data_RFJ # _chem_comp.id RFJ _chem_comp.name "2'-O-methyl-5'-O-thiophosphonoguanosine" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O7 P S" _chem_comp.mon_nstd_parent_comp_id G _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-02-11 _chem_comp.pdbx_modified_date 2020-04-24 _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 393.313 _chem_comp.one_letter_code G _chem_comp.three_letter_code RFJ _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 ? _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 RFJ C C1 C 0 1 N N N ? ? ? 1.933 3.263 -1.719 C RFJ 1 RFJ "C1'" C2 C 0 1 N N R ? ? ? 0.718 0.553 0.477 "C1'" RFJ 2 RFJ C2 C3 C 0 1 N N N ? ? ? 5.173 0.203 0.783 C2 RFJ 3 RFJ "C2'" C4 C 0 1 N N R ? ? ? 0.558 1.638 -0.618 "C2'" RFJ 4 RFJ "C3'" C5 C 0 1 N N R ? ? ? -0.848 2.208 -0.306 "C3'" RFJ 5 RFJ C4 C6 C 0 1 Y N N ? ? ? 3.028 -0.441 0.216 C4 RFJ 6 RFJ "C4'" C7 C 0 1 N N R ? ? ? -1.532 1.097 0.513 "C4'" RFJ 7 RFJ C5 C8 C 0 1 Y N N ? ? ? 3.518 -1.627 -0.343 C5 RFJ 8 RFJ "C5'" C9 C 0 1 N N N ? ? ? -2.813 0.645 -0.191 "C5'" RFJ 9 RFJ C6 C10 C 0 1 N N N ? ? ? 4.912 -1.862 -0.318 C6 RFJ 10 RFJ C8 C11 C 0 1 Y N N ? ? ? 1.364 -1.643 -0.588 C8 RFJ 11 RFJ N1 N1 N 0 1 N N N ? ? ? 5.710 -0.931 0.250 N1 RFJ 12 RFJ N2 N2 N 0 1 N N N ? ? ? 6.007 1.131 1.354 N2 RFJ 13 RFJ N3 N3 N 0 1 N N N ? ? ? 3.879 0.435 0.762 N3 RFJ 14 RFJ N7 N4 N 0 1 Y N N ? ? ? 2.452 -2.318 -0.818 N7 RFJ 15 RFJ N9 N5 N 0 1 Y N N ? ? ? 1.670 -0.475 0.049 N9 RFJ 16 RFJ "O2'" O1 O 0 1 N N N ? ? ? 1.559 2.649 -0.484 "O2'" RFJ 17 RFJ "O3'" O2 O 0 1 N N N ? ? ? -0.745 3.407 0.464 "O3'" RFJ 18 RFJ "O4'" O3 O 0 1 N N N ? ? ? -0.608 -0.002 0.603 "O4'" RFJ 19 RFJ "O5'" O4 O 0 1 N N N ? ? ? -3.501 -0.300 0.631 "O5'" RFJ 20 RFJ O6 O5 O 0 1 N N N ? ? ? 5.383 -2.881 -0.794 O6 RFJ 21 RFJ OP2 O6 O 0 1 N N N ? ? ? -5.573 -1.673 1.490 OP2 RFJ 22 RFJ P P1 P 0 1 N N N ? ? ? -4.893 -0.987 0.201 P RFJ 23 RFJ S S1 S 0 1 N N N ? ? ? -6.039 0.311 -0.489 S RFJ 24 RFJ H1 H1 H 0 1 N N N ? ? ? 1.059 3.733 -2.171 H1 RFJ 25 RFJ H2 H2 H 0 1 N N N ? ? ? 2.696 4.018 -1.533 H2 RFJ 26 RFJ H3 H3 H 0 1 N N N ? ? ? 2.329 2.506 -2.396 H3 RFJ 27 RFJ H4 H4 H 0 1 N N N ? ? ? 1.037 1.002 1.418 H4 RFJ 28 RFJ H5 H5 H 0 1 N N N ? ? ? 0.586 1.194 -1.613 H5 RFJ 29 RFJ H6 H6 H 0 1 N N N ? ? ? -1.395 2.393 -1.231 H6 RFJ 30 RFJ H7 H7 H 0 1 N N N ? ? ? -1.766 1.464 1.512 H7 RFJ 31 RFJ H8 H8 H 0 1 N N N ? ? ? -3.455 1.509 -0.367 H8 RFJ 32 RFJ H9 H9 H 0 1 N N N ? ? ? -2.560 0.181 -1.144 H9 RFJ 33 RFJ H10 H10 H 0 1 N N N ? ? ? 0.368 -1.959 -0.861 H10 RFJ 34 RFJ H11 H11 H 0 1 N N N ? ? ? 6.669 -1.069 0.279 H11 RFJ 35 RFJ H12 H12 H 0 1 N N N ? ? ? 