data_U5M # _chem_comp.id U5M _chem_comp.name "1-(2,6-dideoxy-2-fluoro-5-O-phosphono-alpha-L-talofuranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H14 F N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-08-18 _chem_comp.pdbx_modified_date 2016-06-24 _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 340.199 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U5M _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 5D8T _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 U5M O2 O1 O 0 1 N N N 6.729 -11.382 9.817 3.853 -1.557 -0.813 O2 U5M 1 U5M C2 C1 C 0 1 N N N 6.650 -12.588 9.937 3.618 -0.437 -0.404 C2 U5M 2 U5M N3 N1 N 0 1 N N N 5.479 -13.298 9.772 4.631 0.431 -0.225 N3 U5M 3 U5M C4 C2 C 0 1 N N N 5.368 -14.625 9.917 4.387 1.677 0.228 C4 U5M 4 U5M O4 O2 O 0 1 N N N 4.262 -15.151 9.676 5.304 2.462 0.391 O4 U5M 5 U5M C5 C3 C 0 1 N N N 6.503 -15.336 10.350 3.056 2.064 0.513 C5 U5M 6 U5M C6 C4 C 0 1 N N N 7.665 -14.689 10.556 2.058 1.174 0.323 C6 U5M 7 U5M N1 N2 N 0 1 N N N 7.764 -13.357 10.333 2.347 -0.079 -0.143 N1 U5M 8 U5M "C1'" C5 C 0 1 N N R 9.028 -12.573 10.484 1.264 -1.043 -0.353 "C1'" U5M 9 U5M "O4'" O3 O 0 1 N N N 10.077 -13.530 10.548 0.245 -0.476 -1.204 "O4'" U5M 10 U5M "C2'" C6 C 0 1 N N R 9.084 -11.791 11.745 0.544 -1.342 0.980 "C2'" U5M 11 U5M "F2'" F1 F 0 1 N N N 9.964 -10.721 11.548 1.019 -2.534 1.538 "F2'" U5M 12 U5M "C3'" C7 C 0 1 N N R 9.718 -12.765 12.713 -0.942 -1.486 0.581 "C3'" U5M 13 U5M "O3'" O4 O 0 1 N N N 10.325 -12.113 13.816 -1.419 -2.796 0.891 "O3'" U5M 14 U5M "C4'" C8 C 0 1 N N S 10.744 -13.395 11.814 -0.943 -1.257 -0.947 "C4'" U5M 15 U5M "C5'" C9 C 0 1 N N S 11.145 -14.811 12.226 -2.192 -0.480 -1.368 "C5'" U5M 16 U5M C5M C10 C 0 1 N N N 11.975 -14.833 13.540 -2.076 -0.087 -2.842 C5M U5M 17 U5M "O5'" O5 O 0 1 N N N 11.982 -15.305 11.186 -2.312 0.699 -0.570 "O5'" U5M 18 U5M P P1 P 0 1 N N N 12.275 -16.878 11.019 -3.583 0.995 0.373 P U5M 19 U5M OP1 O6 O 0 1 N N N 13.607 -17.208 11.575 -3.785 -0.141 1.300 OP1 U5M 20 U5M OP2 O7 O 0 1 N N N 11.150 -17.624 11.384 -3.322 2.339 1.220 OP2 U5M 21 U5M H3 H1 H 0 1 N N N 4.655 -12.786 9.527 5.541 0.158 -0.422 H3 U5M 22 U5M H5 H2 H 0 1 N N N 6.441 -16.401 10.517 2.841 3.058 0.877 H5 U5M 23 U5M H6 H3 H 0 1 N N N 8.528 -15.238 10.903 1.036 1.452 0.535 H6 U5M 24 U5M "H1'" H4 H 0 1 N N N 9.158 -11.904 9.620 1.655 -1.962 -0.790 "H1'" U5M 25 U5M "H2'" H5 H 0 1 N N N 8.084 -11.479 12.081 0.675 -0.516 1.679 "H2'" U5M 26 U5M "H3'" H6 H 0 1 N N N 8.981 -13.514 13.038 -1.547 -0.731 1.083 "H3'" U5M 27 U5M H6N H7 H 0 1 N N N 10.709 -12.761 14.395 -1.383 -3.016 1.832 H6N U5M 28 U5M "H4'" H8 H 0 1 N N N 11.635 -12.755 11.736 -0.892 -2.209 -1.474 "H4'" U5M 29 U5M "H5'" H9 H 0 1 N N