# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:52:50 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 1-methyl-3-naphthalen-2-yl-1H-pyrazolo[3,4-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(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
 NPZ  NPZ  1-methyl-3-naphthalen-2-yl-1H-pyrazolo[3,4-d]pyrimidin-4-amine  ligand  34  21  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPZ
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
 NPZ  C6    C  CR6   0   0.433  -1.8886   1.8127  -0.3693
 NPZ  NAF   N  NH2   0  -0.815  -0.7972   2.5100  -0.6925
 NPZ  C5    C  CR56  0  -0.254  -1.8770   0.4280  -0.0752
 NPZ  N1    N  N     0  -0.477  -3.0514   2.4671  -0.3223
 NPZ  C2    C  CR16  0   0.055  -4.1648   1.7891  -0.0499
 NPZ  N3    N  N     0  -0.464  -4.3036   0.4991   0.1726
 NPZ  C4    C  CR56  0   0.570  -3.1337  -0.1451   0.1433
 NPZ  NAT   N  NR5   0  -0.358  -2.9346  -1.4650   0.3064
 NPZ  CAU   C  CH3   0  -0.522  -3.9198  -2.4852   0.5599
 NPZ  NAP   N  N     0  -0.274  -1.6362  -1.7776   0.2207
 NPZ  CAO   C  CR5   0   0.261  -0.9708  -0.6662   0.0007
 NPZ  CAG   C  CR6   0   0.044   0.4902  -0.6949  -0.1109
 NPZ  CAH   C  CR16  0  -0.420   1.2649   0.2782   0.4726
 NPZ  CAA   C  CR16  0  -0.282   1.1210  -1.7659  -0.7931
 NPZ  CAB   C  CR16  0  -0.302   2.4813  -1.8255  -0.8890
 NPZ  CAC   C  CR66  0   0.108   3.2973  -0.8242  -0.3107
 NPZ  CAI   C  CR66  0   0.144   2.6749   0.2445   0.3835
 NPZ  CAD   C  CR16  0  -0.308   4.7077  -0.8577  -0.3994
 NPZ  CAE   C  CR16  0  -0.256   5.4650   0.1252   0.1782
 NPZ  CAK   C  CR16  0  -0.256   4.8461   1.1866   0.8722
 NPZ  CAJ   C  CR16  0  -0.315   3.4828   1.2449   0.9733
 NPZ  H1AF  H  HNH2  0   0.414   0.0686   2.0529  -0.9196
 NPZ  H2AF  H  HNH2  0   0.405  -0.9032   3.4667  -0.9873
 NPZ  H2    H  HCR6  0   0.255  -5.0736   2.3817  -0.0221
 NPZ  H1AU  H  HCH3  0   0.262  -3.9034  -3.2315  -0.2320
 NPZ  H2AU  H  HCH3  0   0.262  -3.7294  -2.9688   1.5161
 NPZ  H3AU  H  HCH3  0   0.263  -4.9004  -2.0196   0.5876
 NPZ  HAH   H  HCR6  0   0.272   0.8037   1.0779   1.0416
 NPZ  HAA   H  HCR6  0   0.256   0.5122  -2.5359  -1.2480
 NPZ  HAB   H  HCR6  0   0.260   2.9519  -2.6467  -1.4158
 NPZ  HAD   H  HCR6  0   0.258   5.1817  -1.6745  -0.9300
 NPZ  HAE   H  HCR6  0   0.261   6.5442   0.0918   0.1050
 NPZ  HAK   H  HCR6  0   0.261   5.4560   1.9577   1.3242
 NPZ  HAJ   H  HCR6  0   0.258   3.0059   2.0613   1.5023

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
 NPZ  N1   C2    aromatic  1.332  0.020  1.332
 NPZ  N1   C6    aromatic  1.335  0.020  1.335
 NPZ  C2   N3    aromatic  1.316  0.020  1.316
