data_VDF
# 
_chem_comp.id                                    VDF 
_chem_comp.name                                  2-O-phosphono-beta-L-arabinopyranose 
_chem_comp.type                                  "L-saccharide, beta linking" 
_chem_comp.pdbx_type                             ATOMS 
_chem_comp.formula                               "C5 H11 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ARB 
_chem_comp.pdbx_synonyms                         "2-O-phosphono-beta-L-arabinose; 2-O-phosphono-L-arabinose; 2-O-phosphono-arabinose; [(2S,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-03-01 
_chem_comp.pdbx_modified_date                    2024-01-19 
_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                        230.110 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VDF 
_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        8CH2 
_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.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 
VDF OP2 O1  O 0 1 N N N N N N 15.236 -2.563 -13.927 2.414  -1.668 0.777  OP2 VDF 1  
VDF P   P1  P 0 1 N N N N N N 14.168 -2.532 -14.990 2.237  -0.325 -0.093 P   VDF 2  
VDF OP1 O2  O 0 1 N N N N N N 13.468 -3.759 -15.332 2.788  0.826  0.657  OP1 VDF 3  
VDF OP3 O3  O 0 1 N Y N N N N 13.318 -1.373 -14.410 3.023  -0.482 -1.489 OP3 VDF 4  
VDF O2  O4  O 0 1 N N N N N N 14.939 -1.972 -16.287 0.673  -0.076 -0.383 O2  VDF 5  
VDF C2  C1  C 0 1 N N R N N N 15.779 -0.892 -16.314 -0.275 0.206  0.648  C2  VDF 6  
VDF C3  C2  C 0 1 N N S N N N 15.008 0.340  -16.873 -1.361 -0.874 0.655  C3  VDF 7  
VDF O3  O5  O 0 1 N N N N N N 14.110 0.843  -15.845 -2.273 -0.628 1.727  O3  VDF 8  
VDF C4  C3  C 0 1 N N S N N N 15.963 1.496  -17.278 -2.115 -0.833 -0.678 C4  VDF 9  
VDF O4  O6  O 0 1 N N N N N N 16.599 1.915  -16.136 -3.178 -1.788 -0.655 O4  VDF 10 
VDF C5  C4  C 0 1 N N N N N N 17.023 0.984  -18.205 -2.692 0.570  -0.886 C5  VDF 11 
VDF O5  O7  O 0 1 N N N N N N 17.705 -0.136 -17.624 -1.633 1.529  -0.851 O5  VDF 12 
VDF C1  C5  C 0 1 N N S N N N 16.883 -1.276 -17.333 -0.922 1.570  0.389  C1  VDF 13 
VDF O1  O8  O 0 1 N Y N N N N 16.351 -1.902 -18.437 0.091  2.575  0.325  O1  VDF 14 
VDF H1A H1  H 0 1 N N N N N N 15.323 -3.447 -13.590 2.073  -2.463 0.346  H1A VDF 15 
VDF H2A H2  H 0 1 N Y N N N N 12.409 -1.643 -14.357 3.973  -0.635 -1.390 H2A VDF 16 
VDF H2  H3  H 0 1 N N N N N N 16.222 -0.657 -15.335 0.231  0.221  1.614  H2  VDF 17 
VDF H3  H4  H 0 1 N N N N N N 14.434 0.027  -17.758 -0.900 -1.853 0.785  H3  VDF 18 
VDF HO3 H5  H 0 1 N Y N N N N 13.514 0.153  -15.579 -2.989 -1.276 1.791  HO3 VDF 19 
VDF H4  H6  H 0 1 N N N N N N 15.388 2.301  -17.758 -1.429 -1.070 -1.492 H4  VDF 20 
VDF HO4 H7  H 0 1 N Y N N N N 15.957 2.248  -15.520 -3.698 -1.816 -1.469 HO4 VDF 21 
VDF H51 H8  H 0 1 N N N N N N 17.749 1.787  -18.402 -3.193 0.617  -1.853 H51 VDF 22 
VDF H52 H9  H 0 1 N N N N N N 16.556 0.672  -19.151 -3.408 0.789  -0.094 H52 VDF 23 
VDF H1  H10 H 0 1 N N N N N N 17.522 -2.005 -16.814 -1.615 1.803  1.198  H1  VDF 24 
VDF HO1 H11 H 0 1 N Y N N N N 15.823 -2.641 -18.159 -0.249 3.466  0.162  HO1 VDF 25 
# 
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 
VDF O1  C1  SING N N 1  
VDF C5  O5  SING N N 2  
VDF C5  C4  SING N N 3  
VDF O5  C1  SING N N 4  
VDF C1  C2  SING N N 5  
VDF C4  C3  SING N N 6  
VDF C4  O4  SING N N 7  
VDF C3  C2  SING N N 8  
VDF C3  O3  SING N N 9  
VDF C2  O2  SING N N 10 
VDF O2  P   SING N N 11 
VDF OP1 P   DOUB N N 12 
VDF P   OP3 SING N N 13 
VDF P   OP2 SING N N 14 
VDF OP2 H1A SING N N 15 
