# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 18:27:10 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 3-(6-ethoxynaphthalen-2-yl)-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOc1ccc2cc(ccc2c1)c3nn(C(C)C)c4ncnc(N)c34
#
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
 BK5  BK5  3-(6-ethoxynaphthalen-2-yl)-1-(propan-2-yl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  47  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BK5
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
 BK5  N1    N  N     0  -0.478   4.1035   2.7895   0.4923
 BK5  C2    C  CR16  0   0.054   5.1375   1.9537   0.4098
 BK5  N3    N  N     0  -0.466   5.1255   0.6523   0.2146
 BK5  C4    C  CR56  0   0.578   3.8861   0.1784   0.0520
 BK5  C5    C  CR56  0  -0.263   2.7059   0.9287   0.0623
 BK5  C6    C  CR6   0   0.432   2.8670   2.3059   0.3461
 BK5  CAA   C  CH3   0  -0.681  -8.4621  -0.3641   0.0737
 BK5  CAB   C  CH3   0  -0.648   4.1776  -3.1575   1.0164
 BK5  CAC   C  CH3   0  -0.650   4.2012  -3.0237  -1.5084
 BK5  NAD   N  NH2   0  -0.817   1.8497   3.1588   0.4780
 BK5  CAE   C  CR16  0  -0.377  -4.2990  -1.2891   0.7235
 BK5  CAF   C  CR16  0  -0.340  -0.3064   1.2395  -1.0088
 BK5  CAG   C  CR16  0  -0.297  -2.9457  -1.4596   0.8343
 BK5  CAH   C  CR16  0  -0.301  -1.6545   1.4234  -1.1236
 BK5  CAJ   C  CR16  0  -0.435  -3.9580   0.6957  -0.6094
 BK5  CAK   C  CR16  0  -0.355  -0.6405  -0.7256   0.3370
 BK5  CAL   C  CH2   0  -0.191  -7.0785  -0.8482   0.4356
 BK5  NAO   N  N     0  -0.274   2.2022  -1.2269  -0.2645
 BK5  CAQ   C  CR6   0   0.406  -4.8201  -0.1952  -0.0098
 BK5  CAR   C  CR6   0   0.034   0.2250   0.1592  -0.2574
 BK5  CAT   C  CR5   0   0.261   1.6748  -0.0288  -0.1534
 BK5  CAU   C  CR66  0   0.134  -2.5647   0.5305  -0.5061
 BK5  CAV   C  CR66  0   0.118  -2.0386  -0.5643   0.2282
 BK5  NAZ   N  NR5   0  -0.362   3.5293  -1.1033  -0.1423
 BK5  H2    H  HCR6  0   0.253   6.1138   2.4112   0.5331
 BK5  HAA   H  HCH3  0   0.238  -9.2033  -1.0257   0.5207
 BK5  HAAA  H  HCH3  0   0.236  -8.6437   0.6438   0.4467
 BK5  HAAB  H  HCH3  0   0.235  -8.6154  -0.3697  -1.0055
 BK5  HAB   H  HCH3  0   0.238   4.8848  -3.9865   1.0046
 BK5  HABA  H  HCH3  0   0.239   4.3253  -2.6021   1.9426
 BK5  HABB  H  HCH3  0   0.231   3.1699  -3.5744   1.0211
 BK5  HAC   H  HCH3  0   0.240   4.3445  -2.3701  -2.3688
 BK5  HACA  H  HCH3  0   0.239   4.9279  -3.8329  -1.5752
 BK5  HACB  H  HCH3  0   0.233   3.2048  -3.4617  -1.5679
 BK5  HNAD  H  HNH2  0   0.405   2.0404   4.1064   0.7580
 BK5  HNAA  H  HNH2  0   0.416   0.8966   2.8443   0.5281
 BK5  HAE   H  HCR6  0   0.285  -4.9555  -2.0016   1.2036
