data_3DG
#

_chem_comp.id                                   3DG
_chem_comp.name                                 "9-(3-DEOXY-BETA-D-RIBOFURANOSYL)GUANINE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H13 N5 O4"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        3-DEOXYGUANOSINE
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2003-11-10
_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                       267.241
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3DG
_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       1V45
_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
3DG  N9      N9      N  0  1  Y  N  N  53.233  129.076  55.619   0.071  -0.460  -0.007  N9      3DG   1  
3DG  "C1'"   "C1'"   C  0  1  N  N  R  52.802  128.394  56.889   1.258   0.359  -0.263  "C1'"   3DG   2  
3DG  "C2'"   "C2'"   C  0  1  N  N  R  53.813  127.833  57.974   1.638   1.164   0.999  "C2'"   3DG   3  
3DG  "C3'"   "C3'"   C  0  1  N  N  N  53.437  128.553  59.373   3.185   1.157   0.995  "C3'"   3DG   4  
3DG  "C4'"   "C4'"   C  0  1  N  N  S  52.490  129.694  58.890   3.553   0.353  -0.271  "C4'"   3DG   5  
3DG  "O4'"   "O4'"   O  0  1  N  N  N  51.923  129.314  57.602   2.402  -0.481  -0.527  "O4'"   3DG   6  
3DG  "C5'"   "C5'"   C  0  1  N  N  N  53.147  131.050  58.636   4.790  -0.511  -0.015  "C5'"   3DG   7  
3DG  "O5'"   "O5'"   O  0  1  N  N  N  52.082  131.925  58.150   5.138  -1.212  -1.211  "O5'"   3DG   8  
3DG  "O2'"   "O2'"   O  0  1  N  N  N  53.584  126.393  58.115   1.143   2.502   0.916  "O2'"   3DG   9  
3DG  C8      C8      C  0  1  Y  N  N  52.268  129.617  54.781   0.062  -1.762   0.405  C8      3DG  10  
3DG  N7      N7      N  0  1  Y  N  N  52.924  130.175  53.725  -1.165  -2.176   0.532  N7      3DG  11  
3DG  C5      C5      C  0  1  Y  N  N  54.258  129.966  53.966  -2.013  -1.169   0.211  C5      3DG  12  
3DG  C6      C6      C  0  1  N  N  N  55.315  130.367  53.174  -3.422  -1.045   0.167  C6      3DG  13  
3DG  O6      O6      O  0  1  N  N  N  55.226  131.026  52.099  -4.142  -1.983   0.462  O6      3DG  14  
3DG  N1      N1      N  0  1  N  N  N  56.556  129.969  53.717  -3.950   0.143  -0.205  N1      3DG  15  
3DG  C2      C2      C  0  1  N  N  N  56.700  129.258  54.895  -3.136   1.184  -0.538  C2      3DG  16  
3DG  N2      N2      N  0  1  N  N  N  57.946  128.970  55.308  -3.700   2.376  -0.917  N2      3DG  17  
3DG  N3      N3      N  0  1  N  N  N  55.681  128.872  55.656  -1.826   1.081  -0.501  N3      3DG  18  
3DG  C4      C4      C  0  1  Y  N  N  54.499  129.257  55.132  -1.232  -0.062  -0.137  C4      3DG  19  
3DG  "H1'"   "H1'"   H  0  1  N  N  N  52.387  127.451  56.464   1.079   1.032  -1.103  "H1'"   3DG  20  
3DG  "H2'"   "H2'"   H  0  1  N  N  N  54.874  128.023  57.688   1.256   0.672   1.894  "H2'"   3DG  21  
3DG  "H3'1"  "1H3'"  H  0  0  N  N  N  54.307  128.884  59.987   3.568   0.663   1.887  "H3'1"  3DG  22  
3DG  "H3'2"  "2H3'"  H  0  0  N  N  N  53.012  127.881  60.155   3.570   2.175   0.926  "H3'2"  3DG  23  
3DG  "H4'"   "H4'"   H  0  1  N  N  N  51.760  129.812  59.724   3.729   1.025  -1.111  "H4'"   3DG  24  
3DG  "H5'1"  "1H5'"  H  0  0  N  N  N  54.027  130.998  57.954   5.621   0.126   0.288  "H5'1"  3DG  25  
3DG  "H5'2"  "2H5'"  H  0  0  N  N  N  53.688  131.456  59.522   4.575  -1.228   0.777  "H5'2"  3DG  26  
