# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 05:53:15 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-{[(3-nitrobenzyl)disulfanyl]methyl}tetrahydrofuran-3,4-diol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CSSCc4cccc(c4)[N+]([O-])=O)[C@@H](O)[C@H]3O
#
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
 A6D  A6D  '(2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-{[(3-nitrobenzyl)disulfanyl]methyl}tetrahydrofuran-3,4-diol (non-preferred name)'  ligand  48  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A6D
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
 A6D  N1    N  N      0  -0.475  -6.8101   1.1590   1.3186
 A6D  C2    C  CR16   0   0.047  -6.5827  -0.1408   1.1508
 A6D  N3    N  N      0  -0.457  -5.5004  -0.7314   0.6743
 A6D  C4    C  CR56   0   0.493  -4.5617   0.1527   0.3468
 A6D  C5    C  CR56   0  -0.012  -4.6490   1.5301   0.4677
 A6D  C6    C  CR6    0   0.461  -5.8561   2.0359   0.9846
 A6D  N6    N  NH2    0  -0.816  -6.0789   3.3393   1.1525
 A6D  N7    N  N      0  -0.448  -3.4902   2.1313   0.0472
 A6D  C8    C  CR15   0   0.114  -2.7300   1.1448  -0.3209
 A6D  N9    N  NR5    0  -0.540  -3.3188  -0.0823  -0.1689
 A6D  OAC   O  OH1    0  -0.666  -1.8022  -3.8900  -1.5689
 A6D  OAD   O  OH1    0  -0.652  -3.5478  -1.9999  -2.6254
 A6D  CAF   C  CR16   0  -0.239   6.0811   0.6723   2.1117
 A6D  CAG   C  CR16   0  -0.261   5.3443  -0.4896   1.9484
 A6D  CAH   C  CR16   0  -0.276   6.1236   1.6229   1.1041
 A6D  CAK   C  CR16   0  -0.302   4.6754   0.2169  -0.2439
 A6D  CAL   C  CH2    0  -0.669   3.8255  -1.9702   0.6095
 A6D  OAQ   O  O      0  -0.485  -1.5272  -1.4977   0.2222
 A6D  SAR   S  S2     0  -0.022   2.2105  -1.8561   1.4660
 A6D  SAS   S  S2     0  -0.011   1.2937  -0.3117   0.4852
 A6D  CAT   C  CR6    0   0.159   4.6401  -0.7303   0.7700
 A6D  CAV   C  CR6    0   0.264   5.4150   1.3775  -0.0615
 A6D  CAY   C  CR15   0  -0.025  -1.2863  -2.6139  -1.8403
 A6D  CAZ   C  CR15   0  -0.049  -2.4094  -1.5782  -1.9386
 A6D  CBA   C  CR15   0   0.024  -0.5422  -2.1168  -0.6047
 A6D  CBB   C  CR15   0   0.213  -2.7419  -1.3683  -0.4620
 A6D  NBD   N  N      1   0.329   5.4455   2.3668  -1.1291
 A6D  H2    H  HCR6   0   0.253  -7.3942  -0.7976   1.4460
 A6D  HN6   H  HNH2   0   0.404  -6.9558   3.6615   1.5234
 A6D  HN6A  H  HNH2   0   0.412  -5.3856   4.0227   0.9040
 A6D  H8    H  HCR5   0   0.290  -1.7248   1.2526  -0.7003
 A6D  HOAC  H  HOH1   0   0.451  -2.5230  -4.0578  -2.1872
 A6D  HOAD  H  HOH1   0   0.470  -3.4161  -1.8544  -3.5677
 A6D  HAG   H  HCR6   0   0.276   5.3165  -1.2211   2.7465
 A6D  HAH   H  HCR6   0   0.299   6.6985   2.5280   1.2344
 A6D  HAK   H  HCR6   0   0.289   4.1385   0.0402  -1.1651
 A6D  HAL   H  HCH2   0   0.317   4.3092  -2.8306   1.0764
 A6D  HALA  H  HCH2   0   0.306   3.6561  -2.2136  -0.4386
 A6D  HAY   H  HCR5   0   0.256  -0.6456  -2.6126  -2.7315
 A6D  HAZ   H  HCR5   0   0.250  -2.0046  -0.6486  -2.3607
 A6D  HBA   H  HCR5   0   0.266  -0.1060  -2.9569  -0.0567
 A6D  HBB   H  HCR5   0   0.264  -3.4748  -2.1116  -0.1302
 A6D  CAM   C  CH2    0  -0.614   0.5625  -1.1375  -0.9578
 A6D  HAF   H  HCR6   0   0.279   6.6289   0.8426   3.0282