 NPZ  NAF  C6    single    1.335  0.020  1.335
 NPZ  C6   C5    aromatic  1.416  0.020  1.416
 NPZ  N3   C4    aromatic  1.336  0.020  1.336
 NPZ  CAB  CAA   aromatic  1.365  0.020  1.365
 NPZ  CAB  CAC   aromatic  1.415  0.020  1.415
 NPZ  CAA  CAG   aromatic  1.418  0.020  1.418
 NPZ  C5   C4    aromatic  1.398  0.020  1.398
 NPZ  C5   CAO   aromatic  1.423  0.020  1.423
 NPZ  C4   NAT   aromatic  1.345  0.020  1.345
 NPZ  CAD  CAC   aromatic  1.414  0.020  1.414
 NPZ  CAD  CAE   aromatic  1.369  0.020  1.369
 NPZ  CAC  CAI   aromatic  1.418  0.020  1.418
 NPZ  NAT  CAU   single    1.441  0.020  1.441
 NPZ  NAT  NAP   aromatic  1.338  0.020  1.338
 NPZ  CAO  CAG   single    1.466  0.020  1.466
 NPZ  CAO  NAP   aromatic  1.314  0.020  1.314
 NPZ  CAG  CAH   aromatic  1.374  0.020  1.374
 NPZ  CAE  CAK   aromatic  1.411  0.020  1.411
 NPZ  CAI  CAH   aromatic  1.413  0.020  1.413
 NPZ  CAI  CAJ   aromatic  1.415  0.020  1.415
 NPZ  CAK  CAJ   aromatic  1.368  0.020  1.368
 NPZ  NAF  H1AF  single    0.860  0.020  1.020
 NPZ  NAF  H2AF  single    0.860  0.020  1.020
 NPZ  C2   H2    single    0.930  0.020  1.080
 NPZ  CAU  H1AU  single    0.970  0.020  1.090
 NPZ  CAU  H2AU  single    0.970  0.020  1.090
 NPZ  CAU  H3AU  single    0.970  0.020  1.090
 NPZ  CAH  HAH   single    0.930  0.020  1.080
 NPZ  CAA  HAA   single    0.930  0.020  1.080
 NPZ  CAB  HAB   single    0.930  0.020  1.080
 NPZ  CAD  HAD   single    0.930  0.020  1.080
 NPZ  CAE  HAE   single    0.930  0.020  1.080
 NPZ  CAK  HAK   single    0.930  0.020  1.080
 NPZ  CAJ  HAJ   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
 NPZ  N1    C6   C5    118.64  3.000
 NPZ  C5    C6   NAF   123.68  3.000
 NPZ  N1    C6   NAF   117.68  3.000
 NPZ  H2AF  NAF  H1AF  117.18  3.000
 NPZ  H2AF  NAF  C6    118.77  3.000
 NPZ  H1AF  NAF  C6    121.43  3.000
 NPZ  CAO   C5   C4    104.41  3.000
 NPZ  CAO   C5   C6    140.23  3.000
 NPZ  C4    C5   C6    115.21  3.000
 NPZ  C2    N1   C6    119.07  3.000
 NPZ  H2    C2   N3    116.26  3.000
 NPZ  H2    C2   N1    115.30  3.000
 NPZ  N3    C2   N1    128.43  3.000
 NPZ  C4    N3   C2    112.12  3.000
 NPZ  NAT   C4   N3    126.89  3.000
 NPZ  NAT   C4   C5    106.75  3.000
 NPZ  N3    C4   C5    126.36  3.000
 NPZ  NAP   NAT  CAU   120.62  3.000
 NPZ  NAP   NAT  C4    111.42  3.000
 NPZ  CAU   NAT  C4    127.96  3.000
 NPZ  H3AU  CAU  H2AU  109.03  3.000
 NPZ  H3AU  CAU  H1AU  109.04  3.000
 NPZ  H2AU  CAU  H1AU  109.39  3.000
 NPZ  H3AU  CAU  NAT   108.57  3.000
 NPZ  H2AU  CAU  NAT   110.46  3.000
 NPZ  H1AU  CAU  NAT   110.32  3.000
 NPZ  CAO   NAP  NAT   107.73  3.000
