# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 10:12:47 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 3,7-dimethyl-1-[3-(3-methyl-2,6-dioxo-9H-purin-1-yl)propyl]purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2N(C)C(=O)N(CCCN3C(=O)N(C)c4[nH]cnc4C3=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
 CX9  CX9  3,7-dimethyl-1-[3-(3-methyl-2,6-dioxo-9H-purin-1-yl)propyl]purine-2,6-dione  ligand  46  28  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CX9
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
 CX9  O6    O  O     0  -0.465   2.4761  -1.9323  -0.9925
 CX9  C6    C  CR6   0   0.565   2.9073  -0.8712  -0.5769
 CX9  C5    C  CR56  0   0.133   4.0819  -0.6870   0.2032
 CX9  N1    N  NR6   0  -0.615   2.2625   0.3437  -0.8386
 CX9  N7    N  NR5   0  -0.467   5.0181  -1.5752   0.6783
 CX9  C4    C  CR56  0   0.432   4.4886   0.5392   0.6624
 CX9  CAA   C  CH3   0  -0.518   5.0592  -3.0072   0.4708
 CX9  C8    C  CR15  0   0.129   5.9003  -0.8456   1.3675
 CX9  N9    N  N     0  -0.471   5.6163   0.4463   1.3849
 CX9  N3    N  NR6   0  -0.592   3.7826   1.6754   0.3889
 CX9  CAC   C  CH3   0  -0.532   4.2075   2.9746   0.8824
 CX9  C2    C  CR6   0   0.758   2.6423   1.5987  -0.3669
 CX9  O2    O  O     0  -0.492   1.9887   2.5938  -0.6161
 CX9  CAK   C  CH2   0  -0.314   1.0357   0.2920  -1.6324
 CX9  CAL   C  CH2   0  -0.443  -0.2106   0.1615  -0.7682
 CX9  CA0   C  CH2   0  -0.313  -1.4503   0.0962  -1.6498
 CX9  N10   N  NR6   0  -0.614  -2.6832  -0.0253  -0.8720
 CX9  CAP   C  CR6   0   0.543  -3.3165   1.1711  -0.4926
 CX9  CAR   C  CR6   0   0.748  -3.0668  -1.3170  -0.5307
 CX9  OAF   O  O     0  -0.461  -2.8621   2.2544  -0.8062
 CX9  CAV   C  CR56  0  -0.059  -4.5046   0.9464   0.2685
 CX9  NAX   N  N     0  -0.426  -5.3890   1.8461   0.8032
 CX9  CAT   C  CR56  0   0.645  -4.8931  -0.3318   0.5671
 CX9  CAJ   C  CR15  0   0.097  -6.2810   1.1205   1.4023
 CX9  NAN   N  NR15  0  -0.649  -6.0249  -0.2219   1.2892
 CX9  NAZ   N  NR6   0  -0.592  -4.2314  -1.4543   0.1948
 CX9  CAD   C  CH3   0  -0.560  -4.7223  -2.7610   0.6003
 CX9  OAH   O  O     0  -0.480  -2.4097  -2.2835  -0.8604
 CX9  HAA   H  HCH3  0   0.267   5.1482  -3.2358  -0.5881
 CX9  HAAA  H  HCH3  0   0.267   5.9248  -3.4038   0.9929
 CX9  HAAB  H  HCH3  0   0.267   4.1615  -3.4754   0.8655
 CX9  H8    H  HCR5  0   0.301   6.7542  -1.2947   1.8513
 CX9  HAC   H  HCH3  0   0.258   4.4482   3.6420   0.0572
 CX9  HACA  H  HCH3  0   0.259   3.4297   3.4286   1.4923
 CX9  HACB  H  HCH3  0   0.268   5.0945   2.8352   1.4909
 CX9  HAK   H  HCH2  0   0.269   0.9868   1.1888  -2.2465
 CX9  HAKA  H  HCH2  0   0.269   1.1165  -0.5563  -2.3086
 CX9  HAL   H  HCH2  0   0.246  -0.1418  -0.7406  -0.1571
 CX9  HALA  H  HCH2  0   0.247  -0.2849   1.0142  -0.0907
 CX9  HA0   H  HCH2  0   0.269  -1.5298   0.9961  -2.2557
 CX9  HA0A  H  HCH2  0   0.270  -1.3892  -0.7468  -2.3346
 CX9  HAJ   H  HCR5  0   0.294  -7.1427   1.4809   1.9411
 CX9  HNAN  H  HNR5  0   0.442  -6.5886  -0.9645   1.6763
