data_VNB # _chem_comp.id VNB _chem_comp.name "(2~{R},3~{R},4~{S},5~{R})-2-[(dimethylamino)methyl]-5-(hydroxymethyl)pyrrolidine-3,4-diol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C8 H18 N2 O3" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-08-01 _chem_comp.pdbx_modified_date 2024-04-05 _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 190.240 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VNB _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 8K7J _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 VNB CAA C1 C 0 1 N N N N N N -29.613 16.248 -0.569 3.709 1.153 -0.756 CAA VNB 1 VNB CAB C2 C 0 1 N N R N N N -27.035 18.283 -4.737 -1.480 0.623 -0.521 CAB VNB 2 VNB CAC C3 C 0 1 N N S N N N -28.062 19.236 -4.196 -1.808 -0.891 -0.477 CAC VNB 3 VNB CAD C4 C 0 1 N N R N N N -29.084 18.271 -3.652 -0.398 -1.521 -0.625 CAD VNB 4 VNB CAE C5 C 0 1 N N R N N N -28.191 17.257 -2.932 0.504 -0.541 0.154 CAE VNB 5 VNB CAG C6 C 0 1 N N N N N N -25.704 19.002 -4.887 -2.576 1.426 0.181 CAG VNB 6 VNB CAK C7 C 0 1 N N N N N N -28.790 15.847 -2.862 1.842 -0.377 -0.572 CAK VNB 7 VNB CAM C8 C 0 1 N N N N N N -30.269 14.301 -1.802 3.227 0.079 1.360 CAM VNB 8 VNB NAF N1 N 0 1 N N N N N N -26.945 17.206 -3.735 -0.200 0.753 0.207 NAF VNB 9 VNB NAL N2 N 0 1 N N N N N N -29.921 15.736 -1.920 2.656 0.628 0.123 NAL VNB 10 VNB OAH O1 O 0 1 N N N N N N -27.445 19.969 -3.111 -2.401 -1.249 0.773 OAH VNB 11 VNB OAI O2 O 0 1 N N N N N N -29.971 18.933 -2.749 -0.362 -2.821 -0.032 OAI VNB 12 VNB OAJ O3 O 0 1 N N N N N N -24.774 18.112 -5.524 -2.315 2.823 0.028 OAJ VNB 13 VNB H1 H1 H 0 1 N N N N N N -30.496 16.134 0.077 3.260 1.540 -1.671 H1 VNB 14 VNB H2 H2 H 0 1 N N N N N N -28.773 15.679 -0.144 4.243 1.954 -0.246 H2 VNB 15 VNB H3 H3 H 0 1 N N N N N N -29.340 17.312 -0.633 4.406 0.352 -1.005 H3 VNB 16 VNB H4 H4 H 0 1 N N N N N N -27.360 17.884 -5.709 -1.365 0.956 -1.553 H4 VNB 17 VNB H5 H5 H 0 1 N N N N N N -28.480 19.888 -4.977 -2.452 -1.175 -1.309 H5 VNB 18 VNB H6 H6 H 0 1 N N N N N N -29.629 17.782 -4.473 -0.104 -1.566 -1.673 H6 VNB 19 VNB H7 H7 H 0 1 N N N N N N -27.973 17.615 -1.915 0.674 -0.916 1.163 H7 VNB 20 VNB H8 H8 H 0 1 N N N N N N -25.323 19.289 -3.896 -3.543 1.187 -0.262 H8 VNB 21 VNB H9 H9 H 0 1 N N N N N N -25.837 19.903 -5.504 -2.590 1.173 1.241 H9 VNB 22 VNB H10 H10 H 0 1 N N N N N N -29.144 15.568 -3.866 2.370 -1.330 -0.580 H10 VNB 23 VNB H11 H11 H 0 1 N N N N N N -28.002 15.149 -2.544 1.661 -0.053 -1.597 H11 VNB 24 VNB H12 H12 H 0 1 N N N N N N -31.111 14.184 -1.105 3.859 -0.776 1.120 H12 VNB 25 VNB H13 H13 H 0 1 N N N N N N -30.554 13.911 -2.790 3.825 0.845 1.855 H13 VNB 26 VNB H14 H14 H 0 1 N N N N N N -29.400 13.743 -1.424 2.422 -0.238 2.023 H14 VNB 27 VNB H15 H15 H 0 1 N N N N N N -26.866 16.319 -4.190 0.367 1.489 -0.187 H15 VNB 28 VNB H18 H18 H 0 1 N N N N N N -28.072 20.583 -2.746 -2.624 -2.187 0.848 H18 VNB 29 VNB H19 H19 H 0 1 N N N N N N -30.607 18.311 -2.416 -0.970 -3.455 -0.437 H19 VNB 30 VNB H20 H20 H 0 1 N N N N N N -23.936 18.548 -5.625 -2.972 3.394 0.449 H20 VNB 31 # 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 VNB OAJ CAG SING N N 1 VNB CAG CAB SING N N 2 VNB CAB CAC SING N N 3 VNB CAB NAF SING N N 4 VNB CAC CAD SING N N 5 VNB CAC OAH SING N N 6 VNB NAF CAE SING N N 7 VNB CAD CAE SING N N 8 VNB CAD OAI SING N N 9 VNB CAE CAK SING N N 10 VNB CAK NAL SING N N 11 VNB NAL CAM SING N N 12 VNB NAL CAA SING N N 13 VNB CAA H1 SING N N 14 VNB CAA H2 SING N N 15 VNB CAA H3 SING N N 16 VNB CAB H4 SING N N 17 VNB CAC H5 SING N N 18 VNB CAD H6 SING N N 19 VNB CAE H7 SING N N 20 VNB CAG H8 SING N N 21 VNB CAG H9 SING N N 22 VNB CAK H10 SING N N 23 VNB CAK H11 SING N N 24 VNB CAM H12 SING N N 25 VNB CAM H13 SING N N 26 VNB CAM H14 SING N N 27 VNB NAF H15 SING N N 28 VNB OAH H18 SING N N 29 VNB OAI H19 SING N N 30 VNB OAJ H20 SING N N 31 # 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 VNB InChI InChI 1.06 "InChI=1S/C8H18N2O3/c1-10(2)3-5-7(12)8(13)6(4-11)9-5/h5-9,11-13H,3-4H2,1-2H3/t5-,6-,7-,8+/m1/s1" VNB InChIKey InChI 1.06 UTJUIABWRUKQDR-XUTVFYLZSA-N VNB SMILES_CANONICAL CACTVS 3.385 "CN(C)C[C@H]1N[C@H](CO)[C@H](O)[C@@H]1O" VNB SMILES CACTVS 3.385 "CN(C)C[CH]1N[CH](CO)[CH](O)[CH]1O" VNB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN(C)C[C@@H]1[C@H]([C@H]([C@H](N1)CO)O)O" VNB SMILES "OpenEye OEToolkits" 2.0.7 "CN(C)CC1C(C(C(N1)CO)O)O" # _pdbx_chem_comp_identifier.comp_id VNB _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},3~{R},4~{S},5~{R})-2-[(dimethylamino)methyl]-5-(hydroxymethyl)pyrrolidine-3,4-diol" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site VNB "Create component" 2023-08-01 PDBJ VNB "Initial release" 2024-04-10 RCSB #