# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 01:07:17 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: (2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-[(benzyldisulfanyl)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](CSSCc4ccccc4)[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
 A5D  A5D  '(2R,3R,4S,5S)-2-(6-amino-9H-purin-9-yl)-5-[(benzyldisulfanyl)methyl]tetrahydrofuran-3,4-diol (non-preferred name)'  ligand  46  27  .  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_A5D
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
 A5D  N1    N  N     0  -0.475  -6.2919   1.1867   1.1337
 A5D  C2    C  CR16  0   0.046  -5.8590  -0.0214   1.4830
 A5D  N3    N  N     0  -0.457  -4.7256  -0.6157   1.1524
 A5D  C4    C  CR56  0   0.492  -3.9741   0.1579   0.3735
 A5D  C5    C  CR56  0  -0.012  -4.2860   1.4333  -0.0691
 A5D  C6    C  CR6   0   0.461  -5.5254   1.9525   0.3484
 A5D  N6    N  NH2   0  -0.816  -5.9577   3.1630  -0.0046
 A5D  N7    N  N     0  -0.448  -3.2760   1.9400  -0.8466
 A5D  C8    C  CR15  0   0.113  -2.3849   0.9959  -0.8746
 A5D  N9    N  NR5   0  -0.540  -2.7458  -0.1148  -0.1587
 A5D  OAB   O  OH1   0  -0.667  -0.7321  -3.9516  -0.0921
 A5D  OAC   O  OH1   0  -0.652  -2.8014  -2.8793  -1.6053
 A5D  CAD   C  CR16  0  -0.266   6.8955   2.5516  -0.3254
 A5D  CAE   C  CR16  0  -0.244   6.9776   1.9620   0.9315
 A5D  CAF   C  CR16  0  -0.245   6.1001   1.9738  -1.3044
 A5D  CAG   C  CR16  0  -0.288   6.2651   0.8050   1.2050
 A5D  CAH   C  CR16  0  -0.285   5.3880   0.8126  -1.0285
 A5D  CAK   C  CH2   0  -0.668   4.6824  -1.0189   0.5290
 A5D  OAP   O  O     0  -0.485  -0.7306  -1.0102   0.5574
 A5D  SAQ   S  S2    0  -0.033   3.1456  -0.6776   1.4661
 A5D  SAR   S  S2    0  -0.015   2.0165   0.3811   0.1261
 A5D  CAS   C  CR6   0   0.158   5.4646   0.2166   0.2268
 A5D  CAW   C  CR15  0  -0.026  -0.4340  -2.8432  -0.8998
 A5D  CAX   C  CR15  0  -0.048  -1.7060  -2.0810  -1.2749
 A5D  CAY   C  CR15  0   0.023   0.2903  -1.8056  -0.0468
 A5D  CAZ   C  CR15  0   0.212  -1.9862  -1.3246   0.0225
 A5D  H2    H  HCR6  0   0.253  -6.5271  -0.5888   2.1220
 A5D  HN6   H  HNH2  0   0.404  -6.8465   3.4997   0.3232
 A5D  HN6A  H  HNH2  0   0.412  -5.4108   3.7594  -0.6000
 A5D  H8    H  HCR5  0   0.292  -1.4415   1.0573  -1.3966
 A5D  HOAB  H  HOH1  0   0.451  -1.4474  -4.4440  -0.5119
 A5D  HOAC  H  HOH1  0   0.470  -2.7361  -3.1291  -2.5328
 A5D  HAE   H  HCR6  0   0.256   7.6008   2.4045   1.6978
 A5D  HAF   H  HCR6  0   0.255   6.0342   2.4238  -2.2867
 A5D  HAG   H  HCR6  0   0.253   6.3303   0.3534   2.1881
 A5D  HAH   H  HCR6  0   0.249   4.7712   0.3637  -1.7972
 A5D  HAK   H  HCH2  0   0.307   5.2361  -1.6976   1.1818
 A5D  HAKA  H  HCH2  0   0.297   4.4242  -1.5709  -0.3748
 A5D  HAW   H  HCR5  0   0.255   0.1509  -3.1292  -1.7835
 A5D  HAX   H  HCR5  0   0.249  -1.4728  -1.3661  -2.0750
 A5D  HAY   H  HCR5  0   0.265   0.8628  -2.3023   0.7429
 A5D  HAZ   H  HCR5  0   0.263  -2.5715  -1.9503   0.7048
