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 
# 
