data_PYO
# 
_chem_comp.id                                    PYO 
_chem_comp.name                                  "1-(BETA-D-RIBOFURANOSYL)-PYRIMIDIN-2-ONE-5'-PHOSPHATE" 
_chem_comp.type                                  "RNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H13 N2 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2000-09-13 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        308.182 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     PYO 
_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        ? 
_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 
PYO OP3    O3P  O 0 1 N Y N -16.115 106.143 5.841 -1.825 1.007  -4.603 OP3    PYO 1  
PYO P      P    P 0 1 N N N -15.321 107.173 6.777 -0.773 0.044  -3.855 P      PYO 2  
PYO OP1    O1P  O 0 1 N N N -15.917 107.091 8.137 0.502  -0.196 -4.805 OP1    PYO 3  
PYO OP2    O2P  O 0 1 N N N -15.244 108.489 6.093 -1.419 -1.253 -3.557 OP2    PYO 4  
PYO "O5'"  O5*  O 0 1 N N N -13.845 106.592 6.871 -0.297 0.735  -2.481 "O5'"  PYO 5  
PYO "C5'"  C5*  C 0 1 N N N -12.839 107.388 7.463 0.629  -0.163 -1.867 "C5'"  PYO 6  
PYO "C4'"  C4*  C 0 1 N N R -11.479 106.765 7.312 1.123  0.436  -0.549 "C4'"  PYO 7  
PYO "O4'"  O4*  O 0 1 N N N -11.264 106.277 5.958 0.018  0.625  0.364  "O4'"  PYO 8  
PYO "C3'"  C3*  C 0 1 N N S -10.391 107.794 7.565 2.068  -0.547 0.176  "C3'"  PYO 9  
PYO "C1'"  C1*  C 0 1 N N R -10.199 106.995 5.356 0.615  0.707  1.676  "C1'"  PYO 10 
PYO "O3'"  O3*  O 0 1 N N N -9.271  107.152 8.144 3.433  -0.205 -0.070 "O3'"  PYO 11 
PYO "C2'"  C2*  C 0 1 N N R -10.087 108.295 6.157 1.726  -0.366 1.672  "C2'"  PYO 12 
PYO "O2'"  O2*  O 0 1 N N N -8.814  108.902 6.048 2.870  0.089  2.395  "O2'"  PYO 13 
PYO N1     N1   N 0 1 N N N -10.486 107.151 3.915 -0.377 0.409  2.711  N1     PYO 14 
PYO C6     C6   C 0 1 N N N -11.658 106.769 3.415 -0.606 1.302  3.708  C6     PYO 15 
PYO C2     C2   C 0 1 N N N -9.482  107.700 3.104 -1.066 -0.746 2.668  C2     PYO 16 
PYO C5     C5   C 0 1 N N N -11.885 106.900 2.097 -1.531 1.010  4.661  C5     PYO 17 
PYO O2     O2   O 0 1 N N N -8.371  108.077 3.581 -0.852 -1.540 1.767  O2     PYO 18 
PYO N3     N3   N 0 1 N N N -9.730  107.823 1.767 -1.972 -1.041 3.603  N3     PYO 19 
PYO C4     C4   C 0 1 N N N -10.900 107.427 1.299 -2.223 -0.201 4.588  C4     PYO 20 
PYO HOP3   3HOP H 0 0 N N N -15.734 106.195 4.972 -2.084 0.558  -5.419 HOP3   PYO 21 
PYO HOP1   1HOP H 0 0 N N N -15.446 107.701 8.691 0.893  0.671  -4.975 HOP1   PYO 22 
PYO "H5''" 2H5* H 0 0 N N N -12.856 108.429 7.064 0.136  -1.115 -1.671 "H5''" PYO 23 
PYO "H5'"  1H5* H 0 1 N N N -13.069 107.607 8.531 1.476  -0.322 -2.534 "H5'"  PYO 24 
PYO "H4'"  H4*  H 0 1 N N N -11.434 105.927 8.046 1.631  1.383  -0.731 "H4'"  PYO 25 
PYO "H3'"  H3*  H 0 1 N N N -10.672 108.617 8.262 1.869  -1.571 -0.140 "H3'"  PYO 26 
PYO "H1'"  H1*  H 0 1 N N N -9.207  106.485 5.387 1.044  1.696  1.836  "H1'"  PYO 27 
PYO HO3    3HO  H 0 1 N Y N -8.590  107.795 8.302 3.973  -0.831 0.430  HO3    PYO 28 
PYO "H2'"  H2*  H 0 1 N N N -10.767 109.106 5.806 1.356  -1.300 2.094  "H2'"  PYO 29 
