# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 19:27:43 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 3-(naphthalen-1-ylmethyl)-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1nc(Cc2cccc3ccccc23)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
 BK1  BK1  3-(naphthalen-1-ylmethyl)-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  43  24  .  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_BK1
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
 BK1  N1    N  N     0  -0.485  -2.5029   1.8397   1.6008
 BK1  C2    C  CR16  0   0.068  -3.2907   0.7992   1.8629
 BK1  N3    N  N     0  -0.434  -3.2704  -0.3998   1.3220
 BK1  C4    C  CR56  0   0.586  -2.3154  -0.5185   0.3936
 BK1  C5    C  CR56  0  -0.245  -1.4092   0.4752   0.0010
 BK1  C6    C  CR6   0   0.433  -1.5462   1.7126   0.6759
 BK1  CAA   C  CH3   0  -0.633  -3.3534  -3.2295  -1.6274
 BK1  CAB   C  CH3   0  -0.635  -1.6922  -3.9801   0.1250
 BK1  NAC   N  NH2   0  -0.823  -0.7848   2.7798   0.4324
 BK1  CAD   C  CR16  0  -0.228   3.9521  -1.0694   1.7792
 BK1  CAE   C  CR16  0  -0.221   2.9347  -1.7401   1.0731
 BK1  CAF   C  CR16  0  -0.221   3.0202   2.9778  -0.6886
 BK1  CAG   C  CR16  0  -0.364   1.9751   2.3221  -1.3715
 BK1  CAH   C  CR16  0  -0.285   4.2057   0.2490   1.5195
 BK1  CAI   C  CR16  0  -0.302   3.7356   2.3125   0.2640
 BK1  CAJ   C  CR16  0  -0.317   2.1824  -1.0797   0.1388
 BK1  NAO   N  N     0  -0.261  -1.0269  -1.3782  -1.1862
 BK1  CAQ   C  CR6   0   0.110   1.6443   1.0157  -1.1064
 BK1  CAR   C  CR5   0   0.312  -0.6195  -0.1448  -1.0093
 BK1  CAS   C  CR66  0   0.132   3.4518   0.9567   0.5541
 BK1  CAT   C  CR66  0   0.112   2.4066   0.2904  -0.1425
 BK1  NAX   N  NR5   0  -0.371  -2.0447  -1.6065  -0.3446
 BK1  H2    H  HCR6  0   0.233  -4.0452   0.9691   2.6242
 BK1  HAA   H  HCH3  0   0.222  -3.8760  -4.1834  -1.5592
 BK1  HAAA  H  HCH3  0   0.233  -4.0811  -2.4653  -1.9001
 BK1  HAAB  H  HCH3  0   0.235  -2.6157  -3.3067  -2.4264
 BK1  HAB   H  HCH3  0   0.222  -2.1971  -4.9422   0.2109
 BK1  HABA  H  HCH3  0   0.233  -0.8929  -4.0814  -0.6093
 BK1  HABB  H  HCH3  0   0.233  -1.2447  -3.7449   1.0907
 BK1  HNAC  H  HNH2  0   0.413   0.0381   2.7258  -0.1426
 BK1  HNAA  H  HNH2  0   0.374  -0.8992   3.5996   1.0047
 BK1  HAE   H  HCR6  0   0.231   2.7478  -2.7877   1.2704
 BK1  HAF   H  HCR6  0   0.231   3.2424   4.0106  -0.9218
 BK1  HAG   H  HCR6  0   0.240   1.4160   2.8699  -2.1220
 BK1  HAH   H  HCR6  0   0.224   4.9959   0.7694   2.0473
 BK1  HAI   H  HCR6  0   0.226   4.5335   2.8100   0.8012
 BK1  HAJ   H  HCR6  0   0.249   1.4142  -1.6237  -0.3922
 BK1  CAL   C  CH2   0  -0.636   0.5006   0.3786  -1.8551
 BK1  CAW   C  CH1   0  -0.119  -2.6895  -2.9102  -0.2959
 BK1  HAD   H  HCR6  0   0.231   4.5346  -1.6029   2.5187
 BK1  HAL   H  HCH2  0   0.256   0.1013   1.1110  -2.5616
 BK1  HALA  H  HCH2  0   0.278   0.8650  -0.4557  -2.4598
 BK1  HAW   H  HCH1  0   0.262  -3.4578  -2.8164   0.4729

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
 BK1  C2   N1    aromatic  1.331  0.020  1.331
 BK1  C6   N1    aromatic  1.337  0.020  1.337
