data_FDM # _chem_comp.id FDM _chem_comp.name "3'-FLUORO-3'-DEOXYTHYMIDINE MONOPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H14 F N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "PHOSPHORIC ACID MONO-[3-FLUORO-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYRO-FURAN-2-YLMETHYL] ESTER" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2003-01-14 _chem_comp.pdbx_modified_date 2021-03-13 _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 324.200 _chem_comp.one_letter_code ? _chem_comp.three_letter_code FDM _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1NMX _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 FDM N1 N1 N 0 1 Y N N 13.400 77.886 24.234 -0.383 -0.175 2.257 N1 FDM 1 FDM C6 C6 C 0 1 Y N N 12.643 77.015 23.466 -0.485 -0.940 3.387 C6 FDM 2 FDM C2 C2 C 0 1 Y N N 13.814 79.166 23.811 0.551 0.787 2.164 C2 FDM 3 FDM O2 O2 O 0 1 N N N 14.504 79.894 24.564 0.624 1.456 1.151 O2 FDM 4 FDM N3 N3 N 0 1 Y N N 13.372 79.576 22.613 1.407 1.021 3.176 N3 FDM 5 FDM C4 C4 C 0 1 Y N N 12.612 78.739 21.767 1.336 0.291 4.308 C4 FDM 6 FDM O4 O4 O 0 1 N N N 12.278 79.181 20.588 2.110 0.502 5.224 O4 FDM 7 FDM C5 C5 C 0 1 Y N N 12.216 77.417 22.270 0.360 -0.728 4.417 C5 FDM 8 FDM C7 C7 C 0 1 N N N 11.362 76.583 21.298 0.263 -1.560 5.669 C7 FDM 9 FDM "O4'" O4* O 0 1 N N N 14.615 76.171 25.278 -0.567 -0.681 -0.072 "O4'" FDM 10 FDM F F F 0 1 N N N 14.449 76.772 28.430 -3.769 0.173 -0.788 F FDM 11 FDM "C1'" C1* C 0 1 N N R 13.869 77.326 25.476 -1.301 -0.405 1.139 "C1'" FDM 12 FDM "C2'" C2* C 0 1 N N N 12.859 76.973 26.585 -2.088 0.886 0.803 "C2'" FDM 13 FDM "C3'" C3* C 0 1 N N S 13.682 76.079 27.490 -2.462 0.662 -0.681 "C3'" FDM 14 FDM "C4'" C4* C 0 1 N N R 14.650 75.382 26.491 -1.449 -0.389 -1.171 "C4'" FDM 15 FDM "O5'" O5* O 0 1 N N N 13.284 73.555 26.047 0.286 -0.814 -2.799 "O5'" FDM 16 FDM "C5'" C5* C 0 1 N N N 14.639 73.791 26.440 -0.650 0.167 -2.352 "C5'" FDM 17 FDM P1 P1 P 0 1 N N N 12.647 72.156 26.796 1.086 -0.165 -4.035 P1 FDM 18 FDM OP2 OP2 O 0 1 N N N 12.369 72.720 28.241 2.165 -1.222 -4.592 OP2 FDM 19 FDM OP1 OP1 O 0 1 N N N 11.445 71.919 26.064 1.784 1.059 -3.582 OP1 FDM 20 FDM OP3 OP3 O 0 1 N N N 13.674 71.131 27.043 0.049 0.211 -5.208 OP3 FDM 21 FDM HC61 1HC6 H 0 0 N N N 12.379 75.999 23.807 -1.239 -1.711 3.453 HC61 FDM 22 FDM HN31 1HN3 H 0 0 N N N 13.615 80.529 22.343 2.075 1.719 3.092 HN31 FDM 23 FDM HC71 1HC7 H 0 0 N N N 11.004 76.919 20.296 1.025 -1.240 6.379 HC71 FDM 24 FDM HC72 2HC7 H 0 0 N N N 11.910 75.626 21.134 -0.723 -1.433 6.114 HC72 FDM 25 FDM HC73 3HC7 H 0 0 N N N 10.458 76.260 21.865 0.417 -2.610 5.420 HC73 FDM 26 FDM "H1'1" 1H1* H 0 0 N N N 14.448 78.203 25.847 -1.985 -1.223 1.368 "H1'1" FDM 27 FDM "H2'1" 1H2* H 0 0 N N N 12.386 77.848 27.089 -2.982 0.969 1.422 "H2'1" FDM 28 FDM "H2'2" 2H2* H 0 0 N N N 11.901 76.528 26.226 -1.455 1.767 0.916 "H2'2" FDM 29 