# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 16:24:11 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 1,1'-ethane-1,2-diylbis(3,7-dimethyl-3,7-dihydro-1H-purine-2,6-dione)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2N(C)C(=O)N(CCN3C(=O)N(C)c4ncn(C)c4C3=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
 D1H  D1H  1,1'-ethane-1,2-diylbis(3,7-dimethyl-3,7-dihydro-1H-purine-2,6-dione)  ligand  46  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D1H
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
 D1H  O6    O  OC    0  -0.458   1.7616   1.8951  -0.5515
 D1H  C6    C  CR6   0   0.565   2.4225   0.8888  -0.3703
 D1H  C5    C  CR56  0   0.133   3.8184   0.8296  -0.1071
 D1H  N7    N  NR5   0  -0.467   4.7716   1.8125   0.0224
 D1H  CAA   C  CH3   0  -0.519   4.5823   3.2427  -0.0962
 D1H  C8    C  CR15  0   0.131   5.9203   1.1790   0.2754
 D1H  N9    N  N     0  -0.471   5.7965  -0.1371   0.3249
 D1H  C4    C  CR56  0   0.432   4.4921  -0.3484   0.0879
 D1H  N3    N  NR6   0  -0.593   3.8540  -1.5547   0.0412
 D1H  CAC   C  CH3   0  -0.532   4.5669  -2.8026   0.2583
 D1H  C2    C  CR6   0   0.756   2.5031  -1.5997  -0.1837
 D1H  O2    O  OC    0  -0.486   1.9048  -2.6574  -0.1953
 D1H  N1    N  NR6   0  -0.620   1.8460  -0.3890  -0.4057
 D1H  CAK   C  CH2   0  -0.316   0.4095  -0.4588  -0.6584
 D1H  CAL   C  CH2   0  -0.315  -0.3838  -0.3465   0.6407
 D1H  NBB   N  NR6   0  -0.617  -1.8208  -0.3037   0.3826
 D1H  CAP   C  CR6   0   0.566  -2.4252   0.9614   0.3374
 D1H  OAF   O  OC    0  -0.457  -1.7890   1.9864   0.4994
 D1H  CAV   C  CR56  0   0.141  -3.8222   0.8660   0.0925
 D1H  NAX   N  NR5   0  -0.468  -4.8067   1.8184  -0.0195
 D1H  CAB   C  CH3   0  -0.519  -4.6632   3.2523   0.1183
 D1H  CAJ   C  CR15  0   0.127  -5.9382   1.1502  -0.2645
 D1H  NAN   N  N     0  -0.469  -5.7736  -0.1613  -0.3240
 D1H  CAT   C  CR56  0   0.434  -4.4607  -0.3304  -0.1011
 D1H  NAZ   N  NR6   0  -0.593  -3.7961  -1.5214  -0.0667
 D1H  CAD   C  CH3   0  -0.536  -4.5335  -2.7524  -0.2965
 D1H  CAR   C  CR6   0   0.743  -2.4469  -1.5356   0.1815
 D1H  OAH   O  OC    0  -0.483  -1.8104  -2.5698   0.2283
 D1H  HAA1  H  HCH3  0   0.267   4.2517   3.5009  -1.0987
 D1H  HAA2  H  HCH3  0   0.267   3.8463   3.5880   0.6247
 D1H  HAA3  H  HCH3  0   0.268   5.5305   3.7326   0.1044
 D1H  H8    H  HCR5  0   0.301   6.8448   1.7160   0.4240
 D1H  HAC1  H  HCH3  0   0.258   4.2164  -3.2974   1.1620
 D1H  HAC2  H  HCH3  0   0.259   4.4355  -3.4710  -0.5894
 D1H  HAC3  H  HCH3  0   0.268   5.6225  -2.5786   0.3676
 D1H  HAK1  H  HCH2  0   0.274   0.1458   0.3537  -1.3309
 D1H  HAK2  H  HCH2  0   0.281   0.1902  -1.3971  -1.1580
 D1H  HAL1  H  HCH2  0   0.275  -0.1682  -1.1859   1.2971
