# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 11:55:33 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 3,7-dimethyl-1-(5-oxohexyl)-3,7-dihydro-1H-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2N(C)C(=O)N(CCCCC(C)=O)C(=O)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
 PNX  PNX  3,7-dimethyl-1-(5-oxohexyl)-3,7-dihydro-1H-purine-2,6-dione  ligand  38  20  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PNX
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
 PNX  CAA   C  CH3   0  -0.768  -6.7698   0.3217   1.3971
 PNX  CAM   C  C     0   0.395  -5.7595   0.3519   0.2821
 PNX  OAD   O  O     0  -0.409  -6.0874   0.4418  -0.8803
 PNX  CAJ   C  CH2   0  -0.561  -4.3177   0.2472   0.7063
 PNX  CAH   C  CH2   0  -0.425  -3.3163   0.1215  -0.4287
 PNX  CAI   C  CH2   0  -0.429  -1.8868   0.0249   0.0901
 PNX  CAK   C  CH2   0  -0.302  -0.8954  -0.1339  -1.0540
 PNX  N1    N  NR6   0  -0.615   0.4908  -0.2373  -0.5947
 PNX  C6    C  CR6   0   0.564   1.2209   0.9516  -0.4883
 PNX  O6    O  OC    0  -0.467   0.7346   2.0339  -0.7661
 PNX  C5    C  CR56  0   0.132   2.5485   0.7173  -0.0349
 PNX  N7    N  NR5   0  -0.467   3.6044   1.5674   0.1964
 PNX  CAB   C  CH3   0  -0.518   3.6352   3.0026   0.0102
 PNX  C8    C  CR15  0   0.129   4.6084   0.7977   0.6266
 PNX  N9    N  N     0  -0.471   4.2954  -0.4855   0.6980
 PNX  C4    C  CR56  0   0.432   3.0181  -0.5301   0.2864
 PNX  N3    N  NR6   0  -0.592   2.2294  -1.6395   0.1829
 PNX  CAC   C  CH3   0  -0.532   2.7139  -2.9579   0.5567
 PNX  C2    C  CR6   0   0.756   0.9351  -1.5117  -0.2496
 PNX  O2    O  OC    0  -0.494   0.2054  -2.4816  -0.3313
 PNX  HAA1  H  HCH3  0   0.256  -6.4381   0.9126   2.2511
 PNX  HAA2  H  HCH3  0   0.259  -7.7443   0.6733   1.0646
 PNX  HAA3  H  HCH3  0   0.270  -6.8751  -0.7074   1.7497
 PNX  HAJ1  H  HCH2  0   0.263  -4.2288  -0.5976   1.3984
 PNX  HAJ2  H  HCH2  0   0.269  -4.1014   1.1304   1.3194
 PNX  HAH1  H  HCH2  0   0.230  -3.4057   0.9785  -1.1015
 PNX  HAH2  H  HCH2  0   0.228  -3.5465  -0.7652  -1.0258
 PNX  HAI1  H  HCH2  0   0.231  -1.7975  -0.8236   0.7736
 PNX  HAI2  H  HCH2  0   0.230  -1.6409   0.9224   0.6642
 PNX  HAK1  H  HCH2  0   0.261  -0.9576   0.7183  -1.7269
 PNX  HAK2  H  HCH2  0   0.261  -1.1270  -1.0211  -1.6394
 PNX  HAB1  H  HCH3  0   0.267   3.4194   3.2559  -1.0244
 PNX  HAB2  H  HCH3  0   0.267   2.9074   3.4858   0.6567
 PNX  HAB3  H  HCH3  0   0.267   4.6285   3.3609   0.2644
 PNX  H8    H  HCR5  0   0.301   5.5720   1.2110   0.8826
 PNX  HAC1  H  HCH3  0   0.258   2.1551  -3.3481   1.4050
 PNX  HAC2  H  HCH3  0   0.259   2.6260  -3.6496  -0.2776
 PNX  HAC3  H  HCH3  0   0.268   3.7590  -2.8723   0.8339

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
 PNX  CAA  CAM   single    1.505  0.020  1.505
 PNX  CAA  HAA1  single    0.970  0.020  1.090
 PNX  CAA  HAA2  single    0.970  0.020  1.090
 PNX  CAA  HAA3  single    0.970  0.020  1.090
 PNX  CAM  OAD   double    1.211  0.020  1.211
 PNX  CAM  CAJ   single    1.507  0.020  1.507
 PNX  CAJ  CAH   single    1.519  0.020  1.519
 PNX  CAJ  HAJ1  single    0.970  0.020  1.090
 PNX  CAJ  HAJ2  single    0.970  0.020  1.090
 PNX  CAH  CAI   single    1.524  0.020  1.524
 PNX  CAH  HAH1  single    0.970  0.020  1.090
 PNX  CAH  HAH2  single    0.970  0.020  1.090
 PNX  CAI  CAK   single    1.522  0.020  1.522
