# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 19:08:47 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-(naphthalen-1-ylmethyl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CC3CCNCC3)nc(Cc4cccc5ccccc45)c12
#
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
 BK3  BK3  3-(naphthalen-1-ylmethyl)-1-(piperidin-4-ylmethyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  52  28  .  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_BK3
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
 BK3  N1    N  N     0  -0.480   0.4364   4.1543  -0.3078
 BK3  C2    C  CR16  0   0.056   1.4457   3.7265  -1.0654
 BK3  N3    N  N     0  -0.464   1.8714   2.4935  -1.2422
 BK3  C4    C  CR56  0   0.582   1.1362   1.6059  -0.5647
 BK3  C5    C  CR56  0  -0.264   0.0373   1.8904   0.2524
 BK3  C6    C  CR6   0   0.436  -0.2813   3.2621   0.3786
 BK3  NAA   N  NH2   0  -0.822  -1.2756   3.7259   1.1428
 BK3  NBB   N  NR5   0  -0.369   1.3021   0.2733  -0.5426
 BK3  NAR   N  N     0  -0.262   0.3821  -0.3165   0.2396
 BK3  NAS   N  NH1   0  -0.576   5.7384  -2.1593   0.9826
 BK3  CAB   C  CR16  0  -0.260  -3.7001  -3.7165  -1.0009
 BK3  CAC   C  CR16  0  -0.249  -2.5145  -3.5514  -0.2585
 BK3  CAD   C  CR16  0  -0.242  -4.9069   0.8783  -0.1227
 BK3  CAE   C  CR16  0  -0.329  -3.7292   1.0466   0.6317
 BK3  CAG   C  CR16  0  -0.310  -4.5627  -2.6656  -1.1462
 BK3  CAH   C  CR16  0  -0.333  -5.1802  -0.3253  -0.7061
 BK3  CAI   C  CR16  0  -0.320  -2.2154  -2.3466   0.3192
 BK3  CAJ   C  CH2   0  -0.315   5.9560  -1.5613  -0.3245
 BK3  CAK   C  CH2   0  -0.314   4.7364  -1.4287   1.7416
 BK3  CAL   C  CH2   0  -0.432   4.6788  -1.3781  -1.1417
 BK3  CAM   C  CH2   0  -0.427   3.4086  -1.2446   1.0088
 BK3  CAO   C  CH2   0  -0.285   2.3484  -0.4924  -1.1803
 BK3  CAU   C  CR6   0   0.158  -2.8244   0.0291   0.7961
 BK3  CAV   C  CR5   0   0.305  -0.3945   0.6198   0.7253
 BK3  CAW   C  CR66  0   0.111  -4.2837  -1.4093  -0.5580
 BK3  CAX   C  CR66  0   0.063  -3.0883  -1.2373   0.1944
 BK3  CBA   C  CH1   0  -0.258   3.6283  -0.5946  -0.3553
 BK3  H2    H  HCR6  0   0.254   1.9872   4.5021  -1.5972
 BK3  HNAA  H  HNH2  0   0.406  -1.3735   4.7210   1.2582
 BK3  HNAB  H  HNH2  0   0.411  -1.7319   3.1462   1.8233
 BK3  HNAS  H  HNH1  0   0.337   5.4194  -3.1136   0.8554
 BK3  HAC   H  HCR6  0   0.258  -1.8333  -4.3846  -0.1448
 BK3  HAD   H  HCR6  0   0.259  -5.5920   1.7088  -0.2311
 BK3  HAE   H  HCR6  0   0.241  -3.5440   2.0099   1.0898
 BK3  HAG   H  HCR6  0   0.255  -5.4771  -2.7823  -1.7156
 BK3  HAH   H  HCR6  0   0.255  -6.0849  -0.4651  -1.2856
 BK3  HAI   H  HCR6  0   0.245  -1.2898  -2.2469   0.8670
 BK3  HAJ   H  HCH2  0   0.214   6.4307  -0.5848  -0.1763
 BK3  HAJA  H  HCH2  0   0.235   6.6710  -2.1747  -0.8768
 BK3  HAK   H  HCH2  0   0.234   4.5722  -1.9411   2.6920
 BK3  HAKA  H  HCH2  0   0.214   5.1505  -0.4443   1.9868
