data_6NW # _chem_comp.id 6NW _chem_comp.name "2'-O-methyl-5'-O-thiophosphonoadenosine" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H16 N5 O6 P S" _chem_comp.mon_nstd_parent_comp_id A _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-05-11 _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 377.313 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6NW _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 6NW P P1 P 0 1 N N N -23.527 31.189 33.282 -4.550 1.165 -0.011 P 6NW 1 6NW SP1 S1 S 0 1 N N N -22.273 29.695 33.465 -6.129 -0.246 0.094 SP1 6NW 2 6NW OP2 O1 O 0 1 N N N -24.822 30.574 32.810 -4.321 1.749 1.329 OP2 6NW 3 6NW "O5'" O2 O 0 1 N N N -23.678 31.769 34.643 -3.208 0.432 -0.514 "O5'" 6NW 4 6NW "C5'" C1 C 0 1 N N N -24.269 30.882 35.470 -2.544 -0.582 0.243 "C5'" 6NW 5 6NW "C4'" C2 C 0 1 N N R -24.629 31.660 36.769 -1.308 -1.062 -0.520 "C4'" 6NW 6 6NW "O4'" O3 O 0 1 N N N -25.254 32.733 36.518 -0.341 -0.001 -0.601 "O4'" 6NW 7 6NW "C3'" C3 C 0 1 N N R -25.584 30.783 37.494 -0.646 -2.229 0.237 "C3'" 6NW 8 6NW "O3'" O4 O 0 1 N N N -24.860 30.230 38.418 -0.618 -3.402 -0.578 "O3'" 6NW 9 6NW "C2'" C4 C 0 1 N N R -26.678 31.731 37.987 0.793 -1.731 0.518 "C2'" 6NW 10 6NW "O2'" O5 O 0 1 N N N -26.222 32.358 39.220 1.744 -2.778 0.315 "O2'" 6NW 11 6NW "C1'" C5 C 0 1 N N R -26.744 32.598 37.079 0.964 -0.616 -0.545 "C1'" 6NW 12 6NW "CM'" C6 C 0 1 N N N -27.267 32.963 39.874 2.033 -3.536 1.492 "CM'" 6NW 13 6NW N9 N1 N 0 1 Y N N -27.526 32.049 36.014 1.973 0.355 -0.116 N9 6NW 14 6NW C8 C7 C 0 1 Y N N -27.029 31.397 34.961 1.747 1.488 0.609 C8 6NW 15 6NW N7 N2 N 0 1 Y N N -28.012 31.005 34.165 2.867 2.117 0.813 N7 6NW 16 6NW C5 C8 C 0 1 Y N N -29.218 31.432 34.736 3.882 1.430 0.234 C5 6NW 17 6NW C6 C9 C 0 1 Y N N -30.623 31.340 34.404 5.270 1.620 0.128 C6 6NW 18 6NW N6 N3 N 0 1 N N N -30.990 30.664 33.198 5.879 2.723 0.702 N6 6NW 19 6NW N1 N4 N 0 1 Y N N -31.574 31.905 35.240 5.984 0.717 -0.535 N1 6NW 20 6NW C2 C10 C 0 1 Y N N -31.264 32.530 36.349 5.411 -0.338 -1.085 C2 6NW 21 6NW N3 N5 N 0 1 Y N N -29.966 32.636 36.698 4.115 -0.557 -1.012 N3 6NW 22 6NW C4 C11 C 0 1 Y N N -28.935 32.088 35.896 3.321 0.289 -0.364 C4 6NW 23 6NW H1 H1 H 0 1 N N N -23.006 28.682 33.111 -7.168 0.494 0.520 H1 6NW 24 6NW "H5''" H2 H 0 0 N N N -25.180 30.477 35.005 -2.240 -0.174 1.207 "H5''" 6NW 25 6NW "H4'" H3 H 0 1 N N N -23.718 31.806 37.368 -1.593 -1.381 -1.523 "H4'" 6NW 26 6NW "H3'" H4 H 0 1 N N N -26.023 30.052 36.799 -1.172 -2.427 1.170 "H3'" 6NW 27 6NW "HO3'" H5 H 0 0 N Y N -25.400 29.645 38.936 -1.494 -3.725 -0.834 "HO3'" 6NW 28 6NW "H2'" H6 H 0 1 N N N -27.611 31.172 38.152 0.874 -1.324 1.526 "H2'" 6NW 29 6NW H7 H7 H 0 1 N N N -27.112 33.585 37.396 1.229 -1.044 -1.512 H7 6NW 30 6NW H11 H8 H 0 1 N N N -26.900 33.429 40.800 2.440 -2.877 2.258 H11 6NW 31 6NW H9 H9 H 0 1 N N