VDF OP3 H2A SING N N 16 
VDF C2  H2  SING N N 17 
VDF C3  H3  SING N N 18 
VDF O3  HO3 SING N N 19 
VDF C4  H4  SING N N 20 
VDF O4  HO4 SING N N 21 
VDF C5  H51 SING N N 22 
VDF C5  H52 SING N N 23 
VDF C1  H1  SING N N 24 
VDF O1  HO1 SING N N 25 
# 
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 
VDF InChI            InChI                1.06  "InChI=1S/C5H11O8P/c6-2-1-12-5(8)4(3(2)7)13-14(9,10)11/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4+,5-/m0/s1" 
VDF InChIKey         InChI                1.06  QIAIUTJEZJIPSH-KLVWXMOXSA-N                                                                       
VDF SMILES_CANONICAL CACTVS               3.385 "O[C@H]1CO[C@H](O)[C@H](O[P](O)(O)=O)[C@H]1O"                                                     
VDF SMILES           CACTVS               3.385 "O[CH]1CO[CH](O)[CH](O[P](O)(O)=O)[CH]1O"                                                         
VDF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@@H]([C@H]([C@H](O1)O)OP(=O)(O)O)O)O"                                                 
VDF SMILES           "OpenEye OEToolkits" 2.0.7 "C1C(C(C(C(O1)O)OP(=O)(O)O)O)O"                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           VDF 
_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~{S},3~{R},4~{S},5~{S})-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_feature.comp_id 
_pdbx_chem_comp_feature.type 
_pdbx_chem_comp_feature.value 
_pdbx_chem_comp_feature.source 
_pdbx_chem_comp_feature.support 
VDF "CARBOHYDRATE ISOMER"                 L        PDB ? 
VDF "CARBOHYDRATE RING"                   pyranose PDB ? 
VDF "CARBOHYDRATE ANOMER"                 beta     PDB ? 
VDF "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose   PDB ? 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 VDF 2-O-phosphono-beta-L-arabinose                                       PDB ? 
2 VDF 2-O-phosphono-L-arabinose                                            PDB ? 
3 VDF 2-O-phosphono-arabinose                                              PDB ? 
4 VDF "[(2S,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl] dihydrogen phosphate" PDB ? 
# 
_pdbx_chem_comp_related.comp_id             VDF 
_pdbx_chem_comp_related.related_comp_id     ARB 
_pdbx_chem_comp_related.relationship_type   "Carbohydrate core" 
_pdbx_chem_comp_related.details             ? 
# 
loop_
_pdbx_chem_comp_atom_related.ordinal 
_pdbx_chem_comp_atom_related.comp_id 
_pdbx_chem_comp_atom_related.atom_id 
_pdbx_chem_comp_atom_related.related_comp_id 
_pdbx_chem_comp_atom_related.related_atom_id 
_pdbx_chem_comp_atom_related.related_type 
1  VDF O2  ARB O2  "Carbohydrate core" 
2  VDF C2  ARB C2  "Carbohydrate core" 
3  VDF C3  ARB C3  "Carbohydrate core" 
4  VDF O3  ARB O3  "Carbohydrate core" 
5  VDF C4  ARB C4  "Carbohydrate core" 
6  VDF O4  ARB O4  "Carbohydrate core" 
7  VDF C5  ARB C5  "Carbohydrate core" 
8  VDF O5  ARB O5  "Carbohydrate core" 
9  VDF C1  ARB C1  "Carbohydrate core" 
10 VDF O1  ARB O1  "Carbohydrate core" 
11 VDF H2  ARB H2  "Carbohydrate core" 
12 VDF H3  ARB H3  "Carbohydrate core" 
13 VDF HO3 ARB HO3 "Carbohydrate core" 
14 VDF H4  ARB H4  "Carbohydrate core" 
15 VDF HO4 ARB HO4 "Carbohydrate core" 
16 VDF H51 ARB H51 "Carbohydrate core" 
17 VDF H52 ARB H52 "Carbohydrate core" 
18 VDF H1  ARB H1  "Carbohydrate core" 
19 VDF HO1 ARB HO1 "Carbohydrate core" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VDF "Create component"     2023-03-01 PDBE 
VDF "Modify internal type" 2023-05-17 PDBE 
VDF "Initial release"      2024-01-24 RCSB 
# 
