data_C5L # _chem_comp.id C5L _chem_comp.name ;2'-O-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate) ; _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H22 N3 O9 P" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-01-22 _chem_comp.pdbx_modified_date 2013-11-22 _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 395.302 _chem_comp.one_letter_code ? _chem_comp.three_letter_code C5L _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 2M3F _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 C5L P P P 0 1 N N N 12.091 4.299 23.932 5.146 -0.175 0.045 P C5L 1 C5L N1 N1 N 0 1 N N N 8.794 1.249 20.898 -1.357 -1.110 -0.392 N1 C5L 2 C5L C2 C2 C 0 1 N N N 8.192 0.666 19.778 -1.005 -1.778 0.722 C2 C5L 3 C5L O2 O2 O 0 1 N N N 7.455 -0.313 19.863 -0.067 -1.376 1.391 O2 C5L 4 C5L N3 N3 N 0 1 N N N 8.402 1.164 18.545 -1.664 -2.869 1.106 N3 C5L 5 C5L C4 C4 C 0 1 N N N 9.228 2.177 18.419 -2.688 -3.327 0.398 C4 C5L 6 C5L N4 N4 N 0 1 N N N 9.326 2.580 17.189 -3.361 -4.455 0.805 N4 C5L 7 C5L C5 C5 C 0 1 N N N 9.944 2.778 19.515 -3.081 -2.651 -0.775 C5 C5L 8 C5L C6 C6 C 0 1 N N N 9.684 2.283 20.746 -2.405 -1.539 -1.150 C6 C5L 9 C5L C7 C7 C 0 1 N N N 10.883 3.964 19.355 -4.241 -3.154 -1.596 C7 C5L 10 C5L "C1'" "C1'" C 0 1 N N R 8.424 0.712 22.230 -0.613 0.088 -0.790 "C1'" C5L 11 C5L "C2'" "C2'" C 0 1 N N R 9.249 -0.491 22.663 -0.794 1.216 0.258 "C2'" C5L 12 C5L "O2'" "O2'" O 0 1 N N N 8.441 -1.365 23.460 -1.972 1.978 -0.013 "O2'" C5L 13 C5L "C3'" "C3'" C 0 1 N N R 10.353 0.163 23.495 0.478 2.069 0.039 "C3'" C5L 14 C5L "O3'" "O3'" O 0 1 N N N 10.979 -0.745 24.392 0.191 3.190 -0.799 "O3'" C5L 15 C5L "C4'" "C4'" C 0 1 N N R 9.543 1.261 24.191 1.461 1.110 -0.660 "C4'" C5L 16 C5L "O4'" "O4'" O 0 1 N N N 8.557 1.695 23.253 0.808 -0.166 -0.768 "O4'" C5L 17 C5L "C5'" "C5'" C 0 1 N N N 10.395 2.423 24.723 2.737 0.973 0.174 "C5'" C5L 18 C5L "O5'" "O5'" O 0 1 N N N 11.166 3.013 23.687 3.687 0.176 -0.536 "O5'" C5L 19 C5L "CA'" "CA'" C 0 1 N N N 7.693 -2.299 22.694 -2.586 2.533 1.153 "CA'" C5L 20 C5L "CB'" "CB'" C 0 1 N N N 6.969 -3.270 23.633 -3.831 3.324 0.746 "CB'" C5L 21 C5L "OC'" "OC'" O 0 1 N N N 6.192 -4.248 22.943 -4.803 2.433 0.196 "OC'" C5L 22 C5L "CD'" "CD'" C 0 1 N N N 6.949 -5.162 22.156 -6.011 3.074 -0.219 "CD'" C5L 23 C5L OP1 OP1 O 0 1 N N N 12.833 4.114 25.205 6.010 1.177 0.179 OP1 C5L 24 C5L OP2 OP2 O 0 1 N N N 12.859 4.551 22.691 5.008 -0.805 1.377 OP2 C5L 25 C5L OP3 OP3 O 0 1 N Y N 11.074 5.515 24.132 5.892 -1.192 -0.955 OP3 C5L 26 C5L H6 H6 H 0 1 N N N 10.177 2.702 21.611 -2.688 -1.004 -2.044 H6 C5L 27 C5L "H5'" "H5'" H 0 1 N N N 9.731 3.186 25.155 3.157 1.961 0.359 "H5'" C5L 28 C5L "H1'" "H1'" H 0 1 N N N 7.373 0.391 22.185 -0.930 0.426 -1.776 "H1'" C5L 29 C5L "H2'" "H2'" H 0 1 N N N 9.676 -1.005 21.789 -0.821 0.808 1.268 "H2'" C5L 30 C5L "H3'" "H3'" H 0 1 N N N 11.092 0.625 22.823 0.884 2.401 0.995 "H3'" C5L 31 C5L "H4'" "H4'" H 0 1 N N N 9.036 0.802 25.053 1.706 1.489 -1.652 "H4'" C5L 32 C5L H41 H41 H 0 1 N N N 8.802 2.123 16.470 -3.088 -4.918 1.612 H41 C5L 33 C5L H42 H42 H 0 1 N N N 9.925 3.347 16.960 -4.109 -4.788 0.284 H42 C5L 34 C5L "H5''" "H5''" H 0 0 N N N 11.072 2.043 25.502 2.500 0.495 1.124 "H5''" C5L 35 C5L H71 H71 H 0 1 N N N 10.326 4.820 18.947 -4.653 -4.049 -1.132 H71 C5L 36 C5L H72 H72 H 0 1 N N N 11.304 4.234 20.335 -5.010 -2.384 -1.648 H72 C5L 37 