 D1H  HAL2  H  HCH2  0   0.279  -0.1150   0.5669   1.1627
 D1H  HAB1  H  HCH3  0   0.267  -4.3176   3.5045   1.1174
 D1H  HAB2  H  HCH3  0   0.268  -3.9574   3.6353  -0.6137
 D1H  HAB3  H  HCH3  0   0.268  -5.6326   3.7120  -0.0497
 D1H  HAJ   H  HCR5  0   0.300  -6.8809   1.6593  -0.3967
 D1H  HAD1  H  HCH3  0   0.272  -3.8484  -3.5910  -0.2817
 D1H  HAD2  H  HCH3  0   0.259  -5.2851  -2.8921   0.4784
 D1H  HAD3  H  HCH3  0   0.259  -5.0281  -2.7150  -1.2650

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
 D1H  O6   C6    double    1.217  0.020  1.217
 D1H  C6   C5    aromatic  1.422  0.020  1.422
 D1H  C6   N1    aromatic  1.402  0.020  1.402
 D1H  C5   N7    aromatic  1.375  0.020  1.375
 D1H  C5   C4    aromatic  1.371  0.020  1.371
 D1H  N7   CAA   single    1.448  0.020  1.448
 D1H  N7   C8    aromatic  1.336  0.020  1.336
 D1H  CAA  HAA1  single    0.970  0.020  1.090
 D1H  CAA  HAA2  single    0.970  0.020  1.090
 D1H  CAA  HAA3  single    0.970  0.020  1.090
 D1H  C8   N9    aromatic  1.323  0.020  1.323
 D1H  C8   H8    single    0.930  0.020  1.080
 D1H  N9   C4    aromatic  1.342  0.020  1.342
 D1H  C4   N3    aromatic  1.365  0.020  1.365
 D1H  N3   CAC   single    1.453  0.020  1.453
 D1H  N3   C2    aromatic  1.370  0.020  1.370
 D1H  CAC  HAC1  single    0.970  0.020  1.090
 D1H  CAC  HAC2  single    0.970  0.020  1.090
 D1H  CAC  HAC3  single    0.970  0.020  1.090
 D1H  C2   O2    double    1.215  0.020  1.215
 D1H  C2   N1    aromatic  1.395  0.020  1.395
 D1H  N1   CAK   single    1.460  0.020  1.460
 D1H  CAK  CAL   single    1.526  0.020  1.526
 D1H  CAK  HAK1  single    0.970  0.020  1.090
 D1H  CAK  HAK2  single    0.970  0.020  1.090
 D1H  CAL  NBB   single    1.461  0.020  1.461
 D1H  CAL  HAL1  single    0.970  0.020  1.090
 D1H  CAL  HAL2  single    0.970  0.020  1.090
 D1H  NBB  CAP   aromatic  1.403  0.020  1.403
 D1H  NBB  CAR   aromatic  1.396  0.020  1.396
 D1H  CAP  OAF   double    1.217  0.020  1.217
 D1H  CAP  CAV   aromatic  1.422  0.020  1.422
 D1H  CAV  NAX   aromatic  1.374  0.020  1.374
 D1H  CAV  CAT   aromatic  1.370  0.020  1.370
 D1H  NAX  CAB   single    1.448  0.020  1.448
 D1H  NAX  CAJ   aromatic  1.337  0.020  1.337
 D1H  CAB  HAB1  single    0.970  0.020  1.090
 D1H  CAB  HAB2  single    0.970  0.020  1.090
 D1H  CAB  HAB3  single    0.970  0.020  1.090
 D1H  CAJ  NAN   aromatic  1.323  0.020  1.323
 D1H  CAJ  HAJ   single    0.930  0.020  1.080
 D1H  NAN  CAT   aromatic  1.342  0.020  1.342
 D1H  CAT  NAZ   aromatic  1.364  0.020  1.364
 D1H  NAZ  CAD   single    1.453  0.020  1.453
 D1H  NAZ  CAR   aromatic  1.372  0.020  1.372
 D1H  CAD  HAD1  single    0.970  0.020  1.090
 D1H  CAD  HAD2  single    0.970  0.020  1.090
