data_T0N # _chem_comp.id T0N _chem_comp.name "~{N}-(1,3-dimethylimidazolidin-2-yl)-[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy]phosphonamidic acid" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C15 H26 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms "phosphoryl thymidine moiety, Rp-diastereomer" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-12-09 _chem_comp.pdbx_modified_date 2023-08-15 _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 419.370 _chem_comp.one_letter_code T _chem_comp.three_letter_code T0N _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 7B72 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 T0N P P1 P 0 1 N N N -8.675 -4.671 11.584 -2.495 1.335 0.656 P T0N 1 T0N OP1 O1 O 0 1 N N N -9.788 -5.262 10.803 -2.126 1.836 1.999 OP1 T0N 2 T0N C6 C1 C 0 1 N N N -10.010 -1.189 8.079 4.801 -0.229 -1.406 C6 T0N 3 T0N C5 C2 C 0 1 N N N -10.194 -1.412 6.752 5.939 0.468 -1.200 C5 T0N 4 T0N C4 C3 C 0 1 N N N -10.062 -0.317 5.793 6.166 1.056 0.068 C4 T0N 5 T0N N3 N1 N 0 1 N N N -9.787 0.911 6.349 5.244 0.909 1.041 N3 T0N 6 T0N C2 C4 C 0 1 N N N -9.610 1.166 7.688 4.119 0.208 0.808 C2 T0N 7 T0N N1 N2 N 0 1 N N N -9.703 0.070 8.558 3.891 -0.355 -0.392 N1 T0N 8 T0N "C1'" C5 C 0 1 N N R -9.463 0.294 10.011 2.654 -1.107 -0.618 "C1'" T0N 9 T0N "C2'" C6 C 0 1 N N N -10.587 -0.221 10.906 2.585 -2.326 0.329 "C2'" T0N 10 T0N "C3'" C7 C 0 1 N N S -9.866 -0.368 12.243 1.091 -2.418 0.713 "C3'" T0N 11 T0N "O3'" O2 O 0 1 N N N -9.908 0.823 13.026 0.540 -3.665 0.283 "O3'" T0N 12 T0N "O4'" O3 O 0 1 N N N -8.295 -0.386 10.430 1.506 -0.303 -0.268 "O4'" T0N 13 T0N "C4'" C8 C 0 1 N N R -8.419 -0.677 11.817 0.434 -1.245 -0.047 "C4'" T0N 14 T0N "C5'" C9 C 0 1 N N N -8.014 -2.137 12.078 -0.667 -0.609 0.803 "C5'" T0N 15 T0N "O5'" O4 O 0 1 N N N -8.850 -3.077 11.401 -1.290 0.445 0.066 "O5'" T0N 16 T0N C7 C10 C 0 1 N N N -10.536 -2.813 6.271 6.953 0.618 -2.304 C7 T0N 17 T0N O4 O5 O 0 1 N N N -10.155 -0.400 4.571 7.185 1.689 0.278 O4 T0N 18 T0N O2 O6 O 0 1 N N N -9.387 2.320 8.053 3.296 0.083 1.695 O2 T0N 19 T0N NP N3 N 0 1 N N N -8.704 -5.102 13.102 -3.884 0.392 0.772 N2 T0N 20 T0N CN C11 C 0 1 N N N -7.470 -5.011 13.715 -4.281 -0.124 -0.545 CN T0N 21 T0N NC1 N4 N 0 1 N N N -7.344 -4.425 14.979 -5.124 -1.323 -0.378 NC1 T0N 22 T0N NC2 N5 N 0 1 N N N -6.471 -5.990 13.576 -5.078 0.895 -1.263 NC2 T0N 23 T0N C31 C12 C 0 1 N N N -6.188 -4.960 15.710 -6.432 -1.025 -1.007 C31 T0N 24 T0N C32 C13 C 0 1 N N N -8.466 -3.860 15.759 -5.288 -1.658 1.043 C32 T0N 25 T0N C33 C14 C 0 1 N N N -6.695 -7.305 12.935 -5.709 1.829 -0.321 C33 T0N 26 T0N C34 C15 C 0 1 N N N -5.577 -5.988 14.749 -6.102 0.113 -2.006 C34 T0N 27 T0N H6 H2 H 0 1 N N N -10.105 -2.011 8.773 4.608 -0.680 -2.368 H6 T0N 28 T0N H3 H3 H 0 1 N N N -9.709 1.687 5.723 5.393 1.308 1.912 H3 T0N 29 T0N "H1'" H4 H 0 1 N N N -9.349 1.374 10.188 2.590 -1.428 -1.657 "H1'" T0N 30 T0N "H2'" H5 H 0 1 N N N -11.412 0.503 10.972 2.903 -3.230 -0.189 "H2'" T0N 31 T0N "H2''" H6 H 0 0 N N N -10.974 -1.187 10.550 3.197 -2.156 1.215 "H2''" T0N 32 T0N "H3'" H7 H 0 1 N N N -10.279 -1.224 12.797 0.965 -2.297 1.789 "H3'" T0N 33 T0N "HO3'" H8 H 0 0 N Y N -9.448 0.681 13.845 0.958 -4.439 0.685 "HO3'" T0N 34 T0N "H4'" H9 H 0 1 N N N -7.746 -0.026 12.394 0.027 -1.588 -0.999 "H4'" T0N 35 T0N "H5'" H10 H 0 1 N N N -8.074 -2.330 13.159 -1.412 -1.364 1.058 "H5'" T0N 36 T0N "H5''" H11 H 0 0 N N N -6.978 -2.280 11.737 -0.233 -0.205 1.718 "H5''" T0N 37 T0N H73 H12 H 0 1 N N N -10.591 -3.494 7.133 6.729 1.513 -2.885 H73 T0N 38 T0N H72 H13 H 0 1 N N N -11.507 -2.796 5.754 7.950 0.706 -1.872 H72 T0N 39 T0N H71 H14 H 0 1 N N N -9.757 -3.163 5.577 6.915 -0.256 -2.954 H71 T0N 40 T0N H5 H16 H 0 1 N N N -7.023 -4.213 13.103 -3.393 -0.375 -1.126 H5 T0N 41 T0N H12 H19 H 0 1 N N N -6.507 -5.442 16.646 -6.813 -1.899 -1.534 H12 T0N 42 T0N H11 H20 H 0 1 N N N -5.466 -4.161 15.937 -7.149 -0.686 -0.260 H11 T0N 43 T0N H23 H21 H 0 1 N N N -8.088 -3.465 16.714 -5.646 -0.782 1.583 H23 T0N 44 T0N H21 H22 H 0 1 N N N -8.937 -3.047 15.187 -6.010 -2.468 1.145 H21 T0N 45 T0N H22 H23 H 0 1 N N N -9.208 -4.647 15.956 -4.329 -1.972 1.455 H22 T0N 46 T0N H33 H24 H 0 1 N N N -5.761 -7.886 12.952 -4.938 2.334 0.261 H33 T0N 47 T0N H31 H25 H 0 1 N N N -7.476 -7.852 13.483 -6.288 2.567 -0.876 H31 T0N 48 T0N H32 H26 H 0 1 N N N -7.015 -7.155 11.893 -6.368 1.278 0.350 H32 T0N 49 T0N H42 H27 H 0 1 N N N -5.548 -6.984 15.215 -6.985 0.721 -2.207 H42 T0N 50 T0N H41 H28 H 0 1 N N N -4.559 -5.689 14.459 -5.689 -0.290 -2.931 H41 T0N 51 T0N OP3 OP1 O 0 1 N Y N ? ? ? -2.772 2.581 -0.325 OP3 T0N 52 T0N HOP3 H29 H 0 0 N Y N ? ? ? -3.019 2.326 -1.224 HOP3 T0N 53 T0N HNP H30 H 0 1 N N N -9.346 -4.509 13.589 -3.757 -0.360 1.432 H1 T0N 54 # 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 T0N O4 C4 DOUB N N 1 T0N C4 N3 SING N N 2 T0N C4 C5 SING N N 3 T0N C7 C5 SING N N 4 T0N N3 C2 SING N N 5 T0N C5 C6 DOUB N N 6 T0N C2 O2 DOUB N N 7 T0N C2 N1 SING N N 8 T0N C6 N1 SING N N 9 T0N N1 "C1'" SING N N 10 T0N "C1'" "O4'" SING N N 11 T0N "C1'" "C2'" SING N N 12 T0N "O4'" "C4'" SING N N 13 T0N OP1 P DOUB N N 14 T0N "C2'" "C3'" SING N N 15 T0N "O5'" P SING N N 16 T0N "O5'" "C5'" SING N N 17 T0N P NP SING N N 18 T0N "C4'" "C5'" SING N N 19 T0N "C4'" "C3'" SING N N 20 T0N "C3'" "O3'" SING N N 21 T0N C33 NC2 SING N N 22 T0N NP CN SING N N 23 T0N NC2 CN SING N N 24 T0N NC2 C34 SING N N 25 T0N CN NC1 SING N N 26 T0N C34 C31 SING N N 27 T0N NC1 C31 SING N N 28 T0N NC1 C32 SING N N 29 T0N C6 H6 SING N N 30 T0N N3 H3 SING N N 31 T0N "C1'" "H1'" SING N N 32 T0N "C2'" "H2'" SING N N 33 T0N "C2'" "H2''" SING N N 34 T0N "C3'" "H3'" SING N N 35 T0N "O3'" "HO3'" SING N N 36 T0N "C4'" "H4'" SING N N 37 T0N "C5'" "H5'" SING N N 38 T0N "C5'" "H5''" SING N N 39 T0N C7 H73 SING N N 40 T0N C7 H72 SING N N 41 T0N C7 H71 SING N N 42 T0N CN H5 SING N N 43 T0N C31 H12 SING N N 44 T0N C31 H11 SING N N 45 T0N C32 H23 SING N N 46 T0N C32 H21 SING N N 47 T0N C32 H22 SING N N 48 T0N C33 H33 SING N N 49 T0N C33 H31 SING N N 50 T0N C33 H32 SING N N 51 T0N C34 H42 SING N N 52 T0N C34 H41 SING N N 53 T0N P OP3 SING N N 54 T0N OP3 HOP3 SING N N 55 T0N NP HNP SING N N 56 # 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 T0N InChI InChI 1.06 "InChI=1S/C15H26N5O7P/c1-9-7-20(15(23)16-13(9)22)12-6-10(21)11(27-12)8-26-28(24,25)17-14-18(2)4-5-19(14)3/h7,10-12,14,21H,4-6,8H2,1-3H3,(H,16,22,23)(H2,17,24,25)/t10-,11+,12+/m0/s1" T0N InChIKey InChI 1.06 NZONXHNEUWVHKC-QJPTWQEYSA-N T0N SMILES_CANONICAL CACTVS 3.385 "CN1CCN(C)C1N[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O" T0N SMILES CACTVS 3.385 "CN1CCN(C)C1N[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O" T0N SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(NC3N(CCN3C)C)O)O" T0N SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(NC3N(CCN3C)C)O)O" # _pdbx_chem_comp_identifier.comp_id T0N _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "~{N}-(1,3-dimethylimidazolidin-2-yl)-[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy]phosphonamidic acid" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id T0N _pdbx_chem_comp_synonyms.name "phosphoryl thymidine moiety, Rp-diastereomer" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site T0N "Create component" 2020-12-09 PDBE T0N "Initial release" 2021-01-13 RCSB T0N "Modify synonyms" 2021-03-13 RCSB T0N "Other modification" 2021-07-29 PDBE T0N "Modify leaving atom flag" 2023-08-15 PDBE T0N "Other modification" 2023-08-15 PDBE #