 BK1  N3   C2    aromatic  1.316  0.020  1.316
 BK1  C2   H2    single    0.930  0.020  1.080
 BK1  C4   N3    aromatic  1.337  0.020  1.337
 BK1  NAX  C4    aromatic  1.342  0.020  1.342
 BK1  C4   C5    aromatic  1.401  0.020  1.401
 BK1  CAR  C5    aromatic  1.424  0.020  1.424
 BK1  C5   C6    aromatic  1.416  0.020  1.416
 BK1  C6   NAC   single    1.333  0.020  1.333
 BK1  CAW  CAA   single    1.522  0.020  1.522
 BK1  CAA  HAA   single    0.970  0.020  1.090
 BK1  CAA  HAAA  single    0.970  0.020  1.090
 BK1  CAA  HAAB  single    0.970  0.020  1.090
 BK1  CAB  CAW   single    1.522  0.020  1.522
 BK1  CAB  HAB   single    0.970  0.020  1.090
 BK1  CAB  HABA  single    0.970  0.020  1.090
 BK1  CAB  HABB  single    0.970  0.020  1.090
 BK1  NAC  HNAC  single    0.860  0.020  1.020
 BK1  NAC  HNAA  single    0.860  0.020  1.020
 BK1  CAE  CAD   aromatic  1.408  0.020  1.408
 BK1  CAD  CAH   aromatic  1.367  0.020  1.367
 BK1  CAD  HAD   single    0.930  0.020  1.080
 BK1  CAJ  CAE   aromatic  1.369  0.020  1.369
 BK1  CAE  HAE   single    0.930  0.020  1.080
 BK1  CAG  CAF   aromatic  1.410  0.020  1.410
 BK1  CAF  CAI   aromatic  1.364  0.020  1.364
 BK1  CAF  HAF   single    0.930  0.020  1.080
 BK1  CAQ  CAG   aromatic  1.373  0.020  1.373
 BK1  CAG  HAG   single    0.930  0.020  1.080
 BK1  CAS  CAH   aromatic  1.415  0.020  1.415
 BK1  CAH  HAH   single    0.930  0.020  1.080
 BK1  CAS  CAI   aromatic  1.415  0.020  1.415
 BK1  CAI  HAI   single    0.930  0.020  1.080
 BK1  CAJ  CAT   aromatic  1.416  0.020  1.416
 BK1  CAJ  HAJ   single    0.930  0.020  1.080
 BK1  CAR  CAL   single    1.498  0.020  1.498
 BK1  CAL  CAQ   single    1.508  0.020  1.508
 BK1  CAL  HAL   single    0.970  0.020  1.090
 BK1  CAL  HALA  single    0.970  0.020  1.090
 BK1  NAX  NAO   aromatic  1.340  0.020  1.340
 BK1  NAO  CAR   aromatic  1.311  0.020  1.311
 BK1  CAQ  CAT   aromatic  1.427  0.020  1.427
 BK1  CAT  CAS   aromatic  1.422  0.020  1.422
 BK1  CAW  NAX   single    1.455  0.020  1.455
 BK1  CAW  HAW   single    0.970  0.020  1.090

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
 BK1  C6    N1   C2    119.05  3.000
 BK1  H2    C2   N3    116.22  3.000
 BK1  H2    C2   N1    115.29  3.000
 BK1  N3    C2   N1    128.49  3.000
 BK1  C4    N3   C2    112.17  3.000
 BK1  NAX   C4   C5    106.88  3.000
 BK1  C5    C4   N3    126.41  3.000
 BK1  NAX   C4   N3    126.71  3.000
 BK1  CAR   C5   C6    140.54  3.000
 BK1  C6    C5   C4    115.06  3.000
 BK1  CAR   C5   C4    104.40  3.000
 BK1  NAC   C6   C5    123.85  3.000
 BK1  NAC   C6   N1    117.32  3.000
 BK1  C5    C6   N1    118.82  3.000
 BK1  HAAB  CAA  HAAA  108.54  3.000
 BK1  HAAB  CAA  HAA   107.96  3.000
 BK1  HAAA  CAA  HAA   108.01  3.000
 BK1  HAAB  CAA  CAW   111.16  3.000
 BK1  HAAA  CAA  CAW   111.29  3.000
 BK1  HAA   CAA  CAW   109.76  3.000
 BK1  HABB  CAB  HABA  108.41  3.000
 BK1  HABB  CAB  HAB   108.11  3.000
 BK1  HABA  CAB  HAB   108.10  3.000
 BK1  HABB  CAB  CAW   111.24  3.000
 BK1  HABA  CAB  CAW   111.06  3.000
 BK1  HAB   CAB  CAW   109.80  3.000
 BK1  HNAA  NAC  HNAC  117.52  3.000
