data_CDF
# 
_chem_comp.id                                    CDF 
_chem_comp.name                                  4-AMINO-1-{5-O-[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]-ALPHA-D-ARABINOFURANOSYL}PYRIMIDIN-2(1H)-ONE 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             ? 
_chem_comp.formula                               "C9 H15 N3 O11 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2008-04-23 
_chem_comp.pdbx_modified_date                    2008-12-26 
_chem_comp.pdbx_ambiguous_flag                   ? 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        403.176 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     CDF 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        2VSI 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
CDF O3B    O3B    O 0 1 N N N -15.604 -14.502 4.270  5.970  -0.906 1.158  O3B    CDF 1  
CDF PB     PB     P 0 1 N N N -15.355 -14.868 2.822  5.375  -1.126 -0.179 PB     CDF 2  
CDF O1B    O1B    O 0 1 N N N -16.590 -15.353 2.089  6.151  -0.228 -1.266 O1B    CDF 3  
CDF O2B    O2B    O 0 1 N N N -14.146 -15.758 2.614  5.506  -2.681 -0.575 O2B    CDF 4  
CDF O3A    O3A    O 0 1 N N N -15.026 -13.452 2.094  3.820  -0.710 -0.149 O3A    CDF 5  
CDF PA     PA     P 0 1 N N R -13.668 -12.593 2.311  3.010  0.548  0.446  PA     CDF 6  
CDF O1A    O1A    O 0 1 N N N -13.701 -11.391 1.391  2.911  0.414  2.047  O1A    CDF 7  
CDF O2A    O2A    O 0 1 N N N -13.507 -12.355 3.793  3.719  1.800  0.099  O2A    CDF 8  
CDF "O5'"  "O5'"  O 0 1 N N N -12.536 -13.623 1.782  1.528  0.579  -0.183 "O5'"  CDF 9  
CDF "C5'"  "C5'"  C 0 1 N N N -11.166 -13.252 1.625  0.598  1.634  0.068  "C5'"  CDF 10 
CDF "C4'"  "C4'"  C 0 1 N N R -10.565 -13.740 0.310  -0.707 1.352  -0.679 "C4'"  CDF 11 
CDF "O4'"  "O4'"  O 0 1 N N N -11.566 -13.944 -0.696 -1.342 0.193  -0.125 "O4'"  CDF 12 
CDF "C3'"  "C3'"  C 0 1 N N S -9.640  -12.646 -0.203 -1.676 2.541  -0.508 "C3'"  CDF 13 
CDF "O3'"  "O3'"  O 0 1 N N N -8.295  -13.119 -0.308 -1.672 3.371  -1.671 "O3'"  CDF 14 
CDF "C2'"  "C2'"  C 0 1 N N S -10.222 -12.216 -1.536 -3.046 1.829  -0.342 "C2'"  CDF 15 
CDF "O2'"  "O2'"  O 0 1 N N N -10.134 -10.794 -1.635 -3.946 2.619  0.438  "O2'"  CDF 16 
CDF "C1'"  "C1'"  C 0 1 N N S -11.662 -12.719 -1.419 -2.622 0.549  0.422  "C1'"  CDF 17 
CDF N1     N1     N 0 1 N N N -12.513 -12.729 -2.633 -3.590 -0.525 0.191  N1     CDF 18 
CDF C2     C2     C 0 1 N N N -12.106 -13.097 -3.946 -4.863 -0.379 0.602  C2     CDF 19 
CDF O2     O2     O 0 1 N N N -10.955 -13.488 -4.209 -5.197 0.651  1.165  O2     CDF 20 
CDF N3     N3     N 0 1 N N N -12.989 -13.031 -4.968 -5.765 -1.339 0.405  N3     CDF 21 
CDF C4     C4     C 0 1 N N N -14.259 -12.613 -4.767 -5.428 -2.469 -0.204 C4     CDF 22 
CDF N4     N4     N 0 1 N N N -15.117 -12.558 -5.805 -6.368 -3.454 -0.403 N4     CDF 23 
CDF C6     C6     C 0 1 N N N -13.778 -12.314 -2.446 -3.199 -1.666 -0.443 C6     CDF 24 
CDF C5     C5     C 0 1 N N N -14.684 -12.242 -3.499 -4.102 -2.654 -0.646 C5     CDF 25 
CDF H1B    H1B    H 0 1 N N N -17.305 -15.454 2.706  5.813  -0.322 -2.168 H1B    CDF 26 
CDF H2B    H2B    H 0 1 N N N -14.045 -15.944 1.688  6.418  -3.002 -0.612 H2B    CDF 27 
CDF H1A    H1A    H 0 1 N N N -13.708 -10.595 1.909  2.457  -0.386 2.348  H1A    CDF 28 
CDF "H5'1" "H5'1" H 0 0 N N N -11.100 -12.154 1.649  0.399  1.697  1.138  "H5'1" CDF 29 
CDF "H5'2" "H5'2" H 0 0 N N N -10.599 -13.721 2.443  1.018  2.579  -0.279 "H5'2" CDF 30 
CDF "H4'"  "H4'"  H 0 1 N N N -10.050 -14.694 0.498  -0.500 1.190  -1.737 "H4'"  CDF 31 
CDF "H3'"  "H3'"  H 0 1 N N N -9.583  -11.789 0.485  -1.426 3.121  0.381  "H3'"  CDF 32 
CDF "H1'"  "H1'"  H 0 1 N N N -12.265 -11.973 -0.880 -2.532 0.757  1.488  "H1'"  CDF 33 
CDF HA     HA     H 0 1 N N N -8.066  -13.224 -1.224 -2.266 4.133  -1.613 HA     CDF 34 