N 10.246 -15.434 12.348 -3.073 -1.105 -1.227 "H5'" U5M 30 U5M H6L H10 H 0 1 N N N 12.237 -15.871 13.791 -1.195 0.538 -2.984 H6L U5M 31 U5M H6M H11 H 0 1 N N N 12.895 -14.246 13.402 -1.985 -0.987 -3.452 H6M U5M 32 U5M H5M H12 H 0 1 N N N 11.380 -14.397 14.356 -2.966 0.466 -3.142 H5M U5M 33 U5M H1 H14 H 0 1 N N N 11.406 -18.306 11.994 -4.049 2.578 1.811 H1 U5M 34 U5M OP3 O8 O 0 1 N Y N 12.496 -16.937 9.393 -4.896 1.183 -0.540 O1 U5M 35 U5M H2 H15 H 0 1 N Y N 13.399 -17.162 9.204 -4.834 1.911 -1.173 H2 U5M 36 # 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 U5M O2 C2 DOUB N N 1 U5M C2 N3 SING N N 2 U5M C2 N1 SING N N 3 U5M N3 C4 SING N N 4 U5M C4 O4 DOUB N N 5 U5M C4 C5 SING N N 6 U5M C5 C6 DOUB N N 7 U5M C6 N1 SING N N 8 U5M N1 "C1'" SING N N 9 U5M "C1'" "O4'" SING N N 10 U5M "C1'" "C2'" SING N N 11 U5M "O4'" "C4'" SING N N 12 U5M "C2'" "F2'" SING N N 13 U5M "C2'" "C3'" SING N N 14 U5M "C3'" "O3'" SING N N 15 U5M "C3'" "C4'" SING N N 16 U5M "C4'" "C5'" SING N N 17 U5M "C5'" C5M SING N N 18 U5M "C5'" "O5'" SING N N 19 U5M "O5'" P SING N N 20 U5M P OP1 DOUB N N 21 U5M P OP2 SING N N 22 U5M N3 H3 SING N N 23 U5M C5 H5 SING N N 24 U5M C6 H6 SING N N 25 U5M "C1'" "H1'" SING N N 26 U5M "C2'" "H2'" SING N N 27 U5M "C3'" "H3'" SING N N 28 U5M "O3'" H6N SING N N 29 U5M "C4'" "H4'" SING N N 30 U5M "C5'" "H5'" SING N N 31 U5M C5M H6L SING N N 32 U5M C5M H6M SING N N 33 U5M C5M H5M SING N N 34 U5M OP2 H1 SING N N 35 U5M P OP3 SING N N 36 U5M OP3 H2 SING N N 37 # 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 U5M SMILES ACDLabs 12.01 "O=C1NC(=O)C=CN1C2OC(C(C2F)O)C(C)OP(=O)(O)O" U5M InChI InChI 1.03 "InChI=1S/C10H14FN2O8P/c1-4(21-22(17,18)19)8-7(15)6(11)9(20-8)13-3-2-5(14)12-10(13)16/h2-4,6-9,15H,1H3,(H,12,14,16)(H2,17,18,19)/t4-,6+,7-,8+,9+/m0/s1" U5M InChIKey InChI 1.03 AVNIYVQWHJOOLV-VEMNEOHVSA-N U5M SMILES_CANONICAL CACTVS 3.385 "C[C@H](O[P](O)(O)=O)[C@H]1O[C@H]([C@H](F)[C@@H]1O)N2C=CC(=O)NC2=O" U5M SMILES CACTVS 3.385 "C[CH](O[P](O)(O)=O)[CH]1O[CH]([CH](F)[CH]1O)N2C=CC(=O)NC2=O" U5M SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C[C@@H]([C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)F)O)OP(=O)(O)O" U5M SMILES "OpenEye OEToolkits" 1.9.2 "CC(C1C(C(C(O1)N2C=CC(=O)NC2=O)F)O)OP(=O)(O)O" # 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 U5M "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2,6-dideoxy-2-fluoro-5-O-phosphono-alpha-L-talofuranosyl)pyrimidine-2,4(1H,3H)-dione" U5M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(1S)-1-[(2S,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]ethyl] 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 U5M "Create component" 2015-08-18 RCSB U5M "Initial release" 2016-06-29 RCSB #