 BK3  HAL   H  HCH2  0   0.230   4.9084  -0.8701  -2.0831
 BK3  HALA  H  HCH2  0   0.215   4.2747  -2.3628  -1.4052
 BK3  HAM   H  HCH2  0   0.211   2.9301  -2.2224   0.8756
 BK3  HAMA  H  HCH2  0   0.232   2.7341  -0.6440   1.6241
 BK3  HAO   H  HCH2  0   0.258   1.9433  -1.4847  -1.3836
 BK3  HAOA  H  HCH2  0   0.264   2.5636  -0.0232  -2.1418
 BK3  HBA   H  HCH1  0   0.230   4.0103   0.4228  -0.1963
 BK3  CAN   C  CH2   0  -0.687  -1.5633   0.2689   1.5946
 BK3  HAB   H  HCR6  0   0.258  -3.9243  -4.6736  -1.4535
 BK3  HAN   H  HCH2  0   0.281  -1.7403   1.0665   2.3173
 BK3  HANA  H  HCH2  0   0.291  -1.3097  -0.6071   2.1930

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
 BK3  C2   N1    aromatic  1.333  0.020  1.333
 BK3  N1   C6    aromatic  1.335  0.020  1.335
 BK3  N3   C2    aromatic  1.316  0.020  1.316
 BK3  C2   H2    single    0.930  0.020  1.080
 BK3  N3   C4    aromatic  1.337  0.020  1.337
 BK3  NBB  C4    aromatic  1.343  0.020  1.343
 BK3  C4   C5    aromatic  1.399  0.020  1.399
 BK3  CAV  C5    aromatic  1.423  0.020  1.423
 BK3  C5   C6    aromatic  1.414  0.020  1.414
 BK3  C6   NAA   single    1.337  0.020  1.337
 BK3  NAA  HNAA  single    0.860  0.020  1.020
 BK3  NAA  HNAB  single    0.860  0.020  1.020
 BK3  CAO  NBB   single    1.445  0.020  1.445
 BK3  NBB  NAR   aromatic  1.344  0.020  1.344
 BK3  NAR  CAV   aromatic  1.310  0.020  1.310
 BK3  CAJ  NAS   single    1.454  0.020  1.454
 BK3  NAS  CAK   single    1.454  0.020  1.454
 BK3  NAS  HNAS  single    0.890  0.020  1.040
 BK3  CAC  CAB   aromatic  1.409  0.020  1.409
 BK3  CAG  CAB   aromatic  1.367  0.020  1.367
 BK3  CAB  HAB   single    0.930  0.020  1.080
 BK3  CAI  CAC   aromatic  1.369  0.020  1.369
 BK3  CAC  HAC   single    0.930  0.020  1.080
 BK3  CAE  CAD   aromatic  1.409  0.020  1.409
 BK3  CAD  CAH   aromatic  1.365  0.020  1.365
 BK3  CAD  HAD   single    0.930  0.020  1.080
 BK3  CAE  CAU   aromatic  1.372  0.020  1.372
 BK3  CAE  HAE   single    0.930  0.020  1.080
 BK3  CAW  CAG   aromatic  1.415  0.020  1.415
 BK3  CAG  HAG   single    0.930  0.020  1.080
 BK3  CAH  CAW   aromatic  1.414  0.020  1.414
 BK3  CAH  HAH   single    0.930  0.020  1.080
 BK3  CAX  CAI   aromatic  1.417  0.020  1.417
 BK3  CAI  HAI   single    0.930  0.020  1.080
 BK3  CAJ  CAL   single    1.527  0.020  1.527
 BK3  CAJ  HAJ   single    0.970  0.020  1.090
 BK3  CAJ  HAJA  single    0.970  0.020  1.090
 BK3  CAK  CAM   single    1.528  0.020  1.528
 BK3  CAK  HAK   single    0.970  0.020  1.090
 BK3  CAK  HAKA  single    0.970  0.020  1.090
 BK3  CAL  CBA   single    1.528  0.020  1.528
 BK3  CAL  HAL   single    0.970  0.020  1.090
 BK3  CAL  HALA  single    0.970  0.020  1.090
 BK3  CBA  CAM   single    1.527  0.020  1.527
 BK3  CAM  HAM   single    0.970  0.020  1.090
 BK3  CAM  HAMA  single    0.970  0.020  1.090
