data_F7H # _chem_comp.id F7H _chem_comp.name "4-azanyl-1-[(1~{S},2~{R},4~{S},6~{S},8~{R})-2,6-bis(oxidanyl)-9-oxatricyclo[4.3.0.0^{2,4}]nonan-8-yl]-5-methyl-pyrimidin-2-one" _chem_comp.type "DNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H17 N3 O4" _chem_comp.mon_nstd_parent_comp_id DC _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-06-06 _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 279.292 _chem_comp.one_letter_code C _chem_comp.three_letter_code F7H _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 6GMY _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 F7H "O5'" O1 O 0 1 N N N 1.719 -8.933 -14.485 -3.033 1.800 -1.681 "O5'" F7H 1 F7H "C5'" C1 C 0 1 N N R 2.824 -8.988 -13.624 -3.041 0.885 -0.584 "C5'" F7H 2 F7H "C4'" C2 C 0 1 N N S 4.173 -8.548 -14.188 -2.264 -0.433 -0.760 "C4'" F7H 3 F7H "O4'" O2 O 0 1 N N N 3.998 -7.431 -15.077 -0.931 -0.136 -1.214 "O4'" F7H 4 F7H "C1'" C3 C 0 1 N N R 4.834 -6.338 -14.667 -0.057 -1.147 -0.692 "C1'" F7H 5 F7H N1 N1 N 0 1 N N N 3.989 -5.203 -14.162 1.249 -0.562 -0.377 N1 F7H 6 F7H C6 C4 C 0 1 N N N 2.632 -5.348 -13.891 1.345 0.765 -0.086 C6 F7H 7 F7H C5 C5 C 0 1 N N N 1.877 -4.291 -13.470 2.557 1.294 0.203 C5 F7H 8 F7H C7 C6 C 0 1 N N N 0.392 -4.442 -13.167 2.695 2.759 0.529 C7 F7H 9 F7H C4 C7 C 0 1 N N N 2.560 -3.012 -13.329 3.689 0.453 0.194 C4 F7H 10 F7H N4 N2 N 0 1 N N N 1.921 -1.908 -12.938 4.933 0.964 0.485 N4 F7H 11 F7H N3 N3 N 0 1 N N N 3.874 -2.890 -13.591 3.547 -0.834 -0.095 N3 F7H 12 F7H C2 C8 C 0 1 N N N 4.628 -3.956 -13.990 2.347 -1.340 -0.372 C2 F7H 13 F7H O2 O3 O 0 1 N N N 5.835 -3.829 -14.192 2.242 -2.528 -0.630 O2 F7H 14 F7H "C3'" C9 C 0 1 N N S 5.045 -8.103 -13.039 -2.057 -0.958 0.694 "C3'" F7H 15 F7H "C2'" C10 C 0 1 N N N 5.772 -6.879 -13.587 -0.705 -1.699 0.591 "C2'" F7H 16 F7H "C7'" C11 C 0 1 N N N 4.063 -7.783 -11.885 -1.872 0.340 1.512 "C7'" F7H 17 F7H "C6'" C12 C 0 1 N N S 2.738 -8.474 -12.207 -2.838 1.376 0.858 "C6'" F7H 18 F7H "C8'" C13 C 0 1 N N N 2.792 -9.948 -12.464 -4.217 0.906 0.395 "C8'" F7H 19 F7H "O3'" O4 O 0 1 N N N 5.916 -9.183 -12.709 -3.124 -1.782 1.168 "O3'" F7H 20 F7H "HO5'" H1 H 0 0 N N N 0.943 -9.229 -14.024 -3.169 1.382 -2.543 "HO5'" F7H 21 F7H "H4'" H2 H 0 1 N N N 4.647 -9.392 -14.710 -2.787 -1.147 -1.397 "H4'" F7H 22 F7H "H1'" H3 H 0 1 N N N 5.438 -5.987 -15.516 0.062 -1.947 -1.422 "H1'" F7H 23 F7H H6 H4 H 0 1 N N N 2.167 -6.315 -14.016 0.463 1.389 -0.087 H6 F7H 24 F7H H71 H5 H 0 1 N N N -0.018 -3.473 -12.845 2.581 2.904 1.603 H71 F7H 25 F7H H72 H6 H 0 1 N N N -0.134 -4.780 -14.072 3.679 3.110 0.217 H72 F7H 26 F7H H73 H7 H 0 1 N N N 0.255 -5.182 -12.365 1.924 3.323 0.003 H73 F7H 27 F7H H41 H8 H 0 1 N N N 2.420 -1.045 -12.852 5.033 1.905 0.697 H41 F7H 28 F7H H42 H9 H 0 1 N N N 0.943 -1.943 -12.730 