 A6D  OAB   O  O      0  -0.378   6.1085   3.3632  -0.9621
 A6D  OAE   O  O     -1  -0.378   4.8092   2.1424  -2.1319
 A6D  HAM   H  HCH2   0   0.291   0.2027  -0.3184  -1.5882
 A6D  HAMA  H  HCH2   0   0.299   1.3457  -1.6483  -1.5194

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
 A6D  N1   C2    aromatic  1.330  0.020  1.330
 A6D  N1   C6    aromatic  1.338  0.020  1.338
 A6D  C2   N3    aromatic  1.322  0.020  1.322
 A6D  C2   H2    single    0.930  0.020  1.080
 A6D  N3   C4    aromatic  1.330  0.020  1.330
 A6D  C4   C5    aromatic  1.386  0.020  1.386
 A6D  C4   N9    aromatic  1.366  0.020  1.366
 A6D  C5   C6    aromatic  1.407  0.020  1.407
 A6D  C5   N7    aromatic  1.371  0.020  1.371
 A6D  C6   N6    single    1.333  0.020  1.333
 A6D  N6   HN6   single    0.860  0.020  1.020
 A6D  N6   HN6A  single    0.860  0.020  1.020
 A6D  N7   C8    aromatic  1.299  0.020  1.299
 A6D  C8   N9    aromatic  1.369  0.020  1.369
 A6D  C8   H8    single    0.930  0.020  1.080
 A6D  N9   CBB   single    1.440  0.020  1.440
 A6D  OAB  NBD   double    1.208  0.020  1.208
 A6D  OAC  CAY   single    1.403  0.020  1.403
 A6D  OAC  HOAC  single    0.850  0.020  0.980
 A6D  OAD  CAZ   single    1.395  0.020  1.395
 A6D  OAD  HOAD  single    0.850  0.020  0.980
 A6D  OAE  NBD   single    1.209  0.020  1.209
 A6D  CAF  CAG   aromatic  1.385  0.020  1.385
 A6D  CAF  CAH   aromatic  1.386  0.020  1.386
 A6D  CAF  HAF   single    0.930  0.020  1.080
 A6D  CAG  CAT   aromatic  1.394  0.020  1.394
 A6D  CAG  HAG   single    0.930  0.020  1.080
 A6D  CAH  CAV   aromatic  1.386  0.020  1.386
 A6D  CAH  HAH   single    0.930  0.020  1.080
 A6D  CAK  CAT   aromatic  1.388  0.020  1.388
 A6D  CAK  CAV   aromatic  1.388  0.020  1.388
 A6D  CAK  HAK   single    0.930  0.020  1.080
 A6D  CAL  SAR   single    1.832  0.020  1.832
 A6D  CAL  CAT   single    1.492  0.020  1.492
 A6D  CAL  HAL   single    0.970  0.020  1.090
 A6D  CAL  HALA  single    0.970  0.020  1.090
 A6D  CAM  SAS   single    1.816  0.020  1.816
 A6D  CAM  CBA   single    1.518  0.020  1.518
 A6D  CAM  HAM   single    0.970  0.020  1.090
 A6D  CAM  HAMA  single    0.970  0.020  1.090
 A6D  OAQ  CBA   single    1.427  0.020  1.427
 A6D  OAQ  CBB   single    1.400  0.020  1.400
 A6D  SAR  SAS   single    2.046  0.020  2.046
 A6D  CAV  NBD   single    1.456  0.020  1.456
 A6D  CAY  CAZ   single    1.531  0.020  1.531
 A6D  CAY  CBA   single    1.526  0.020  1.526
 A6D  CAY  HAY   single    0.970  0.020  1.090
 A6D  CAZ  CBB   single    1.528  0.020  1.528
 A6D  CAZ  HAZ   single    0.970  0.020  1.090
 A6D  CBA  HBA   single    0.970  0.020  1.090
 A6D  CBB  HBB   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
 A6D  C6    N1   C2   119.14  3.000
 A6D  H2    C2   N3   116.11  3.000
 A6D  H2    C2   N1   115.43  3.000
 A6D  N3    C2   N1   128.46  3.000
 A6D  C4    N3   C2   111.69  3.000
 A6D  N9    C4   C5   105.15  3.000
 A6D  N9    C4   N3   128.36  3.000
 A6D  C5    C4   N3   126.49  3.000
 A6D  N7    C5   C6   132.83  3.000
 A6D  N7    C5   C4   110.84  3.000
 A6D  C6    C5   C4   116.33  3.000
 A6D  N6    C6   C5   122.76  3.000
 A6D  N6    C6   N1   119.35  3.000
 A6D  C5    C6   N1   117.89  3.000