 BK1  HNAA  NAC  C6    118.89  3.000
 BK1  HNAC  NAC  C6    121.93  3.000
 BK1  HAD   CAD  CAH   120.35  3.000
 BK1  HAD   CAD  CAE   119.78  3.000
 BK1  CAH   CAD  CAE   119.87  3.000
 BK1  HAE   CAE  CAJ   119.76  3.000
 BK1  HAE   CAE  CAD   119.63  3.000
 BK1  CAJ   CAE  CAD   120.61  3.000
 BK1  HAF   CAF  CAI   120.55  3.000
 BK1  HAF   CAF  CAG   119.45  3.000
 BK1  CAI   CAF  CAG   119.99  3.000
 BK1  HAG   CAG  CAQ   119.34  3.000
 BK1  HAG   CAG  CAF   118.84  3.000
 BK1  CAQ   CAG  CAF   121.83  3.000
 BK1  HAH   CAH  CAS   118.74  3.000
 BK1  HAH   CAH  CAD   120.39  3.000
 BK1  CAS   CAH  CAD   120.87  3.000
 BK1  HAI   CAI  CAS   119.08  3.000
 BK1  HAI   CAI  CAF   120.57  3.000
 BK1  CAS   CAI  CAF   120.34  3.000
 BK1  HAJ   CAJ  CAT   120.12  3.000
 BK1  HAJ   CAJ  CAE   118.88  3.000
 BK1  CAT   CAJ  CAE   121.00  3.000
 BK1  NAX   NAO  CAR   108.15  3.000
 BK1  CAT   CAQ  CAL   121.72  3.000
 BK1  CAT   CAQ  CAG   119.03  3.000
 BK1  CAL   CAQ  CAG   119.25  3.000
 BK1  NAO   CAR  CAL   119.01  3.000
 BK1  NAO   CAR  C5    109.45  3.000
 BK1  CAL   CAR  C5    131.53  3.000
 BK1  CAT   CAS  CAI   119.73  3.000
 BK1  CAT   CAS  CAH   119.45  3.000
 BK1  CAI   CAS  CAH   120.82  3.000
 BK1  CAS   CAT  CAQ   119.04  3.000
 BK1  CAS   CAT  CAJ   118.18  3.000
 BK1  CAQ   CAT  CAJ   122.77  3.000
 BK1  CAW   NAX  NAO   120.67  3.000
 BK1  CAW   NAX  C4    128.20  3.000
 BK1  NAO   NAX  C4    111.12  3.000
 BK1  HALA  CAL  HAL   106.00  3.000
 BK1  HALA  CAL  CAR   107.15  3.000
 BK1  HAL   CAL  CAR   109.02  3.000
 BK1  HALA  CAL  CAQ   110.14  3.000
 BK1  HAL   CAL  CAQ   108.35  3.000
 BK1  CAR   CAL  CAQ   115.74  3.000
 BK1  HAW   CAW  NAX   104.99  3.000
 BK1  HAW   CAW  CAB   109.09  3.000
 BK1  NAX   CAW  CAB   110.41  3.000
 BK1  HAW   CAW  CAA   109.11  3.000
 BK1  NAX   CAW  CAA   110.61  3.000
 BK1  CAB   CAW  CAA   112.36  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
 BK1  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 BK1  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 BK1  CONST_03  CAR   C5   C6   N1    180.00   0.0  0
 BK1  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 BK1  CONST_05  NAX   C4   N3   C2    180.00   0.0  0
 BK1  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 BK1  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 BK1  CONST_08  NAO   NAX  C4   N3    180.00   0.0  0
 BK1  CONST_09  CAR   C5   C4   N3    180.00   0.0  0
 BK1  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 BK1  CONST_11  CAR   NAO  NAX  C4      0.00   0.0  0
 BK1  CONST_12  NAO   CAR  C5   C4      0.00   0.0  0
 BK1  CONST_13  NAO   NAX  C4   C5      0.00   0.0  0
 BK1  CONST_14  NAX   NAO  CAR  C5      0.00   0.0  0
 BK1  CONST_15  NAX   C4   C5   C6    180.00   0.0  0
 BK1  CONST_16  NAO   CAR  C5   C6    180.00   0.0  0
 BK1  CONST_17  CAT   CAJ  CAE  CAD     0.00   0.0  0
 BK1  CONST_18  CAI   CAS  CAH  CAD   180.00   0.0  0
 BK1  CONST_19  CAT   CAS  CAH  CAD     0.00   0.0  0
 BK1  CONST_20  CAS   CAH  CAD  CAE     0.00   0.0  0
 BK1  CONST_21  CAQ   CAT  CAJ  CAE   180.00   0.0  0
 BK1  CONST_22  CAS   CAT  CAJ  CAE     0.00   0.0  0
