data_6OP # _chem_comp.id 6OP _chem_comp.name "1-[(5E)-5,6-dideoxy-2-O-(2-methoxyethyl)-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C14 H21 N2 O9 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-05-13 _chem_comp.pdbx_modified_date 2016-07-15 _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 392.298 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6OP _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 5JS2 _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 6OP P P1 P 0 1 N N N -18.447 30.666 29.630 5.126 0.069 0.038 P 6OP 1 6OP OP1 O1 O 0 1 N N N -18.421 29.079 29.846 5.653 -1.418 -0.285 OP1 6OP 2 6OP OP2 O2 O 0 1 N N N -17.121 31.169 29.204 5.901 0.633 1.166 OP2 6OP 3 6OP OP3 O3 O 0 1 N Y N -18.773 31.355 30.969 5.316 1.000 -1.262 OP3 6OP 4 6OP "C6'" C1 C 0 1 N N N -19.645 31.071 28.374 3.369 0.004 0.483 "C6'" 6OP 5 6OP "C5'" C2 C 0 1 N N N -20.899 30.195 28.389 2.740 -1.145 0.502 "C5'" 6OP 6 6OP "C4'" C3 C 0 1 N N R -21.927 30.738 27.295 1.280 -1.199 0.872 "C4'" 6OP 7 6OP "O4'" O4 O 0 1 N N N -21.768 29.976 25.979 0.730 0.134 0.946 "O4'" 6OP 8 6OP "C3'" C4 C 0 1 N N R -23.091 30.565 27.637 0.469 -1.900 -0.241 "C3'" 6OP 9 6OP "O3'" O5 O 0 1 N N N -23.854 31.754 27.351 0.235 -3.269 0.096 "O3'" 6OP 10 6OP "C2'" C5 C 0 1 N N R -23.622 29.293 26.748 -0.862 -1.116 -0.285 "C2'" 6OP 11 6OP "O2'" O6 O 0 1 N N N -25.057 29.244 26.784 -1.960 -1.976 0.025 "O2'" 6OP 12 6OP "C1'" C6 C 0 1 N N R -23.166 29.506 25.622 -0.697 -0.035 0.806 "C1'" 6OP 13 6OP "CB'" C7 C 0 1 N N N -25.684 28.238 25.966 -2.557 -2.591 -1.119 "CB'" 6OP 14 6OP "CG'" C8 C 0 1 N N N -25.512 26.845 26.622 -3.716 -3.484 -0.671 "CG'" 6OP 15 6OP "OD'" O7 O 0 1 N N N -26.221 26.903 27.890 -4.745 -2.677 -0.096 "OD'" 6OP 16 6OP "CE'" C9 C 0 1 N N N -25.632 26.175 28.954 -5.880 -3.418 0.357 "CE'" 6OP 17 6OP N1 N1 N 0 1 N N N -23.000 28.252 24.790 -1.319 1.221 0.379 N1 6OP 18 6OP C2 C10 C 0 1 N N N -23.385 28.245 23.510 -0.866 1.848 -0.722 C2 6OP 19 6OP O2 O8 O 0 1 N N N -23.883 29.230 23.030 0.059 1.368 -1.347 O2 6OP 20 6OP N3 N2 N 0 1 N N N -23.247 27.163 22.732 -1.423 3.000 -1.140 N3 6OP 21 6OP C4 C11 C 0 1 N N N -22.696 26.042 23.239 -2.451 3.545 -0.458 C4 6OP 22 6OP O4 O9 O 0 1 N N N -22.554 25.021 22.534 -2.956 4.587 -0.837 O4 6OP 23 6OP C5 C12 C 0 1 N N N -22.268 25.988 24.557 -2.937 2.895 0.702 C5 6OP 24 6OP C7 C13 C 0 1 N N N -21.637 24.693 25.137 -4.084 3.484 1.483 C7 6OP 25 6OP C6 C14 C 0 1 N N N -22.425 27.135 25.338 -2.360 1.741 1.099 C6 6OP 26 6OP H1 H1 H 0 1 N N N -17.550 28.748 29.659 5.189 -1.850 -1.016 H1 6OP 27 6OP HOP3 H2 H 0 0 N Y N -18.060 31.935 31.209 6.233 1.080 -1.558 H2 6OP 28 6OP "H6'" H3 H 0 1 N N N -19.498 31.869 27.661 2.841 0.912 0.734 H3 6OP 29 6OP "H5'" H5 H 0 1 N N N -21.063 29.346 29.036 3.267 -2.054 0.251 H5 6OP 30 6OP "H4'" H7 H 0 1 N N N -21.686 31.795 27.112 1.149 -1.719 1.821 H7 6OP 31 6OP "H3'" H8 H 0 1 N N N -23.203 30.295 28.697 0.988 -1.825 -1.196 H8 6OP 32 6OP "HO3'" H9 H 0 0 N Y N -23.528 32.474 27.877 1.042 -3.792 0.194 H9 6OP 33 6OP "H2'" H10 H 0 1 N N N -23.212 28.383 27.211 -1.002 -0.656 -1.263 H10 6OP 34 6OP "H1'" H11 H 0 1 N N N -23.691 30.280 25.044 -1.133 -0.374 1.746 H11 6OP 35 6OP H12 H12 H 0 1 N N N -25.216 28.233 24.971 -2.932 -1.819 -1.792 H12 6OP 36 6OP H13 H13 H 0 1 N N N -26.756 28.465 25.866 -1.812 -3.194 -1.638 H13 6OP 37 6OP H14 