data_3PD
#

_chem_comp.id                                   3PD
_chem_comp.name                                 "2-AMINO-9-(2-DEOXY-3-O-PHOSPHONOPENTOFURANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H14 N5 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2'-DEOXYGUANOSINE-3'-MONOPHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2006-04-14
_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                       347.221
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3PD
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       ?
_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
3PD  "O5'"   "O5'"   O  0  1  N  N  N   0.929  11.162  13.419   3.235   3.702  -2.745  "O5'"   3PD   1  
3PD  "C5'"   "C5'"   C  0  1  N  N  N   1.922  11.969  12.786   2.240   2.706  -2.896  "C5'"   3PD   2  
3PD  "C4'"   "C4'"   C  0  1  N  N  R   2.431  13.049  13.724   2.219   1.846  -1.646  "C4'"   3PD   3  
3PD  "O4'"   "O4'"   O  0  1  N  N  N   1.382  13.999  14.095   1.879   2.654  -0.508  "O4'"   3PD   4  
3PD  "C1'"   "C1'"   C  0  1  N  N  R   1.567  14.465  15.412   1.171   1.827   0.433  "C1'"   3PD   5  
3PD  "C2'"   "C2'"   C  0  1  N  N  N   2.807  13.768  16.007   0.970   0.461  -0.212  "C2'"   3PD   6  
3PD  "C3'"   "C3'"   C  0  1  N  N  S   3.019  12.553  15.059   1.177   0.741  -1.684  "C3'"   3PD   7  
3PD  "O3'"   "O3'"   O  0  1  N  N  N   4.418  12.253  14.819   1.636  -0.408  -2.366  "O3'"   3PD   8  
3PD  N9      N9      N  0  1  Y  N  N   0.267  14.282  16.183  -0.077   2.488   0.819  N9      3PD   9  
3PD  C4      C4      C  0  1  Y  N  N  -0.407  13.104  16.516  -0.705   2.429   2.031  C4      3PD  10  
3PD  N3      N3      N  0  1  Y  N  N  -0.006  11.798  16.192  -0.281   1.738   3.113  N3      3PD  11  
3PD  C2      C2      C  0  1  Y  N  N  -0.858  10.835  16.654  -1.083   1.861   4.148  C2      3PD  12  
3PD  N2      N2      N  0  1  N  N  N  -0.624   9.536  16.441  -0.830   1.237   5.342  N2      3PD  13  
3PD  N1      N1      N  0  1  Y  N  N  -2.023  11.153  17.382  -2.263   2.641   4.111  N1      3PD  14  
3PD  C6      C6      C  0  1  Y  N  N  -2.453  12.488  17.721  -2.721   3.365   3.001  C6      3PD  15  
3PD  O6      O6      O  0  1  N  N  N  -3.493  12.639  18.363  -3.741   4.041   2.966  O6      3PD  16  
3PD  C5      C5      C  0  1  Y  N  N  -1.550  13.505  17.234  -1.825   3.211   1.888  C5      3PD  17  
3PD  N7      N7      N  0  1  Y  N  N  -1.600  14.885  17.352  -1.918   3.751   0.639  N7      3PD  18  
3PD  C8      C8      C  0  1  Y  N  N  -0.523  15.291  16.725  -0.848   3.296   0.017  C8      3PD  19  
3PD  P       P       P  0  1  N  N  N   5.526  12.056  15.963   0.705  -1.727  -2.352  P       3PD  20  
3PD  O1P     O1P     O  0  1  N  N  N   6.284  13.310  16.097   1.453  -2.739  -3.368  O1P     3PD  21  
3PD  O2P     O2P     O  0  1  N  N  N   4.890  11.528  17.191  -0.594  -1.252  -3.188  O2P     3PD  22  
3PD  O1      O1      O  0  1  N  N  N       ?       ?       ?   0.413  -2.287  -0.990  O1      3PD  23  
3PD  "H5'"   "H5'"   H  0  1  N  N  N   1.273  10.288  13.560   3.079   4.368  -3.436  "H5'"   3PD  24  
3PD  "H5'1"  "1H5'"  H  0  0  N  N  N   1.471  12.453  11.908   1.270   3.186  -3.037  "H5'1"  3PD  25  
3PD  "H5'2"  "2H5'"  H  0  0  N  N  N   2.765  11.328  12.489   2.475   2.094  -3.768  "H5'2"  3PD  26  
3PD  "H4'"   "H4'"   H  0  1  N  N  N   3.231  13.507  13.125   3.224   1.436  -1.487  "H4'"   3PD  27  
3PD  "H1'"   "H1'"   H  0  1  N  N  N   1.783  15.542  15.462   1.753   1.756   1.357  "H1'"   3PD  28  
3PD  "H2'1"  "1H2'"  H  0  0  N  N  N   2.671  13.474  17.058  -0.002   0.004   0.001  "H2'1"  3PD  29  