 BK1  CONST_23  CAT   CAQ  CAG  CAF     0.00   0.0  0
 BK1  CONST_24  CAH   CAS  CAI  CAF   180.00   0.0  0
 BK1  CONST_25  CAT   CAS  CAI  CAF     0.00   0.0  0
 BK1  CONST_26  CAS   CAI  CAF  CAG     0.00   0.0  0
 BK1  CONST_27  CAJ   CAT  CAQ  CAG   180.00   0.0  0
 BK1  CONST_28  CAS   CAT  CAQ  CAG     0.00   0.0  0
 BK1  CONST_29  CAJ   CAE  CAD  CAH     0.00   0.0  0
 BK1  CONST_30  CAJ   CAT  CAS  CAH     0.00   0.0  0
 BK1  CONST_31  CAQ   CAT  CAS  CAH   180.00   0.0  0
 BK1  CONST_32  CAQ   CAG  CAF  CAI     0.00   0.0  0
 BK1  CONST_33  CAJ   CAT  CAS  CAI   180.00   0.0  0
 BK1  CONST_34  CAQ   CAT  CAS  CAI     0.00   0.0  0
 BK1  CONST_35  NAX   C4   C5   CAR     0.00   0.0  0
 BK1  CONST_36  NAC   C6   N1   C2    180.00   0.0  0
 BK1  CONST_37  CAW   NAX  C4   N3      0.00   0.0  0
 BK1  CONST_38  CAL   CAR  C5   C4    180.00   0.0  0
 BK1  CONST_39  NAC   C6   C5   C4    180.00   0.0  0
 BK1  CONST_40  CAW   NAX  C4   C5    180.00   0.0  0
 BK1  CONST_41  CAL   CAR  C5   C6      0.00   0.0  0
 BK1  CONST_42  CAR   C5   C6   NAC     0.00   0.0  0
 BK1  CONST_43  CAL   CAQ  CAG  CAF   180.00   0.0  0
 BK1  CONST_44  CAL   CAQ  CAT  CAJ     0.00   0.0  0
 BK1  CONST_45  NAX   NAO  CAR  CAL   180.00   0.0  0
 BK1  CONST_46  CAS   CAT  CAQ  CAL   180.00   0.0  0
 BK1  CONST_47  CAW   NAX  NAO  CAR   180.00   0.0  0
 BK1  CONST_48  H2    C2   N3   C4    180.00   0.0  0
 BK1  CONST_49  HAJ   CAJ  CAE  CAD   180.00   0.0  0
 BK1  CONST_50  HAH   CAH  CAD  CAE   180.00   0.0  0
 BK1  CONST_51  HAI   CAI  CAF  CAG   180.00   0.0  0
 BK1  CONST_52  HAE   CAE  CAD  CAH   180.00   0.0  0
 BK1  CONST_53  HAG   CAG  CAF  CAI   180.00   0.0  0
 BK1  CONST_54  HAD   CAD  CAE  CAJ   180.00   0.0  0
 BK1  CONST_55  HAF   CAF  CAG  CAQ   180.00   0.0  0
 BK1  CONST_56  HNAC  NAC  C6   N1    180.00   0.0  0
 BK1  CONST_57  HNAA  NAC  C6   N1      0.00   0.0  0
 BK1  Var_01    CAQ   CAL  CAR  C5     53.25  30.0  2
 BK1  Var_02    CAR   CAL  CAQ  CAG  -121.38  30.0  2
 BK1  Var_03    CAA   CAW  NAX  C4    118.03  30.0  3
 BK1  Var_04    HAA   CAA  CAW  NAX  -177.02  30.0  3
 BK1  Var_05    HAB   CAB  CAW  NAX   176.94  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
 BK1  plan-1  N1    0.020
 BK1  plan-1  C2    0.020
 BK1  plan-1  N3    0.020
 BK1  plan-1  C4    0.020
 BK1  plan-1  C5    0.020
 BK1  plan-1  C6    0.020
 BK1  plan-1  NAC   0.020
 BK1  plan-1  NAO   0.020
 BK1  plan-1  CAR   0.020
 BK1  plan-1  NAX   0.020
 BK1  plan-1  H2    0.020
 BK1  plan-1  CAL   0.020
 BK1  plan-1  CAW   0.020
 BK1  plan-2  CAD   0.020
 BK1  plan-2  CAE   0.020
 BK1  plan-2  CAF   0.020
 BK1  plan-2  CAG   0.020
 BK1  plan-2  CAH   0.020
 BK1  plan-2  CAI   0.020
 BK1  plan-2  CAJ   0.020
 BK1  plan-2  CAQ   0.020
 BK1  plan-2  CAS   0.020
 BK1  plan-2  CAT   0.020
 BK1  plan-2  HAE   0.020
 BK1  plan-2  HAF   0.020
 BK1  plan-2  HAG   0.020
 BK1  plan-2  HAH   0.020
 BK1  plan-2  HAI   0.020
 BK1  plan-2  HAJ   0.020
 BK1  plan-2  CAL   0.020
 BK1  plan-2  HAD   0.020
 BK1  plan-3  C6    0.020
 BK1  plan-3  NAC   0.020
 BK1  plan-3  HNAC  0.020
 BK1  plan-3  HNAA  0.020