 D1H  CAD  HAD3  single    0.970  0.020  1.090
 D1H  CAR  OAH   double    1.215  0.020  1.215

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
 D1H  N1    C6   C5    111.74  3.000
 D1H  N1    C6   O6    121.75  3.000
 D1H  C5    C6   O6    126.51  3.000
 D1H  C4    C5   N7    105.08  3.000
 D1H  C4    C5   C6    123.00  3.000
 D1H  N7    C5   C6    131.92  3.000
 D1H  C8    N7   CAA   126.62  3.000
 D1H  C8    N7   C5    105.95  3.000
 D1H  CAA   N7   C5    127.43  3.000
 D1H  HAA3  CAA  HAA2  109.00  3.000
 D1H  HAA3  CAA  HAA1  109.19  3.000
 D1H  HAA2  CAA  HAA1  109.30  3.000
 D1H  HAA3  CAA  N7    108.45  3.000
 D1H  HAA2  CAA  N7    110.38  3.000
 D1H  HAA1  CAA  N7    110.49  3.000
 D1H  H8    C8   N9    124.75  3.000
 D1H  H8    C8   N7    121.78  3.000
 D1H  N9    C8   N7    113.48  3.000
 D1H  C4    N9   C8    103.94  3.000
 D1H  N3    C4   N9    126.80  3.000
 D1H  N3    C4   C5    121.64  3.000
 D1H  N9    C4   C5    111.55  3.000
 D1H  C2    N3   CAC   118.68  3.000
 D1H  C2    N3   C4    119.69  3.000
 D1H  CAC   N3   C4    121.62  3.000
 D1H  HAC3  CAC  HAC2  108.85  3.000
 D1H  HAC3  CAC  HAC1  108.88  3.000
 D1H  HAC2  CAC  HAC1  109.21  3.000
 D1H  HAC3  CAC  N3    108.36  3.000
 D1H  HAC2  CAC  N3    110.61  3.000
 D1H  HAC1  CAC  N3    110.88  3.000
 D1H  N1    C2   O2    121.45  3.000
 D1H  N1    C2   N3    117.51  3.000
 D1H  O2    C2   N3    121.03  3.000
 D1H  CAK   N1   C2    116.70  3.000
 D1H  CAK   N1   C6    116.90  3.000
 D1H  C2    N1   C6    126.37  3.000
 D1H  HAK2  CAK  HAK1  108.20  3.000
 D1H  HAK2  CAK  CAL   110.51  3.000
 D1H  HAK1  CAK  CAL   110.21  3.000
 D1H  HAK2  CAK  N1    108.65  3.000
 D1H  HAK1  CAK  N1    108.06  3.000
 D1H  CAL   CAK  N1    111.13  3.000
 D1H  HAL2  CAL  HAL1  108.07  3.000
 D1H  HAL2  CAL  NBB   107.69  3.000
 D1H  HAL1  CAL  NBB   108.93  3.000
 D1H  HAL2  CAL  CAK   110.02  3.000
 D1H  HAL1  CAL  CAK   110.73  3.000
 D1H  NBB   CAL  CAK   111.29  3.000
 D1H  CAR   NBB  CAP   126.71  3.000
 D1H  CAR   NBB  CAL   116.15  3.000
 D1H  CAP   NBB  CAL   117.13  3.000
 D1H  CAV   CAP  OAF   126.38  3.000
 D1H  CAV   CAP  NBB   111.62  3.000
 D1H  OAF   CAP  NBB   122.00  3.000
 D1H  CAT   CAV  NAX   105.06  3.000
 D1H  CAT   CAV  CAP   122.76  3.000
 D1H  NAX   CAV  CAP   132.18  3.000
 D1H  CAJ   NAX  CAB   126.62  3.000
 D1H  CAJ   NAX  CAV   105.95  3.000
 D1H  CAB   NAX  CAV   127.42  3.000
 D1H  HAB3  CAB  HAB2  109.05  3.000
 D1H  HAB3  CAB  HAB1  109.14  3.000
 D1H  HAB2  CAB  HAB1  109.33  3.000
 D1H  HAB3  CAB  NAX   108.43  3.000
 D1H  HAB2  CAB  NAX   110.45  3.000
 D1H  HAB1  CAB  NAX   110.42  3.000
 D1H  HAJ   CAJ  NAN   124.79  3.000
 D1H  HAJ   CAJ  NAX   121.72  3.000