6.964 0.976 1.374 H12 RFJ 36 RFJ H13 H13 H 0 1 N N N ? ? ? 5.639 1.943 1.737 H13 RFJ 37 RFJ "HO3'" H14 H 0 0 N Y N ? ? ? -1.597 3.774 0.735 "HO3'" RFJ 38 RFJ HOP2 H15 H 0 0 N N N ? ? ? -6.417 -2.107 1.304 HOP2 RFJ 39 RFJ OP3 O3P O 0 1 N Y N ? ? ? -4.614 -2.108 -0.920 OP3 RFJ 40 RFJ HOP3 H16 H 0 0 N Y N ? ? ? -4.024 -2.817 -0.629 HOP3 RFJ 41 # # 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 RFJ S P DOUB N N 1 RFJ OP2 P SING N N 2 RFJ P "O5'" SING N N 3 RFJ "O3'" "C3'" SING N N 4 RFJ "C5'" "O5'" SING N N 5 RFJ "C5'" "C4'" SING N N 6 RFJ "C3'" "C4'" SING N N 7 RFJ "C3'" "C2'" SING N N 8 RFJ "C4'" "O4'" SING N N 9 RFJ "C2'" "O2'" SING N N 10 RFJ "C2'" "C1'" SING N N 11 RFJ "O4'" "C1'" SING N N 12 RFJ C8 N7 DOUB Y N 13 RFJ C8 N9 SING Y N 14 RFJ "O2'" C SING N N 15 RFJ N7 C5 SING Y N 16 RFJ "C1'" N9 SING N N 17 RFJ N9 C4 SING Y N 18 RFJ C5 C4 DOUB Y N 19 RFJ C5 C6 SING N N 20 RFJ C4 N3 SING N N 21 RFJ O6 C6 DOUB N N 22 RFJ C6 N1 SING N N 23 RFJ N3 C2 DOUB N N 24 RFJ N1 C2 SING N N 25 RFJ C2 N2 SING N N 26 RFJ C H1 SING N N 27 RFJ C H2 SING N N 28 RFJ C H3 SING N N 29 RFJ "C1'" H4 SING N N 30 RFJ "C2'" H5 SING N N 31 RFJ "C3'" H6 SING N N 32 RFJ "C4'" H7 SING N N 33 RFJ "C5'" H8 SING N N 34 RFJ "C5'" H9 SING N N 35 RFJ C8 H10 SING N N 36 RFJ N1 H11 SING N N 37 RFJ N2 H12 SING N N 38 RFJ N2 H13 SING N N 39 RFJ "O3'" "HO3'" SING N N 40 RFJ OP2 HOP2 SING N N 41 RFJ P OP3 SING N N 42 RFJ OP3 HOP3 SING N N 43 # # 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 RFJ SMILES ACDLabs 12.01 "COC3C(n2c1N=C(N)NC(c1nc2)=O)OC(C3O)COP(O)(O)=S" RFJ InChI InChI 1.03 "InChI=1S/C11H16N5O7PS/c1-21-7-6(17)4(2-22-24(19,20)25)23-10(7)16-3-13-5-8(16)14-11(12)15-9(5)18/h3-4,6-7,10,17H,2H2,1H3,(H2,19,20,25)(H3,12,14,15,18)/t4-,6-,7-,10-/m1/s1" RFJ InChIKey InChI 1.03 QUDYZWLGVZGRFN-KQYNXXCUSA-N RFJ SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=S)O[C@H]1n2cnc3C(=O)NC(=Nc23)N" RFJ SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(O)=S)O[CH]1n2cnc3C(=O)NC(=Nc23)N" RFJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)O" RFJ SMILES "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1n2cnc3c2N=C(NC3=O)N)COP(=S)(O)O)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 RFJ "SYSTEMATIC NAME" ACDLabs 12.01 "2'-O-methyl-5'-O-thiophosphonoguanosine" RFJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-azanyl-9-[(2~{R},3~{R},4~{R},5~{R})-5-[bis(oxidanyl)phosphinothioyloxymethyl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-1~{H}-purin-6-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 RFJ "Create component" 2020-02-11 RCSB RFJ "Initial release" 2020-04-29 RCSB ##