 A6D  HN6A  N6   HN6  118.38  3.000
 A6D  HN6A  N6   C6   121.24  3.000
 A6D  HN6   N6   C6   120.38  3.000
 A6D  C8    N7   C5   104.39  3.000
 A6D  H8    C8   N9   121.92  3.000
 A6D  H8    C8   N7   124.66  3.000
 A6D  N9    C8   N7   113.42  3.000
 A6D  CBB   N9   C8   127.26  3.000
 A6D  CBB   N9   C4   126.52  3.000
 A6D  C8    N9   C4   106.20  3.000
 A6D  HOAC  OAC  CAY  108.01  3.000
 A6D  HOAD  OAD  CAZ  108.95  3.000
 A6D  HAF   CAF  CAH  119.52  3.000
 A6D  HAF   CAF  CAG  120.09  3.000
 A6D  CAH   CAF  CAG  120.39  3.000
 A6D  HAG   CAG  CAT  119.57  3.000
 A6D  HAG   CAG  CAF  119.56  3.000
 A6D  CAT   CAG  CAF  120.88  3.000
 A6D  HAH   CAH  CAV  121.46  3.000
 A6D  HAH   CAH  CAF  120.22  3.000
 A6D  CAV   CAH  CAF  118.31  3.000
 A6D  HAK   CAK  CAV  120.88  3.000
 A6D  HAK   CAK  CAT  119.89  3.000
 A6D  CAV   CAK  CAT  119.22  3.000
 A6D  HALA  CAL  HAL  107.71  3.000
 A6D  HALA  CAL  CAT  111.97  3.000
 A6D  HAL   CAL  CAT  111.53  3.000
 A6D  HALA  CAL  SAR  109.07  3.000
 A6D  HAL   CAL  SAR  103.87  3.000
 A6D  CAT   CAL  SAR  112.29  3.000
 A6D  CBB   OAQ  CBA  110.83  3.000
 A6D  SAS   SAR  CAL  102.59  3.000
 A6D  SAR   SAS  CAM  102.59  3.000
 A6D  CAL   CAT  CAK  120.16  3.000
 A6D  CAL   CAT  CAG  120.68  3.000
 A6D  CAK   CAT  CAG  119.14  3.000
 A6D  NBD   CAV  CAK  118.87  3.000
 A6D  NBD   CAV  CAH  119.06  3.000
 A6D  CAK   CAV  CAH  122.07  3.000
 A6D  HAY   CAY  CBA  111.87  3.000
 A6D  HAY   CAY  CAZ  112.04  3.000
 A6D  CBA   CAY  CAZ  100.92  3.000
 A6D  HAY   CAY  OAC  111.89  3.000
 A6D  CBA   CAY  OAC  108.61  3.000
 A6D  CAZ   CAY  OAC  110.97  3.000
 A6D  HAZ   CAZ  CBB  109.59  3.000
 A6D  HAZ   CAZ  CAY  109.08  3.000
 A6D  CBB   CAZ  CAY  100.98  3.000
 A6D  HAZ   CAZ  OAD  111.56  3.000
 A6D  CBB   CAZ  OAD  109.86  3.000
 A6D  CAY   CAZ  OAD  115.21  3.000
 A6D  HBA   CBA  CAY  110.49  3.000
 A6D  HBA   CBA  OAQ  108.55  3.000
 A6D  CAY   CBA  OAQ  105.90  3.000
 A6D  HBA   CBA  CAM  108.77  3.000
 A6D  CAY   CBA  CAM  112.14  3.000
 A6D  OAQ   CBA  CAM  110.92  3.000
 A6D  HBB   CBB  CAZ  110.19  3.000
 A6D  HBB   CBB  OAQ  111.70  3.000
 A6D  CAZ   CBB  OAQ  105.71  3.000
 A6D  HBB   CBB  N9   106.04  3.000
 A6D  CAZ   CBB  N9   114.00  3.000
 A6D  OAQ   CBB  N9   109.31  3.000
 A6D  CAV   NBD  OAE  118.12  3.000
 A6D  CAV   NBD  OAB  118.06  3.000
 A6D  OAE   NBD  OAB  123.82  3.000
 A6D  HAMA  CAM  HAM  106.86  3.000
 A6D  HAMA  CAM  CBA  109.89  3.000
 A6D  HAM   CAM  CBA  112.18  3.000
 A6D  HAMA  CAM  SAS  109.45  3.000
 A6D  HAM   CAM  SAS  104.46  3.000
 A6D  CBA   CAM  SAS  113.67  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
 A6D  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 A6D  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 A6D  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 A6D  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 A6D  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 A6D  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 A6D  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 A6D  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 A6D  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 A6D  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 