# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:09:40 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-tert-butyl-3-(naphthalen-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)n1nc(c2ccc3ccccc3c2)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
 BK2  BK2  1-tert-butyl-3-(naphthalen-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  43  24  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BK2
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
 BK2  N1    N  N     0  -0.478   2.5535  -3.1433  -0.4190
 BK2  C2    C  CR16  0   0.049   3.6636  -2.4100  -0.3551
 BK2  N3    N  N     0  -0.465   3.7784  -1.1085  -0.2045
 BK2  C4    C  CR56  0   0.590   2.5937  -0.5010  -0.0676
 BK2  C5    C  CR56  0  -0.260   1.3490  -1.1391  -0.0579
 BK2  C6    C  CR6   0   0.432   1.3726  -2.5340  -0.2972
 BK2  CAA   C  CH3   0  -0.650   4.1672   1.9196  -1.1464
 BK2  CAB   C  CH3   0  -0.648   4.2502   1.7050   1.3591
 BK2  CAC   C  CH3   0  -0.647   2.6126   3.2466   0.2862
 BK2  NAD   N  NH2   0  -0.818   0.2737  -3.2838  -0.4071
 BK2  CAE   C  CR16  0  -0.256  -6.0183   0.7456   0.0195
 BK2  CAF   C  CR16  0  -0.256  -5.3995   1.7613  -0.7410
 BK2  CAH   C  CR16  0  -0.339  -1.6781  -1.1331   1.0246
 BK2  CAI   C  CR16  0  -0.308  -5.2622  -0.2139   0.6358
 BK2  CAJ   C  CR16  0  -0.314  -4.0383   1.7963  -0.8704
 BK2  CAK   C  CR16  0  -0.293  -3.0382  -1.1710   1.1518
 BK2  CAL   C  CR16  0  -0.363  -1.8234   0.8274  -0.3652
 BK2  NAO   N  N     0  -0.269   1.0476   1.0578   0.2078
 BK2  CAQ   C  CR6   0   0.042  -1.0494  -0.1288   0.2463
 BK2  CAR   C  CR5   0   0.269   0.4117  -0.0875   0.1312
 BK2  CAS   C  CR66  0   0.105  -3.8527  -0.2023   0.5214
 BK2  CAT   C  CR66  0   0.140  -3.2299   0.8175  -0.2440
 BK2  NAW   N  NR5   0  -0.373   2.3589   0.8201   0.0835
 BK2  CAX   C  CT    0   0.061   3.3470   1.9179   0.1444
 BK2  H2    H  HCR6  0   0.253   4.5914  -2.9645  -0.4530
 BK2  HAA   H  HCH3  0   0.235   4.8693   2.7535  -1.1278
 BK2  HAAA  H  HCH3  0   0.248   4.7388   0.9998  -1.2591
 BK2  HAAB  H  HCH3  0   0.236   3.5238   2.0374  -2.0193
 BK2  HAB   H  HCH3  0   0.236   4.9648   2.5259   1.4323
 BK2  HABA  H  HCH3  0   0.236   3.6652   1.6836   2.2796
 BK2  HABB  H  HCH3  0   0.246   4.8160   0.7775   1.2859
 BK2  HAC   H  HCH3  0   0.239   1.9365   3.4354  -0.5468
 BK2  HACA  H  HCH3  0   0.239   2.0388   3.2986   1.2105
 BK2  HACB  H  HCH3  0   0.238   3.3554   4.0439   0.3064
 BK2  HNAD  H  HNH2  0   0.405   0.3694  -4.2533  -0.6598
 BK2  HNAA  H  HNH2  0   0.415  -0.6415  -2.8758  -0.4841
 BK2  HAE   H  HCR6  0   0.261  -7.0962   0.7302   0.1139
 BK2  HAF   H  HCR6  0   0.261  -6.0092   2.5153  -1.2214
 BK2  HAH   H  HCR6  0   0.273  -1.0739  -1.8647   1.5466
 BK2  HAI   H  HCR6  0   0.258  -5.7362  -0.9941   1.2188
 BK2  HAJ   H  HCR6  0   0.257  -3.5621   2.5770  -1.4514
 BK2  HAK   H  HCR6  0   0.261  -3.5049  -1.9432   1.7512
 BK2  HAL   H  HCR6  0   0.253  -1.3546   1.6004  -0.9623

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
 BK2  C2   N1    aromatic  1.332  0.020  1.332
 BK2  N1   C6    aromatic  1.334  0.020  1.334
