data_RY # _chem_comp.id RY _chem_comp.name ;5'-3,6-dihydrocytidylic acid ; _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H16 N3 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-09-06 _chem_comp.pdbx_modified_date 2018-10-26 _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 325.212 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RY _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 6MCF _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 RY P P1 P 0 1 N N N 32.896 6.856 -5.847 -4.067 -1.071 0.048 P RY 1 RY "C5'" C1 C 0 1 N N N 30.597 5.982 -4.718 -2.130 0.726 -0.352 "C5'" RY 2 RY "O5'" O1 O 0 1 N N N 32.002 6.244 -4.634 -2.798 -0.195 0.512 "O5'" RY 3 RY "C4'" C2 C 0 1 N N R 30.220 4.708 -5.495 -0.974 1.387 0.402 "C4'" RY 4 RY "O4'" O2 O 0 1 N N N 30.772 3.540 -4.893 0.033 0.407 0.709 "O4'" RY 5 RY "C3'" C3 C 0 1 N N S 28.695 4.437 -5.549 -0.314 2.459 -0.486 "C3'" RY 6 RY "O3'" O3 O 0 1 N N N 28.104 4.707 -6.821 -0.398 3.743 0.135 "O3'" RY 7 RY "C2'" C4 C 0 1 N N R 28.598 2.927 -5.226 1.162 2.006 -0.595 "C2'" RY 8 RY "O2'" O4 O 0 1 N N N 27.700 2.186 -6.044 2.047 3.123 -0.502 "O2'" RY 9 RY "C1'" C5 C 0 1 N N R 30.032 2.466 -5.441 1.309 1.078 0.638 "C1'" RY 10 RY N1 N1 N 0 1 N N N 30.349 1.152 -4.818 2.390 0.111 0.430 N1 RY 11 RY C2 C6 C 0 1 N N N 30.522 0.027 -5.633 2.303 -0.823 -0.538 C2 RY 12 RY O2 O5 O 0 1 N N N 30.355 0.028 -6.845 1.311 -0.853 -1.242 O2 RY 13 RY N3 N2 N 0 1 N N N 30.838 -1.142 -5.077 3.276 -1.718 -0.748 N3 RY 14 RY C4 C7 C 0 1 N N N 30.973 -1.285 -3.797 4.443 -1.765 -0.001 C4 RY 15 RY N4 N3 N 0 1 N N N 31.297 -2.455 -3.318 5.402 -2.730 -0.289 N4 RY 16 RY C5 C8 C 0 1 N N N 30.748 -0.198 -2.910 4.661 -0.901 0.989 C5 RY 17 RY C6 C9 C 0 1 N N N 30.446 1.012 -3.455 3.598 0.140 1.270 C6 RY 18 RY OP1 O6 O 0 1 N N N 32.002 7.206 -6.975 -3.717 -1.840 -1.167 OP1 RY 19 RY OP2 O7 O 0 1 N N N 33.735 7.954 -5.302 -4.477 -2.087 1.227 OP2 RY 20 RY OP3 O8 O 0 1 N Y N 33.875 5.682 -6.362 -5.305 -0.093 -0.273 OP3 RY 21 RY "H5''" H1 H 0 0 N N N 30.119 6.839 -5.215 -1.740 0.193 -1.220 "H5''" RY 22 RY "H5'" H2 H 0 1 N N N 30.206 5.886 -3.694 -2.833 1.491 -0.681 "H5'" RY 23 RY "H4'" H3 H 0 1 N N N 30.589 4.808 -6.526 -1.343 1.840 1.322 "H4'" RY 24 RY "H3'" H4 H 0 1 N N N 28.197 5.011 -4.754 -0.781 2.479 -1.471 "H3'" RY 25 RY H1 H5 H 0 1 N N N 27.173 4.521 -6.784 0.002 4.457 -0.381 H1 RY 26 RY "H2'" H6 H 0 1 N N N 28.338 2.809 -4.164 1.332 1.453 -1.520 "H2'" RY 27 RY "HO2'" H7 H 0 0 N N N 27.705 1.275 -5.776 1.930 3.778 -1.204 "HO2'" RY 28 RY "H1'" H8 H 0 1 N N N 30.217 2.399 -6.523 1.485 1.664 1.540 "H1'" RY 29 RY H3 H9 H 0 1 N N N 30.976 -1.936 -5.669 3.159 -2.367 -1.459 H3 RY 30 RY H41 H10 H 0 1 N N N 31.362 -2.401 -2.322 5.251 -3.363 -1.009 H41 RY 31 RY H42 H11 H 0 1 N N N 30.598 -3.124 -3.571 6.221 -2.770 0.229 H42 RY 32 RY H5 H12 H 0 1 N N N 30.814 -0.328 -1.840 5.571 -0.939 1.571 H5 RY 33 RY H6 H13 H 0 1 N N N 31.224 1.713 -3.120 4.053 1.125 1.168 H6 RY 34 RY H2 H14 H 0 1 N N N 29.475 1.314 -3.036 3.287 0.025 2.309 H2 RY 35 RY H4 H15 H 0 1 N N N 33.562 8.754 -5.784 -5.236 -2.648 1.016 H4 RY 36 RY H7 H16 H 0 1 N N N 33.670 5.471 -7.265 -5.588 0.443 0.480 H7 RY 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 RY OP1 P DOUB N N 1 RY O2 C2 DOUB N N 2 RY "O3'" "C3'" SING N N 3 RY "O2'" "C2'" SING N N 4 RY P OP2 SING N N 5 RY P "O5'" SING N N 6 RY C2 N3 SING N N 7 RY C2 N1 SING N N 8 RY "C3'" "C4'" SING N N 9 RY "C3'" "C2'" SING N N 10 RY "C4'" "O4'" SING N N 11 RY "C4'" "C5'" SING N N 12 RY "C1'" "C2'" SING N N 13 RY "C1'" "O4'" SING N N 14 RY "C1'" N1 SING N N 15 RY N3 C4 SING N N 16 RY N1 C6 SING N N 17 RY "C5'" "O5'" SING N N 18 RY C4 N4 SING N N 19 RY C4 C5 DOUB N N 20 RY C6 C5 SING N N 21 RY P OP3 SING N N 22 RY "C5'" "H5''" SING N N 23 RY "C5'" "H5'" SING N N 24 RY "C4'" "H4'" SING N N 25 RY "C3'" "H3'" SING N N 26 RY "O3'" H1 SING N N 27 RY "C2'" "H2'" SING N N 28 RY "O2'" "HO2'" SING N N 29 RY "C1'" "H1'" SING N N 30 RY N3 H3 SING N N 31 RY N4 H41 SING N N 32 RY N4 H42 SING N N 33 RY C5 H5 SING N N 34 RY C6 H6 SING N N 35 RY C6 H2 SING N N 36 RY OP2 H4 SING N N 37 RY OP3 H7 SING N N 38 # 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 RY SMILES ACDLabs 12.01 "P(O)(OCC1OC(C(C1O)O)N2CC=C(NC2=O)N)(O)=O" RY InChI InChI 1.03 "InChI=1S/C9H16N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1,4,6-8,13-14H,2-3,10H2,(H,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1" RY InChIKey InChI 1.03 NWPXZYGTNOANAA-XVFCMESISA-N RY SMILES_CANONICAL CACTVS 3.385 "NC1=CCN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)N1" RY SMILES CACTVS 3.385 "NC1=CCN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)N1" RY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1C=C(NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N" RY SMILES "OpenEye OEToolkits" 2.0.6 "C1C=C(NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)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 RY "SYSTEMATIC NAME" ACDLabs 12.01 ;5'-3,6-dihydrocytidylic acid ; RY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-oxidanylidene-1,4-dihydropyrimidin-3-yl)-3,4-bis(oxidanyl)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 RY "Create component" 2018-09-06 RCSB RY "Initial release" 2018-10-31 RCSB #