 A5D  CAL   C  CH2   0  -0.605   1.2345  -0.9370  -0.8540
 A5D  HAD   H  HCR6  0   0.256   7.4516   3.4552  -0.5387
 A5D  HAL   H  HCH2  0   0.289   0.7209  -0.4099  -1.6638
 A5D  HALA  H  HCH2  0   0.294   2.0090  -1.5516  -1.3152

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
 A5D  N1   C2    aromatic  1.330  0.020  1.330
 A5D  N1   C6    aromatic  1.338  0.020  1.338
 A5D  C2   N3    aromatic  1.322  0.020  1.322
 A5D  N3   C4    aromatic  1.330  0.020  1.330
 A5D  C4   C5    aromatic  1.386  0.020  1.386
 A5D  C4   N9    aromatic  1.366  0.020  1.366
 A5D  C5   C6    aromatic  1.407  0.020  1.407
 A5D  C5   N7    aromatic  1.372  0.020  1.372
 A5D  C6   N6    single    1.333  0.020  1.333
 A5D  N7   C8    aromatic  1.299  0.020  1.299
 A5D  C8   N9    aromatic  1.370  0.020  1.370
 A5D  N9   CAZ   single    1.440  0.020  1.440
 A5D  OAB  CAW   single    1.404  0.020  1.404
 A5D  OAC  CAX   single    1.395  0.020  1.395
 A5D  CAD  CAE   aromatic  1.391  0.020  1.391
 A5D  CAD  CAF   aromatic  1.387  0.020  1.387
 A5D  CAE  CAG   aromatic  1.386  0.020  1.386
 A5D  CAF  CAH   aromatic  1.390  0.020  1.390
 A5D  CAG  CAS   aromatic  1.394  0.020  1.394
 A5D  CAH  CAS   aromatic  1.392  0.020  1.392
 A5D  CAK  SAQ   single    1.832  0.020  1.832
 A5D  CAK  CAS   single    1.493  0.020  1.493
 A5D  CAL  SAR   single    1.819  0.020  1.819
 A5D  CAL  CAY   single    1.516  0.020  1.516
 A5D  OAP  CAY   single    1.428  0.020  1.428
 A5D  OAP  CAZ   single    1.401  0.020  1.401
 A5D  SAQ  SAR   single    2.047  0.020  2.047
 A5D  CAW  CAX   single    1.530  0.020  1.530
 A5D  CAW  CAY   single    1.526  0.020  1.526
 A5D  CAX  CAZ   single    1.528  0.020  1.528
 A5D  C2   H2    single    0.930  0.020  1.080
 A5D  N6   HN6   single    0.860  0.020  1.020
 A5D  N6   HN6A  single    0.860  0.020  1.020
 A5D  C8   H8    single    0.930  0.020  1.080
 A5D  OAB  HOAB  single    0.850  0.020  0.980
 A5D  OAC  HOAC  single    0.850  0.020  0.980
 A5D  CAD  HAD   single    0.930  0.020  1.080
 A5D  CAE  HAE   single    0.930  0.020  1.080
 A5D  CAF  HAF   single    0.930  0.020  1.080
 A5D  CAG  HAG   single    0.930  0.020  1.080
 A5D  CAH  HAH   single    0.930  0.020  1.080
 A5D  CAK  HAK   single    0.970  0.020  1.090
 A5D  CAK  HAKA  single    0.970  0.020  1.090
 A5D  CAL  HAL   single    0.970  0.020  1.090
 A5D  CAL  HALA  single    0.970  0.020  1.090
 A5D  CAW  HAW   single    0.970  0.020  1.090
 A5D  CAX  HAX   single    0.970  0.020  1.090
 A5D  CAY  HAY   single    0.970  0.020  1.090
 A5D  CAZ  HAZ   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
 A5D  C6    N1   C2   119.18  3.000
 A5D  H2    C2   N3   116.12  3.000
 A5D  H2    C2   N1   115.43  3.000
 A5D  N3    C2   N1   128.45  3.000
 A5D  C4    N3   C2   111.68  3.000
 A5D  N9    C4   C5   105.17  3.000
 A5D  N9    C4   N3   128.31  3.000
 A5D  C5    C4   N3   126.52  3.000
 A5D  N7    C5   C6   132.88  3.000
 A5D  N7    C5   C4   110.82  3.000
 A5D  C6    C5   C4   116.30  3.000