H14 H 0 1 N N N -25.945 26.065 25.979 -4.114 -4.021 -1.532 H14 6OP 38 6OP H15 H15 H 0 1 N N N -24.446 26.632 26.791 -3.358 -4.199 0.069 H15 6OP 39 6OP H16 H16 H 0 1 N N N -26.246 26.287 29.860 -5.567 -4.132 1.120 H16 6OP 40 6OP H17 H17 H 0 1 N N N -25.572 25.111 28.681 -6.615 -2.734 0.781 H17 6OP 41 6OP H18 H18 H 0 1 N N N -24.620 26.562 29.147 -6.323 -3.954 -0.482 H18 6OP 42 6OP H3 H19 H 0 1 N N N -23.551 27.187 21.780 -1.084 3.439 -1.936 H19 6OP 43 6OP H20 H20 H 0 1 N N N -21.367 24.856 26.191 -4.410 4.409 1.007 H20 6OP 44 6OP H21 H21 H 0 1 N N N -22.363 23.869 25.068 -4.911 2.775 1.504 H21 6OP 45 6OP H22 H22 H 0 1 N N N -20.735 24.436 24.563 -3.759 3.694 2.502 H22 6OP 46 6OP H6 H23 H 0 1 N N N -22.096 27.142 26.367 -2.720 1.229 1.979 H23 6OP 47 # 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 6OP O4 C4 DOUB N N 1 6OP N3 C4 SING N N 2 6OP N3 C2 SING N N 3 6OP O2 C2 DOUB N N 4 6OP C4 C5 SING N N 5 6OP C2 N1 SING N N 6 6OP C5 C7 SING N N 7 6OP C5 C6 DOUB N N 8 6OP N1 C6 SING N N 9 6OP N1 "C1'" SING N N 10 6OP "C1'" "O4'" SING N N 11 6OP "C1'" "C2'" SING N N 12 6OP "CB'" "CG'" SING N N 13 6OP "CB'" "O2'" SING N N 14 6OP "O4'" "C4'" SING N N 15 6OP "CG'" "OD'" SING N N 16 6OP "C2'" "O2'" SING N N 17 6OP "C2'" "C3'" SING N N 18 6OP "C4'" "C3'" SING N N 19 6OP "C4'" "C5'" SING N N 20 6OP "O3'" "C3'" SING N N 21 6OP "OD'" "CE'" SING N N 22 6OP "C6'" "C5'" DOUB N E 23 6OP "C6'" P SING N N 24 6OP OP2 P DOUB N N 25 6OP P OP1 SING N N 26 6OP P OP3 SING N N 27 6OP OP1 H1 SING N N 28 6OP OP3 HOP3 SING N N 29 6OP "C6'" "H6'" SING N N 30 6OP "C5'" "H5'" SING N N 31 6OP "C4'" "H4'" SING N N 32 6OP "C3'" "H3'" SING N N 33 6OP "O3'" "HO3'" SING N N 34 6OP "C2'" "H2'" SING N N 35 6OP "C1'" "H1'" SING N N 36 6OP "CB'" H12 SING N N 37 6OP "CB'" H13 SING N N 38 6OP "CG'" H14 SING N N 39 6OP "CG'" H15 SING N N 40 6OP "CE'" H16 SING N N 41 6OP "CE'" H17 SING N N 42 6OP "CE'" H18 SING N N 43 6OP N3 H3 SING N N 44 6OP C7 H20 SING N N 45 6OP C7 H21 SING N N 46 6OP C7 H22 SING N N 47 6OP C6 H6 SING N N 48 # 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 6OP SMILES ACDLabs 12.01 "P(O)(O)(=O)C=[C@H]C1C(O)C(OCCOC)C(O1)N2C=C(C(NC2=O)=O)C" 6OP InChI InChI 1.03 "InChI=1S/C14H21N2O9P/c1-8-7-16(14(19)15-12(8)18)13-11(24-5-4-23-2)10(17)9(25-13)3-6-26(20,21)22/h3,6-7,9-11,13,17H,4-5H2,1-2H3,(H,15,18,19)(H2,20,21,22)/b6-3+/t9-,10-,11-,13-/m1/s1" 6OP InChIKey InChI 1.03 MIWMWNWNEZHLGC-PSDJLLRUSA-N 6OP SMILES_CANONICAL CACTVS 3.385 "COCCO[C@@H]1[C@H](O)[C@H](O[C@H]1N2C=C(C)C(=O)NC2=O)/C=C/[P](O)(O)=O" 6OP SMILES CACTVS 3.385 "COCCO[CH]1[CH](O)[CH](O[CH]1N2C=C(C)C(=O)NC2=O)C=C[P](O)(O)=O" 6OP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)/C=C/P(=O)(O)O)O)OCCOC" 6OP SMILES "OpenEye OEToolkits" 2.0.4 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)C=CP(=O)(O)O)O)OCCOC" # 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 6OP "SYSTEMATIC NAME" ACDLabs 12.01 "1-[(5E)-5,6-dideoxy-2-O-(2-methoxyethyl)-6-phosphono-beta-D-ribo-hex-5-enofuranosyl]-5-methylpyrimidine-2,4(1H,3H)-dione" 6OP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(~{E})-2-[(2~{R},3~{R},4~{R},5~{R})-4-(2-methoxyethoxy)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]ethenyl]phosphonic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 6OP "Create component" 2016-05-13 RCSB 6OP "Initial release" 2016-07-20 RCSB #