 NPZ  CAG   CAO  NAP   120.07  3.000
 NPZ  NAP   CAO  C5    109.69  3.000
 NPZ  CAG   CAO  C5    130.23  3.000
 NPZ  CAA   CAG  CAH   119.24  3.000
 NPZ  CAH   CAG  CAO   121.07  3.000
 NPZ  CAA   CAG  CAO   119.66  3.000
 NPZ  HAH   CAH  CAI   118.36  3.000
 NPZ  HAH   CAH  CAG   120.35  3.000
 NPZ  CAI   CAH  CAG   121.26  3.000
 NPZ  HAA   CAA  CAB   120.02  3.000
 NPZ  HAA   CAA  CAG   119.31  3.000
 NPZ  CAB   CAA  CAG   120.67  3.000
 NPZ  HAB   CAB  CAC   118.99  3.000
 NPZ  HAB   CAB  CAA   120.01  3.000
 NPZ  CAC   CAB  CAA   121.00  3.000
 NPZ  CAD   CAC  CAI   119.11  3.000
 NPZ  CAI   CAC  CAB   118.69  3.000
 NPZ  CAD   CAC  CAB   122.20  3.000
 NPZ  CAJ   CAI  CAC   119.10  3.000
 NPZ  CAJ   CAI  CAH   121.77  3.000
 NPZ  CAC   CAI  CAH   119.13  3.000
 NPZ  HAD   CAD  CAE   120.40  3.000
 NPZ  HAD   CAD  CAC   119.03  3.000
 NPZ  CAE   CAD  CAC   120.57  3.000
 NPZ  HAE   CAE  CAK   119.59  3.000
 NPZ  HAE   CAE  CAD   120.07  3.000
 NPZ  CAK   CAE  CAD   120.33  3.000
 NPZ  HAK   CAK  CAJ   120.03  3.000
 NPZ  HAK   CAK  CAE   119.61  3.000
 NPZ  CAJ   CAK  CAE   120.36  3.000
 NPZ  HAJ   CAJ  CAK   120.45  3.000
 NPZ  HAJ   CAJ  CAI   119.02  3.000
 NPZ  CAK   CAJ  CAI   120.53  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
 NPZ  CONST_01  N3    C2   N1   C6     0.00   0.0  0
 NPZ  CONST_02  N3    C4   C5   C6     0.00   0.0  0
 NPZ  CONST_03  NAT   C4   C5   C6   180.00   0.0  0
 NPZ  CONST_04  CAG   CAO  C5   C6     0.00   0.0  0
 NPZ  CONST_05  NAP   CAO  C5   C6   180.00   0.0  0
 NPZ  CONST_06  C2    N1   C6   C5     0.00   0.0  0
 NPZ  CONST_07  C2    N3   C4   C5     0.00   0.0  0
 NPZ  CONST_08  NAP   NAT  C4   C5     0.00   0.0  0
 NPZ  CONST_11  NAT   NAP  CAO  C5     0.00   0.0  0
 NPZ  CONST_12  C4    N3   C2   N1     0.00   0.0  0
 NPZ  CONST_13  C4    C5   C6   N1     0.00   0.0  0
 NPZ  CONST_14  CAO   C5   C6   N1   180.00   0.0  0
 NPZ  CONST_15  NAT   C4   N3   C2   180.00   0.0  0
 NPZ  CONST_16  CAO   C5   C4   N3   180.00   0.0  0
 NPZ  CONST_17  NAP   NAT  C4   N3   180.00   0.0  0
 NPZ  CONST_18  CAG   CAO  C5   C4   180.00   0.0  0
 NPZ  CONST_19  NAP   CAO  C5   C4     0.00   0.0  0
 NPZ  CONST_20  CAO   NAP  NAT  C4     0.00   0.0  0
 NPZ  CONST_21  CAO   C5   C4   NAT    0.00   0.0  0
 NPZ  CONST_22  CAG   CAO  NAP  NAT  180.00   0.0  0
 NPZ  CONST_25  CAB   CAA  CAG  CAO  180.00   0.0  0
 NPZ  CONST_26  CAI   CAH  CAG  CAO  180.00   0.0  0
 NPZ  CONST_27  CAC   CAB  CAA  CAG    0.00   0.0  0
 NPZ  CONST_28  CAC   CAI  CAH  CAG    0.00   0.0  0
 NPZ  CONST_29  CAJ   CAI  CAH  CAG  180.00   0.0  0
 NPZ  CONST_30  CAB   CAA  CAG  CAH    0.00   0.0  0
