data_P1D
#

_chem_comp.id                                   P1D
_chem_comp.name                                 
;((2S,3AS,4R,6S)-4-(HYDROXYMETHYL)-6-(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)-TETRAHYDROFURO[3,4-D][1,3]DIOXO
L-2-YL)METHYLPHOSPHONIC ACID
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C13 H16 N3 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "9-DEAZAINOSINE-2',3'-O-ETHYLIDENEPHOSPHONATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2005-08-04
_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                       373.255
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    P1D
_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       2AI2
_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
P1D  O3      O3      O  0  1  N  N  N  68.130  -40.506   96.449   4.319   0.185   0.389  O3      P1D   1  
P1D  P       P       P  0  1  N  N  N  66.583  -40.898   96.634   3.741  -1.317   0.441  P       P1D   2  
P1D  O4      O4      O  0  1  N  N  N  65.769  -39.618   97.137   4.883  -2.313   0.987  O4      P1D   3  
P1D  O2      O2      O  0  1  N  N  N  65.966  -41.382   95.372   2.571  -1.365   1.346  O2      P1D   4  
P1D  C1P     C1P     C  0  1  N  N  N  66.457  -42.156   97.927   3.236  -1.833  -1.233  C1P     P1D   5  
P1D  C1      C1      C  0  1  N  N  S  65.218  -43.061   97.773   2.067  -0.965  -1.703  C1      P1D   6  
P1D  "O3'"   "O3'"   O  0  1  N  N  N  65.041  -43.786   99.008   2.431   0.424  -1.660  "O3'"   P1D   7  
P1D  "O2'"   "O2'"   O  0  1  N  N  N  65.318  -44.106   96.783   0.948  -1.113  -0.804  "O2'"   P1D   8  
P1D  "C2'"   "C2'"   C  0  1  N  N  S  65.798  -45.317   97.404   0.165   0.082  -1.032  "C2'"   P1D   9  
P1D  "C3'"   "C3'"   C  0  1  N  N  R  65.548  -45.129   98.894   1.242   1.174  -1.314  "C3'"   P1D  10  
P1D  "C4'"   "C4'"   C  0  1  N  N  R  66.899  -45.269   99.587   1.438   1.807   0.084  "C4'"   P1D  11  
P1D  "C5'"   "C5'"   C  0  1  N  N  N  67.007  -46.598  100.351   1.931   3.250  -0.044  "C5'"   P1D  12  
P1D  "O5'"   "O5'"   O  0  1  N  N  N  68.339  -46.808  100.827   2.171   3.789   1.257  "O5'"   P1D  13  
P1D  "O4'"   "O4'"   O  0  1  N  N  N  67.854  -45.049   98.522   0.120   1.773   0.670  "O4'"   P1D  14  
P1D  "C1'"   "C1'"   C  0  1  N  N  S  67.310  -45.546   97.278  -0.469   0.515   0.303  "C1'"   P1D  15  
P1D  C9      C9      C  0  1  Y  N  N  67.848  -46.939   96.900  -1.958   0.676   0.137  C9      P1D  16  
P1D  C8      C8      C  0  1  Y  N  N  69.111  -47.316   97.103  -2.607   1.826  -0.140  C8      P1D  17  
P1D  N7      N7      N  0  1  Y  N  N  69.255  -48.597   96.767  -3.944   1.584  -0.217  N7      P1D  18  
P1D  C5      C5      C  0  1  Y  N  N  68.084  -49.071   96.347  -4.167   0.247   0.016  C5      P1D  19  
P1D  C4      C4      C  0  1  Y  N  N  67.145  -48.037   96.404  -2.921  -0.350   0.237  C4      P1D  20  
