data_XAD
#

_chem_comp.id                                   XAD
_chem_comp.name                                 "9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-9H-PURIN-6-AMINE"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C11 H16 N5 O6 P"
_chem_comp.mon_nstd_parent_comp_id              DA
_chem_comp.pdbx_synonyms                        "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL ADENINE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2006-06-20
_chem_comp.pdbx_modified_date                   2020-06-17
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       345.248
_chem_comp.one_letter_code                      A
_chem_comp.three_letter_code                    XAD
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       2H9S
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
XAD  OP3     O3P     O  0  1  N  Y  N  -16.283   9.480  12.323  -4.403   1.735   1.310  OP3     XAD   1  
XAD  P       P       P  0  1  N  N  N  -17.059  10.187  13.539  -4.330   1.368  -0.256  P       XAD   2  
XAD  OP1     O1P     O  0  1  N  N  N  -18.186  10.965  12.986  -5.410   0.413  -0.590  OP1     XAD   3  
XAD  OP2     O2P     O  0  1  N  N  N  -17.274   9.118  14.523  -4.511   2.709  -1.130  OP2     XAD   4  
XAD  "O6'"   "O6'"   O  0  1  N  N  N  -16.055  11.231  14.161  -2.903   0.701  -0.586  "O6'"   XAD   5  
XAD  "C6'"   "C6'"   C  0  1  N  N  N  -14.801  10.769  14.637  -2.851  -0.537   0.125  "C6'"   XAD   6  
XAD  "C5'"   "C5'"   C  0  1  N  N  R  -13.724  11.759  14.272  -1.512  -1.226  -0.146  "C5'"   XAD   7  
XAD  "C4'"   "C4'"   C  0  1  N  N  S  -12.331  11.233  14.617  -1.508  -2.607   0.513  "C4'"   XAD   8  
XAD  "O4'"   "O4'"   O  0  1  N  N  N  -12.033  10.208  13.667  -2.585  -3.390  -0.005  "O4'"   XAD   9  
XAD  "C3'"   "C3'"   C  0  1  N  N  N  -11.325  12.390  14.530  -0.175  -3.301   0.209  "C3'"   XAD  10  
XAD  "C2'"   "C2'"   C  0  1  N  N  N  -11.768  13.596  15.342   0.969  -2.373   0.630  "C2'"   XAD  11  
XAD  "C1'"   "C1'"   C  0  1  N  N  R  -13.060  13.989  14.665   0.777  -1.009  -0.038  "C1'"   XAD  12  
XAD  "O5'"   "O5'"   O  0  1  N  N  N  -13.993  12.986  14.979  -0.455  -0.432   0.390  "O5'"   XAD  13  
XAD  N9      N9      N  0  1  Y  N  N  -13.705  15.202  15.119   1.884  -0.125   0.333  N9      XAD  14  
XAD  C8      C8      C  0  1  Y  N  N  -14.103  15.479  16.409   1.887   0.781   1.352  C8      XAD  15  
XAD  N7      N7      N  0  1  Y  N  N  -14.764  16.613  16.468   3.032   1.396   1.397  N7      XAD  16  
XAD  C5      C5      C  0  1  Y  N  N  -14.883  17.029  15.141   3.838   0.922   0.417  C5      XAD  17  
XAD  C4      C4      C  0  1  Y  N  N  -14.237  16.172  14.308   3.109  -0.055  -0.282  C4      XAD  18  
XAD  C6      C6      C  0  1  Y  N  N  -15.473  18.141  14.538   5.146   1.207  -0.012  C6      XAD  19  
XAD  N6      N6      N  0  1  N  N  N  -16.119  19.080  15.222   5.910   2.163   0.633  N6      XAD  20  
XAD  N1      N1      N  0  1  Y  N  N  -15.408  18.260  13.183   5.633   0.532  -1.048  N1      XAD  21  
XAD  C2      C2      C  0  1  Y  N  N  -14.766  17.327  12.451   4.911  -0.382  -1.670  C2      XAD  22  
XAD  N3      N3      N  0  1  Y  N  N  -14.152  16.248  12.952   3.681  -0.678  -1.307  N3      XAD  23  
XAD  HOP3    3HOP    H  0  0  N  N  N  -16.885   9.340  11.601  -3.685   2.358   1.484  HOP3    XAD  24  
XAD  HOP2    2HOP    H  0  0  N  N  N  -17.320   8.281  14.077  -5.377   3.075  -0.903  HOP2    XAD  25  
XAD  "H6'1"  "1H6'"  H  0  0  N  N  N  -14.573   9.796  14.178  -3.665  -1.181  -0.208  "H6'1"  XAD  26  
XAD  "H6'2"  "2H6'"  H  0  0  N  N  N  -14.843  10.661  15.731  -2.952  -0.347   1.194  "H6'2"  XAD  27  
XAD  "H5'"   "H5'"   H  0  1  N  N  N  -13.736  11.929  13.185  -1.374  -1.337  -1.222  "H5'"   XAD  28  
XAD  "H4'"   "H4'"   H  0  1  N  N  N  -12.280  10.824  15.637  -1.623  -2.496   1.591  "H4'"   XAD  29  
XAD  "H4T'"  "H4T'"  H  0  0  N  N  N  -11.967  10.589  12.799  -2.539  -4.251   0.432  "H4T'"  XAD  30  