N -27.708 33.734 39.225 1.117 -4.000 1.860 H9 6NW 32 6NW H10 H10 H 0 1 N N N -28.031 32.210 40.120 2.763 -4.311 1.255 H10 6NW 33 6NW H8 H11 H 0 1 N N N -25.979 31.216 34.784 0.780 1.814 0.961 H8 6NW 34 6NW H61 H12 H 0 1 N N N -31.984 30.683 33.094 5.347 3.375 1.184 H61 6NW 35 6NW H62 H13 H 0 1 N N N -30.565 31.121 32.417 6.839 2.843 0.622 H62 6NW 36 6NW H2 H14 H 0 1 N N N -32.036 32.954 36.974 6.029 -1.048 -1.615 H2 6NW 37 6NW "H5'" "H5'" H 0 1 N N N -23.578 30.058 35.700 -3.223 -1.420 0.401 "H5'" 6NW 38 6NW OP3 OP3 O 0 1 N Y N -23.254 32.445 32.415 -4.943 2.334 -1.046 OP3 6NW 39 6NW HOP3 HOP3 H 0 0 N Y N -23.955 32.552 31.782 -5.108 2.023 -1.947 HOP3 6NW 40 # 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 6NW P SP1 SING N N 1 6NW P OP2 DOUB N N 2 6NW P "O5'" SING N N 3 6NW "O5'" "C5'" SING N N 4 6NW "C5'" "C4'" SING N N 5 6NW "C4'" "O4'" SING N N 6 6NW "C4'" "C3'" SING N N 7 6NW "O4'" "C1'" SING N N 8 6NW "C3'" "O3'" SING N N 9 6NW "C3'" "C2'" SING N N 10 6NW "C2'" "O2'" SING N N 11 6NW "C2'" "C1'" SING N N 12 6NW "O2'" "CM'" SING N N 13 6NW "C1'" N9 SING N N 14 6NW N9 C8 SING Y N 15 6NW N9 C4 SING Y N 16 6NW C8 N7 DOUB Y N 17 6NW N7 C5 SING Y N 18 6NW C5 C6 DOUB Y N 19 6NW C5 C4 SING Y N 20 6NW C6 N6 SING N N 21 6NW C6 N1 SING Y N 22 6NW N1 C2 DOUB Y N 23 6NW C2 N3 SING Y N 24 6NW N3 C4 DOUB Y N 25 6NW SP1 H1 SING N N 26 6NW "C5'" "H5''" SING N N 27 6NW "C4'" "H4'" SING N N 28 6NW "C3'" "H3'" SING N N 29 6NW "O3'" "HO3'" SING N N 30 6NW "C2'" "H2'" SING N N 31 6NW "C1'" H7 SING N N 32 6NW "CM'" H11 SING N N 33 6NW "CM'" H9 SING N N 34 6NW "CM'" H10 SING N N 35 6NW C8 H8 SING N N 36 6NW N6 H61 SING N N 37 6NW N6 H62 SING N N 38 6NW C2 H2 SING N N 39 6NW "C5'" "H5'" SING N N 40 6NW P OP3 SING N N 41 6NW OP3 HOP3 SING N N 42 # 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 6NW SMILES ACDLabs 12.01 "P(S)(=O)(OCC1OC(C(C1O)OC)n2cnc3c(N)ncnc23)O" 6NW InChI InChI 1.03 "InChI=1S/C11H16N5O6PS/c1-20-8-7(17)5(2-21-23(18,19)24)22-11(8)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17H,2H2,1H3,(H2,12,13,14)(H2,18,19,24)/t5-,7-,8-,11-/m1/s1" 6NW InChIKey InChI 1.03 OXNLMRLCWQEYRW-IOSLPCCCSA-N 6NW SMILES_CANONICAL CACTVS 3.385 "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(S)=O)O[C@H]1n2cnc3c(N)ncnc23" 6NW SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](CO[P](O)(S)=O)O[CH]1n2cnc3c(N)ncnc23" 6NW SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)COP(=O)(O)S)O" 6NW SMILES "OpenEye OEToolkits" 2.0.4 "COC1C(C(OC1n2cnc3c2ncnc3N)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 6NW "SYSTEMATIC NAME" ACDLabs 12.01 "2'-O-methyl-5'-O-thiophosphonoadenosine" 6NW "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-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 6NW "Create component" 2016-05-11 RCSB 6NW "Initial release" 2016-07-20 RCSB #