 D1H  NAN   CAJ  NAX   113.48  3.000
 D1H  CAT   NAN  CAJ   103.83  3.000
 D1H  NAZ   CAT  NAN   126.20  3.000
 D1H  NAZ   CAT  CAV   122.12  3.000
 D1H  NAN   CAT  CAV   111.67  3.000
 D1H  CAR   NAZ  CAD   121.26  3.000
 D1H  CAR   NAZ  CAT   119.52  3.000
 D1H  CAD   NAZ  CAT   119.23  3.000
 D1H  HAD3  CAD  HAD2  108.91  3.000
 D1H  HAD3  CAD  HAD1  109.04  3.000
 D1H  HAD2  CAD  HAD1  109.13  3.000
 D1H  HAD3  CAD  NAZ   110.02  3.000
 D1H  HAD2  CAD  NAZ   110.28  3.000
 D1H  HAD1  CAD  NAZ   109.44  3.000
 D1H  OAH   CAR  NAZ   122.07  3.000
 D1H  OAH   CAR  NBB   120.69  3.000
 D1H  NAZ   CAR  NBB   117.25  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
 D1H  CONST_01  C8    N7   C5   C6   180.00   0.0  0
 D1H  CONST_02  N9    C4   C5   C6   180.00   0.0  0
 D1H  CONST_03  N3    C4   C5   C6     0.00   0.0  0
 D1H  CONST_04  N3    C2   N1   C6     0.00   0.0  0
 D1H  CONST_05  C2    N1   C6   C5     0.00   0.0  0
 D1H  CONST_06  N9    C8   N7   C5     0.00   0.0  0
 D1H  CONST_07  C8    N9   C4   C5     0.00   0.0  0
 D1H  CONST_08  C2    N3   C4   C5     0.00   0.0  0
 D1H  CONST_09  N1    C6   C5   N7   180.00   0.0  0
 D1H  CONST_10  N9    C4   C5   N7     0.00   0.0  0
 D1H  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 D1H  CONST_12  C4    N9   C8   N7     0.00   0.0  0
 D1H  CONST_13  C4    C5   N7   C8     0.00   0.0  0
 D1H  CONST_14  N3    C4   N9   C8   180.00   0.0  0
 D1H  CONST_15  C2    N3   C4   N9   180.00   0.0  0
 D1H  CONST_16  N1    C6   C5   C4     0.00   0.0  0
 D1H  CONST_17  N1    C2   N3   C4     0.00   0.0  0
 D1H  CONST_18  NAX   CAV  CAP  NBB  180.00   0.0  0
 D1H  CONST_19  CAT   CAV  CAP  NBB    0.00   0.0  0
 D1H  CONST_20  CAT   NAZ  CAR  NBB    0.00   0.0  0
 D1H  CONST_21  NAZ   CAR  NBB  CAP    0.00   0.0  0
 D1H  CONST_22  CAJ   NAX  CAV  CAP  180.00   0.0  0
 D1H  CONST_23  NAN   CAT  CAV  CAP  180.00   0.0  0
 D1H  CONST_24  NAZ   CAT  CAV  CAP    0.00   0.0  0
 D1H  CONST_25  CAR   NBB  CAP  CAV    0.00   0.0  0
 D1H  CONST_26  NAN   CAJ  NAX  CAV    0.00   0.0  0
 D1H  CONST_27  CAJ   NAN  CAT  CAV    0.00   0.0  0
 D1H  CONST_28  CAR   NAZ  CAT  CAV    0.00   0.0  0
 D1H  CONST_29  NAN   CAT  CAV  NAX    0.00   0.0  0
 D1H  CONST_30  NAZ   CAT  CAV  NAX  180.00   0.0  0
 D1H  CONST_31  CAT   NAN  CAJ  NAX    0.00   0.0  0
 D1H  CONST_32  CAT   CAV  NAX  CAJ    0.00   0.0  0
 D1H  CONST_33  NAZ   CAT  NAN  CAJ  180.00   0.0  0
 D1H  CONST_34  CAR   NAZ  CAT  NAN  180.00   0.0  0
 D1H  CONST_35  N7    C5   C6   O6     0.00   0.0  0
 D1H  CONST_36  C4    C5   C6   O6   180.00   0.0  0
 D1H  CONST_37  C2    N1   C6   O6   180.00   0.0  0
 D1H  CONST_38  CAA   N7   C5   C6     0.00   0.0  0
 D1H  CONST_39  O2    C2   N1   C6   180.00   0.0  0
