data_O2C # _chem_comp.id O2C _chem_comp.name "3'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-10-31 _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 307.197 _chem_comp.one_letter_code N _chem_comp.three_letter_code O2C _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 O2C P P P 0 1 N N N 9.887 11.933 21.470 -0.731 5.255 2.799 P O2C 1 O2C O1P O1P O 0 1 N N N 9.244 13.041 22.197 -1.330 5.696 4.103 O1P O2C 2 O2C O2P O2P O 0 1 N N N 10.564 12.200 20.171 -1.299 6.012 1.488 O2P O2C 3 O2C "O5'" O5* O 0 1 N N N 10.939 11.219 22.430 -0.925 3.686 2.453 "O5'" O2C 4 O2C "C5'" C5* C 0 1 N N N 10.650 11.012 23.810 -0.387 3.192 1.237 "C5'" O2C 5 O2C "C4'" C4* C 0 1 N N S 11.873 10.491 24.524 -0.692 1.703 1.132 "C4'" O2C 6 O2C "O4'" O4* O 0 1 N N N 12.190 9.160 24.031 -2.120 1.530 1.107 "O4'" O2C 7 O2C "C1'" C1* C 0 1 N N R 13.595 8.972 24.041 -2.520 1.128 -0.211 "C1'" O2C 8 O2C N1 N1 N 0 1 N N N 14.036 8.625 22.675 -3.631 1.935 -0.629 N1 O2C 9 O2C C6 C6 C 0 1 N N N 13.328 9.030 21.577 -3.700 3.248 -0.190 C6 O2C 10 O2C C2 C2 C 0 1 N N N 15.191 7.855 22.521 -4.651 1.429 -1.472 C2 O2C 11 O2C O2 O2 O 0 1 N N N 15.838 7.541 23.524 -4.618 0.267 -1.880 O2 O2C 12 O2C N3 N3 N 0 1 N N N 15.575 7.475 21.282 -5.693 2.265 -1.835 N3 O2C 13 O2C C4 C4 C 0 1 N N N 14.860 7.847 20.218 -5.744 3.502 -1.413 C4 O2C 14 O2C N4 N4 N 0 1 N N N 15.253 7.413 19.019 -6.788 4.316 -1.785 N4 O2C 15 O2C C5 C5 C 0 1 N N N 13.704 8.668 20.338 -4.693 4.068 -0.527 C5 O2C 16 O2C "C2'" C2* C 0 1 N N R 14.222 10.249 24.611 -1.308 1.289 -1.113 "C2'" O2C 17 O2C "O2'" O2* O 0 1 N N N 14.403 10.095 26.008 -1.310 0.329 -2.151 "O2'" O2C 18 O2C "C3'" C3* C 0 1 N N N 13.151 11.283 24.285 -0.167 1.075 -0.146 "C3'" O2C 19 O2C O3P O3P O 0 1 N Y N ? ? ? 0.869 5.455 2.680 O3P O2C 20 O2C HOP2 2HOP H 0 0 N N N 9.914 12.257 19.480 -1.349 6.991 1.489 HOP2 O2C 21 O2C "H5'1" 1H5* H 0 0 N N N 9.838 10.275 23.901 -0.841 3.733 0.403 "H5'1" O2C 22 O2C "H5'2" 2H5* H 0 0 N N N 10.344 11.966 24.264 0.693 3.360 1.232 "H5'2" O2C 23 O2C "H4'" H4* H 0 1 N N N 11.602 10.546 25.589 -0.294 1.197 2.016 "H4'" O2C 24 O2C "H1'" H1* H 0 1 N N N 13.919 8.138 24.681 -2.872 0.091 -0.168 "H1'" O2C 25 O2C H6 H6 H 0 1 N N N 12.453 9.650 21.707 -2.892 3.579 0.453 H6 O2C 26 O2C HN41 1HN4 H 0 0 N N N 16.046 6.827 18.854 -7.355 4.703 -1.070 HN41 O2C 27 O2C HN42 2HN4 H 0 0 N N N 14.639 7.759 18.309 -6.929 4.481 -2.752 HN42 O2C 28 O2C H5 H5 H 0 1 N N N 13.150 8.988 19.468 -4.754 5.093 -0.188 H5 O2C 29 O2C "H2'" H2* H 0 1 N N N 15.211 10.514 24.209 -1.257 2.290 -1.556 "H2'" O2C 30 O2C "HO'2" 2HO* H 0 0 N N N 15.332 10.061 26.206 -0.440 -0.100 -2.133 "HO'2" O2C 31 O2C "H3'1" 1H3* H 0 0 N N N 13.223 12.201 24.887 0.001 0.000 -0.001 "H3'1" O2C 32 O2C "H3'2" 2H3* H 0 0 N N N 13.226 11.645 23.249 0.779 1.503 -0.494 "H3'2" O2C 33 O2C HOP3 3HOP H 0 0 N N N 0.415 -0.715 -0.469 1.260 6.317 2.937 HOP3 O2C 34 # 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 O2C P O1P DOUB N N 1 O2C P O2P SING N N 2 O2C P "O5'" SING N N 3 O2C P O3P SING N N 4 O2C O2P HOP2 SING N N 5 O2C "O5'" "C5'" SING N N 6 O2C "C5'" "C4'" SING N N 7 O2C "C5'" "H5'1" SING N N 8 O2C "C5'" "H5'2" SING N N 9 O2C "C4'" "O4'" SING N N 10 O2C "C4'" "C3'" SING N N 11 O2C "C4'" "H4'" SING N N 12 O2C "O4'" "C1'" SING N N 13 O2C "C1'" N1 SING N N 14 O2C "C1'" "C2'" SING N N 15 O2C "C1'" "H1'" SING N N 16 O2C N1 C6 SING N N 17 O2C N1 C2 SING N N 18 O2C C6 C5 DOUB N N 19 O2C C6 H6 SING N N 20 O2C C2 O2 DOUB N N 21 O2C C2 N3 SING N N 22 O2C N3 C4 DOUB N N 23 O2C C4 N4 SING N N 24 O2C C4 C5 SING N N 25 O2C N4 HN41 SING N N 26 O2C N4 HN42 SING N N 27 O2C C5 H5 SING N N 28 O2C "C2'" "O2'" SING N N 29 O2C "C2'" "C3'" SING N N 30 O2C "C2'" "H2'" SING N N 31 O2C "O2'" "HO'2" SING N N 32 O2C "C3'" "H3'1" SING N N 33 O2C "C3'" "H3'2" SING N N 34 O2C O3P HOP3 SING N N 35 # 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 O2C SMILES ACDLabs 10.04 "O=C1N=C(N)C=CN1C2OC(CC2O)COP(=O)(O)O" O2C SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)C[C@H]2O" O2C SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)C[CH]2O" O2C SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H](O[C@H]([C@@H]1O)N2C=CC(=NC2=O)N)COP(=O)(O)O" O2C SMILES "OpenEye OEToolkits" 1.5.0 "C1C(OC(C1O)N2C=CC(=NC2=O)N)COP(=O)(O)O" O2C InChI InChI 1.03 "InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-6(13)3-5(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1" O2C InChIKey InChI 1.03 SCVBZIYRQRHLNC-SHYZEUOFSA-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 O2C "SYSTEMATIC NAME" ACDLabs 10.04 ;3'-deoxy-5'-cytidylic acid ; O2C "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-4-hydroxy-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 O2C "Create component" 2005-10-31 RCSB O2C "Modify linking type" 2011-06-04 RCSB O2C "Modify descriptor" 2011-06-04 RCSB #