data_6OO # _chem_comp.id 6OO _chem_comp.name "2'-O-methyl-5'-O-thiophosphonocytidine" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O7 P S" _chem_comp.mon_nstd_parent_comp_id C _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 353.289 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6OO _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 6OO C2 C1 C 0 1 N N N -31.350 24.700 38.316 -2.465 1.068 -0.540 C2 6OO 1 6OO C4 C2 C 0 1 N N N -29.178 24.622 37.520 -4.483 2.098 -0.087 C4 6OO 2 6OO C5 C3 C 0 1 N N N -28.708 24.473 38.810 -4.661 1.254 1.028 C5 6OO 3 6OO C6 C4 C 0 1 N N N -29.669 24.438 39.858 -3.711 0.331 1.310 C6 6OO 4 6OO O2 O1 O 0 1 N N N -32.499 24.810 38.037 -1.469 0.980 -1.239 O2 6OO 5 6OO P P1 P 0 1 N N N -27.546 25.691 42.946 3.898 1.098 0.002 P 6OO 6 6OO SP1 S1 S 0 1 N N N -27.861 25.811 44.845 5.463 -0.297 -0.305 SP1 6OO 7 6OO OP2 O2 O 0 1 N N N -26.378 24.839 42.448 3.572 1.764 -1.280 OP2 6OO 8 6OO "O5'" O3 O 0 1 N N N -28.936 25.407 42.387 2.595 0.330 0.554 "O5'" 6OO 9 6OO "C5'" C5 C 0 1 N N N -29.786 24.640 43.280 1.877 -0.637 -0.214 "C5'" 6OO 10 6OO "C4'" C6 C 0 1 N N R -31.022 24.243 42.718 0.700 -1.168 0.605 "C4'" 6OO 11 6OO "O4'" O4 O 0 1 N N N -31.516 25.186 41.677 -0.261 -0.120 0.817 "O4'" 6OO 12 6OO "C3'" C7 C 0 1 N N R -30.971 22.844 41.974 -0.011 -2.296 -0.168 "C3'" 6OO 13 6OO "O3'" O5 O 0 1 N N N -31.146 21.650 42.864 0.023 -3.514 0.579 "O3'" 6OO 14 6OO "C2'" C8 C 0 1 N N R -31.767 22.934 41.050 -1.467 -1.794 -0.318 "C2'" 6OO 15 6OO "O2'" O6 O 0 1 N N N -33.098 22.336 41.154 -2.398 -2.858 -0.109 "O2'" 6OO 16 6OO "C1'" C9 C 0 1 N N R -31.858 24.505 40.639 -1.566 -0.738 0.818 "C1'" 6OO 17 6OO "CM'" C10 C 0 1 N N N -33.555 21.881 39.893 -2.767 -3.550 -1.304 "CM'" 6OO 18 6OO N1 N1 N 0 1 N N N -30.943 24.564 39.564 -2.606 0.248 0.518 N1 6OO 19 6OO N3 N2 N 0 1 N N N -30.478 24.732 37.303 -3.393 1.978 -0.834 N3 6OO 20 6OO N4 N3 N 0 1 N N N -28.274 24.664 36.419 -5.432 3.045 -0.397 N4 6OO 21 6OO O1 O7 O 0 1 N Y N -27.302 27.211 42.604 4.366 2.202 1.076 O1 6OO 22 6OO H1 H1 H 0 1 N N N -27.651 24.386 39.015 -5.543 1.340 1.646 H1 6OO 23 6OO H2 H2 H 0 1 N N N -29.355 24.309 40.883 -3.824 -0.327 2.159 H2 6OO 24 6OO H3 H3 H 0 1 N N N -26.912 25.063 45.324 5.651 -0.817 0.921 H3 6OO 25 6OO H4 H4 H 0 1 N N N -29.239 23.734 43.581 1.504 -0.172 -1.127 H4 6OO 26 6OO H5 H5 H 0 1 N N N -29.994 25.255 44.168 2.542 -1.462 -0.473 H5 6OO 27 6OO H6 H6 H 0 1 N N N -31.781 24.167 43.511 1.056 -1.544 1.565 H6 6OO 28 6OO H7 H7 H 0 1 N N N -29.949 22.773 41.574 0.449 -2.437 -1.146 H7 6OO 29 6OO H8 H8 H 0 1 N N N -30.487 21.665 43.548 0.916 -3.843 