 PNX  CAI  HAI1  single    0.970  0.020  1.090
 PNX  CAI  HAI2  single    0.970  0.020  1.090
 PNX  CAK  N1    single    1.464  0.020  1.464
 PNX  CAK  HAK1  single    0.970  0.020  1.090
 PNX  CAK  HAK2  single    0.970  0.020  1.090
 PNX  N1   C6    aromatic  1.399  0.020  1.399
 PNX  N1   C2    aromatic  1.393  0.020  1.393
 PNX  C6   O6    double    1.219  0.020  1.219
 PNX  C6   C5    aromatic  1.422  0.020  1.422
 PNX  C5   N7    aromatic  1.375  0.020  1.375
 PNX  C5   C4    aromatic  1.371  0.020  1.371
 PNX  N7   CAB   single    1.448  0.020  1.448
 PNX  N7   C8    aromatic  1.336  0.020  1.336
 PNX  CAB  HAB1  single    0.970  0.020  1.090
 PNX  CAB  HAB2  single    0.970  0.020  1.090
 PNX  CAB  HAB3  single    0.970  0.020  1.090
 PNX  C8   N9    aromatic  1.323  0.020  1.323
 PNX  C8   H8    single    0.930  0.020  1.080
 PNX  N9   C4    aromatic  1.343  0.020  1.343
 PNX  C4   N3    aromatic  1.365  0.020  1.365
 PNX  N3   CAC   single    1.454  0.020  1.454
 PNX  N3   C2    aromatic  1.371  0.020  1.371
 PNX  CAC  HAC1  single    0.970  0.020  1.090
 PNX  CAC  HAC2  single    0.970  0.020  1.090
 PNX  CAC  HAC3  single    0.970  0.020  1.090
 PNX  C2   O2    double    1.217  0.020  1.217

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
 PNX  HAA3  CAA  HAA2  108.46  3.000
 PNX  HAA3  CAA  HAA1  106.68  3.000
 PNX  HAA2  CAA  HAA1  109.67  3.000
 PNX  HAA3  CAA  CAM   108.82  3.000
 PNX  HAA2  CAA  CAM   111.61  3.000
 PNX  HAA1  CAA  CAM   111.42  3.000
 PNX  CAJ   CAM  OAD   122.31  3.000
 PNX  CAJ   CAM  CAA   115.62  3.000
 PNX  OAD   CAM  CAA   122.06  3.000
 PNX  HAJ2  CAJ  HAJ1  104.59  3.000
 PNX  HAJ2  CAJ  CAH   110.75  3.000
 PNX  HAJ1  CAJ  CAH   110.77  3.000
 PNX  HAJ2  CAJ  CAM   106.87  3.000
 PNX  HAJ1  CAJ  CAM   108.00  3.000
 PNX  CAH   CAJ  CAM   115.23  3.000
 PNX  HAH2  CAH  HAH1  106.40  3.000
 PNX  HAH2  CAH  CAI   109.39  3.000
 PNX  HAH1  CAH  CAI   109.63  3.000
 PNX  HAH2  CAH  CAJ   109.66  3.000
 PNX  HAH1  CAH  CAJ   109.94  3.000
 PNX  CAI   CAH  CAJ   111.68  3.000
 PNX  HAI2  CAI  HAI1  106.89  3.000
 PNX  HAI2  CAI  CAK   109.50  3.000
 PNX  HAI1  CAI  CAK   109.62  3.000
 PNX  HAI2  CAI  CAH   109.73  3.000
 PNX  HAI1  CAI  CAH   109.80  3.000
 PNX  CAK   CAI  CAH   111.20  3.000
 PNX  HAK2  CAK  HAK1  107.10  3.000
 PNX  HAK2  CAK  N1    108.23  3.000
 PNX  HAK1  CAK  N1    107.67  3.000
 PNX  HAK2  CAK  CAI   110.54  3.000
 PNX  HAK1  CAK  CAI   110.25  3.000
 PNX  N1    CAK  CAI   112.84  3.000
 PNX  C2    N1   C6    126.30  3.000
 PNX  C2    N1   CAK   116.38  3.000
 PNX  C6    N1   CAK   117.25  3.000
 PNX  C5    C6   O6    126.26  3.000
 PNX  C5    C6   N1    111.80  3.000
 PNX  O6    C6   N1    121.94  3.000
 PNX  C4    C5   N7    105.07  3.000
 PNX  C4    C5   C6    122.98  3.000
 PNX  N7    C5   C6    131.95  3.000
 PNX  C8    N7   CAB   126.62  3.000
 PNX  C8    N7   C5    105.96  3.000
 PNX  CAB   N7   C5    127.42  3.000
 PNX  HAB3  CAB  HAB2  109.05  3.000
 PNX  HAB3  CAB  HAB1  109.11  3.000
 PNX  HAB2  CAB  HAB1  109.25  3.000
 PNX  HAB3  CAB  N7    108.45  3.000
 PNX  HAB2  CAB  N7    110.49  3.000
 PNX  HAB1  CAB  N7    110.45  3.000
 PNX  H8    C8   N9    124.74  3.000
 PNX  H8    C8   N7    121.78  3.000
 PNX  N9    C8   N7    113.48  3.000
 PNX  C4    N9   C8    103.93  3.000
 PNX  N3    C4   N9    126.86  3.000