PYO HO2    2HO  H 0 1 N N N -8.624  109.214 5.170 3.548  -0.593 2.306  HO2    PYO 30 
PYO HC6    HC6  H 0 1 N N N -12.429 106.350 4.082 -0.059 2.233  3.745  HC6    PYO 31 
PYO HC5    HC5  H 0 1 N N N -12.855 106.582 1.680 -1.729 1.706  5.464  HC5    PYO 32 
PYO HC4    HC4  H 0 1 N N N -11.058 107.539 0.213 -2.962 -0.450 5.336  HC4    PYO 33 
# 
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 
PYO OP3   P      SING N N 1  
PYO OP3   HOP3   SING N N 2  
PYO P     OP1    SING N N 3  
PYO P     OP2    DOUB N N 4  
PYO P     "O5'"  SING N N 5  
PYO OP1   HOP1   SING N N 6  
PYO "O5'" "C5'"  SING N N 7  
PYO "C5'" "C4'"  SING N N 8  
PYO "C5'" "H5''" SING N N 9  
PYO "C5'" "H5'"  SING N N 10 
PYO "C4'" "O4'"  SING N N 11 
PYO "C4'" "C3'"  SING N N 12 
PYO "C4'" "H4'"  SING N N 13 
PYO "O4'" "C1'"  SING N N 14 
PYO "C3'" "O3'"  SING N N 15 
PYO "C3'" "C2'"  SING N N 16 
PYO "C3'" "H3'"  SING N N 17 
PYO "C1'" "C2'"  SING N N 18 
PYO "C1'" N1     SING N N 19 
PYO "C1'" "H1'"  SING N N 20 
PYO "O3'" HO3    SING N N 21 
PYO "C2'" "O2'"  SING N N 22 
PYO "C2'" "H2'"  SING N N 23 
PYO "O2'" HO2    SING N N 24 
PYO N1    C6     SING N N 25 
PYO N1    C2     SING N N 26 
PYO C6    C5     DOUB N N 27 
PYO C6    HC6    SING N N 28 
PYO C2    O2     DOUB N N 29 
PYO C2    N3     SING N N 30 
PYO C5    C4     SING N N 31 
PYO C5    HC5    SING N N 32 
PYO N3    C4     DOUB N N 33 
PYO C4    HC4    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 
PYO SMILES           ACDLabs              10.04 "O=C1N=CC=CN1C2OC(C(O)C2O)COP(=O)(O)O"                                                                                              
PYO SMILES_CANONICAL CACTVS               3.341 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC=NC2=O"                                                                         
PYO SMILES           CACTVS               3.341 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC=NC2=O"                                                                                
PYO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"                                                                      
PYO SMILES           "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1)C2C(C(C(O2)COP(=O)(O)O)O)O"                                                                                        
PYO InChI            InChI                1.03  "InChI=1S/C9H13N2O8P/c12-6-5(4-18-20(15,16)17)19-8(7(6)13)11-3-1-2-10-9(11)14/h1-3,5-8,12-13H,4H2,(H2,15,16,17)/t5-,6-,7-,8-/m1/s1" 
PYO InChIKey         InChI                1.03  LBWXMAFPEFFHIJ-WCTZXXKLSA-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 
PYO "SYSTEMATIC NAME" ACDLabs              10.04 "1-(5-O-phosphono-beta-D-ribofuranosyl)pyrimidin-2(1H)-one"                                   
PYO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-oxopyrimidin-1-yl)oxolan-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 
PYO "Create component"  2000-09-13 EBI  
PYO "Modify descriptor" 2011-06-04 RCSB 
# 