A6D  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 A6D  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 A6D  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 A6D  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 A6D  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 A6D  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 A6D  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 A6D  CONST_18  CAK   CAT  CAG  CAF    0.00   0.0  0
 A6D  CONST_19  CAK   CAV  CAH  CAF    0.00   0.0  0
 A6D  CONST_20  CAV   CAH  CAF  CAG    0.00   0.0  0
 A6D  CONST_21  CAV   CAK  CAT  CAG    0.00   0.0  0
 A6D  CONST_22  CAT   CAG  CAF  CAH    0.00   0.0  0
 A6D  CONST_23  CAT   CAK  CAV  CAH    0.00   0.0  0
 A6D  CONST_24  CBB   N9   C4   N3     0.00   0.0  0
 A6D  CONST_25  CBB   N9   C4   C5   180.00   0.0  0
 A6D  CONST_26  CBB   N9   C8   N7   180.00   0.0  0
 A6D  CONST_27  N6    C6   N1   C2   180.00   0.0  0
 A6D  CONST_28  N6    C6   C5   C4   180.00   0.0  0
 A6D  CONST_29  N7    C5   C6   N6     0.00   0.0  0
 A6D  CONST_30  CAL   CAT  CAG  CAF  180.00   0.0  0
 A6D  CONST_31  NBD   CAV  CAH  CAF  180.00   0.0  0
 A6D  CONST_32  CAV   CAK  CAT  CAL  180.00   0.0  0
 A6D  CONST_33  NBD   CAV  CAK  CAT  180.00   0.0  0
 A6D  CONST_34  H2    C2   N3   C4   180.00   0.0  0
 A6D  CONST_35  H8    C8   N9   C4   180.00   0.0  0
 A6D  CONST_36  HAH   CAH  CAF  CAG  180.00   0.0  0
 A6D  CONST_37  HAK   CAK  CAT  CAG  180.00   0.0  0
 A6D  CONST_38  HAG   CAG  CAF  CAH  180.00   0.0  0
 A6D  CONST_39  HAF   CAF  CAG  CAT  180.00   0.0  0
 A6D  CONST_40  CAH   CAV  NBD  OAB    0.00   0.0  0
 A6D  CONST_41  CAK   CAV  NBD  OAB  180.00   0.0  0
 A6D  CONST_42  CAH   CAV  NBD  OAE  180.00   0.0  0
 A6D  CONST_43  CAK   CAV  NBD  OAE    0.00   0.0  0
 A6D  CONST_44  HN6   N6   C6   N1     0.00   0.0  0
 A6D  CONST_45  HN6A  N6   C6   N1   180.00   0.0  0
 A6D  Var_01    SAR   CAL  CAT  CAG   78.83  30.0  3
 A6D  Var_02    CBA   CAM  SAS  SAR   66.26  30.0  2
 A6D  Var_03    CAT   CAL  SAR  SAS   62.74  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
 A6D  chir_01  CAY  OAC  CAZ  CBA  negativ
 A6D  chir_02  CAZ  OAD  CBB  CAY  negativ
 A6D  chir_03  CBA  OAQ  CAY  CAM  negativ
 A6D  chir_04  CBB  OAQ  N9   CAZ  negativ

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
 A6D  plan-1  CAF   0.020
 A6D  plan-1  CAG   0.020
 A6D  plan-1  CAH   0.020
 A6D  plan-1  CAK   0.020
 A6D  plan-1  CAL   0.020
 A6D  plan-1  CAT   0.020
 A6D  plan-1  CAV   0.020
 A6D  plan-1  NBD   0.020
 A6D  plan-1  HAG   0.020
 A6D  plan-1  HAH   0.020
 A6D  plan-1  HAK   0.020
 A6D  plan-1  HAF   0.020
 A6D  plan-2  N1    0.020
 A6D  plan-2  C2    0.020
 A6D  plan-2  N3    0.020
 A6D  plan-2  C4    0.020
 A6D  plan-2  C5    0.020
 A6D  plan-2  C6    0.020
 A6D  plan-2  N6    0.020
 A6D  plan-2  N7    0.020
 A6D  plan-2  C8    0.020
 A6D  plan-2  N9    0.020
 A6D  plan-2  CBB   0.020
 A6D  plan-2  H2    0.020
 A6D  plan-2  H8    0.020
 A6D  plan-3  C6    0.020
 A6D  plan-3  N6    0.020
 A6D  plan-3  HN6   0.020
 A6D  plan-3  HN6A  0.020
 A6D  plan-4  CAV   0.020
 A6D  plan-4  NBD   0.020
 A6D  plan-4  OAB   0.020
 A6D  plan-4  OAE   0.020