 PNX  N3    C4   C5    121.58  3.000
 PNX  N9    C4   C5    111.56  3.000
 PNX  C2    N3   CAC   118.72  3.000
 PNX  C2    N3   C4    119.59  3.000
 PNX  CAC   N3   C4    121.67  3.000
 PNX  HAC3  CAC  HAC2  108.92  3.000
 PNX  HAC3  CAC  HAC1  108.89  3.000
 PNX  HAC2  CAC  HAC1  109.18  3.000
 PNX  HAC3  CAC  N3    108.38  3.000
 PNX  HAC2  CAC  N3    110.66  3.000
 PNX  HAC1  CAC  N3    110.77  3.000
 PNX  O2    C2   N3    120.88  3.000
 PNX  O2    C2   N1    121.43  3.000
 PNX  N3    C2   N1    117.69  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
 PNX  CONST_01  N7    C5   C6   N1    180.00   0.0  0
 PNX  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 PNX  CONST_03  C4    N3   C2   N1      0.00   0.0  0
 PNX  CONST_04  N3    C2   N1   C6      0.00   0.0  0
 PNX  CONST_05  C8    N7   C5   C6    180.00   0.0  0
 PNX  CONST_06  N9    C4   C5   C6    180.00   0.0  0
 PNX  CONST_07  N3    C4   C5   C6      0.00   0.0  0
 PNX  CONST_08  C2    N1   C6   C5      0.00   0.0  0
 PNX  CONST_09  N9    C8   N7   C5      0.00   0.0  0
 PNX  CONST_10  C8    N9   C4   C5      0.00   0.0  0
 PNX  CONST_11  C2    N3   C4   C5      0.00   0.0  0
 PNX  CONST_12  N9    C4   C5   N7      0.00   0.0  0
 PNX  CONST_13  N3    C4   C5   N7    180.00   0.0  0
 PNX  CONST_14  C4    N9   C8   N7      0.00   0.0  0
 PNX  CONST_15  C4    C5   N7   C8      0.00   0.0  0
 PNX  CONST_16  N3    C4   N9   C8    180.00   0.0  0
 PNX  CONST_17  C2    N3   C4   N9    180.00   0.0  0
 PNX  CONST_18  C5    C6   N1   CAK   180.00   0.0  0
 PNX  CONST_19  N3    C2   N1   CAK   180.00   0.0  0
 PNX  CONST_20  CAC   N3   C2   N1    180.00   0.0  0
 PNX  CONST_21  O2    C2   N1   C6    180.00   0.0  0
 PNX  CONST_22  CAB   N7   C5   C6      0.00   0.0  0
 PNX  CONST_23  C2    N1   C6   O6    180.00   0.0  0
 PNX  CONST_24  N7    C5   C6   O6      0.00   0.0  0
 PNX  CONST_25  C4    C5   C6   O6    180.00   0.0  0
 PNX  CONST_26  CAC   N3   C4   C5    180.00   0.0  0
 PNX  CONST_27  C4    C5   N7   CAB   180.00   0.0  0
 PNX  CONST_28  N9    C8   N7   CAB   180.00   0.0  0
 PNX  CONST_29  CAC   N3   C4   N9      0.00   0.0  0
 PNX  CONST_30  O2    C2   N3   C4    180.00   0.0  0
 PNX  CONST_31  H8    C8   N7   C5    180.00   0.0  0
 PNX  CONST_32  O6    C6   N1   CAK     0.00   0.0  0
 PNX  CONST_33  O2    C2   N1   CAK     0.00   0.0  0
 PNX  CONST_34  O2    C2   N3   CAC     0.00   0.0  0
 PNX  Var_01    C6    N1   CAK  CAI   -91.14  30.0  2
 PNX  Var_02    HAB1  CAB  N7   C5    -59.23  30.0  2
 PNX  Var_03    HAC1  CAC  N3   C4    115.52  30.0  2
 PNX  Var_04    N1    CAK  CAI  CAH  -179.70  30.0  3
 PNX  Var_05    CAH   CAJ  CAM  CAA   173.43  30.0  3
 PNX  Var_06    CAI   CAH  CAJ  CAM   179.86  30.0  3
 PNX  Var_07    CAK   CAI  CAH  CAJ   178.65  30.0  3
 PNX  Var_08    HAA1  CAA  CAM  OAD  -139.52  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
 PNX  plan-1  CAK  0.020
 PNX  plan-1  N1   0.020
 PNX  plan-1  C6   0.020
 PNX  plan-1  O6   0.020
 PNX  plan-1  C5   0.020
 PNX  plan-1  N7   0.020
 PNX  plan-1  CAB  0.020
 PNX  plan-1  C8   0.020
 PNX  plan-1  N9   0.020
 PNX  plan-1  C4   0.020
 PNX  plan-1  N3   0.020
 PNX  plan-1  CAC  0.020
 PNX  plan-1  C2   0.020
 PNX  plan-1  O2   0.020
 PNX  plan-1  H8   0.020
 PNX  plan-2  CAA  0.020
 PNX  plan-2  CAM  0.020
 PNX  plan-2  OAD  0.020
 PNX  plan-2  CAJ  0.020