CDF "H2'"  "H2'"  H 0 1 N N N -9.719  -12.605 -2.434 -3.481 1.583  -1.310 "H2'"  CDF 35 
CDF HB     HB     H 0 1 N N N -10.114 -10.416 -0.764 -4.155 3.479  0.047  HB     CDF 36 
CDF H41N   H41N   H 0 0 N N N -16.010 -12.231 -5.495 -7.279 -3.323 -0.098 H41N   CDF 37 
CDF H42N   H42N   H 0 0 N N N -14.894 -12.807 -6.747 -6.119 -4.279 -0.848 H42N   CDF 38 
CDF H6     H6     H 0 1 N N N -14.098 -12.030 -1.455 -2.178 -1.782 -0.777 H6     CDF 39 
CDF H5     H5     H 0 1 N N N -15.696 -11.905 -3.333 -3.813 -3.568 -1.143 H5     CDF 40 
# 
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 
CDF O3B   PB     DOUB N N 1  
CDF PB    O1B    SING N N 2  
CDF PB    O2B    SING N N 3  
CDF PB    O3A    SING N N 4  
CDF O3A   PA     SING N N 5  
CDF PA    O1A    SING N N 6  
CDF PA    O2A    DOUB N N 7  
CDF PA    "O5'"  SING N N 8  
CDF "O5'" "C5'"  SING N N 9  
CDF "C5'" "C4'"  SING N N 10 
CDF "C4'" "O4'"  SING N N 11 
CDF "C4'" "C3'"  SING N N 12 
CDF "O4'" "C1'"  SING N N 13 
CDF "C3'" "O3'"  SING N N 14 
CDF "C3'" "C2'"  SING N N 15 
CDF "C2'" "O2'"  SING N N 16 
CDF "C2'" "C1'"  SING N N 17 
CDF "C1'" N1     SING N N 18 
CDF N1    C2     SING N N 19 
CDF N1    C6     SING N N 20 
CDF C2    O2     DOUB N N 21 
CDF C2    N3     SING N N 22 
CDF N3    C4     DOUB N N 23 
CDF C4    N4     SING N N 24 
CDF C4    C5     SING N N 25 
CDF O1B   H1B    SING N N 26 
CDF O2B   H2B    SING N N 27 
CDF O1A   H1A    SING N N 28 
CDF "C5'" "H5'1" SING N N 29 
CDF "C5'" "H5'2" SING N N 30 
CDF "C4'" "H4'"  SING N N 31 
CDF "C3'" "H3'"  SING N N 32 
CDF "C1'" "H1'"  SING N N 33 
CDF "O3'" HA     SING N N 34 
CDF "C2'" "H2'"  SING N N 35 
CDF "O2'" HB     SING N N 36 
CDF N4    H41N   SING N N 37 
CDF N4    H42N   SING N N 38 
CDF C6    C5     DOUB N N 39 
CDF C5    H5     SING N N 40 
CDF C6    H6     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 
CDF SMILES           ACDLabs              10.04 O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O                                                                                                                                         
CDF InChI            InChI                1.02b InChI=1/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7+,8+/m1/s1/f/h16-17,19H,10H2 
CDF InChIKey         InChI                1.02b ZWIADYZPOWUWEW-UZNUKESGDC                                                                                                                                                                  
CDF SMILES_CANONICAL CACTVS               3.341 NC1=NC(=O)N(C=C1)[C@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]2O                                                                                                                  
CDF SMILES           CACTVS               3.341 NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O                                                                                                                         
CDF SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1N)[C@@H]2[C@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O                                                                                                                 
CDF SMILES           "OpenEye OEToolkits" 1.5.0 C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O                                                                                                                                       
# 
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 
CDF "SYSTEMATIC NAME" ACDLabs              10.04 4-amino-1-{5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-alpha-D-arabinofuranosyl}pyrimidin-2(1H)-one               
CDF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4S,5S)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen phosphate" 
# 