 BK5  HAF   H  HCR6  0   0.272   0.3646   1.9148  -1.5258
 BK5  HAG   H  HCR6  0   0.263  -2.5604  -2.3023   1.3954
 BK5  HAH   H  HCR6  0   0.258  -2.0392   2.2536  -1.7032
 BK5  HAJ   H  HCR6  0   0.259  -4.3564   1.5350  -1.1676
 BK5  HAK   H  HCR6  0   0.252  -0.2539  -1.5593   0.9111
 BK5  HAL   H  HCH2  0   0.227  -6.9488  -0.8599   1.5228
 BK5  HALA  H  HCH2  0   0.227  -6.9283  -1.8700   0.0722
 BK5  HAY   H  HCH1  0   0.263   5.4102  -1.8674  -0.1706
 BK5  CAY   C  CH1   0  -0.119   4.3972  -2.2709  -0.2013
 BK5  OAP   O  O2    0  -0.472  -6.1356   0.0333  -0.1630

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
 BK5  N1   C6    aromatic  1.336  0.020  1.336
 BK5  C2   N1    aromatic  1.332  0.020  1.332
 BK5  N3   C2    aromatic  1.316  0.020  1.316
 BK5  N3   C4    aromatic  1.337  0.020  1.337
 BK5  C4   NAZ   aromatic  1.344  0.020  1.344
 BK5  C4   C5    aromatic  1.399  0.020  1.399
 BK5  C5   C6    aromatic  1.415  0.020  1.415
 BK5  C5   CAT   aromatic  1.424  0.020  1.424
 BK5  C6   NAD   single    1.334  0.020  1.334
 BK5  CAC  CAY   single    1.521  0.020  1.521
 BK5  CAF  CAH   aromatic  1.365  0.020  1.365
 BK5  CAF  CAR   aromatic  1.419  0.020  1.419
 BK5  CAG  CAE   aromatic  1.369  0.020  1.369
 BK5  CAH  CAU   aromatic  1.417  0.020  1.417
 BK5  CAJ  CAQ   aromatic  1.377  0.020  1.377
 BK5  CAK  CAV   aromatic  1.412  0.020  1.412
 BK5  CAL  CAA   single    1.510  0.020  1.510
 BK5  CAL  OAP   single    1.423  0.020  1.423
 BK5  NAO  CAT   aromatic  1.314  0.020  1.314
 BK5  CAQ  CAE   aromatic  1.416  0.020  1.416
 BK5  CAQ  OAP   single    1.344  0.020  1.344
 BK5  CAR  CAK   aromatic  1.373  0.020  1.373
 BK5  CAT  CAR   single    1.466  0.020  1.466
 BK5  CAU  CAJ   aromatic  1.407  0.020  1.407
 BK5  CAU  CAV   aromatic  1.419  0.020  1.419
 BK5  CAV  CAG   aromatic  1.411  0.020  1.411
 BK5  CAY  CAB   single    1.522  0.020  1.522
 BK5  CAY  NAZ   single    1.456  0.020  1.456
 BK5  NAZ  NAO   aromatic  1.338  0.020  1.338
 BK5  C2   H2    single    0.930  0.020  1.080
 BK5  CAA  HAA   single    0.970  0.020  1.090
 BK5  CAA  HAAA  single    0.970  0.020  1.090
 BK5  CAA  HAAB  single    0.970  0.020  1.090
 BK5  CAB  HAB   single    0.970  0.020  1.090
 BK5  CAB  HABA  single    0.970  0.020  1.090
 BK5  CAB  HABB  single    0.970  0.020  1.090
 BK5  CAC  HAC   single    0.970  0.020  1.090
 BK5  CAC  HACA  single    0.970  0.020  1.090
 BK5  CAC  HACB  single    0.970  0.020  1.090
 BK5  NAD  HNAD  single    0.860  0.020  1.020
 BK5  NAD  HNAA  single    0.860  0.020  1.020
 BK5  CAE  HAE   single    0.930  0.020  1.080