 NPZ  CONST_31  CAB   CAC  CAI  CAH    0.00   0.0  0
 NPZ  CONST_32  CAD   CAC  CAI  CAH  180.00   0.0  0
 NPZ  CONST_33  CAK   CAJ  CAI  CAH  180.00   0.0  0
 NPZ  CONST_34  CAD   CAC  CAB  CAA  180.00   0.0  0
 NPZ  CONST_35  CAI   CAC  CAB  CAA    0.00   0.0  0
 NPZ  CONST_36  CAI   CAH  CAG  CAA    0.00   0.0  0
 NPZ  CONST_37  CAE   CAD  CAC  CAB  180.00   0.0  0
 NPZ  CONST_38  CAJ   CAI  CAC  CAB  180.00   0.0  0
 NPZ  CONST_39  CAK   CAE  CAD  CAC    0.00   0.0  0
 NPZ  CONST_40  CAK   CAJ  CAI  CAC    0.00   0.0  0
 NPZ  CONST_41  CAE   CAD  CAC  CAI    0.00   0.0  0
 NPZ  CONST_42  CAE   CAK  CAJ  CAI    0.00   0.0  0
 NPZ  CONST_43  CAJ   CAI  CAC  CAD    0.00   0.0  0
 NPZ  CONST_44  CAJ   CAK  CAE  CAD    0.00   0.0  0
 NPZ  CONST_45  C2    N1   C6   NAF  180.00   0.0  0
 NPZ  CONST_46  C4    C5   C6   NAF  180.00   0.0  0
 NPZ  CONST_47  CAO   C5   C6   NAF    0.00   0.0  0
 NPZ  CONST_48  CAU   NAT  C4   C5   180.00   0.0  0
 NPZ  CONST_49  CAU   NAT  C4   N3     0.00   0.0  0
 NPZ  CONST_50  CAO   NAP  NAT  CAU  180.00   0.0  0
 NPZ  CONST_51  H2    C2   N1   C6   180.00   0.0  0
 NPZ  CONST_52  HAA   CAA  CAG  CAO    0.00   0.0  0
 NPZ  CONST_53  HAH   CAH  CAG  CAO    0.00   0.0  0
 NPZ  CONST_54  HAB   CAB  CAA  CAG  180.00   0.0  0
 NPZ  CONST_55  HAJ   CAJ  CAI  CAH    0.00   0.0  0
 NPZ  CONST_56  HAD   CAD  CAC  CAB    0.00   0.0  0
 NPZ  CONST_57  HAE   CAE  CAD  CAC  180.00   0.0  0
 NPZ  CONST_58  HAK   CAK  CAJ  CAI  180.00   0.0  0
 NPZ  CONST_59  H1AF  NAF  C6   C5     0.00   0.0  0
 NPZ  CONST_60  H2AF  NAF  C6   C5   180.00   0.0  0
 NPZ  Var_01    H1AU  CAU  NAT  C4   120.34  30.0  2

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
 NPZ  plan-1  C6    0.020
 NPZ  plan-1  NAF   0.020
 NPZ  plan-1  C5    0.020
 NPZ  plan-1  N1    0.020
 NPZ  plan-1  C2    0.020
 NPZ  plan-1  N3    0.020
 NPZ  plan-1  C4    0.020
 NPZ  plan-1  NAT   0.020
 NPZ  plan-1  CAU   0.020
 NPZ  plan-1  NAP   0.020
 NPZ  plan-1  CAO   0.020
 NPZ  plan-1  CAG   0.020
 NPZ  plan-1  H2    0.020
 NPZ  plan-2  CAO   0.020
 NPZ  plan-2  CAG   0.020
 NPZ  plan-2  CAH   0.020
 NPZ  plan-2  CAA   0.020
 NPZ  plan-2  CAB   0.020
 NPZ  plan-2  CAC   0.020
 NPZ  plan-2  CAI   0.020
 NPZ  plan-2  CAD   0.020
 NPZ  plan-2  CAE   0.020
 NPZ  plan-2  CAK   0.020
 NPZ  plan-2  CAJ   0.020
 NPZ  plan-2  HAH   0.020
 NPZ  plan-2  HAA   0.020
 NPZ  plan-2  HAB   0.020
 NPZ  plan-2  HAD   0.020
 NPZ  plan-2  HAE   0.020
 NPZ  plan-2  HAK   0.020
 NPZ  plan-2  HAJ   0.020
 NPZ  plan-3  C6    0.020
 NPZ  plan-3  NAF   0.020
 NPZ  plan-3  H1AF  0.020
 NPZ  plan-3  H2AF  0.020

