data_TCJ # _chem_comp.id TCJ _chem_comp.name "[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl] dihydrogen phosphate" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H18 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-03-12 _chem_comp.pdbx_modified_date 2019-05-06 _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 359.272 _chem_comp.one_letter_code C _chem_comp.three_letter_code TCJ _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 6FW6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 TCJ P P1 P 0 1 N N N -3.913 -4.784 16.470 3.080 1.596 0.396 P TCJ 1 TCJ O1P O1 O 0 1 N N N -3.281 -5.938 15.792 1.909 1.638 1.299 O1P TCJ 2 TCJ O2P O2 O 0 1 N N N -4.601 -4.986 17.764 4.327 0.928 1.164 O2P TCJ 3 TCJ "O5'" O3 O 0 1 N N N -2.782 -3.652 16.680 2.721 0.722 -0.908 "O5'" TCJ 4 TCJ "C5'" C1 C 0 1 N N R -1.607 -3.974 17.395 2.238 -0.621 -0.835 "C5'" TCJ 5 TCJ "C4'" C2 C 0 1 N N S -0.454 -4.630 16.653 1.392 -1.001 0.394 "C4'" TCJ 6 TCJ "O4'" O4 O 0 1 N N N -0.375 -4.110 15.320 0.340 -0.032 0.558 "O4'" TCJ 7 TCJ "C1'" C3 C 0 1 N N R 0.923 -3.544 15.083 -0.788 -0.706 1.136 "C1'" TCJ 8 TCJ N1 N1 N 0 1 N N N 0.828 -2.050 14.947 -2.031 -0.139 0.608 N1 TCJ 9 TCJ C6 C4 C 0 1 N N N -0.329 -1.347 15.265 -2.035 0.470 -0.611 C6 TCJ 10 TCJ C5 C5 C 0 1 N N N -0.386 0.011 15.146 -3.190 0.991 -1.088 C5 TCJ 11 TCJ C7 C6 C 0 1 N N N -1.643 0.794 15.488 -3.226 1.669 -2.433 C7 TCJ 12 TCJ C4 C7 C 0 1 N N N 0.809 0.687 14.674 -4.359 0.888 -0.306 C4 TCJ 13 TCJ N4 N2 N 0 1 N N N 0.823 2.022 14.534 -5.547 1.408 -0.767 N4 TCJ 14 TCJ N3 N3 N 0 1 N N N 1.928 -0.007 14.367 -4.308 0.287 0.875 N3 TCJ 15 TCJ C2 C8 C 0 1 N N N 1.980 -1.376 14.488 -3.165 -0.226 1.328 C2 TCJ 16 TCJ O2 O5 O 0 1 N N N 3.004 -2.000 14.208 -3.143 -0.774 2.417 O2 TCJ 17 TCJ "C3'" C9 C 0 1 N N S 0.837 -4.279 17.376 0.643 -2.299 -0.036 "C3'" TCJ 18 TCJ "C2'" C10 C 0 1 N N N 1.815 -3.914 16.267 -0.685 -2.192 0.746 "C2'" TCJ 19 TCJ "C7'" C11 C 0 1 N N N 0.493 -3.092 18.313 0.375 -2.067 -1.539 "C7'" TCJ 20 TCJ "C6'" C12 C 0 1 N N S -1.025 -3.011 18.397 1.590 -1.297 -2.054 "C6'" TCJ 21 TCJ "C8'" C13 C 0 1 N N N -1.723 -4.251 18.866 2.984 -1.723 -1.591 "C8'" TCJ 22 TCJ "O3'" O6 O 0 1 N N N 1.310 -5.391 18.121 1.369 -3.500 0.235 "O3'" TCJ 23 TCJ H2 H2 H 0 1 N N N -4.545 -5.901 18.014 5.131 0.867 0.630 H2 TCJ 24 TCJ "H4'" H3 H 0 1 N N N -0.590 -5.721 16.644 1.994 -1.137 1.293 "H4'" TCJ 25 TCJ "H1'" H4 H 0 1 N N N 1.358 -3.964 14.164 -0.764 -0.605 2.221 "H1'" TCJ 26 TCJ H6 H5 H 0 1 N N N -1.198 -1.886 15.612 -1.126 0.536 -1.191 H6 TCJ 27 TCJ H73 H6 H 0 1 N N N -2.428 0.100 15.824 -3.455 0.934 -3.205 H73 TCJ 28 TCJ H71 H7 H 0 1 N N N -1.420 1.512 16.291 -3.993 2.443 -2.429 H71 TCJ 29 TCJ H72 H8 H 0 1 N N N -1.991 1.337 14.597 -2.255 2.121 -2.638 H72 TCJ 30 TCJ H41 H9 H 0 1 N N N 1.649 2.482 14.209 -5.582 1.847 -1.631 H41 TCJ 31 TCJ H42 H10 H 0 1 N N N 0.007 2.556 14.755 -6.350 1.336 -0.227 H42 TCJ 32 TCJ "H2'" H11 H 0 1 N N N 2.458 -4.771 16.017 -0.652 -2.818 1.638 "H2'" TCJ 33 TCJ "H2''" H12 H 0 0 N N N 2.441 -3.060 16.565 -1.524 -2.478 0.111 "H2''" TCJ 34 TCJ "H7'" H13 H 0 1 N N N 0.917 -3.266 19.313 0.268 -3.020 -2.058 "H7'" TCJ 35 TCJ "H7''" H14 H 0 0 N N N 0.898 -2.156 17.900 -0.518 -1.457 -1.676 "H7''" TCJ 36 TCJ "H6'" H15 H 0 1 N N N -1.501 -2.030 18.544 1.474 -0.761 -2.997 "H6'" TCJ 37 TCJ "H8'" H16 H 0 1 N N N -2.701 -4.176 19.364 3.832 -1.424 -2.207 "H8'" TCJ 38 TCJ "H8''" H17 H 0 0 N N N -1.144 -5.070 19.318 3.077 -2.694 -1.103 "H8''" TCJ 39 TCJ H3T H18 H 0 1 N N N 0.687 -5.602 18.806 0.907 -4.307 -0.031 H3T TCJ 40 TCJ OP3 OP3 O 0 1 N Y N -5.097 -4.261 15.336 3.466 3.094 -0.053 OP3 TCJ 41 TCJ H1 H1 H 0 1 N N N -5.067 -4.818 14.567 3.694 3.678 0.683 H1 TCJ 42 # # 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 TCJ O2 C2 DOUB N N 1 TCJ N3 C2 SING N N 2 TCJ N3 C4 DOUB N N 3 TCJ C2 N1 SING N N 4 TCJ N4 C4 SING N N 5 TCJ C4 C5 SING N N 6 TCJ N1 "C1'" SING N N 7 TCJ N1 C6 SING N N 8 TCJ "C1'" "O4'" SING N N 9 TCJ "C1'" "C2'" SING N N 10 TCJ C5 C6 DOUB N N 11 TCJ C5 C7 SING N N 12 TCJ "O4'" "C4'" SING N N 13 TCJ O1P P DOUB N N 14 TCJ "C2'" "C3'" SING N N 15 TCJ P "O5'" SING N N 16 TCJ P O2P SING N N 17 TCJ "C4'" "C3'" SING N N 18 TCJ "C4'" "C5'" SING N N 19 TCJ "O5'" "C5'" SING N N 20 TCJ "C3'" "O3'" SING N N 21 TCJ "C3'" "C7'" SING N N 22 TCJ "C5'" "C6'" SING N N 23 TCJ "C5'" "C8'" SING N N 24 TCJ "C7'" "C6'" SING N N 25 TCJ "C6'" "C8'" SING N N 26 TCJ O2P H2 SING N N 27 TCJ "C4'" "H4'" SING N N 28 TCJ "C1'" "H1'" SING N N 29 TCJ C6 H6 SING N N 30 TCJ C7 H73 SING N N 31 TCJ C7 H71 SING N N 32 TCJ C7 H72 SING N N 33 TCJ N4 H41 SING N N 34 TCJ N4 H42 SING N N 35 TCJ "C2'" "H2'" SING N N 36 TCJ "C2'" "H2''" SING N N 37 TCJ "C7'" "H7'" SING N N 38 TCJ "C7'" "H7''" SING N N 39 TCJ "C6'" "H6'" SING N N 40 TCJ "C8'" "H8'" SING N N 41 TCJ "C8'" "H8''" SING N N 42 TCJ "O3'" H3T SING N N 43 TCJ P OP3 SING N N 44 TCJ OP3 H1 SING N N 45 # # 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 TCJ InChI InChI 1.03 "InChI=1S/C13H18N3O7P/c1-6-5-16(11(17)15-9(6)14)8-4-12(18)2-7-3-13(7,10(12)22-8)23-24(19,20)21/h5,7-8,10,18H,2-4H2,1H3,(H2,14,15,17)(H2,19,20,21)/t7-,8-,10+,12+,13-/m1/s1" TCJ InChIKey InChI 1.03 QNNOIYJQVYUYLR-ZIDZYHNGSA-N TCJ SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@@]3(O)C[C@@H]4C[C@]4(O[P](O)(O)=O)[C@H]3O2)C(=O)N=C1N" TCJ SMILES CACTVS 3.385 "CC1=CN([CH]2C[C]3(O)C[CH]4C[C]4(O[P](O)(O)=O)[CH]3O2)C(=O)N=C1N" TCJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)N=C1N)[C@H]2C[C@]3(C[C@@H]4C[C@@]4([C@H]3O2)OP(=O)(O)O)O" TCJ SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)N=C1N)C2CC3(CC4CC4(C3O2)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id TCJ _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl] 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 TCJ "Create component" 2018-03-12 EBI TCJ "Initial release" 2018-06-06 RCSB TCJ "Modify one letter code" 2019-05-06 EBI ##