data_C2L # _chem_comp.id C2L _chem_comp.name ;5-METHYL-3'-O-METHOXYETHYL CYTIDINE 5'-MONOPHOSPHATE ; _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 2004-10-29 _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 395.302 _chem_comp.one_letter_code C _chem_comp.three_letter_code C2L _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 C2L OP3 O3P O 0 1 N Y N ? ? ? 1.198 0.588 -4.548 OP3 C2L 1 C2L P P P 0 1 N N N 9.194 -7.166 11.808 2.787 0.324 -4.407 P C2L 2 C2L OP1 O1P O 0 1 N N N 9.354 -8.268 12.783 3.659 1.172 -5.286 OP1 C2L 3 C2L OP2 O2P O 0 1 N N N 10.384 -6.400 11.367 2.921 -1.270 -4.647 OP2 C2L 4 C2L "O5'" O5* O 0 1 N N N 8.481 -7.741 10.486 3.063 0.476 -2.819 "O5'" C2L 5 C2L "C5'" C5* C 0 1 N N N 7.425 -8.675 10.568 2.282 -0.292 -1.921 "C5'" C2L 6 C2L "C4'" C4* C 0 1 N N R 6.661 -8.731 9.246 2.725 0.023 -0.498 "C4'" C2L 7 C2L "O4'" O4* O 0 1 N N N 6.013 -7.497 8.989 2.470 1.422 -0.246 "O4'" C2L 8 C2L "C3'" C3* C 0 1 N N S 7.515 -9.005 8.011 1.940 -0.742 0.560 "C3'" C2L 9 C2L "O3'" O3* O 0 1 N N N 7.899 -10.370 7.891 2.742 -0.809 1.739 "O3'" C2L 10 C2L "C2'" C2* C 0 1 N N R 6.556 -8.525 6.922 0.748 0.163 0.786 "C2'" C2L 11 C2L "O2'" O2* O 0 1 N N N 5.561 -9.520 6.688 0.137 -0.058 2.041 "O2'" C2L 12 C2L "C1'" C1* C 0 1 N N R 5.907 -7.315 7.581 1.373 1.543 0.675 "C1'" C2L 13 C2L N1 N1 N 0 1 N N N 6.445 -6.016 7.117 0.452 2.524 0.177 N1 C2L 14 C2L C2 C2 C 0 1 N N N 5.823 -5.340 6.063 -0.308 3.346 1.042 C2 C2L 15 C2L O2 O2 O 0 1 N N N 4.829 -5.801 5.509 -0.204 3.247 2.266 O2 C2L 16 C2L N3 N3 N 0 1 N N N 6.340 -4.145 5.653 -1.176 4.269 0.491 N3 C2L 17 C2L C4 C4 C 0 1 N N N 7.419 -3.614 6.243 -1.306 4.396 -0.806 C4 C2L 18 C2L N4 N4 N 0 1 N N N 7.854 -2.437 5.783 -2.189 5.336 -1.292 N4 C2L 19 C2L C5 C5 C 0 1 N N N 8.070 -4.303 7.335 -0.522 3.547 -1.759 C5 C2L 20 C2L C6 C6 C 0 1 N N N 7.543 -5.490 7.719 0.307 2.665 -1.195 C6 C2L 21 C2L "CA'" CA* C 0 1 N N N 8.728 -10.614 6.765 3.867 -1.652 1.551 "CA'" C2L 22 C2L "CB'" CB* C 0 1 N N N 9.142 -12.085 6.734 4.693 -1.667 2.823 "CB'" C2L 23 C2L "OC'" OC* O 0 1 N N N 9.998 -12.362 7.830 5.141 -0.346 3.101 "OC'" C2L 24 C2L "CD'" CD* C 0 1 N N N 10.417 -13.714 7.854 5.904 -0.296 4.298 "CD'" C2L 25 C2L C7 C7 C 0 1 N N N 9.289 -3.768 8.048 -0.687 3.708 -3.234 C7 C2L 26 C2L HOP3 3HOP H 0 0 N N N -0.103 0.707 -0.626 0.799 0.616 -5.443 HOP3 C2L 27 C2L HOP2 2HOP H 0 0 N N N 10.910 -6.810 12.043 2.886 -1.617 -5.563 HOP2 C2L 28 C2L "H5'" 1H5* H 0 1 N N N 7.832 -9.660 10.800 1.229 -0.035 -2.051 "H5'" C2L 29 C2L "H5''" 2H5* H 0 0 N N N 6.735 -8.378 11.358 2.428 -1.352 -2.133 "H5''" C2L 30 C2L "H4'" H4* H 0 1 N N N 5.896 -9.507 9.319 3.804 -0.139 -0.410 "H4'" C2L 31 C2L "H3'" H3* H 0 1 N N N 8.396 -8.365 8.018 1.675 -1.764 0.277 "H3'" C2L 32 C2L "H2'" H2* H 0 1 N N N 7.118 -8.221 6.044 -0.000 0.004 -0.000 "H2'" C2L 33 C2L "HO2'" 2HO* H 0 0 N N N 4.965 -9.222 6.011 -0.494 0.669 2.185 "HO2'" C2L 34 C2L "H1'" H1* H 0 1 N N N 4.865 -7.263 7.353 1.754 1.910 1.633 "H1'" C2L 35 C2L H41 1H4 H 0 1 N N N 7.359 -1.996 5.014 -2.573 5.189 -2.193 H41 C2L 36 C2L H42 2H4 H 0 1 N N N 8.663 -1.997 6.193 -2.398 6.116 -0.718 H42 C2L 37 C2L H6 H6 H 0 1 N N N 7.947 -6.089 8.507 0.921 2.002 -1.796 H6 