 CX9  HAD   H  HCH3  0   0.286  -4.1062  -3.5321   0.1544
 CX9  HADA  H  HCH3  0   0.269  -4.6839  -2.8622   1.6843
 CX9  HADB  H  HCH3  0   0.268  -5.7476  -2.8955   0.2590

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
 CX9  O6   C6    double    1.218  0.020  1.218
 CX9  C6   C5    single    1.422  0.020  1.422
 CX9  C6   N1    single    1.400  0.020  1.400
 CX9  C5   N7    aromatic  1.375  0.020  1.375
 CX9  C5   C4    aromatic  1.371  0.020  1.371
 CX9  N1   C2    single    1.393  0.020  1.393
 CX9  N1   CAK   single    1.462  0.020  1.462
 CX9  N7   CAA   single    1.448  0.020  1.448
 CX9  N7   C8    aromatic  1.336  0.020  1.336
 CX9  C4   N9    aromatic  1.342  0.020  1.342
 CX9  C4   N3    single    1.365  0.020  1.365
 CX9  CAA  HAA   single    0.970  0.020  1.090
 CX9  CAA  HAAA  single    0.970  0.020  1.090
 CX9  CAA  HAAB  single    0.970  0.020  1.090
 CX9  C8   N9    aromatic  1.323  0.020  1.323
 CX9  C8   H8    single    0.930  0.020  1.080
 CX9  N3   CAC   single    1.453  0.020  1.453
 CX9  N3   C2    single    1.370  0.020  1.370
 CX9  CAC  HAC   single    0.970  0.020  1.090
 CX9  CAC  HACA  single    0.970  0.020  1.090
 CX9  CAC  HACB  single    0.970  0.020  1.090
 CX9  C2   O2    double    1.216  0.020  1.216
 CX9  CAK  CAL   single    1.522  0.020  1.522
 CX9  CAK  HAK   single    0.970  0.020  1.090
 CX9  CAK  HAKA  single    0.970  0.020  1.090
 CX9  CAL  CA0   single    1.523  0.020  1.523
 CX9  CAL  HAL   single    0.970  0.020  1.090
 CX9  CAL  HALA  single    0.970  0.020  1.090
 CX9  CA0  N10   single    1.463  0.020  1.463
 CX9  CA0  HA0   single    0.970  0.020  1.090
 CX9  CA0  HA0A  single    0.970  0.020  1.090
 CX9  N10  CAP   single    1.406  0.020  1.406
 CX9  N10  CAR   single    1.390  0.020  1.390
 CX9  CAP  OAF   double    1.216  0.020  1.216
 CX9  CAP  CAV   single    1.429  0.020  1.429
 CX9  CAR  NAZ   single    1.379  0.020  1.379
 CX9  CAR  OAH   double    1.214  0.020  1.214
 CX9  CAV  NAX   aromatic  1.370  0.020  1.370
 CX9  CAV  CAT   aromatic  1.369  0.020  1.369
 CX9  NAX  CAJ   aromatic  1.296  0.020  1.296
 CX9  CAT  NAN   aromatic  1.347  0.020  1.347
 CX9  CAT  NAZ   single    1.355  0.020  1.355
 CX9  CAJ  NAN   aromatic  1.371  0.020  1.371
 CX9  CAJ  HAJ   single    0.930  0.020  1.080
 CX9  NAN  HNAN  single    0.860  0.020  1.020
 CX9  NAZ  CAD   single    1.454  0.020  1.454
 CX9  CAD  HAD   single    0.970  0.020  1.090
 CX9  CAD  HADA  single    0.970  0.020  1.090
 CX9  CAD  HADB  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
 CX9  N1    C6   C5    111.75  3.000
 CX9  N1    C6   O6    121.93  3.000
 CX9  C5    C6   O6    126.32  3.000
 CX9  C4    C5   N7    105.07  3.000
 CX9  C4    C5   C6    123.00  3.000
 CX9  N7    C5   C6    131.93  3.000
 CX9  CAK   N1   C2    116.38  3.000
 CX9  CAK   N1   C6    117.21  3.000
 CX9  C2    N1   C6    126.35  3.000
 CX9  C8    N7   CAA   126.53  3.000
 CX9  C8    N7   C5    105.96  3.000
 CX9  CAA   N7   C5    127.50  3.000
 CX9  N3    C4   N9    126.85  3.000
 CX9  N3    C4   C5    121.58  3.000