P1D  N3      N3      N  0  1  Y  N  N  65.842  -48.212   96.066  -2.858  -1.678   0.500  N3      P1D  21  
P1D  C2      C2      C  0  1  Y  N  N  65.356  -49.383   95.660  -3.936  -2.405   0.538  C2      P1D  22  
P1D  N1      N1      N  0  1  Y  N  N  66.257  -50.467   95.574  -5.170  -1.880   0.326  N1      P1D  23  
P1D  C6      C6      C  0  1  Y  N  N  67.618  -50.322   95.920  -5.320  -0.563   0.063  C6      P1D  24  
P1D  O6      O6      O  0  1  N  N  N  68.350  -51.314   95.901  -6.426  -0.086  -0.128  O6      P1D  25  
P1D  HO3     HO3     H  0  1  N  N  N  68.613  -41.266   96.150   5.078   0.172  -0.210  HO3     P1D  26  
P1D  HO4     HO4     H  0  1  N  N  N  64.854  -39.849   97.246   5.121  -2.006   1.873  HO4     P1D  27  
P1D  H1P1    1H1P    H  0  0  N  N  N  67.389  -42.765   97.980   2.929  -2.878  -1.214  H1P1    P1D  28  
P1D  H1P2    2H1P    H  0  0  N  N  N  66.484  -41.689   98.939   4.075  -1.713  -1.919  H1P2    P1D  29  
P1D  H1      H1      H  0  1  N  N  N  64.399  -42.363   97.478   1.775  -1.246  -2.715  H1      P1D  30  
P1D  "H2'"   "H2'"   H  0  1  N  N  N  65.282  -46.174   96.912  -0.562  -0.028  -1.836  "H2'"   P1D  31  
P1D  "H3'"   "H3'"   H  0  1  N  N  N  64.837  -45.859   99.347   0.957   1.896  -2.080  "H3'"   P1D  32  
P1D  "H4'"   "H4'"   H  0  1  N  N  N  67.083  -44.535  100.406   2.136   1.216   0.677  "H4'"   P1D  33  
P1D  "H5'1"  "1H5'"  H  0  0  N  N  N  66.260  -46.659  101.176   1.175   3.849  -0.552  "H5'1"  P1D  34  
P1D  "H5'2"  "2H5'"  H  0  0  N  N  N  66.649  -47.456   99.735   2.856   3.268  -0.621  "H5'2"  P1D  35  
P1D  "H5'"   "H5'"   H  0  1  N  N  N  68.405  -47.629  101.299   2.480   4.696   1.132  "H5'"   P1D  36  
P1D  "H1'"   "H1'"   H  0  1  N  N  N  67.650  -45.006   96.363  -0.261  -0.230   1.071  "H1'"   P1D  37  
P1D  H8      H8      H  0  1  N  N  N  69.914  -46.666   97.490  -2.138   2.789  -0.279  H8      P1D  38  
P1D  HN7     HN7     H  0  1  N  N  N  70.123  -49.129   96.822  -4.628   2.247  -0.405  HN7     P1D  39  
P1D  H2      H2      H  0  1  N  N  N  64.283  -49.450   95.412  -3.847  -3.462   0.746  H2      P1D  40  
P1D  HN1     HN1     H  0  1  N  N  N  65.917  -51.374   95.255  -5.951  -2.454   0.363  HN1     P1D  41  
#   #
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
P1D  O3     P       SING  N  N   1  
P1D  O3     HO3     SING  N  N   2  
P1D  P      O4      SING  N  N   3  
P1D  P      O2      DOUB  N  N   4  
P1D  P      C1P     SING  N  N   5  
P1D  O4     HO4     SING  N  N   6  
P1D  C1P    C1      SING  N  N   7  
P1D  C1P    H1P1    SING  N  N   8  
P1D  C1P    H1P2    SING  N  N   9  
P1D  C1     "O3'"   SING  N  N  10  
P1D  C1     "O2'"   SING  N  N  11  
P1D  C1     H1      SING  N  N  12  
P1D  "O3'"  "C3'"   SING  N  N  13  
P1D  "O2'"  "C2'"   SING  N  N  14  