C5L H73 H73 H 0 1 N N N 11.698 3.696 18.667 -3.897 -3.392 -2.603 H73 C5L 38 C5L HCA1 HCA1 H 0 0 N N N 6.954 -1.762 22.082 -2.872 1.730 1.831 HCA1 C5L 39 C5L HCA2 HCA2 H 0 0 N N N 8.373 -2.862 22.038 -1.881 3.197 1.653 HCA2 C5L 40 C5L HCB1 HCB1 H 0 0 N N N 6.301 -2.691 24.287 -4.248 3.821 1.622 HCB1 C5L 41 C5L HCB2 HCB2 H 0 0 N N N 7.721 -3.790 24.245 -3.559 4.071 -0.000 HCB2 C5L 42 C5L HCD1 HCD1 H 0 0 N N N 6.269 -5.874 21.665 -6.696 2.330 -0.624 HCD1 C5L 43 C5L HCD2 HCD2 H 0 0 N N N 7.514 -4.608 21.392 -6.473 3.566 0.637 HCD2 C5L 44 C5L HCD3 HCD3 H 0 0 N N N 7.649 -5.711 22.803 -5.784 3.816 -0.985 HCD3 C5L 45 C5L "HO3'" "HO3'" H 0 0 N N N 11.654 -0.291 24.883 0.954 3.760 -0.970 "HO3'" C5L 46 C5L HOP1 HOP1 H 0 0 N N N 13.766 4.187 25.042 6.141 1.644 -0.658 HOP1 C5L 47 C5L HOP3 HOP3 H 0 0 N Y N 11.177 6.135 23.420 6.779 -1.447 -0.666 HOP3 C5L 48 # 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 C5L OP2 P DOUB N N 1 C5L "O5'" P SING N N 2 C5L P OP3 SING N N 3 C5L P OP1 SING N N 4 C5L C2 N1 SING N N 5 C5L C6 N1 SING N N 6 C5L N1 "C1'" SING N N 7 C5L N3 C2 SING N N 8 C5L C2 O2 DOUB N N 9 C5L C4 N3 DOUB N N 10 C5L N4 C4 SING N N 11 C5L C4 C5 SING N N 12 C5L H41 N4 SING N N 13 C5L H42 N4 SING N N 14 C5L C7 C5 SING N N 15 C5L C5 C6 DOUB N N 16 C5L C6 H6 SING N N 17 C5L H72 C7 SING N N 18 C5L H73 C7 SING N N 19 C5L C7 H71 SING N N 20 C5L "H1'" "C1'" SING N N 21 C5L "C1'" "C2'" SING N N 22 C5L "C1'" "O4'" SING N N 23 C5L "H2'" "C2'" SING N N 24 C5L "C2'" "O2'" SING N N 25 C5L "C2'" "C3'" SING N N 26 C5L "CA'" "O2'" SING N N 27 C5L "H3'" "C3'" SING N N 28 C5L "C3'" "C4'" SING N N 29 C5L "C3'" "O3'" SING N N 30 C5L "O3'" "HO3'" SING N N 31 C5L "O4'" "C4'" SING N N 32 C5L "C4'" "C5'" SING N N 33 C5L "C4'" "H4'" SING N N 34 C5L "O5'" "C5'" SING N N 35 C5L "C5'" "H5'" SING N N 36 C5L "C5'" "H5''" SING N N 37 C5L HCA1 "CA'" SING N N 38 C5L HCA2 "CA'" SING N N 39 C5L "CA'" "CB'" SING N N 40 C5L "OC'" "CB'" SING N N 41 C5L "CB'" HCB2 SING N N 42 C5L "CB'" HCB1 SING N N 43 C5L "CD'" "OC'" SING N N 44 C5L HCD1 "CD'" SING N N 45 C5L HCD2 "CD'" SING N N 46 C5L "CD'" HCD3 SING N N 47 C5L OP1 HOP1 SING N N 48 C5L OP3 HOP3 SING N N 49 # 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 C5L SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(=C1)C)C(OCCOC)C2O" C5L InChI InChI 1.03 "InChI=1S/C13H22N3O9P/c1-7-5-16(13(18)15-11(7)14)12-10(23-4-3-22-2)9(17)8(25-12)6-24-26(19,20)21/h5,8-10,12,17H,3-4,6H2,1-2H3,(H2,14,15,18)(H2,19,20,21)/t8-,9-,10-,12-/m1/s1" C5L InChIKey InChI 1.03 RRWZBUGVTSQGAI-DNRKLUKYSA-N C5L SMILES_CANONICAL CACTVS 3.370 "COCCO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=NC2=O)N" C5L SMILES CACTVS 3.370 "COCCO[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=NC2=O)N" C5L SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)OCCOC" C5L SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)OCCOC" # 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 C5L "SYSTEMATIC NAME" ACDLabs 12.01 ;2'-O-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate) ; C5L "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3R,4R,5R)-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-4-(2-methoxyethoxy)-3-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 C5L "Create component" 2013-01-22 RCSB C5L "Modify atom id" 2013-01-23 RCSB C5L "Initial release" 2013-11-27 RCSB #