 CX9  N9    C4   C5    111.56  3.000
 CX9  HAAB  CAA  HAAA  109.06  3.000
 CX9  HAAB  CAA  HAA   109.32  3.000
 CX9  HAAA  CAA  HAA   109.05  3.000
 CX9  HAAB  CAA  N7    110.53  3.000
 CX9  HAAA  CAA  N7    108.36  3.000
 CX9  HAA   CAA  N7    110.49  3.000
 CX9  H8    C8   N9    124.77  3.000
 CX9  H8    C8   N7    121.76  3.000
 CX9  N9    C8   N7    113.47  3.000
 CX9  C8    N9   C4    103.94  3.000
 CX9  C2    N3   CAC   118.73  3.000
 CX9  C2    N3   C4    119.62  3.000
 CX9  CAC   N3   C4    121.65  3.000
 CX9  HACB  CAC  HACA  108.90  3.000
 CX9  HACB  CAC  HAC   108.86  3.000
 CX9  HACA  CAC  HAC   109.11  3.000
 CX9  HACB  CAC  N3    108.35  3.000
 CX9  HACA  CAC  N3    110.76  3.000
 CX9  HAC   CAC  N3    110.82  3.000
 CX9  O2    C2   N3    120.96  3.000
 CX9  O2    C2   N1    121.40  3.000
 CX9  N3    C2   N1    117.64  3.000
 CX9  HAKA  CAK  HAK   107.17  3.000
 CX9  HAKA  CAK  CAL   110.29  3.000
 CX9  HAK   CAK  CAL   110.75  3.000
 CX9  HAKA  CAK  N1    107.63  3.000
 CX9  HAK   CAK  N1    108.36  3.000
 CX9  CAL   CAK  N1    112.44  3.000
 CX9  HALA  CAL  HAL   107.60  3.000
 CX9  HALA  CAL  CA0   109.72  3.000
 CX9  HAL   CAL  CA0   109.87  3.000
 CX9  HALA  CAL  CAK   109.95  3.000
 CX9  HAL   CAL  CAK   109.70  3.000
 CX9  CA0   CAL  CAK   109.97  3.000
 CX9  HA0A  CA0  HA0   107.13  3.000
 CX9  HA0A  CA0  N10   108.53  3.000
 CX9  HA0   CA0  N10   107.65  3.000
 CX9  HA0A  CA0  CAL   110.61  3.000
 CX9  HA0   CA0  CAL   110.28  3.000
 CX9  N10   CA0  CAL   112.45  3.000
 CX9  CAR   N10  CAP   126.89  3.000
 CX9  CAR   N10  CA0   116.13  3.000
 CX9  CAP   N10  CA0   116.90  3.000
 CX9  CAV   CAP  OAF   126.03  3.000
 CX9  CAV   CAP  N10   112.61  3.000
 CX9  OAF   CAP  N10   121.35  3.000
 CX9  OAH   CAR  NAZ   121.37  3.000
 CX9  OAH   CAR  N10   121.57  3.000
 CX9  NAZ   CAR  N10   117.05  3.000
 CX9  CAT   CAV  NAX   110.17  3.000
 CX9  CAT   CAV  CAP   119.94  3.000
 CX9  NAX   CAV  CAP   129.89  3.000
 CX9  CAJ   NAX  CAV   104.89  3.000
 CX9  NAZ   CAT  NAN   128.69  3.000
 CX9  NAZ   CAT  CAV   125.09  3.000
 CX9  NAN   CAT  CAV   106.21  3.000
 CX9  HAJ   CAJ  NAN   121.17  3.000
 CX9  HAJ   CAJ  NAX   126.42  3.000
 CX9  NAN   CAJ  NAX   112.42  3.000
 CX9  HNAN  NAN  CAJ   125.75  3.000
 CX9  HNAN  NAN  CAT   127.93  3.000
 CX9  CAJ   NAN  CAT   106.32  3.000
 CX9  CAD   NAZ  CAT   120.20  3.000
 CX9  CAD   NAZ  CAR   121.43  3.000
 CX9  CAT   NAZ  CAR   118.32  3.000
 CX9  HADB  CAD  HADA  109.48  3.000
 CX9  HADB  CAD  HAD   108.58  3.000
 CX9  HADA  CAD  HAD   108.87  3.000
 CX9  HADB  CAD  NAZ   109.98  3.000
 CX9  HADA  CAD  NAZ   110.44  3.000
 CX9  HAD   CAD  NAZ   109.45  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
 CX9  CONST_01  N9    C8   N7   C5      0.00   0.0  0
 CX9  CONST_02  C8    N9   C4   C5      0.00   0.0  0
 CX9  CONST_03  N9    C4   C5   N7      0.00   0.0  0
 CX9  CONST_04  C4    N9   C8   N7      0.00   0.0  0
 CX9  CONST_05  C8    N7   C5   C4      0.00   0.0  0
 CX9  CONST_06  NAN   CAJ  NAX  CAV     0.00   0.0  0