 BK5  CAF  HAF   single    0.930  0.020  1.080
 BK5  CAG  HAG   single    0.930  0.020  1.080
 BK5  CAH  HAH   single    0.930  0.020  1.080
 BK5  CAJ  HAJ   single    0.930  0.020  1.080
 BK5  CAK  HAK   single    0.930  0.020  1.080
 BK5  CAL  HAL   single    0.970  0.020  1.090
 BK5  CAL  HALA  single    0.970  0.020  1.090
 BK5  CAY  HAY   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
 BK5  C6    N1   C2    118.99  3.000
 BK5  H2    C2   N3    116.22  3.000
 BK5  H2    C2   N1    115.27  3.000
 BK5  N3    C2   N1    128.50  3.000
 BK5  C4    N3   C2    112.15  3.000
 BK5  NAZ   C4   C5    106.77  3.000
 BK5  C5    C4   N3    126.25  3.000
 BK5  NAZ   C4   N3    126.98  3.000
 BK5  CAT   C5   C6    140.11  3.000
 BK5  CAT   C5   C4    104.43  3.000
 BK5  C6    C5   C4    115.31  3.000
 BK5  NAD   C6   C5    123.72  3.000
 BK5  NAD   C6   N1    117.62  3.000
 BK5  C5    C6   N1    118.66  3.000
 BK5  HAAB  CAA  HAAA  108.67  3.000
 BK5  HAAB  CAA  HAA   107.90  3.000
 BK5  HAAA  CAA  HAA   107.92  3.000
 BK5  HAAB  CAA  CAL   111.38  3.000
 BK5  HAAA  CAA  CAL   111.54  3.000
 BK5  HAA   CAA  CAL   109.29  3.000
 BK5  HABB  CAB  HABA  108.44  3.000
 BK5  HABB  CAB  HAB   107.99  3.000
 BK5  HABA  CAB  HAB   107.99  3.000
 BK5  HABB  CAB  CAY   111.06  3.000
 BK5  HABA  CAB  CAY   111.31  3.000
 BK5  HAB   CAB  CAY   109.93  3.000
 BK5  HACB  CAC  HACA  107.93  3.000
 BK5  HACB  CAC  HAC   108.55  3.000
 BK5  HACA  CAC  HAC   108.01  3.000
 BK5  HACB  CAC  CAY   111.32  3.000
 BK5  HACA  CAC  CAY   109.53  3.000
 BK5  HAC   CAC  CAY   111.38  3.000
 BK5  HNAA  NAD  HNAD  117.43  3.000
 BK5  HNAA  NAD  C6    121.87  3.000
 BK5  HNAD  NAD  C6    119.01  3.000
 BK5  HAE   CAE  CAQ   121.03  3.000
 BK5  HAE   CAE  CAG   118.84  3.000
 BK5  CAQ   CAE  CAG   120.13  3.000
 BK5  HAF   CAF  CAR   119.69  3.000
 BK5  HAF   CAF  CAH   119.18  3.000
 BK5  CAR   CAF  CAH   121.11  3.000
 BK5  HAG   CAG  CAV   119.17  3.000
 BK5  HAG   CAG  CAE   119.38  3.000
 BK5  CAV   CAG  CAE   121.45  3.000
 BK5  HAH   CAH  CAU   119.22  3.000
 BK5  HAH   CAH  CAF   119.92  3.000
 BK5  CAU   CAH  CAF   120.85  3.000
 BK5  HAJ   CAJ  CAU   119.52  3.000
 BK5  HAJ   CAJ  CAQ   119.68  3.000
 BK5  CAU   CAJ  CAQ   120.80  3.000
 BK5  HAK   CAK  CAV   118.83  3.000
 BK5  HAK   CAK  CAR   120.02  3.000
 BK5  CAV   CAK  CAR   121.15  3.000
 BK5  HALA  CAL  HAL   107.66  3.000
 BK5  HALA  CAL  OAP   110.34  3.000
 BK5  HAL   CAL  OAP   110.24  3.000
 BK5  HALA  CAL  CAA   110.20  3.000
 BK5  HAL   CAL  CAA   110.49  3.000
 BK5  OAP   CAL  CAA   107.92  3.000
 BK5  NAZ   NAO  CAT   107.83  3.000
 BK5  OAP   CAQ  CAJ   116.94  3.000