C2L 38 C2L "HA'1" 1HA* H 0 0 N N N 9.620 -9.989 6.812 3.504 -2.655 1.304 "HA'1" C2L 39 C2L "HA'2" 2HA* H 0 0 N N N 8.181 -10.391 5.849 4.455 -1.258 0.717 "HA'2" C2L 40 C2L "HB'1" 1HB* H 0 0 N N N 8.250 -12.711 6.779 5.572 -2.309 2.715 "HB'1" C2L 41 C2L "HB'2" 2HB* H 0 0 N N N 9.672 -12.279 5.800 4.088 -2.009 3.668 "HB'2" C2L 42 C2L "HD'1" 1HD* H 0 0 N N N 9.552 -14.374 7.933 5.249 -0.053 5.138 "HD'1" C2L 43 C2L "HD'2" 2HD* H 0 0 N N N 11.062 -13.871 8.719 6.686 0.461 4.201 "HD'2" C2L 44 C2L "HD'3" 3HD* H 0 0 N N N 10.976 -13.949 6.948 6.363 -1.273 4.468 "HD'3" C2L 45 C2L H71 1H7 H 0 1 N N N 9.572 -4.521 8.785 -0.306 2.826 -3.748 H71 C2L 46 C2L H72 2H7 H 0 1 N N N 9.042 -2.827 8.577 -0.139 4.587 -3.575 H72 C2L 47 C2L H73 3H7 H 0 1 N N N 10.095 -3.618 7.336 -1.742 3.837 -3.477 H73 C2L 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 C2L OP3 P SING N N 1 C2L OP3 HOP3 SING N N 2 C2L P OP1 DOUB N N 3 C2L P OP2 SING N N 4 C2L P "O5'" SING N N 5 C2L OP2 HOP2 SING N N 6 C2L "O5'" "C5'" SING N N 7 C2L "C5'" "C4'" SING N N 8 C2L "C5'" "H5'" SING N N 9 C2L "C5'" "H5''" SING N N 10 C2L "C4'" "O4'" SING N N 11 C2L "C4'" "C3'" SING N N 12 C2L "C4'" "H4'" SING N N 13 C2L "O4'" "C1'" SING N N 14 C2L "C3'" "O3'" SING N N 15 C2L "C3'" "C2'" SING N N 16 C2L "C3'" "H3'" SING N N 17 C2L "O3'" "CA'" SING N N 18 C2L "C2'" "O2'" SING N N 19 C2L "C2'" "C1'" SING N N 20 C2L "C2'" "H2'" SING N N 21 C2L "O2'" "HO2'" SING N N 22 C2L "C1'" N1 SING N N 23 C2L "C1'" "H1'" SING N N 24 C2L N1 C2 SING N N 25 C2L N1 C6 SING N N 26 C2L C2 O2 DOUB N N 27 C2L C2 N3 SING N N 28 C2L N3 C4 DOUB N N 29 C2L C4 N4 SING N N 30 C2L C4 C5 SING N N 31 C2L N4 H41 SING N N 32 C2L N4 H42 SING N N 33 C2L C5 C6 DOUB N N 34 C2L C5 C7 SING N N 35 C2L C6 H6 SING N N 36 C2L "CA'" "CB'" SING N N 37 C2L "CA'" "HA'1" SING N N 38 C2L "CA'" "HA'2" SING N N 39 C2L "CB'" "OC'" SING N N 40 C2L "CB'" "HB'1" SING N N 41 C2L "CB'" "HB'2" SING N N 42 C2L "OC'" "CD'" SING N N 43 C2L "CD'" "HD'1" SING N N 44 C2L "CD'" "HD'2" SING N N 45 C2L "CD'" "HD'3" SING N N 46 C2L C7 H71 SING N N 47 C2L C7 H72 SING N N 48 C2L C7 H73 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 C2L SMILES ACDLabs 10.04 "O=C1N=C(N)C(=CN1C2OC(C(OCCOC)C2O)COP(=O)(O)O)C" C2L SMILES_CANONICAL CACTVS 3.341 "COCCO[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C)C(=NC2=O)N" C2L SMILES CACTVS 3.341 "COCCO[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C)C(=NC2=O)N" C2L SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)OCCOC)O" C2L SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)OCCOC)O" C2L InChI InChI 1.03 "InChI=1S/C13H22N3O9P/c1-7-5-16(13(18)15-11(7)14)12-9(17)10(23-4-3-22-2)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" C2L InChIKey InChI 1.03 DVYXLKQTQMTZSH-DNRKLUKYSA-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 C2L "SYSTEMATIC NAME" ACDLabs 10.04 ;3'-O-(2-methoxyethyl)-5-methylcytidine 5'-(dihydrogen phosphate) ; C2L "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(4-amino-5-methyl-2-oxo-pyrimidin-1-yl)-4-hydroxy-3-(2-methoxyethoxy)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 C2L "Create component" 2004-10-29 RCSB C2L "Modify descriptor" 2011-06-04 RCSB #