 BK2  N3   C2    aromatic  1.315  0.020  1.315
 BK2  C2   H2    single    0.930  0.020  1.080
 BK2  N3   C4    aromatic  1.338  0.020  1.338
 BK2  NAW  C4    aromatic  1.350  0.020  1.350
 BK2  C4   C5    aromatic  1.399  0.020  1.399
 BK2  C5   CAR   aromatic  1.421  0.020  1.421
 BK2  C5   C6    aromatic  1.416  0.020  1.416
 BK2  C6   NAD   single    1.335  0.020  1.335
 BK2  CAA  CAX   single    1.529  0.020  1.529
 BK2  CAA  HAA   single    0.970  0.020  1.090
 BK2  CAA  HAAA  single    0.970  0.020  1.090
 BK2  CAA  HAAB  single    0.970  0.020  1.090
 BK2  CAX  CAB   single    1.529  0.020  1.529
 BK2  CAB  HAB   single    0.970  0.020  1.090
 BK2  CAB  HABA  single    0.970  0.020  1.090
 BK2  CAB  HABB  single    0.970  0.020  1.090
 BK2  CAC  CAX   single    1.525  0.020  1.525
 BK2  CAC  HAC   single    0.970  0.020  1.090
 BK2  CAC  HACA  single    0.970  0.020  1.090
 BK2  CAC  HACB  single    0.970  0.020  1.090
 BK2  NAD  HNAD  single    0.860  0.020  1.020
 BK2  NAD  HNAA  single    0.860  0.020  1.020
 BK2  CAI  CAE   aromatic  1.368  0.020  1.368
 BK2  CAE  CAF   aromatic  1.412  0.020  1.412
 BK2  CAE  HAE   single    0.930  0.020  1.080
 BK2  CAJ  CAF   aromatic  1.368  0.020  1.368
 BK2  CAF  HAF   single    0.930  0.020  1.080
 BK2  CAH  CAK   aromatic  1.367  0.020  1.367
 BK2  CAH  CAQ   aromatic  1.418  0.020  1.418
 BK2  CAH  HAH   single    0.930  0.020  1.080
 BK2  CAS  CAI   aromatic  1.414  0.020  1.414
 BK2  CAI  HAI   single    0.930  0.020  1.080
 BK2  CAT  CAJ   aromatic  1.416  0.020  1.416
 BK2  CAJ  HAJ   single    0.930  0.020  1.080
 BK2  CAK  CAS   aromatic  1.414  0.020  1.414
 BK2  CAK  HAK   single    0.930  0.020  1.080
 BK2  CAQ  CAL   aromatic  1.374  0.020  1.374
 BK2  CAL  CAT   aromatic  1.412  0.020  1.412
 BK2  CAL  HAL   single    0.930  0.020  1.080
 BK2  NAW  NAO   aromatic  1.339  0.020  1.339
 BK2  NAO  CAR   aromatic  1.312  0.020  1.312
 BK2  CAR  CAQ   single    1.466  0.020  1.466
 BK2  CAS  CAT   aromatic  1.419  0.020  1.419
 BK2  CAX  NAW   single    1.478  0.020  1.478

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
 BK2  C6    N1   C2    118.81  3.000
 BK2  H2    C2   N3    116.18  3.000
 BK2  H2    C2   N1    115.27  3.000
 BK2  N3    C2   N1    128.54  3.000
 BK2  C4    N3   C2    112.56  3.000
 BK2  NAW   C4   C5    106.91  3.000
 BK2  C5    C4   N3    125.54  3.000
 BK2  NAW   C4   N3    127.55  3.000
 BK2  CAR   C5   C6    139.70  3.000
 BK2  C6    C5   C4    115.69  3.000
 BK2  CAR   C5   C4    104.49  3.000
 BK2  NAD   C6   C5    123.62  3.000
 BK2  NAD   C6   N1    117.69  3.000
 BK2  C5    C6   N1    118.69  3.000
 BK2  HAAB  CAA  HAAA  108.55  3.000
 BK2  HAAB  CAA  HAA   108.11  3.000
 BK2  HAAA  CAA  HAA   108.05  3.000
 BK2  HAAB  CAA  CAX   111.05  3.000
 BK2  HAAA  CAA  CAX   111.59  3.000
 BK2  HAA   CAA  CAX   109.38  3.000
 BK2  HABB  CAB  HABA  108.58  3.000
 BK2  HABB  CAB  HAB   107.76  3.000
 BK2  HABA  CAB  HAB   108.02  3.000
 BK2  HABB  CAB  CAX   111.85  3.000
 BK2  HABA  CAB  CAX   110.88  3.000
 BK2  HAB   CAB  CAX   109.62  3.000
