9  CAC  CAX  CAB  109.37  3.000
 0J9  NAW  CAX  CAB  109.00  3.000
 0J9  CAB  CAX  CAA  111.05  3.000
 0J9  CAC  CAX  CAA  109.38  3.000
 0J9  NAW  CAX  CAA  108.66  3.000
 0J9  H19  CAG  CAK  120.54  3.000
 0J9  H19  CAG  CAI  119.44  3.000
 0J9  CAK  CAG  CAI  120.02  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
 0J9  CONST_01  C4   N3   C2   N1     0.00   0.0  0
 0J9  CONST_02  C4   C5   C6   N1     0.00   0.0  0
 0J9  CONST_03  CAR  C5   C6   N1   180.00   0.0  0
 0J9  CONST_04  C5   C6   N1   C2     0.00   0.0  0
 0J9  CONST_05  C5   C4   N3   C2     0.00   0.0  0
 0J9  CONST_06  NAW  C4   N3   C2   180.00   0.0  0
 0J9  CONST_07  C6   N1   C2   N3     0.00   0.0  0
 0J9  CONST_08  C6   C5   C4   N3     0.00   0.0  0
 0J9  CONST_09  CAR  C5   C4   N3   180.00   0.0  0
 0J9  CONST_10  NAO  NAW  C4   N3   180.00   0.0  0
 0J9  CONST_11  CAQ  CAR  C5   C4   180.00   0.0  0
 0J9  CONST_12  NAO  CAR  C5   C4     0.00   0.0  0
 0J9  CONST_13  CAR  NAO  NAW  C4     0.00   0.0  0
 0J9  CONST_14  NAO  NAW  C4   C5     0.00   0.0  0
 0J9  CONST_17  NAW  NAO  CAR  C5     0.00   0.0  0
 0J9  CONST_18  NAW  C4   C5   C6   180.00   0.0  0
 0J9  CONST_19  CAQ  CAR  C5   C6     0.00   0.0  0
 0J9  CONST_20  NAO  CAR  C5   C6   180.00   0.0  0
 0J9  CONST_21  CAK  CAS  CAJ  CAE  180.00   0.0  0
 0J9  CONST_22  CAT  CAS  CAJ  CAE    0.00   0.0  0
 0J9  CONST_23  CAT  CAL  CAF  CAE    0.00   0.0  0
 0J9  CONST_24  CAQ  CAT  CAL  CAF  180.00   0.0  0
 0J9  CONST_25  CAS  CAT  CAL  CAF    0.00   0.0  0
 0J9  CONST_26  CAS  CAJ  CAE  CAF    0.00   0.0  0
 0J9  CONST_27  CAS  CAK  CAG  CAI    0.00   0.0  0
 0J9  CONST_29  CAS  CAT  CAQ  CAI    0.00   0.0  0
 0J9  CONST_30  CAL  CAT  CAQ  CAI  180.00   0.0  0
 0J9  CONST_31  CAG  CAK  CAS  CAJ  180.00   0.0  0
 0J9  CONST_32  CAQ  CAT  CAS  CAJ  180.00   0.0  0
 0J9  CONST_33  CAL  CAT  CAS  CAJ    0.00   0.0  0
 0J9  CONST_34  CAL  CAF  CAE  CAJ    0.00   0.0  0
 0J9  CONST_35  CAQ  CAI  CAG  CAK    0.00   0.0  0
 0J9  CONST_36  CAQ  CAT  CAS  CAK    0.00   0.0  0
 0J9  CONST_37  CAL  CAT  CAS  CAK  180.00   0.0  0
 0J9  CONST_38  CAR  CAQ  CAT  CAL    0.00   0.0  0
 0J9  CONST_40  NAW  NAO  CAR  CAQ  180.00   0.0  0
 0J9  CONST_41  NAW  C4   C5   CAR    0.00   0.0  0
 0J9  CONST_42  CAG  CAI  CAQ  CAR  180.00   0.0  0
 0J9  CONST_43  CAS  CAT  CAQ  CAR  180.00   0.0  0
 0J9  CONST_44  CAG  CAI  CAQ  CAT    0.00   0.0  0
 0J9  CONST_45  CAG  CAK  CAS  CAT    0.00   0.0  0
 0J9  CONST_46  NAD  C6   N1   C2   180.00   0.0  0
 0J9  CONST_47  CAX  NAW  C4   N3     0.00   0.0  0
 0J9  CONST_48  NAD  C6   C5   C4   180.00   0.0  0
 0J9  CONST_49  CAX  NAW  C4   C5   180.00   0.0  0
 0J9  CONST_50  CAR  C5   C6   NAD    0.00   0.0  0
 0J9  CONST_51  CAX  NAW  NAO  CAR  180.00   0.0  0
 0J9  CONST_52  H1   C2   N3   C4   180.00   0.0  0
 0J9  CONST_53  H18  CAL  CAF  CAE  180.00   0.0  0
 0J9  CONST_54  H16  CAJ  CAE  CAF  180.00   0.0  0
 0J9  CONST_55  H17  CAK  CAG  CAI  180.00   0.0  0
 0J9  CONST_56  H14  CAF  CAE  CAJ  180.00   0.0  0
 0J9  CONST_57  H15  CAI  CAG  CAK  180.00   0.0  0
 0J9  CONST_58  H13  CAE  CAF  CAL  180.00   0.0  0
 0J9  CONST_59  H19  CAG  CAI  CAQ  180.00   0.0  0
 0J9  CONST_60  H11  NAD  C6   N1     0.00   0.0  0
 0J9  CONST_61  H12  NAD  C6   N1   180.00   0.0  0
 0J9  Var_01    CAA  CAX  NAW  C4    61.32  30.0  2
 0J9  Var_02    H2   CAA  CAX  NAW   59.89  30.0  3
 0J9  Var_03    H8   CAC  CAX  NAW  -60.68  30.0  3
 0J9  Var_04    H5   CAB  CAX  NAW  179.87  30.0  3

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
 0J9  plan-1  N1   0.020
 0J9  plan-1  C2   0.020
 0J9  plan-1  N3   0.020
 0J9  plan-1  C4   0.020
 0J9  plan-1  C5   0.020
 0J9  plan-1  C6   0.020
 0J9  plan-1  NAD  0.020
 0J9  plan-1  NAO  0.020
 0J9  plan-1  CAQ  0.020
 0J9  plan-1  CAR  0.020
 0J9  plan-1  NAW  0.020
 0J9  plan-1  CAX  0.020
 0J9  plan-1  H1   0.020
 0J9  plan-2  CAE  0.020
 0J9  plan-2  CAF  0.020
 0J9  plan-2  CAI  0.020
 0J9  plan-2  CAJ  0.020
 0J9  plan-2  CAK  0.020
 0J9  plan-2  CAL  0.020
 0J9  plan-2  CAQ  0.020
 0J9  plan-2  CAR  0.020
 0J9  plan-2  CAS  0.020
 0J9  plan-2  CAT  0.020
 0J9  plan-2  CAG  0.020
 0J9  plan-2  H13  0.020
 0J9  plan-2  H14  0.020
 0J9  plan-2  H15  0.020
 0J9  plan-2  H16  0.020
 0J9  plan-2  H17  0.020
 0J9  plan-2  H18  0.020
 0J9  plan-2  H19  0.020
 0J9  plan-3  C6   0.020
 0J9  plan-3  NAD  0.020
 0J9  plan-3  H11  0.020
 0J9  plan-3  H12  0.020