XAD  "H3'1"  "1H3'"  H  0  0  N  N  N  -11.251  12.698  13.477  -0.106  -3.506  -0.860  "H3'1"  XAD  31  
XAD  "H3'2"  "2H3'"  H  0  0  N  N  N  -10.356  12.042  14.918  -0.113  -4.235   0.768  "H3'2"  XAD  32  
XAD  "H2'1"  "1H2'"  H  0  0  N  N  N  -11.023  14.405  15.362   1.921  -2.802   0.317  "H2'1"  XAD  33  
XAD  "H2'2"  "2H2'"  H  0  0  N  N  N  -11.921  13.343  16.401   0.961  -2.252   1.713  "H2'2"  XAD  34  
XAD  "H1'"   "H1'"   H  0  1  N  N  N  -12.787  14.134  13.609   0.761  -1.136  -1.121  "H1'"   XAD  35  
XAD  H8      H8      H  0  1  N  N  N  -13.898  14.847  17.260   1.059   0.961   2.022  H8      XAD  36  
XAD  HN61    1HN6    H  0  0  N  N  N  -16.562  19.884  14.826   6.812   2.348   0.331  HN61    XAD  37  
XAD  HN62    2HN6    H  0  0  N  N  N  -16.090  18.853  16.196   5.541   2.652   1.386  HN62    XAD  38  
XAD  H2      H2      H  0  1  N  N  N  -14.746  17.460  11.379   5.347  -0.907  -2.508  H2      XAD  39  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
XAD  OP3    P       SING  N  N   1  
XAD  OP3    HOP3    SING  N  N   2  
XAD  P      OP1     DOUB  N  N   3  
XAD  P      OP2     SING  N  N   4  
XAD  P      "O6'"   SING  N  N   5  
XAD  OP2    HOP2    SING  N  N   6  
XAD  "O6'"  "C6'"   SING  N  N   7  
XAD  "C6'"  "C5'"   SING  N  N   8  
XAD  "C6'"  "H6'1"  SING  N  N   9  
XAD  "C6'"  "H6'2"  SING  N  N  10  
XAD  "C5'"  "C4'"   SING  N  N  11  
XAD  "C5'"  "O5'"   SING  N  N  12  
XAD  "C5'"  "H5'"   SING  N  N  13  
XAD  "C4'"  "O4'"   SING  N  N  14  
XAD  "C4'"  "C3'"   SING  N  N  15  
XAD  "C4'"  "H4'"   SING  N  N  16  
XAD  "O4'"  "H4T'"  SING  N  N  17  
XAD  "C3'"  "C2'"   SING  N  N  18  
XAD  "C3'"  "H3'1"  SING  N  N  19  
XAD  "C3'"  "H3'2"  SING  N  N  20  
XAD  "C2'"  "C1'"   SING  N  N  21  
XAD  "C2'"  "H2'1"  SING  N  N  22  
XAD  "C2'"  "H2'2"  SING  N  N  23  
XAD  "C1'"  "O5'"   SING  N  N  24  
XAD  "C1'"  N9      SING  N  N  25  
XAD  "C1'"  "H1'"   SING  N  N  26  
XAD  N9     C8      SING  Y  N  27  
XAD  N9     C4      SING  Y  N  28  
XAD  C8     N7      DOUB  Y  N  29  
XAD  C8     H8      SING  N  N  30  
XAD  N7     C5      SING  Y  N  31  
XAD  C5     C4      DOUB  Y  N  32  
XAD  C5     C6      SING  Y  N  33  
XAD  C4     N3      SING  Y  N  34  
XAD  C6     N6      SING  N  N  35  
XAD  C6     N1      DOUB  Y  N  36  
XAD  N6     HN61    SING  N  N  37  
XAD  N6     HN62    SING  N  N  38  
XAD  N1     C2      SING  Y  N  39  
XAD  C2     N3      DOUB  Y  N  40  
XAD  C2     H2      SING  N  N  41  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
XAD  SMILES            ACDLabs               10.04  "O=P(O)(O)OCC3OC(n1cnc2c(ncnc12)N)CCC3O"  
XAD  SMILES_CANONICAL  CACTVS                3.341  "Nc1ncnc2n(cnc12)[C@H]3CC[C@H](O)[C@@H](CO[P](O)(O)=O)O3"  
XAD  SMILES            CACTVS                3.341  "Nc1ncnc2n(cnc12)[CH]3CC[CH](O)[CH](CO[P](O)(O)=O)O3"  
XAD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)[C@H]3CC[C@@H]([C@H](O3)COP(=O)(O)O)O)N"  
XAD  SMILES            "OpenEye OEToolkits"  1.5.0  "c1nc(c2c(n1)n(cn2)C3CCC(C(O3)COP(=O)(O)O)O)N"  
XAD  InChI             InChI                 1.03   "InChI=1S/C11H16N5O6P/c12-10-9-11(14-4-13-10)16(5-15-9)8-2-1-6(17)7(22-8)3-21-23(18,19)20/h4-8,17H,1-3H2,(H2,12,13,14)(H2,18,19,20)/t6-,7+,8+/m0/s1"  
XAD  InChIKey          InChI                 1.03   NNMDAQXJNWKVBU-XLPZGREQSA-N  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
XAD  "SYSTEMATIC NAME"  ACDLabs               10.04  "9-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)-9H-purin-6-amine"  
XAD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,6R)-6-(6-aminopurin-9-yl)-3-hydroxy-oxan-2-yl]methyl dihydrogen phosphate"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XAD  "Create component"   2006-06-20  RCSB  
XAD  "Modify descriptor"  2011-06-04  RCSB  
XAD  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     XAD
_pdbx_chem_comp_synonyms.name        "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL ADENINE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