3PD  "H2'2"  "2H2'"  H  0  0  N  N  N   3.682  14.434  16.014   1.736  -0.240   0.147  "H2'2"  3PD  30  
3PD  "H3'"   "H3'"   H  0  1  N  N  N   2.567  11.646  15.487   0.241   1.086  -2.140  "H3'"   3PD  31  
3PD  HN21    1HN2    H  0  0  N  N  N   0.164   9.171  15.945  -1.587   0.804   5.817  HN21    3PD  32  
3PD  HN22    2HN2    H  0  0  N  N  N  -1.349   8.981  16.849   0.102   1.241   5.687  HN22    3PD  33  
3PD  HN1     HN1     H  0  1  N  N  N  -2.597  10.393  17.688  -2.824   2.680   4.958  HN1     3PD  34  
3PD  H8      H8      H  0  1  N  N  N  -0.267  16.336  16.635  -0.576   3.514  -1.007  H8      3PD  35  
3PD  H1P     H1P     H  0  1  N  N  N   5.681  14.044  16.126   1.101  -3.648  -3.477  H1P     3PD  36  
3PD  H2P     H2P     H  0  1  N  N  N   5.549  11.415  17.866  -1.366  -1.854  -3.248  H2P     3PD  37  
#   #
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
3PD  "O5'"  "C5'"   SING  N  N   1  
3PD  "O5'"  "H5'"   SING  N  N   2  
3PD  "C5'"  "C4'"   SING  N  N   3  
3PD  "C5'"  "H5'1"  SING  N  N   4  
3PD  "C5'"  "H5'2"  SING  N  N   5  
3PD  "C4'"  "O4'"   SING  N  N   6  
3PD  "C4'"  "C3'"   SING  N  N   7  
3PD  "C4'"  "H4'"   SING  N  N   8  
3PD  "O4'"  "C1'"   SING  N  N   9  
3PD  "C1'"  "C2'"   SING  N  N  10  
3PD  "C1'"  N9      SING  N  N  11  
3PD  "C1'"  "H1'"   SING  N  N  12  
3PD  "C2'"  "C3'"   SING  N  N  13  
3PD  "C2'"  "H2'1"  SING  N  N  14  
3PD  "C2'"  "H2'2"  SING  N  N  15  
3PD  "C3'"  "O3'"   SING  N  N  16  
3PD  "C3'"  "H3'"   SING  N  N  17  
3PD  "O3'"  P       SING  N  N  18  
3PD  N9     C4      SING  Y  N  19  
3PD  N9     C8      SING  Y  N  20  
3PD  C4     N3      SING  Y  N  21  
3PD  C4     C5      DOUB  Y  N  22  
3PD  N3     C2      DOUB  Y  N  23  
3PD  C2     N2      SING  N  N  24  
3PD  C2     N1      SING  Y  N  25  
3PD  N2     HN21    SING  N  N  26  
3PD  N2     HN22    SING  N  N  27  
3PD  N1     C6      SING  Y  N  28  
3PD  N1     HN1     SING  N  N  29  
3PD  C6     O6      DOUB  N  N  30  
3PD  C6     C5      SING  Y  N  31  
3PD  C5     N7      SING  Y  N  32  
3PD  N7     C8      DOUB  Y  N  33  
3PD  C8     H8      SING  N  N  34  
3PD  P      O1P     SING  N  N  35  
3PD  P      O2P     SING  N  N  36  
3PD  P      O1      DOUB  N  N  37  
3PD  O1P    H1P     SING  N  N  38  
3PD  O2P    H2P     SING  N  N  39  
#   #
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
3PD  SMILES            ACDLabs               10.04  "O=C1c2ncn(c2N=C(N)N1)C3OC(C(OP(=O)(O)O)C3)CO"  
3PD  SMILES_CANONICAL  CACTVS                3.341  "NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O[P](O)(O)=O)[C@@H](CO)O3"  
3PD  SMILES            CACTVS                3.341  "NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O[P](O)(O)=O)[CH](CO)O3"  
3PD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO)OP(=O)(O)O)N=C(NC2=O)N"  
3PD  SMILES            "OpenEye OEToolkits"  1.5.0  "c1nc2c(n1C3CC(C(O3)CO)OP(=O)(O)O)N=C(NC2=O)N"  
3PD  InChI             InChI                 1.03   "InChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(5(2-16)21-6)22-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1"  
3PD  InChIKey          InChI                 1.03   QQMSZHORHNORLP-KVQBGUIXSA-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
3PD  "SYSTEMATIC NAME"  ACDLabs               10.04  "2'-deoxy-3'-guanylic acid"  
3PD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] 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
3PD  "Create component"   2006-04-14  RCSB  
3PD  "Modify descriptor"  2011-06-04  RCSB  
3PD  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     3PD
_pdbx_chem_comp_synonyms.name        "2'-DEOXYGUANOSINE-3'-MONOPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