0.754 H8 6OO 30 6OO H9 H9 H 0 1 N N N -31.314 22.465 40.165 -1.620 -1.331 -1.293 H9 6OO 31 6OO H10 H10 H 0 1 N N N -32.883 24.714 40.300 -1.760 -1.222 1.776 H10 6OO 32 6OO H11 H11 H 0 1 N N N -34.556 21.438 40.003 -3.229 -2.851 -2.001 H11 6OO 33 6OO H12 H12 H 0 1 N N N -33.605 22.728 39.194 -1.878 -3.985 -1.761 H12 6OO 34 6OO H13 H13 H 0 1 N N N -32.859 21.124 39.503 -3.475 -4.342 -1.060 H13 6OO 35 6OO H14 H14 H 0 1 N N N -28.624 24.776 35.489 -6.226 3.133 0.153 H14 6OO 36 6OO H15 H15 H 0 1 N N N -27.290 24.581 36.577 -5.307 3.624 -1.165 H15 6OO 37 6OO H16 H16 H 0 1 N N N -26.472 27.305 42.152 5.147 2.705 0.808 H16 6OO 38 # 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 6OO N4 C4 SING N N 1 6OO N3 C4 DOUB N N 2 6OO N3 C2 SING N N 3 6OO C4 C5 SING N N 4 6OO O2 C2 DOUB N N 5 6OO C2 N1 SING N N 6 6OO C5 C6 DOUB N N 7 6OO N1 C6 SING N N 8 6OO N1 "C1'" SING N N 9 6OO "CM'" "O2'" SING N N 10 6OO "C1'" "C2'" SING N N 11 6OO "C1'" "O4'" SING N N 12 6OO "C2'" "O2'" SING N N 13 6OO "C2'" "C3'" SING N N 14 6OO "O4'" "C4'" SING N N 15 6OO "C3'" "C4'" SING N N 16 6OO "C3'" "O3'" SING N N 17 6OO "O5'" P SING N N 18 6OO "O5'" "C5'" SING N N 19 6OO OP2 P DOUB N N 20 6OO "C4'" "C5'" SING N N 21 6OO P SP1 SING N N 22 6OO P O1 SING N N 23 6OO C5 H1 SING N N 24 6OO C6 H2 SING N N 25 6OO SP1 H3 SING N N 26 6OO "C5'" H4 SING N N 27 6OO "C5'" H5 SING N N 28 6OO "C4'" H6 SING N N 29 6OO "C3'" H7 SING N N 30 6OO "O3'" H8 SING N N 31 6OO "C2'" H9 SING N N 32 6OO "C1'" H10 SING N N 33 6OO "CM'" H11 SING N N 34 6OO "CM'" H12 SING N N 35 6OO "CM'" H13 SING N N 36 6OO N4 H14 SING N N 37 6OO N4 H15 SING N N 38 6OO O1 H16 SING N N 39 # 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 6OO InChI InChI 1.03 "InChI=1S/C10H16N3O7PS/c1-18-8-7(14)5(4-19-21(16,17)22)20-9(8)13-3-2-6(11)12-10(13)15/h2-3,5,7-9,14H,4H2,1H3,(H2,11,12,15)(H2,16,17,22)/t5-,7-,8-,9-/m1/s1" 6OO InChIKey InChI 1.03 JKIZWHJBBPPNBB-ZOQUXTDFSA-N 6OO SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1N2C=CC(=NC2=O)N" 6OO SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1N2C=CC(=NC2=O)N" 6OO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)S)O" 6OO SMILES "OpenEye OEToolkits" 2.0.5 "COC1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)S)O" # 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 6OO "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.5 "[(2~{R},3~{R},4~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic 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 6OO "Create component" 2016-05-13 RCSB 6OO "Other modification" 2016-06-21 RCSB 6OO "Initial release" 2016-07-20 RCSB #