5.709 0.383 0.479 H42 F7H 29 F7H "H2'" H10 H 0 1 N N N 6.743 -7.163 -14.020 -0.867 -2.773 0.504 "H2'" F7H 30 F7H "H2''" H11 H 0 0 N N N 5.928 -6.131 -12.796 -0.083 -1.476 1.458 "H2''" F7H 31 F7H "H7'" H12 H 0 1 N N N 4.464 -8.163 -10.934 -2.152 0.176 2.552 "H7'" F7H 32 F7H "H7''" H13 H 0 0 N N N 3.912 -6.696 -11.811 -0.840 0.685 1.447 "H7''" F7H 33 F7H "H6'" H14 H 0 1 N N N 1.801 -8.018 -11.855 -2.670 2.432 1.073 "H6'" F7H 34 F7H "H8'" H15 H 0 1 N N N 1.901 -10.569 -12.289 -4.983 1.666 0.244 "H8'" F7H 35 F7H "H8''" H16 H 0 0 N N N 3.694 -10.519 -12.199 -4.574 -0.053 0.772 "H8''" F7H 36 F7H H1 H17 H 0 1 N N N 6.477 -8.928 -11.986 -2.998 -2.109 2.069 H1 F7H 37 # # 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 F7H "O4'" "C1'" SING N N 1 F7H "O4'" "C4'" SING N N 2 F7H "C1'" N1 SING N N 3 F7H "C1'" "C2'" SING N N 4 F7H "O5'" "C5'" SING N N 5 F7H O2 C2 DOUB N N 6 F7H "C4'" "C5'" SING N N 7 F7H "C4'" "C3'" SING N N 8 F7H N1 C2 SING N N 9 F7H N1 C6 SING N N 10 F7H C2 N3 SING N N 11 F7H C6 C5 DOUB N N 12 F7H "C5'" "C8'" SING N N 13 F7H "C5'" "C6'" SING N N 14 F7H N3 C4 DOUB N N 15 F7H "C2'" "C3'" SING N N 16 F7H C5 C4 SING N N 17 F7H C5 C7 SING N N 18 F7H C4 N4 SING N N 19 F7H "C3'" "O3'" SING N N 20 F7H "C3'" "C7'" SING N N 21 F7H "C8'" "C6'" SING N N 22 F7H "C6'" "C7'" SING N N 23 F7H "O5'" "HO5'" SING N N 24 F7H "C4'" "H4'" SING N N 25 F7H "C1'" "H1'" SING N N 26 F7H C6 H6 SING N N 27 F7H C7 H71 SING N N 28 F7H C7 H72 SING N N 29 F7H C7 H73 SING N N 30 F7H N4 H41 SING N N 31 F7H N4 H42 SING N N 32 F7H "C2'" "H2'" SING N N 33 F7H "C2'" "H2''" SING N N 34 F7H "C7'" "H7'" SING N N 35 F7H "C7'" "H7''" SING N N 36 F7H "C6'" "H6'" SING N N 37 F7H "C8'" "H8'" SING N N 38 F7H "C8'" "H8''" SING N N 39 F7H "O3'" H1 SING N N 40 # # 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 F7H InChI InChI 1.03 "InChI=1S/C13H17N3O4/c1-6-5-16(11(17)15-9(6)14)8-4-12(18)2-7-3-13(7,19)10(12)20-8/h5,7-8,10,18-19H,2-4H2,1H3,(H2,14,15,17)/t7-,8-,10+,12+,13-/m1/s1" F7H InChIKey InChI 1.03 GKRDGXCEGWQOOW-ZIDZYHNGSA-N F7H SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@@]3(O)C[C@@H]4C[C@]4(O)[C@H]3O2)C(=O)N=C1N" F7H SMILES CACTVS 3.385 "CC1=CN([CH]2C[C]3(O)C[CH]4C[C]4(O)[CH]3O2)C(=O)N=C1N" F7H 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)O)O" F7H SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)N=C1N)C2CC3(CC4CC4(C3O2)O)O" # _pdbx_chem_comp_identifier.comp_id F7H _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 "4-azanyl-1-[(1~{S},2~{R},4~{S},6~{S},8~{R})-2,6-bis(oxidanyl)-9-oxatricyclo[4.3.0.0^{2,4}]nonan-8-yl]-5-methyl-pyrimidin-2-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site F7H "Create component" 2018-06-06 EBI F7H "Initial release" 2018-06-13 RCSB F7H "Modify one letter code" 2019-05-06 EBI ##