data_XM7 # _chem_comp.id XM7 _chem_comp.name "5'-O-[(R)-hydroxy(methoxy)phosphoryl]adenosine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H16 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-12-18 _chem_comp.pdbx_modified_date 2020-12-25 _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 361.248 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XM7 _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 7L3Q _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 XM7 C2 C1 C 0 1 Y N N 4.580 1.923 -20.779 5.480 -0.455 -0.861 C2 XM7 1 XM7 N1 N1 N 0 1 Y N N 4.072 2.914 -20.042 5.990 0.680 -0.421 N1 XM7 2 XM7 C6 C2 C 0 1 Y N N 4.214 2.890 -18.714 5.217 1.623 0.108 C6 XM7 3 XM7 "C4'" C3 C 0 1 N N R 8.286 -2.584 -17.479 -1.210 -1.441 -0.337 "C4'" XM7 4 XM7 "C3'" C4 C 0 1 N N S 8.972 -1.449 -18.201 -0.463 -2.514 0.479 "C3'" XM7 5 XM7 "C2'" C5 C 0 1 N N R 8.021 -1.168 -19.362 0.947 -1.912 0.698 "C2'" XM7 6 XM7 "C1'" C6 C 0 1 N N R 6.667 -1.319 -18.631 1.030 -0.860 -0.438 "C1'" XM7 7 XM7 C8 C7 C 0 1 Y N N 5.874 0.375 -16.922 1.686 1.395 0.486 C8 XM7 8 XM7 C5 C8 C 0 1 Y N N 4.896 1.815 -18.151 3.834 1.387 0.190 C5 XM7 9 XM7 C4 C9 C 0 1 Y N N 5.382 0.844 -19.007 3.340 0.163 -0.292 C4 XM7 10 XM7 "C5'" C10 C 0 1 N N N 8.828 -2.805 -16.078 -2.460 -0.989 0.420 "C5'" XM7 11 XM7 C22 C11 C 0 1 N N N 6.272 -1.568 -12.742 -6.194 2.532 -0.817 C22 XM7 12 XM7 N9 N2 N 0 1 Y N N 6.008 -0.076 -18.221 1.984 0.197 -0.093 N9 XM7 13 XM7 N7 N3 N 0 1 Y N N 5.215 1.494 -16.838 2.773 2.092 0.651 N7 XM7 14 XM7 N3 N4 N 0 1 Y N N 5.241 0.863 -20.340 4.192 -0.720 -0.805 N3 XM7 15 XM7 N6 N5 N 0 1 N N N 3.691 3.883 -17.983 5.761 2.810 0.567 N6 XM7 16 XM7 "O3'" O1 O 0 1 N N N 10.181 -1.957 -18.790 -0.379 -3.735 -0.259 "O3'" XM7 17 XM7 "O4'" O2 O 0 1 N N N 6.906 -2.070 -17.447 -0.312 -0.331 -0.506 "O4'" XM7 18 XM7 "O2'" O3 O 0 1 N N N 8.151 -2.148 -20.395 1.957 -2.910 0.543 "O2'" XM7 19 XM7 "O5'" O4 O 0 1 N N N 7.762 -3.025 -15.157 -3.198 -0.069 -0.387 "O5'" XM7 20 XM7 OP3 O5 O 0 1 N N N 7.645 -1.912 -13.002 -5.058 1.684 -1.002 OP3 XM7 21 XM7 OP2 O6 O 0 1 N N N 6.838 -4.449 -13.114 -5.703 -0.524 0.270 OP2 XM7 22 XM7 OP1 O7 O 0 1 N N N 9.460 -3.782 -13.310 -4.360 1.295 1.392 OP1 XM7 23 XM7 P P1 P 0 1 N N N 7.950 -3.464 -13.549 -4.575 0.612 0.097 P XM7 24 XM7 "H4'" H1 H 0 1 N N N 4.436 1.994 -21.847 6.143 -1.193 -1.288 "H4'" XM7 25 XM7 H1 H2 H 0 1 N N N 8.350 -3.511 -18.067 -1.491 -1.842 -1.311 H1 XM7 26 XM7 "H3'" H3 H 0 1 N N N 9.124 -0.568 -17.560 -0.959 -2.681 1.435 "H3'" XM7 27 XM7 "H2'" H4 H 0 1 N N N 8.149 -0.142 -19.737 1.019 -1.436 1.675 "H2'" XM7 28 XM7 "H1'" H5 H 0 1 N N N 5.989 -1.880 -19.290 1.307 -1.333 -1.380 "H1'" XM7 29 XM7 "H5''" H6 H 0 0 N N N 6.274 -0.147 -16.065 0.694 1.719 0.766 "H5''" XM7 30 XM7 "H5'" H7 H 0 1 N N N 9.490 -3.683 -16.081 -3.082 -1.855 0.645 "H5'" XM7 