 BK5  OAP   CAQ  CAE   123.40  3.000
 BK5  CAJ   CAQ  CAE   119.66  3.000
 BK5  CAT   CAR  CAK   120.67  3.000
 BK5  CAT   CAR  CAF   120.37  3.000
 BK5  CAK   CAR  CAF   118.93  3.000
 BK5  CAR   CAT  NAO   120.54  3.000
 BK5  CAR   CAT  C5    129.86  3.000
 BK5  NAO   CAT  C5    109.60  3.000
 BK5  CAV   CAU  CAJ   119.72  3.000
 BK5  CAV   CAU  CAH   118.26  3.000
 BK5  CAJ   CAU  CAH   122.02  3.000
 BK5  CAU   CAV  CAK   119.68  3.000
 BK5  CAU   CAV  CAG   118.24  3.000
 BK5  CAK   CAV  CAG   122.07  3.000
 BK5  CAY   NAZ  NAO   120.88  3.000
 BK5  NAO   NAZ  C4    111.37  3.000
 BK5  CAY   NAZ  C4    127.74  3.000
 BK5  HAY   CAY  NAZ   104.81  3.000
 BK5  HAY   CAY  CAC   109.09  3.000
 BK5  NAZ   CAY  CAC   110.79  3.000
 BK5  HAY   CAY  CAB   109.08  3.000
 BK5  NAZ   CAY  CAB   110.41  3.000
 BK5  CAC   CAY  CAB   112.37  3.000
 BK5  CAQ   OAP  CAL   119.69  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
 BK5  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 BK5  CONST_02  CAT   C5   C6   N1    180.00   0.0  0
 BK5  CONST_03  C4    N3   C2   N1      0.00   0.0  0
 BK5  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 BK5  CONST_05  NAZ   C4   N3   C2    180.00   0.0  0
 BK5  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 BK5  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 BK5  CONST_08  NAO   NAZ  C4   N3    180.00   0.0  0
 BK5  CONST_09  C6    C5   C4   N3      0.00   0.0  0
 BK5  CONST_10  CAT   C5   C4   N3    180.00   0.0  0
 BK5  CONST_11  CAT   NAO  NAZ  C4      0.00   0.0  0
 BK5  CONST_12  NAO   CAT  C5   C4      0.00   0.0  0
 BK5  CONST_13  CAR   CAT  C5   C4    180.00   0.0  0
 BK5  CONST_14  NAO   NAZ  C4   C5      0.00   0.0  0
 BK5  CONST_15  NAZ   NAO  CAT  C5      0.00   0.0  0
 BK5  CONST_18  NAZ   C4   C5   C6    180.00   0.0  0
 BK5  CONST_19  NAO   CAT  C5   C6    180.00   0.0  0
 BK5  CONST_20  CAR   CAT  C5   C6      0.00   0.0  0
 BK5  CONST_21  CAK   CAV  CAG  CAE   180.00   0.0  0
 BK5  CONST_22  CAU   CAV  CAG  CAE     0.00   0.0  0
 BK5  CONST_23  CAU   CAJ  CAQ  CAE     0.00   0.0  0
 BK5  CONST_24  CAJ   CAU  CAH  CAF   180.00   0.0  0
 BK5  CONST_25  CAV   CAU  CAH  CAF     0.00   0.0  0
 BK5  CONST_26  CAV   CAK  CAR  CAF     0.00   0.0  0
 BK5  CONST_28  CAJ   CAQ  CAE  CAG     0.00   0.0  0
 BK5  CONST_29  CAR   CAK  CAV  CAG   180.00   0.0  0
 BK5  CONST_30  CAH   CAU  CAV  CAG   180.00   0.0  0
 BK5  CONST_31  CAJ   CAU  CAV  CAG     0.00   0.0  0
 BK5  CONST_32  CAK   CAR  CAF  CAH     0.00   0.0  0
 BK5  CONST_33  CAT   CAR  CAF  CAH   180.00   0.0  0
 BK5  CONST_34  CAQ   CAJ  CAU  CAH   180.00   0.0  0