 BK2  HACB  CAC  HACA  107.96  3.000
 BK2  HACB  CAC  HAC   108.08  3.000
 BK2  HACA  CAC  HAC   108.28  3.000
 BK2  HACB  CAC  CAX   108.12  3.000
 BK2  HACA  CAC  CAX   111.98  3.000
 BK2  HAC   CAC  CAX   112.27  3.000
 BK2  HNAA  NAD  HNAD  117.29  3.000
 BK2  HNAA  NAD  C6    121.87  3.000
 BK2  HNAD  NAD  C6    118.91  3.000
 BK2  HAE   CAE  CAI   120.08  3.000
 BK2  HAE   CAE  CAF   119.59  3.000
 BK2  CAI   CAE  CAF   120.33  3.000
 BK2  HAF   CAF  CAJ   120.05  3.000
 BK2  HAF   CAF  CAE   119.58  3.000
 BK2  CAJ   CAF  CAE   120.37  3.000
 BK2  HAH   CAH  CAQ   119.72  3.000
 BK2  HAH   CAH  CAK   119.46  3.000
 BK2  CAQ   CAH  CAK   120.80  3.000
 BK2  HAI   CAI  CAS   119.05  3.000
 BK2  HAI   CAI  CAE   120.38  3.000
 BK2  CAS   CAI  CAE   120.57  3.000
 BK2  HAJ   CAJ  CAT   118.98  3.000
 BK2  HAJ   CAJ  CAF   120.44  3.000
 BK2  CAT   CAJ  CAF   120.58  3.000
 BK2  HAK   CAK  CAS   119.14  3.000
 BK2  HAK   CAK  CAH   120.00  3.000
 BK2  CAS   CAK  CAH   120.85  3.000
 BK2  HAL   CAL  CAT   118.91  3.000
 BK2  HAL   CAL  CAQ   119.88  3.000
 BK2  CAT   CAL  CAQ   121.21  3.000
 BK2  NAW   NAO  CAR   108.32  3.000
 BK2  CAR   CAQ  CAL   120.45  3.000
 BK2  CAR   CAQ  CAH   120.33  3.000
 BK2  CAL   CAQ  CAH   119.19  3.000
 BK2  CAQ   CAR  NAO   120.19  3.000
 BK2  CAQ   CAR  C5    130.30  3.000
 BK2  NAO   CAR  C5    109.51  3.000
 BK2  CAT   CAS  CAK   118.69  3.000
 BK2  CAT   CAS  CAI   119.14  3.000
 BK2  CAK   CAS  CAI   122.17  3.000
 BK2  CAS   CAT  CAL   119.25  3.000
 BK2  CAS   CAT  CAJ   119.01  3.000
 BK2  CAL   CAT  CAJ   121.74  3.000
 BK2  CAX   NAW  NAO   121.27  3.000
 BK2  CAX   NAW  C4    127.96  3.000
 BK2  NAO   NAW  C4    110.76  3.000
 BK2  NAW   CAX  CAC   109.21  3.000
 BK2  NAW   CAX  CAB   108.92  3.000
 BK2  CAC   CAX  CAB   109.39  3.000
 BK2  NAW   CAX  CAA   108.94  3.000
 BK2  CAC   CAX  CAA   109.62  3.000
 BK2  CAB   CAX  CAA   110.73  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
 BK2  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 BK2  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 BK2  CONST_03  CAR   C5   C6   N1    180.00   0.0  0
 BK2  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 BK2  CONST_05  NAW   C4   N3   C2    180.00   0.0  0
 BK2  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 BK2  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 BK2  CONST_08  NAO   NAW  C4   N3    180.00   0.0  0
 BK2  CONST_09  CAR   C5   C4   N3    180.00   0.0  0
 BK2  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 BK2  CONST_11  CAR   NAO  NAW  C4      0.00   0.0  0
 BK2  CONST_12  NAO   CAR  C5   C4      0.00   0.0  0
 BK2  CONST_13  CAQ   CAR  C5   C4    180.00   0.0  0
 BK2  CONST_14  NAO   NAW  C4   C5      0.00   0.0  0
 BK2  CONST_15  NAW   NAO  CAR  C5      0.00   0.0  0
 BK2  CONST_18  NAW   C4   C5   C6    180.00   0.0  0
 BK2  CONST_19  NAO   CAR  C5   C6    180.00   0.0  0
 BK2  CONST_20  CAQ   CAR  C5   C6      0.00   0.0  0
 BK2  CONST_21  CAK   CAS  CAI  CAE   180.00   0.0  0
 BK2  CONST_22  CAT   CAS  CAI  CAE     0.00   0.0  0