31 XM7 H2 H8 H 0 1 N N N 9.398 -1.917 -15.766 -2.166 -0.502 1.350 H2 XM7 32 XM7 H9 H9 H 0 1 N N N 6.214 -0.527 -12.391 -6.319 3.168 -1.692 H9 XM7 33 XM7 H10 H10 H 0 1 N N N 5.686 -1.676 -13.666 -7.085 1.920 -0.681 H10 XM7 34 XM7 H11 H11 H 0 1 N N N 5.866 -2.238 -11.970 -6.042 3.154 0.066 H11 XM7 35 XM7 H61 H12 H 0 1 N N N 3.240 4.540 -18.587 6.717 2.961 0.505 H61 XM7 36 XM7 H62 H13 H 0 1 N N N 3.023 3.508 -17.341 5.186 3.490 0.951 H62 XM7 37 XM7 "HO3'" H14 H 0 0 N N N 10.811 -2.149 -18.105 0.082 -4.446 0.208 "HO3'" XM7 38 XM7 "HO2'" H15 H 0 0 N N N 8.988 -2.039 -20.832 1.946 -3.591 1.229 "HO2'" XM7 39 XM7 HOP2 H16 H 0 0 N N N 7.232 -5.213 -12.710 -5.896 -1.014 -0.542 HOP2 XM7 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 XM7 C2 N3 DOUB Y N 1 XM7 C2 N1 SING Y N 2 XM7 "O2'" "C2'" SING N N 3 XM7 N3 C4 SING Y N 4 XM7 N1 C6 DOUB Y N 5 XM7 "C2'" "C1'" SING N N 6 XM7 "C2'" "C3'" SING N N 7 XM7 C4 N9 SING Y N 8 XM7 C4 C5 DOUB Y N 9 XM7 "O3'" "C3'" SING N N 10 XM7 C6 C5 SING Y N 11 XM7 C6 N6 SING N N 12 XM7 "C1'" N9 SING N N 13 XM7 "C1'" "O4'" SING N N 14 XM7 N9 C8 SING Y N 15 XM7 "C3'" "C4'" SING N N 16 XM7 C5 N7 SING Y N 17 XM7 "C4'" "O4'" SING N N 18 XM7 "C4'" "C5'" SING N N 19 XM7 C8 N7 DOUB Y N 20 XM7 "C5'" "O5'" SING N N 21 XM7 "O5'" P SING N N 22 XM7 P OP1 DOUB N N 23 XM7 P OP2 SING N N 24 XM7 P OP3 SING N N 25 XM7 OP3 C22 SING N N 26 XM7 C2 "H4'" SING N N 27 XM7 "C4'" H1 SING N N 28 XM7 "C3'" "H3'" SING N N 29 XM7 "C2'" "H2'" SING N N 30 XM7 "C1'" "H1'" SING N N 31 XM7 C8 "H5''" SING N N 32 XM7 "C5'" "H5'" SING N N 33 XM7 "C5'" H2 SING N N 34 XM7 C22 H9 SING N N 35 XM7 C22 H10 SING N N 36 XM7 C22 H11 SING N N 37 XM7 N6 H61 SING N N 38 XM7 N6 H62 SING N N 39 XM7 "O3'" "HO3'" SING N N 40 XM7 "O2'" "HO2'" SING N N 41 XM7 OP2 HOP2 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 XM7 SMILES ACDLabs 12.01 "c1nc3c(c(n1)N)ncn3C2C(C(C(O2)COP(OC)(O)=O)O)O" XM7 InChI InChI 1.03 "InChI=1S/C11H16N5O7P/c1-21-24(19,20)22-2-5-7(17)8(18)11(23-5)16-4-15-6-9(12)13-3-14-10(6)16/h3-5,7-8,11,17-18H,2H2,1H3,(H,19,20)(H2,12,13,14)/t5-,7-,8-,11-/m1/s1" XM7 InChIKey InChI 1.03 OYQVPLDFZZKUTQ-IOSLPCCCSA-N XM7 SMILES_CANONICAL CACTVS 3.385 "CO[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23" XM7 SMILES CACTVS 3.385 "CO[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23" XM7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" XM7 SMILES "OpenEye OEToolkits" 2.0.7 "COP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)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 XM7 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-hydroxy(methoxy)phosphoryl]adenosine" XM7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl methyl hydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XM7 "Create component" 2020-12-18 RCSB XM7 "Initial release" 2020-12-30 RCSB ##