 BK5  CONST_35  CAK   CAV  CAU  CAH     0.00   0.0  0
 BK5  CONST_36  CAK   CAV  CAU  CAJ   180.00   0.0  0
 BK5  CONST_38  CAV   CAU  CAJ  CAQ     0.00   0.0  0
 BK5  CONST_39  CAV   CAG  CAE  CAQ     0.00   0.0  0
 BK5  CONST_40  CAU   CAH  CAF  CAR     0.00   0.0  0
 BK5  CONST_41  CAU   CAV  CAK  CAR     0.00   0.0  0
 BK5  CONST_42  NAZ   NAO  CAT  CAR   180.00   0.0  0
 BK5  CONST_43  NAZ   C4   C5   CAT     0.00   0.0  0
 BK5  CONST_44  CAV   CAK  CAR  CAT   180.00   0.0  0
 BK5  CONST_45  NAD   C6   N1   C2    180.00   0.0  0
 BK5  CONST_46  CAY   NAZ  C4   N3      0.00   0.0  0
 BK5  CONST_47  NAD   C6   C5   C4    180.00   0.0  0
 BK5  CONST_48  CAY   NAZ  C4   C5    180.00   0.0  0
 BK5  CONST_49  CAT   C5   C6   NAD     0.00   0.0  0
 BK5  CONST_50  OAP   CAQ  CAE  CAG   180.00   0.0  0
 BK5  CONST_51  CAU   CAJ  CAQ  OAP   180.00   0.0  0
 BK5  CONST_52  CAY   NAZ  NAO  CAT   180.00   0.0  0
 BK5  CONST_53  H2    C2   N3   C4    180.00   0.0  0
 BK5  CONST_54  HAJ   CAJ  CAQ  CAE   180.00   0.0  0
 BK5  CONST_55  HAK   CAK  CAR  CAF   180.00   0.0  0
 BK5  CONST_56  HAE   CAE  CAQ  CAJ   180.00   0.0  0
 BK5  CONST_57  HAH   CAH  CAU  CAJ     0.00   0.0  0
 BK5  CONST_58  HAG   CAG  CAV  CAK     0.00   0.0  0
 BK5  CONST_59  HAF   CAF  CAR  CAK   180.00   0.0  0
 BK5  CONST_60  HNAD  NAD  C6   N1      0.00   0.0  0
 BK5  CONST_61  HNAA  NAD  C6   N1    180.00   0.0  0
 BK5  Var_01    CAC   CAY  NAZ  C4   -123.95  30.0  2
 BK5  Var_02    HAL   CAL  OAP  CAQ    60.42  30.0  1
 BK5  Var_03    HAC   CAC  CAY  NAZ    54.95  30.0  3
 BK5  Var_04    HAB   CAB  CAY  NAZ  -175.55  30.0  3
 BK5  Var_05    HAA   CAA  CAL  OAP   179.92  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
 BK5  plan-1  N1    0.020
 BK5  plan-1  C2    0.020
 BK5  plan-1  N3    0.020
 BK5  plan-1  C4    0.020
 BK5  plan-1  C5    0.020
 BK5  plan-1  C6    0.020
 BK5  plan-1  NAD   0.020
 BK5  plan-1  NAO   0.020
 BK5  plan-1  CAR   0.020
 BK5  plan-1  CAT   0.020
 BK5  plan-1  NAZ   0.020
 BK5  plan-1  H2    0.020
 BK5  plan-1  CAY   0.020
 BK5  plan-2  CAE   0.020
 BK5  plan-2  CAF   0.020
 BK5  plan-2  CAG   0.020
 BK5  plan-2  CAH   0.020
 BK5  plan-2  CAJ   0.020
 BK5  plan-2  CAK   0.020
 BK5  plan-2  CAQ   0.020
 BK5  plan-2  CAR   0.020
 BK5  plan-2  CAT   0.020
 BK5  plan-2  CAU   0.020
 BK5  plan-2  CAV   0.020
 BK5  plan-2  HAE   0.020
 BK5  plan-2  HAF   0.020
 BK5  plan-2  HAG   0.020
 BK5  plan-2  HAH   0.020
 BK5  plan-2  HAJ   0.020
 BK5  plan-2  HAK   0.020
 BK5  plan-2  OAP   0.020
 BK5  plan-3  C6    0.020
 BK5  plan-3  NAD   0.020
 BK5  plan-3  HNAD  0.020
 BK5  plan-3  HNAA  0.020