 BK2  CONST_23  CAT   CAJ  CAF  CAE     0.00   0.0  0
 BK2  CONST_24  CAS   CAI  CAE  CAF     0.00   0.0  0
 BK2  CONST_25  CAL   CAT  CAJ  CAF   180.00   0.0  0
 BK2  CONST_26  CAS   CAT  CAJ  CAF     0.00   0.0  0
 BK2  CONST_27  CAI   CAS  CAK  CAH   180.00   0.0  0
 BK2  CONST_28  CAT   CAS  CAK  CAH     0.00   0.0  0
 BK2  CONST_29  CAT   CAL  CAQ  CAH     0.00   0.0  0
 BK2  CONST_31  CAJ   CAF  CAE  CAI     0.00   0.0  0
 BK2  CONST_32  CAJ   CAT  CAS  CAI     0.00   0.0  0
 BK2  CONST_33  CAL   CAT  CAS  CAI   180.00   0.0  0
 BK2  CONST_34  CAQ   CAL  CAT  CAJ   180.00   0.0  0
 BK2  CONST_35  CAK   CAS  CAT  CAJ   180.00   0.0  0
 BK2  CONST_36  CAL   CAQ  CAH  CAK     0.00   0.0  0
 BK2  CONST_37  CAR   CAQ  CAH  CAK   180.00   0.0  0
 BK2  CONST_38  CAL   CAT  CAS  CAK     0.00   0.0  0
 BK2  CONST_40  CAS   CAK  CAH  CAQ     0.00   0.0  0
 BK2  CONST_41  CAS   CAT  CAL  CAQ     0.00   0.0  0
 BK2  CONST_42  NAW   NAO  CAR  CAQ   180.00   0.0  0
 BK2  CONST_43  NAW   C4   C5   CAR     0.00   0.0  0
 BK2  CONST_44  CAT   CAL  CAQ  CAR   180.00   0.0  0
 BK2  CONST_45  NAD   C6   N1   C2    180.00   0.0  0
 BK2  CONST_46  CAX   NAW  C4   N3      0.00   0.0  0
 BK2  CONST_47  NAD   C6   C5   C4    180.00   0.0  0
 BK2  CONST_48  CAX   NAW  C4   C5    180.00   0.0  0
 BK2  CONST_49  CAR   C5   C6   NAD     0.00   0.0  0
 BK2  CONST_50  CAX   NAW  NAO  CAR   180.00   0.0  0
 BK2  CONST_51  H2    C2   N3   C4    180.00   0.0  0
 BK2  CONST_52  HAJ   CAJ  CAF  CAE   180.00   0.0  0
 BK2  CONST_53  HAI   CAI  CAE  CAF   180.00   0.0  0
 BK2  CONST_54  HAL   CAL  CAQ  CAH   180.00   0.0  0
 BK2  CONST_55  HAF   CAF  CAE  CAI   180.00   0.0  0
 BK2  CONST_56  HAK   CAK  CAS  CAI     0.00   0.0  0
 BK2  CONST_57  HAE   CAE  CAF  CAJ   180.00   0.0  0
 BK2  CONST_58  HAH   CAH  CAQ  CAL   180.00   0.0  0
 BK2  CONST_59  HNAD  NAD  C6   N1      0.00   0.0  0
 BK2  CONST_60  HNAA  NAD  C6   N1    180.00   0.0  0
 BK2  Var_01    CAA   CAX  NAW  C4     58.81  30.0  3
 BK2  Var_02    HAA   CAA  CAX  NAW   177.56  30.0  3
 BK2  Var_03    HAB   CAB  CAX  NAW  -178.28  30.0  3
 BK2  Var_04    HAC   CAC  CAX  NAW   -59.59  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
 BK2  plan-1  N1    0.020
 BK2  plan-1  C2    0.020
 BK2  plan-1  N3    0.020
 BK2  plan-1  C4    0.020
 BK2  plan-1  C5    0.020
 BK2  plan-1  C6    0.020
 BK2  plan-1  NAD   0.020
 BK2  plan-1  NAO   0.020
 BK2  plan-1  CAQ   0.020
 BK2  plan-1  CAR   0.020
 BK2  plan-1  NAW   0.020
 BK2  plan-1  CAX   0.020
 BK2  plan-1  H2    0.020
 BK2  plan-2  CAE   0.020
 BK2  plan-2  CAF   0.020
 BK2  plan-2  CAH   0.020
 BK2  plan-2  CAI   0.020
 BK2  plan-2  CAJ   0.020
 BK2  plan-2  CAK   0.020
 BK2  plan-2  CAL   0.020
 BK2  plan-2  CAQ   0.020
 BK2  plan-2  CAR   0.020
 BK2  plan-2  CAS   0.020
 BK2  plan-2  CAT   0.020
 BK2  plan-2  HAE   0.020
 BK2  plan-2  HAF   0.020
 BK2  plan-2  HAH   0.020
 BK2  plan-2  HAI   0.020
 BK2  plan-2  HAJ   0.020
 BK2  plan-2  HAK   0.020
 BK2  plan-2  HAL   0.020
 BK2  plan-3  C6    0.020
 BK2  plan-3  NAD   0.020
 BK2  plan-3  HNAD  0.020
 BK2  plan-3  HNAA  0.020