 BK3  CAV  CAN   single    1.498  0.020  1.498
 BK3  CAN  CAU   single    1.512  0.020  1.512
 BK3  CAN  HAN   single    0.970  0.020  1.090
 BK3  CAN  HANA  single    0.970  0.020  1.090
 BK3  CBA  CAO   single    1.526  0.020  1.526
 BK3  CAO  HAO   single    0.970  0.020  1.090
 BK3  CAO  HAOA  single    0.970  0.020  1.090
 BK3  CAU  CAX   aromatic  1.427  0.020  1.427
 BK3  CAX  CAW   aromatic  1.423  0.020  1.423
 BK3  CBA  HBA   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
 BK3  C6    N1   C2    119.01  3.000
 BK3  H2    C2   N3    116.25  3.000
 BK3  H2    C2   N1    115.28  3.000
 BK3  N3    C2   N1    128.47  3.000
 BK3  C4    N3   C2    112.08  3.000
 BK3  NBB   C4   C5    106.82  3.000
 BK3  C5    C4   N3    126.38  3.000
 BK3  NBB   C4   N3    126.81  3.000
 BK3  CAV   C5   C6    140.20  3.000
 BK3  C6    C5   C4    115.25  3.000
 BK3  CAV   C5   C4    104.53  3.000
 BK3  NAA   C6   C5    123.72  3.000
 BK3  NAA   C6   N1    117.51  3.000
 BK3  C5    C6   N1    118.77  3.000
 BK3  HNAB  NAA  HNAA  116.68  3.000
 BK3  HNAB  NAA  C6    121.69  3.000
 BK3  HNAA  NAA  C6    118.74  3.000
 BK3  CAO   NBB  NAR   121.34  3.000
 BK3  NAR   NBB  C4    111.13  3.000
 BK3  CAO   NBB  C4    127.44  3.000
 BK3  CAV   NAR  NBB   107.94  3.000
 BK3  HNAS  NAS  CAK   108.75  3.000
 BK3  HNAS  NAS  CAJ   108.74  3.000
 BK3  CAK   NAS  CAJ   111.46  3.000
 BK3  HAB   CAB  CAG   120.31  3.000
 BK3  HAB   CAB  CAC   119.90  3.000
 BK3  CAG   CAB  CAC   119.80  3.000
 BK3  HAC   CAC  CAI   119.71  3.000
 BK3  HAC   CAC  CAB   119.66  3.000
 BK3  CAI   CAC  CAB   120.62  3.000
 BK3  HAD   CAD  CAH   120.48  3.000
 BK3  HAD   CAD  CAE   119.42  3.000
 BK3  CAH   CAD  CAE   120.10  3.000
 BK3  HAE   CAE  CAU   119.77  3.000
 BK3  HAE   CAE  CAD   118.42  3.000
 BK3  CAU   CAE  CAD   121.81  3.000
 BK3  HAG   CAG  CAW   118.72  3.000
 BK3  HAG   CAG  CAB   120.36  3.000
 BK3  CAW   CAG  CAB   120.92  3.000
 BK3  HAH   CAH  CAW   119.11  3.000
 BK3  HAH   CAH  CAD   120.63  3.000
 BK3  CAW   CAH  CAD   120.27  3.000
 BK3  HAI   CAI  CAX   120.01  3.000
 BK3  HAI   CAI  CAC   118.84  3.000
 BK3  CAX   CAI  CAC   121.14  3.000
 BK3  HAJA  CAJ  HAJ   106.58  3.000
 BK3  HAJA  CAJ  CAL   110.14  3.000
 BK3  HAJ   CAJ  CAL   109.13  3.000
 BK3  HAJA  CAJ  NAS   108.77  3.000
 BK3  HAJ   CAJ  NAS   108.04  3.000
 BK3  CAL   CAJ  NAS   113.91  3.000
 BK3  HAKA  CAK  HAK   106.48  3.000
 BK3  HAKA  CAK  CAM   109.12  3.000
 BK3  HAK   CAK  CAM   110.08  3.000
 BK3  HAKA  CAK  NAS   107.92  3.000
 BK3  HAK   CAK  NAS   108.80  3.000
 BK3  CAM   CAK  NAS   114.15  3.000
 BK3  HALA  CAL  HAL   106.71  3.000
 BK3  HALA  CAL  CBA   109.31  3.000
 BK3  HAL   CAL  CBA   110.42  3.000
 BK3  HALA  CAL  CAJ   109.21  3.000
 BK3  HAL   CAL  CAJ   109.91  3.000
 BK3  CBA   CAL  CAJ   111.16  3.000
 BK3  HAMA  CAM  HAM   106.80  3.000
 BK3  HAMA  CAM  CBA   110.97  3.000