 A5D  N6    C6   C5   122.83  3.000
 A5D  N6    C6   N1   119.30  3.000
 A5D  C5    C6   N1   117.87  3.000
 A5D  HN6A  N6   HN6  118.40  3.000
 A5D  HN6A  N6   C6   121.31  3.000
 A5D  HN6   N6   C6   120.30  3.000
 A5D  C8    N7   C5   104.41  3.000
 A5D  H8    C8   N9   121.93  3.000
 A5D  H8    C8   N7   124.65  3.000
 A5D  N9    C8   N7   113.42  3.000
 A5D  CAZ   N9   C8   127.44  3.000
 A5D  CAZ   N9   C4   126.37  3.000
 A5D  C8    N9   C4   106.18  3.000
 A5D  HOAB  OAB  CAW  108.07  3.000
 A5D  HOAC  OAC  CAX  108.87  3.000
 A5D  HAD   CAD  CAF  120.21  3.000
 A5D  HAD   CAD  CAE  120.11  3.000
 A5D  CAF   CAD  CAE  119.67  3.000
 A5D  HAE   CAE  CAG  119.84  3.000
 A5D  HAE   CAE  CAD  120.04  3.000
 A5D  CAG   CAE  CAD  120.12  3.000
 A5D  HAF   CAF  CAH  119.76  3.000
 A5D  HAF   CAF  CAD  120.14  3.000
 A5D  CAH   CAF  CAD  120.10  3.000
 A5D  HAG   CAG  CAS  119.68  3.000
 A5D  HAG   CAG  CAE  119.73  3.000
 A5D  CAS   CAG  CAE  120.59  3.000
 A5D  HAH   CAH  CAS  119.61  3.000
 A5D  HAH   CAH  CAF  119.81  3.000
 A5D  CAS   CAH  CAF  120.58  3.000
 A5D  HAKA  CAK  HAK  107.51  3.000
 A5D  HAKA  CAK  CAS  112.04  3.000
 A5D  HAK   CAK  CAS  111.68  3.000
 A5D  HAKA  CAK  SAQ  108.64  3.000
 A5D  HAK   CAK  SAQ  103.61  3.000
 A5D  CAS   CAK  SAQ  112.88  3.000
 A5D  CAZ   OAP  CAY  110.75  3.000
 A5D  SAR   SAQ  CAK  102.96  3.000
 A5D  SAQ   SAR  CAL  102.42  3.000
 A5D  CAK   CAS  CAH  120.54  3.000
 A5D  CAK   CAS  CAG  120.53  3.000
 A5D  CAH   CAS  CAG  118.93  3.000
 A5D  HAW   CAW  CAY  111.97  3.000
 A5D  HAW   CAW  CAX  112.06  3.000
 A5D  CAY   CAW  CAX  101.13  3.000
 A5D  HAW   CAW  OAB  111.76  3.000
 A5D  CAY   CAW  OAB  108.43  3.000
 A5D  CAX   CAW  OAB  110.98  3.000
 A5D  HAX   CAX  CAZ  109.60  3.000
 A5D  HAX   CAX  CAW  109.06  3.000
 A5D  CAZ   CAX  CAW  101.02  3.000
 A5D  HAX   CAX  OAC  111.51  3.000
 A5D  CAZ   CAX  OAC  109.90  3.000
 A5D  CAW   CAX  OAC  115.20  3.000
 A5D  HAY   CAY  CAW  110.06  3.000
 A5D  HAY   CAY  OAP  108.74  3.000
 A5D  CAW   CAY  OAP  106.01  3.000
 A5D  HAY   CAY  CAL  108.57  3.000
 A5D  CAW   CAY  CAL  112.81  3.000
 A5D  OAP   CAY  CAL  110.57  3.000
 A5D  HAZ   CAZ  CAX  110.13  3.000
 A5D  HAZ   CAZ  OAP  111.67  3.000
 A5D  CAX   CAZ  OAP  105.72  3.000
 A5D  HAZ   CAZ  N9   106.05  3.000
 A5D  CAX   CAZ  N9   113.95  3.000
 A5D  OAP   CAZ  N9   109.41  3.000
 A5D  HALA  CAL  HAL  106.97  3.000
 A5D  HALA  CAL  CAY  110.15  3.000
 A5D  HAL   CAL  CAY  112.19  3.000
 A5D  HALA  CAL  SAR  109.32  3.000
 A5D  HAL   CAL  SAR  104.56  3.000
 A5D  CAY   CAL  SAR  113.33  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