 D1H  CONST_40  CAK   N1   C6   C5   180.00   0.0  0
 D1H  CONST_41  CAC   N3   C4   C5   180.00   0.0  0
 D1H  CONST_42  C4    C5   N7   CAA  180.00   0.0  0
 D1H  CONST_43  N9    C8   N7   CAA  180.00   0.0  0
 D1H  CONST_44  CAC   N3   C4   N9     0.00   0.0  0
 D1H  CONST_45  O2    C2   N3   C4   180.00   0.0  0
 D1H  CONST_46  CAK   N1   C2   N3   180.00   0.0  0
 D1H  CONST_47  N1    C2   N3   CAC  180.00   0.0  0
 D1H  CONST_48  CAV   CAP  NBB  CAL  180.00   0.0  0
 D1H  CONST_49  NAZ   CAR  NBB  CAL  180.00   0.0  0
 D1H  CONST_50  CAD   NAZ  CAR  NBB  180.00   0.0  0
 D1H  CONST_51  OAH   CAR  NBB  CAP  180.00   0.0  0
 D1H  CONST_52  CAB   NAX  CAV  CAP    0.00   0.0  0
 D1H  CONST_53  CAR   NBB  CAP  OAF  180.00   0.0  0
 D1H  CONST_54  NAX   CAV  CAP  OAF    0.00   0.0  0
 D1H  CONST_55  CAT   CAV  CAP  OAF  180.00   0.0  0
 D1H  CONST_56  CAD   NAZ  CAT  CAV  180.00   0.0  0
 D1H  CONST_57  CAT   CAV  NAX  CAB  180.00   0.0  0
 D1H  CONST_58  NAN   CAJ  NAX  CAB  180.00   0.0  0
 D1H  CONST_59  CAD   NAZ  CAT  NAN    0.00   0.0  0
 D1H  CONST_60  OAH   CAR  NAZ  CAT  180.00   0.0  0
 D1H  CONST_61  H8    C8   N7   C5   180.00   0.0  0
 D1H  CONST_62  HAJ   CAJ  NAX  CAV  180.00   0.0  0
 D1H  CONST_63  CAK   N1   C6   O6     0.00   0.0  0
 D1H  CONST_64  O2    C2   N3   CAC    0.00   0.0  0
 D1H  CONST_65  CAK   N1   C2   O2     0.00   0.0  0
 D1H  CONST_66  OAF   CAP  NBB  CAL    0.00   0.0  0
 D1H  CONST_67  OAH   CAR  NBB  CAL    0.00   0.0  0
 D1H  CONST_68  OAH   CAR  NAZ  CAD    0.00   0.0  0
 D1H  Var_01    CAL   CAK  N1   C6   -87.39  30.0  2
 D1H  Var_02    NBB   CAL  CAK  N1   175.26  30.0  3
 D1H  Var_03    CAP   NBB  CAL  CAK  -96.73  30.0  2
 D1H  Var_04    HAA1  CAA  N7   C5   -62.75  30.0  2
 D1H  Var_05    HAC1  CAC  N3   C4   115.05  30.0  2
 D1H  Var_06    HAB1  CAB  NAX  CAV  -61.61  30.0  2
 D1H  Var_07    HAD1  CAD  NAZ  CAT  177.26  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
 D1H  plan-1  O6   0.020
 D1H  plan-1  C6   0.020
 D1H  plan-1  C5   0.020
 D1H  plan-1  N7   0.020
 D1H  plan-1  CAA  0.020
 D1H  plan-1  C8   0.020
 D1H  plan-1  N9   0.020
 D1H  plan-1  C4   0.020
 D1H  plan-1  N3   0.020
 D1H  plan-1  CAC  0.020
 D1H  plan-1  C2   0.020
 D1H  plan-1  O2   0.020
 D1H  plan-1  N1   0.020
 D1H  plan-1  CAK  0.020
 D1H  plan-1  H8   0.020
 D1H  plan-2  CAL  0.020
 D1H  plan-2  NBB  0.020
 D1H  plan-2  CAP  0.020
 D1H  plan-2  OAF  0.020
 D1H  plan-2  CAV  0.020
 D1H  plan-2  NAX  0.020
 D1H  plan-2  CAB  0.020
 D1H  plan-2  CAJ  0.020
 D1H  plan-2  NAN  0.020
 D1H  plan-2  CAT  0.020
 D1H  plan-2  NAZ  0.020
 D1H  plan-2  CAD  0.020
 D1H  plan-2  CAR  0.020
 D1H  plan-2  OAH  0.020
 D1H  plan-2  HAJ  0.020