 BK3  HAM   CAM  CBA   109.50  3.000
 BK3  HAMA  CAM  CAK   109.43  3.000
 BK3  HAM   CAM  CAK   109.27  3.000
 BK3  CBA   CAM  CAK   110.78  3.000
 BK3  HAOA  CAO  HAO   107.47  3.000
 BK3  HAOA  CAO  CBA   109.86  3.000
 BK3  HAO   CAO  CBA   110.57  3.000
 BK3  HAOA  CAO  NBB   107.69  3.000
 BK3  HAO   CAO  NBB   107.18  3.000
 BK3  CBA   CAO  NBB   113.84  3.000
 BK3  CAX   CAU  CAN   121.19  3.000
 BK3  CAX   CAU  CAE   119.08  3.000
 BK3  CAN   CAU  CAE   119.73  3.000
 BK3  CAN   CAV  NAR   120.68  3.000
 BK3  CAN   CAV  C5    129.70  3.000
 BK3  NAR   CAV  C5    109.58  3.000
 BK3  CAX   CAW  CAH   119.69  3.000
 BK3  CAX   CAW  CAG   119.52  3.000
 BK3  CAH   CAW  CAG   120.79  3.000
 BK3  CAW   CAX  CAU   119.05  3.000
 BK3  CAW   CAX  CAI   118.00  3.000
 BK3  CAU   CAX  CAI   122.94  3.000
 BK3  HBA   CBA  CAO   107.94  3.000
 BK3  HBA   CBA  CAM   108.37  3.000
 BK3  CAO   CBA  CAM   113.01  3.000
 BK3  HBA   CBA  CAL   108.08  3.000
 BK3  CAO   CBA  CAL   109.42  3.000
 BK3  CAM   CBA  CAL   109.90  3.000
 BK3  HANA  CAN  HAN   105.15  3.000
 BK3  HANA  CAN  CAV   108.97  3.000
 BK3  HAN   CAN  CAV   109.86  3.000
 BK3  HANA  CAN  CAU   110.88  3.000
 BK3  HAN   CAN  CAU   109.30  3.000
 BK3  CAV   CAN  CAU   112.43  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
 BK3  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 BK3  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 BK3  CONST_03  CAV   C5   C6   N1   180.00   0.0  0
 BK3  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 BK3  CONST_05  NBB   C4   N3   C2   180.00   0.0  0
 BK3  CONST_06  C5    C4   N3   C2     0.00   0.0  0
 BK3  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 BK3  CONST_08  NAR   NBB  C4   N3   180.00   0.0  0
 BK3  CONST_09  CAV   C5   C4   N3   180.00   0.0  0
 BK3  CONST_10  C6    C5   C4   N3     0.00   0.0  0
 BK3  CONST_11  CAV   NAR  NBB  C4     0.00   0.0  0
 BK3  CONST_12  NAR   CAV  C5   C4     0.00   0.0  0
 BK3  CONST_13  NAR   NBB  C4   C5     0.00   0.0  0
 BK3  CONST_14  NBB   NAR  CAV  C5     0.00   0.0  0
 BK3  CONST_15  NBB   C4   C5   C6   180.00   0.0  0
 BK3  CONST_16  NAR   CAV  C5   C6   180.00   0.0  0
 BK3  CONST_17  CAV   C5   C4   NBB    0.00   0.0  0
 BK3  CONST_18  CAX   CAI  CAC  CAB    0.00   0.0  0
 BK3  CONST_19  CAH   CAW  CAG  CAB  180.00   0.0  0
 BK3  CONST_20  CAX   CAW  CAG  CAB    0.00   0.0  0
 BK3  CONST_21  CAW   CAG  CAB  CAC    0.00   0.0  0
 BK3  CONST_22  CAU   CAX  CAI  CAC  180.00   0.0  0
 BK3  CONST_23  CAW   CAX  CAI  CAC    0.00   0.0  0
 BK3  CONST_24  CAX   CAU  CAE  CAD    0.00   0.0  0
 BK3  CONST_25  CAG   CAW  CAH  CAD  180.00   0.0  0
 BK3  CONST_26  CAX   CAW  CAH  CAD    0.00   0.0  0
 BK3  CONST_27  CAW   CAH  CAD  CAE    0.00   0.0  0
 BK3  CONST_28  CAI   CAX  CAU  CAE  180.00   0.0  0
 BK3  CONST_29  CAW   CAX  CAU  CAE    0.00   0.0  0