 CX9  CONST_07  CAJ   NAN  CAT  CAV     0.00   0.0  0
 CX9  CONST_08  NAN   CAT  CAV  NAX     0.00   0.0  0
 CX9  CONST_09  CAT   NAN  CAJ  NAX     0.00   0.0  0
 CX9  CONST_10  CAJ   NAX  CAV  CAT     0.00   0.0  0
 CX9  CONST_11  N3    C2   N1   C6      0.00   0.0  0
 CX9  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 CX9  CONST_13  C4    N3   C2   N1      0.00   0.0  0
 CX9  CONST_14  CAT   NAZ  CAR  N10     0.00   0.0  0
 CX9  CONST_15  NAZ   CAR  N10  CAP     0.00   0.0  0
 CX9  CONST_16  CAV   CAP  N10  CAR     0.00   0.0  0
 CX9  CONST_17  CAA   N7   C5   C6      0.00   0.0  0
 CX9  CONST_18  CAA   N7   C5   C4    180.00   0.0  0
 CX9  CONST_19  N9    C8   N7   CAA   180.00   0.0  0
 CX9  CONST_20  C2    N1   C6   O6    180.00   0.0  0
 CX9  CONST_21  O2    C2   N1   C6    180.00   0.0  0
 CX9  CONST_22  CAK   N1   C6   C5    180.00   0.0  0
 CX9  CONST_23  CAC   N3   C2   N1    180.00   0.0  0
 CX9  CONST_24  O2    C2   N3   C4    180.00   0.0  0
 CX9  CONST_25  CAK   N1   C2   N3    180.00   0.0  0
 CX9  CONST_26  CAV   CAP  N10  CA0   180.00   0.0  0
 CX9  CONST_27  NAZ   CAR  N10  CA0   180.00   0.0  0
 CX9  CONST_28  CAD   NAZ  CAR  N10   180.00   0.0  0
 CX9  CONST_29  OAH   CAR  N10  CAP   180.00   0.0  0
 CX9  CONST_30  OAF   CAP  N10  CAR   180.00   0.0  0
 CX9  CONST_31  OAH   CAR  NAZ  CAT   180.00   0.0  0
 CX9  CONST_32  H8    C8   N7   C5    180.00   0.0  0
 CX9  CONST_33  HAJ   CAJ  NAX  CAV   180.00   0.0  0
 CX9  CONST_34  HNAN  NAN  CAT  CAV   180.00   0.0  0
 CX9  CONST_35  CAK   N1   C6   O6      0.00   0.0  0
 CX9  CONST_36  O2    C2   N3   CAC     0.00   0.0  0
 CX9  CONST_37  CAK   N1   C2   O2      0.00   0.0  0
 CX9  CONST_38  OAF   CAP  N10  CA0     0.00   0.0  0
 CX9  CONST_39  OAH   CAR  N10  CA0     0.00   0.0  0
 CX9  CONST_40  OAH   CAR  NAZ  CAD     0.00   0.0  0
 CX9  Var_01    CAL   CAK  N1   C6     91.53  30.0  3
 CX9  Var_02    CAP   N10  CA0  CAL    90.08  30.0  3
 CX9  Var_03    HAA   CAA  N7   C5     61.19  30.0  2
 CX9  Var_04    HAC   CAC  N3   C4    117.01  30.0  3
 CX9  Var_05    HAD   CAD  NAZ  CAR    -6.19  30.0  3
 CX9  Var_06    CA0   CAL  CAK  N1   -179.33  30.0  3
 CX9  Var_07    N10   CA0  CAL  CAK  -179.80  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
 CX9  plan-1  O6    0.020
 CX9  plan-1  C6    0.020
 CX9  plan-1  C5    0.020
 CX9  plan-1  N1    0.020
 CX9  plan-1  N7    0.020
 CX9  plan-1  C4    0.020
 CX9  plan-1  CAA   0.020
 CX9  plan-1  C8    0.020
 CX9  plan-1  N9    0.020
 CX9  plan-1  N3    0.020
 CX9  plan-1  CAC   0.020
 CX9  plan-1  C2    0.020
 CX9  plan-1  O2    0.020
 CX9  plan-1  CAK   0.020
 CX9  plan-1  H8    0.020
 CX9  plan-2  CA0   0.020
 CX9  plan-2  N10   0.020
 CX9  plan-2  CAP   0.020
 CX9  plan-2  CAR   0.020
 CX9  plan-2  OAF   0.020
 CX9  plan-2  CAV   0.020
 CX9  plan-2  NAX   0.020
 CX9  plan-2  CAT   0.020
 CX9  plan-2  CAJ   0.020
 CX9  plan-2  NAN   0.020
 CX9  plan-2  NAZ   0.020
 CX9  plan-2  CAD   0.020
 CX9  plan-2  OAH   0.020
 CX9  plan-2  HAJ   0.020
 CX9  plan-2  HNAN  0.020

