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 
# 