3DG  "H5'"   "H5'"   H  0  1  N  N  N  52.491  132.768  57.992   5.920  -1.743  -1.006  "H5'"   3DG  27  
3DG  H1      H1      H  0  1  N  N  N  54.190  126.057  58.765   1.464   2.968   1.700  H1      3DG  28  
3DG  H8      H8      H  0  1  N  N  N  51.175  129.606  54.928   0.942  -2.358   0.596  H8      3DG  29  
3DG  HN1     HN1     H  0  1  N  N  N  57.413  130.214  53.221  -4.913   0.252  -0.242  HN1     3DG  30  
3DG  HN21    1HN2    H  0  0  N  N  N  58.486  129.833  55.370  -3.133   3.127  -1.153  HN21    3DG  31  
3DG  HN22    2HN2    H  0  0  N  N  N  58.052  128.446  56.177  -4.665   2.466  -0.953  HN22    3DG  32  
#   #
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
3DG  N9     "C1'"   SING  N  N   1  
3DG  N9     C8      SING  Y  N   2  
3DG  N9     C4      SING  Y  N   3  
3DG  "C1'"  "C2'"   SING  N  N   4  
3DG  "C1'"  "O4'"   SING  N  N   5  
3DG  "C1'"  "H1'"   SING  N  N   6  
3DG  "C2'"  "C3'"   SING  N  N   7  
3DG  "C2'"  "O2'"   SING  N  N   8  
3DG  "C2'"  "H2'"   SING  N  N   9  
3DG  "C3'"  "C4'"   SING  N  N  10  
3DG  "C3'"  "H3'1"  SING  N  N  11  
3DG  "C3'"  "H3'2"  SING  N  N  12  
3DG  "C4'"  "O4'"   SING  N  N  13  
3DG  "C4'"  "C5'"   SING  N  N  14  
3DG  "C4'"  "H4'"   SING  N  N  15  
3DG  "C5'"  "O5'"   SING  N  N  16  
3DG  "C5'"  "H5'1"  SING  N  N  17  
3DG  "C5'"  "H5'2"  SING  N  N  18  
3DG  "O5'"  "H5'"   SING  N  N  19  
3DG  "O2'"  H1      SING  N  N  20  
3DG  C8     N7      DOUB  Y  N  21  
3DG  C8     H8      SING  N  N  22  
3DG  N7     C5      SING  Y  N  23  
3DG  C5     C6      SING  N  N  24  
3DG  C5     C4      DOUB  Y  N  25  
3DG  C6     O6      DOUB  N  N  26  
3DG  C6     N1      SING  N  N  27  
3DG  N1     C2      SING  N  N  28  
3DG  N1     HN1     SING  N  N  29  
3DG  C2     N2      SING  N  N  30  
3DG  C2     N3      DOUB  N  N  31  
3DG  N2     HN21    SING  N  N  32  
3DG  N2     HN22    SING  N  N  33  
3DG  N3     C4      SING  N  N  34  
#   #
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
3DG  SMILES            ACDLabs               10.04  "O=C1c2ncn(c2N=C(N)N1)C3OC(CC3O)CO"  
3DG  SMILES_CANONICAL  CACTVS                3.341  "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)C[C@H]3O"  
3DG  SMILES            CACTVS                3.341  "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO)C[CH]3O"  
3DG  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1nc2c(n1[C@H]3[C@@H](C[C@H](O3)CO)O)N=C(NC2=O)N"  
3DG  SMILES            "OpenEye OEToolkits"  1.5.0  "c1nc2c(n1C3C(CC(O3)CO)O)N=C(NC2=O)N"  
3DG  InChI             InChI                 1.03   "InChI=1S/C10H13N5O4/c11-10-13-7-6(8(18)14-10)12-3-15(7)9-5(17)1-4(2-16)19-9/h3-5,9,16-17H,1-2H2,(H3,11,13,14,18)/t4-,5+,9+/m0/s1"  
3DG  InChIKey          InChI                 1.03   OROIAVZITJBGSM-OBXARNEKSA-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
3DG  "SYSTEMATIC NAME"  ACDLabs               10.04  "3'-deoxyguanosine"  
3DG  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "2-amino-9-[(2R,3R,5S)-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1H-purin-6-one"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
3DG  "Create component"   2003-11-10  RCSB  
3DG  "Modify descriptor"  2011-06-04  RCSB  
3DG  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     3DG
_pdbx_chem_comp_synonyms.name        3-DEOXYGUANOSINE
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