 BK3  CONST_30  CAI   CAC  CAB  CAG    0.00   0.0  0
 BK3  CONST_31  CAI   CAX  CAW  CAG    0.00   0.0  0
 BK3  CONST_32  CAU   CAX  CAW  CAG  180.00   0.0  0
 BK3  CONST_33  CAU   CAE  CAD  CAH    0.00   0.0  0
 BK3  CONST_34  CAI   CAX  CAW  CAH  180.00   0.0  0
 BK3  CONST_35  CAU   CAX  CAW  CAH    0.00   0.0  0
 BK3  CONST_36  NAA   C6   N1   C2   180.00   0.0  0
 BK3  CONST_37  CAO   NBB  C4   N3     0.00   0.0  0
 BK3  CONST_38  CAN   CAV  C5   C4   180.00   0.0  0
 BK3  CONST_39  NAA   C6   C5   C4   180.00   0.0  0
 BK3  CONST_40  CAO   NBB  C4   C5   180.00   0.0  0
 BK3  CONST_41  CAN   CAV  C5   C6     0.00   0.0  0
 BK3  CONST_42  CAV   C5   C6   NAA    0.00   0.0  0
 BK3  CONST_43  CAN   CAV  NAR  NBB  180.00   0.0  0
 BK3  CONST_44  CAN   CAU  CAE  CAD  180.00   0.0  0
 BK3  CONST_45  CAN   CAU  CAX  CAI    0.00   0.0  0
 BK3  CONST_46  CAW   CAX  CAU  CAN  180.00   0.0  0
 BK3  CONST_47  CAV   NAR  NBB  CAO  180.00   0.0  0
 BK3  CONST_48  H2    C2   N3   C4   180.00   0.0  0
 BK3  CONST_49  HAI   CAI  CAC  CAB  180.00   0.0  0
 BK3  CONST_50  HAG   CAG  CAB  CAC  180.00   0.0  0
 BK3  CONST_51  HAH   CAH  CAD  CAE  180.00   0.0  0
 BK3  CONST_52  HAC   CAC  CAB  CAG  180.00   0.0  0
 BK3  CONST_53  HAE   CAE  CAD  CAH  180.00   0.0  0
 BK3  CONST_54  HAB   CAB  CAC  CAI  180.00   0.0  0
 BK3  CONST_55  HAD   CAD  CAE  CAU  180.00   0.0  0
 BK3  CONST_56  HNAA  NAA  C6   N1     0.00   0.0  0
 BK3  CONST_57  HNAB  NAA  C6   N1   180.00   0.0  0
 BK3  Var_01    CBA   CAL  CAJ  NAS   54.02  30.0  1
 BK3  Var_02    CBA   CAM  CAK  NAS  -54.39  30.0  1
 BK3  Var_03    CAM   CAK  NAS  CAJ   53.89  30.0  1
 BK3  Var_04    CAL   CAJ  NAS  CAK  -53.54  30.0  1
 BK3  Var_05    CBA   CAO  NBB  C4    84.72  30.0  1
 BK3  Var_06    CAU   CAN  CAV  C5    88.04  30.0  2
 BK3  Var_07    CAV   CAN  CAU  CAE  -95.87  30.0  2

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
 BK3  chir_01  CBA  CAL  CAM  CAO  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
 BK3  plan-1  N1    0.020
 BK3  plan-1  C2    0.020
 BK3  plan-1  N3    0.020
 BK3  plan-1  C4    0.020
 BK3  plan-1  C5    0.020
 BK3  plan-1  C6    0.020
 BK3  plan-1  NAA   0.020
 BK3  plan-1  NBB   0.020
 BK3  plan-1  NAR   0.020
 BK3  plan-1  CAO   0.020
 BK3  plan-1  CAV   0.020
 BK3  plan-1  H2    0.020
 BK3  plan-1  CAN   0.020
 BK3  plan-2  CAB   0.020
 BK3  plan-2  CAC   0.020
 BK3  plan-2  CAD   0.020
 BK3  plan-2  CAE   0.020
 BK3  plan-2  CAG   0.020
 BK3  plan-2  CAH   0.020
 BK3  plan-2  CAI   0.020
 BK3  plan-2  CAU   0.020
 BK3  plan-2  CAW   0.020
 BK3  plan-2  CAX   0.020
 BK3  plan-2  HAC   0.020
 BK3  plan-2  HAD   0.020
 BK3  plan-2  HAE   0.020
 BK3  plan-2  HAG   0.020
 BK3  plan-2  HAH   0.020
 BK3  plan-2  HAI   0.020
 BK3  plan-2  CAN   0.020
 BK3  plan-2  HAB   0.020
 BK3  plan-3  C6    0.020
 BK3  plan-3  NAA   0.020
 BK3  plan-3  HNAA  0.020
 BK3  plan-3  HNAB  0.020