 A5D  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 A5D  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 A5D  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 A5D  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 A5D  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 A5D  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 A5D  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 A5D  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 A5D  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 A5D  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 A5D  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 A5D  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 A5D  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 A5D  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 A5D  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 A5D  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 A5D  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 A5D  CONST_18  CAS   CAG  CAE  CAD    0.00   0.0  0
 A5D  CONST_19  CAS   CAH  CAF  CAD    0.00   0.0  0
 A5D  CONST_20  CAH   CAF  CAD  CAE    0.00   0.0  0
 A5D  CONST_21  CAH   CAS  CAG  CAE    0.00   0.0  0
 A5D  CONST_22  CAG   CAE  CAD  CAF    0.00   0.0  0
 A5D  CONST_23  CAG   CAS  CAH  CAF    0.00   0.0  0
 A5D  CONST_24  CAZ   N9   C4   N3     0.00   0.0  0
 A5D  CONST_25  CAZ   N9   C4   C5   180.00   0.0  0
 A5D  CONST_26  CAZ   N9   C8   N7   180.00   0.0  0
 A5D  CONST_27  N6    C6   N1   C2   180.00   0.0  0
 A5D  CONST_28  N6    C6   C5   C4   180.00   0.0  0
 A5D  CONST_29  N7    C5   C6   N6     0.00   0.0  0
 A5D  CONST_30  CAK   CAS  CAG  CAE  180.00   0.0  0
 A5D  CONST_31  CAK   CAS  CAH  CAF  180.00   0.0  0
 A5D  CONST_32  H2    C2   N3   C4   180.00   0.0  0
 A5D  CONST_33  H8    C8   N9   C4   180.00   0.0  0
 A5D  CONST_34  HAG   CAG  CAE  CAD  180.00   0.0  0
 A5D  CONST_35  HAH   CAH  CAF  CAD  180.00   0.0  0
 A5D  CONST_36  HAF   CAF  CAD  CAE  180.00   0.0  0
 A5D  CONST_37  HAE   CAE  CAD  CAF  180.00   0.0  0
 A5D  CONST_38  HAD   CAD  CAE  CAG  180.00   0.0  0
 A5D  CONST_39  HN6   N6   C6   N1     0.00   0.0  0
 A5D  CONST_40  HN6A  N6   C6   N1   180.00   0.0  0
 A5D  Var_01    SAQ   CAK  CAS  CAG   78.86  30.0  3
 A5D  Var_02    CAY   CAL  SAR  SAQ   64.47  30.0  1
 A5D  Var_03    CAS   CAK  SAQ  SAR   66.46  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
 A5D  chir_01  CAW  OAB  CAX  CAY  negativ
 A5D  chir_02  CAX  OAC  CAZ  CAW  negativ
 A5D  chir_03  CAY  OAP  CAW  CAL  negativ
 A5D  chir_04  CAZ  OAP  N9   CAX  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
 A5D  plan-1  CAD   0.020
 A5D  plan-1  CAE   0.020
 A5D  plan-1  CAF   0.020
 A5D  plan-1  CAG   0.020
 A5D  plan-1  CAH   0.020
 A5D  plan-1  CAK   0.020
 A5D  plan-1  CAS   0.020
 A5D  plan-1  HAE   0.020
 A5D  plan-1  HAF   0.020
 A5D  plan-1  HAG   0.020
 A5D  plan-1  HAH   0.020
 A5D  plan-1  HAD   0.020
 A5D  plan-2  N1    0.020
 A5D  plan-2  C2    0.020
 A5D  plan-2  N3    0.020
 A5D  plan-2  C4    0.020
 A5D  plan-2  C5    0.020
 A5D  plan-2  C6    0.020
 A5D  plan-2  N6    0.020
 A5D  plan-2  N7    0.020
 A5D  plan-2  C8    0.020
 A5D  plan-2  N9    0.020
 A5D  plan-2  CAZ   0.020
 A5D  plan-2  H2    0.020
 A5D  plan-2  H8    0.020
 A5D  plan-3  C6    0.020
 A5D  plan-3  N6    0.020
 A5D  plan-3  HN6   0.020
 A5D  plan-3  HN6A  0.020