FDM "H3'1" 1H3* H 0 0 N N N 13.021 75.407 28.086 -2.355 1.588 -1.246 "H3'1" FDM 30 FDM "H4'1" 1H4* H 0 0 N N N 15.702 75.392 26.858 -1.972 -1.296 -1.473 "H4'1" FDM 31 FDM "H5'1" 1H5* H 0 0 N N N 15.418 73.322 25.794 -1.331 0.416 -3.165 "H5'1" FDM 32 FDM "H5'2" 2H5* H 0 0 N N N 14.969 73.275 27.371 -0.115 1.063 -2.038 "H5'2" FDM 33 FDM HP31 1HP3 H 0 0 N N N 12.015 71.942 28.657 2.621 -0.795 -5.329 HP31 FDM 34 FDM HP21 1HP2 H 0 0 N N N 13.320 70.353 27.459 -0.382 -0.611 -5.474 HP21 FDM 35 # # 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 FDM N1 C6 SING Y N 1 FDM N1 C2 SING Y N 2 FDM N1 "C1'" SING N N 3 FDM C6 C5 DOUB Y N 4 FDM C6 HC61 SING N N 5 FDM C2 O2 DOUB N N 6 FDM C2 N3 SING Y N 7 FDM N3 C4 SING Y N 8 FDM N3 HN31 SING N N 9 FDM C4 O4 DOUB N N 10 FDM C4 C5 SING Y N 11 FDM C5 C7 SING N N 12 FDM C7 HC71 SING N N 13 FDM C7 HC72 SING N N 14 FDM C7 HC73 SING N N 15 FDM "O4'" "C1'" SING N N 16 FDM "O4'" "C4'" SING N N 17 FDM F "C3'" SING N N 18 FDM "C1'" "C2'" SING N N 19 FDM "C1'" "H1'1" SING N N 20 FDM "C2'" "C3'" SING N N 21 FDM "C2'" "H2'1" SING N N 22 FDM "C2'" "H2'2" SING N N 23 FDM "C3'" "C4'" SING N N 24 FDM "C3'" "H3'1" SING N N 25 FDM "C4'" "C5'" SING N N 26 FDM "C4'" "H4'1" SING N N 27 FDM "O5'" "C5'" SING N N 28 FDM "O5'" P1 SING N N 29 FDM "C5'" "H5'1" SING N N 30 FDM "C5'" "H5'2" SING N N 31 FDM P1 OP2 SING N N 32 FDM P1 OP1 DOUB N N 33 FDM P1 OP3 SING N N 34 FDM OP2 HP31 SING N N 35 FDM OP3 HP21 SING N N 36 # # 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 FDM SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1C)C2OC(C(F)C2)COP(=O)(O)O" FDM SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](F)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" FDM SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](F)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" FDM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)F" FDM SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)F" FDM InChI InChI 1.03 "InChI=1S/C10H14FN2O7P/c1-5-3-13(10(15)12-9(5)14)8-2-6(11)7(20-8)4-19-21(16,17)18/h3,6-8H,2,4H2,1H3,(H,12,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1" FDM InChIKey InChI 1.03 GGCAVPJXJISBOA-XLPZGREQSA-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 FDM "SYSTEMATIC NAME" ACDLabs 10.04 "3'-deoxy-3'-fluorothymidine 5'-(dihydrogen phosphate)" FDM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-fluoro-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)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 FDM "Create component" 2003-01-14 RCSB FDM "Modify descriptor" 2011-06-04 RCSB FDM "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id FDM _pdbx_chem_comp_synonyms.name "PHOSPHORIC ACID MONO-[3-FLUORO-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-TETRAHYRO-FURAN-2-YLMETHYL] ESTER" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##