data_VPL # _chem_comp.id VPL _chem_comp.name "(2~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxane-2-carboxamide" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C7 H13 N O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-03-24 _chem_comp.pdbx_modified_date 2023-09-08 _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 191.182 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VPL _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 8OJK _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 VPL C7 C1 C 0 1 N N N 22.884 38.573 34.998 -2.389 0.675 -0.080 C7 VPL 1 VPL "C5'" C2 C 0 1 N N R 24.957 40.529 32.682 1.270 0.526 0.505 "C5'" VPL 2 VPL "C4'" C3 C 0 1 N N R 24.303 40.255 31.310 1.554 -0.914 0.069 "C4'" VPL 3 VPL "C3'" C4 C 0 1 N N R 23.833 38.804 31.267 0.434 -1.825 0.581 "C3'" VPL 4 VPL "C2'" C5 C 0 1 N N N 22.942 38.453 32.464 -0.908 -1.311 0.051 "C2'" VPL 5 VPL "C1'" C6 C 0 1 N N R 23.689 38.829 33.751 -1.098 0.144 0.488 "C1'" VPL 6 VPL "O5'" O1 O 0 1 N N N 23.999 40.223 33.706 -0.006 0.930 0.005 "O5'" VPL 7 VPL "C6'" C7 C 0 1 N N N 25.394 41.964 32.899 2.353 1.451 -0.053 "C6'" VPL 8 VPL "O6'" O2 O 0 1 N N N 26.290 42.017 34.025 2.153 2.775 0.448 "O6'" VPL 9 VPL "O4'" O3 O 0 1 N N N 23.152 41.057 31.102 1.610 -0.979 -1.357 "O4'" VPL 10 VPL "O3'" O4 O 0 1 N N N 23.121 38.535 30.070 0.653 -3.158 0.116 "O3'" VPL 11 VPL N1 N1 N 0 1 N N N 22.609 37.179 35.306 -3.565 0.150 0.317 N1 VPL 12 VPL O7 O5 O 0 1 N N N 22.449 39.439 35.730 -2.370 1.578 -0.889 O7 VPL 13 VPL H1 H1 H 0 1 N N N 25.834 39.874 32.785 1.269 0.583 1.594 H1 VPL 14 VPL H2 H2 H 0 1 N N N 25.046 40.422 30.516 2.507 -1.239 0.486 H2 VPL 15 VPL H3 H3 H 0 1 N N N 24.724 38.160 31.312 0.424 -1.814 1.671 H3 VPL 16 VPL H4 H4 H 0 1 N N N 21.999 39.017 32.403 -0.916 -1.369 -1.038 H4 VPL 17 VPL H5 H5 H 0 1 N N N 22.725 37.375 32.462 -1.717 -1.921 0.455 H5 VPL 18 VPL H6 H6 H 0 1 N N N 24.617 38.240 33.800 -1.130 0.196 1.576 H6 VPL 19 VPL H7 H7 H 0 1 N N N 25.910 42.332 32.000 3.334 1.090 0.256 H7 VPL 20 VPL H8 H8 H 0 1 N N N 24.513 42.591 33.099 2.296 1.462 -1.141 H8 VPL 21 VPL H9 H9 H 0 1 N N N 26.568 42.914 34.167 2.805 3.417 0.134 H9 VPL 22 VPL H10 H10 H 0 1 N N N 23.397 41.975 31.121 1.788 -1.864 -1.704 H10 VPL 23 VPL H11 H11 H 0 1 N N N 22.839 37.628 30.066 -0.021 -3.790 0.404 H11 VPL 24 VPL H12 H12 H 0 1 N N N 22.067 36.943 36.113 -4.397 0.494 -0.045 H12 VPL 25 VPL H13 H13 H 0 1 N N N 22.962 36.457 34.711 -3.580 -0.572 0.964 H13 VPL 26 # 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 VPL "O3'" "C3'" SING N N 1 VPL "O4'" "C4'" SING N N 2 VPL "C3'" "C4'" SING N N 3 VPL "C3'" "C2'" SING N N 4 VPL "C4'" "C5'" SING N N 5 VPL "C2'" "C1'" SING N N 6 VPL "C5'" "C6'" SING N N 7 VPL "C5'" "O5'" SING N N 8 VPL "C6'" "O6'" SING N N 9 VPL "O5'" "C1'" SING N N 10 VPL "C1'" C7 SING N N 11 VPL C7 N1 SING N N 12 VPL C7 O7 DOUB N N 13 VPL "C5'" H1 SING N N 14 VPL "C4'" H2 SING N N 15 VPL "C3'" H3 SING N N 16 VPL "C2'" H4 SING N N 17 VPL "C2'" H5 SING N N 18 VPL "C1'" H6 SING N N 19 VPL "C6'" H7 SING N N 20 VPL "C6'" H8 SING N N 21 VPL "O6'" H9 SING N N 22 VPL "O4'" H10 SING N N 23 VPL "O3'" H11 SING N N 24 VPL N1 H12 SING N N 25 VPL N1 H13 SING N N 26 # 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 VPL InChI InChI 1.06 "InChI=1S/C7H13NO5/c8-7(12)4-1-3(10)6(11)5(2-9)13-4/h3-6,9-11H,1-2H2,(H2,8,12)/t3-,4-,5-,6-/m1/s1" VPL InChIKey InChI 1.06 XSQZVCXBAGPICS-KVTDHHQDSA-N VPL SMILES_CANONICAL CACTVS 3.385 "NC(=O)[C@H]1C[C@@H](O)[C@@H](O)[C@@H](CO)O1" VPL SMILES CACTVS 3.385 "NC(=O)[CH]1C[CH](O)[CH](O)[CH](CO)O1" VPL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@H]([C@H]([C@H](O[C@H]1C(=O)N)CO)O)O" VPL SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(C(OC1C(=O)N)CO)O)O" # _pdbx_chem_comp_identifier.comp_id VPL _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(2~{R},4~{R},5~{R},6~{R})-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxane-2-carboxamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VPL "Create component" 2023-03-24 PDBE VPL "Initial release" 2023-09-13 RCSB #