P1D  "C2'"  "C3'"   SING  N  N  15  
P1D  "C2'"  "C1'"   SING  N  N  16  
P1D  "C2'"  "H2'"   SING  N  N  17  
P1D  "C3'"  "C4'"   SING  N  N  18  
P1D  "C3'"  "H3'"   SING  N  N  19  
P1D  "C4'"  "C5'"   SING  N  N  20  
P1D  "C4'"  "O4'"   SING  N  N  21  
P1D  "C4'"  "H4'"   SING  N  N  22  
P1D  "C5'"  "O5'"   SING  N  N  23  
P1D  "C5'"  "H5'1"  SING  N  N  24  
P1D  "C5'"  "H5'2"  SING  N  N  25  
P1D  "O5'"  "H5'"   SING  N  N  26  
P1D  "O4'"  "C1'"   SING  N  N  27  
P1D  "C1'"  C9      SING  N  N  28  
P1D  "C1'"  "H1'"   SING  N  N  29  
P1D  C9     C8      DOUB  Y  N  30  
P1D  C9     C4      SING  Y  N  31  
P1D  C8     N7      SING  Y  N  32  
P1D  C8     H8      SING  N  N  33  
P1D  N7     C5      SING  Y  N  34  
P1D  N7     HN7     SING  N  N  35  
P1D  C5     C4      DOUB  Y  N  36  
P1D  C5     C6      SING  Y  N  37  
P1D  C4     N3      SING  Y  N  38  
P1D  N3     C2      DOUB  Y  N  39  
P1D  C2     N1      SING  Y  N  40  
P1D  C2     H2      SING  N  N  41  
P1D  N1     C6      SING  Y  N  42  
P1D  N1     HN1     SING  N  N  43  
P1D  C6     O6      DOUB  N  N  44  
#   #
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
P1D  SMILES            ACDLabs               10.04  "O=C1NC=Nc2c1ncc2C3OC(C4OC(OC34)CP(=O)(O)O)CO"  
P1D  SMILES_CANONICAL  CACTVS                3.341  "OC[C@H]1O[C@H]([C@@H]2O[C@H](C[P](O)(O)=O)O[C@H]12)c3c[nH]c4C(=O)NC=Nc34"  
P1D  SMILES            CACTVS                3.341  "OC[CH]1O[CH]([CH]2O[CH](C[P](O)(O)=O)O[CH]12)c3c[nH]c4C(=O)NC=Nc34"  
P1D  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1c(c2c([nH]1)C(=O)NC=N2)[C@H]3[C@H]4[C@@H]([C@H](O3)CO)O[C@H](O4)CP(=O)(O)O"  
P1D  SMILES            "OpenEye OEToolkits"  1.5.0  "c1c(c2c([nH]1)C(=O)NC=N2)C3C4C(C(O3)CO)OC(O4)CP(=O)(O)O"  
P1D  InChI             InChI                 1.03   "InChI=1S/C13H16N3O8P/c17-2-6-11-12(24-7(23-11)3-25(19,20)21)10(22-6)5-1-14-9-8(5)15-4-16-13(9)18/h1,4,6-7,10-12,14,17H,2-3H2,(H,15,16,18)(H2,19,20,21)/t6-,7-,10+,11-,12+/m1/s1"  
P1D  InChIKey          InChI                 1.03   ZOEDLCUBOBTIHG-USQSKNHBSA-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
P1D  "SYSTEMATIC NAME"  ACDLabs               10.04  "(1S)-1,4-anhydro-1-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-2,3-O-[(1S)-2-phosphonoethylidene]-D-ribitol"  
P1D  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2S,3aS,4S,6R,6aR)-6-(hydroxymethyl)-4-(4-oxo-3,5-dihydropyrrolo[4,5-d]pyrimidin-7-yl)-3a,4,6,6a-tetrahydrofuro[4,3-d][1,3]dioxol-2-yl]methylphosphonic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
P1D  "Create component"   2005-08-04  RCSB  
P1D  "Modify descriptor"  2011-06-04  RCSB  
P1D  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     P1D
_pdbx_chem_comp_synonyms.name        "9-DEAZAINOSINE-2',3'-O-ETHYLIDENEPHOSPHONATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
