data_VBL
# 
_chem_comp.id                                    VBL 
_chem_comp.name                                  "(2~{S},3~{R})-2-pentyloctane-1,3-diol" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H28 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-09-11 
_chem_comp.pdbx_modified_date                    2025-02-07 
_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                        216.360 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VBL 
_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        8QHF 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              Y 
# 
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 
VBL C3  C1  C 0 1 N N S N N N 23.072 39.485 17.139 0.663  -0.209 -0.257 C3  VBL 1  
VBL C4  C2  C 0 1 N N R N N N 24.221 40.566 17.204 -0.572 0.638  0.056  C4  VBL 2  
VBL C5  C3  C 0 1 N N N N N N 24.121 41.395 18.499 -1.835 -0.169 -0.250 C5  VBL 3  
VBL C6  C4  C 0 1 N N N N N N 25.251 42.429 18.623 -3.066 0.718  -0.056 C6  VBL 4  
VBL C7  C5  C 0 1 N N N N N N 25.708 42.637 20.082 -4.330 -0.089 -0.363 C7  VBL 5  
VBL C8  C6  C 0 1 N N N N N N 26.933 43.565 20.199 -5.561 0.798  -0.168 C8  VBL 6  
VBL C9  C7  C 0 1 N N N N N N 26.890 44.812 19.310 -6.824 -0.009 -0.475 C9  VBL 7  
VBL C1  C8  C 0 1 N N N N N N 20.622 39.114 17.888 3.159  -0.200 -0.381 C1  VBL 8  
VBL C2  C9  C 0 1 N N N N N N 21.628 40.083 17.219 1.926  0.598  0.049  C2  VBL 9  
VBL C10 C10 C 0 1 N N N N N N 23.228 38.471 15.948 0.645  -1.474 0.602  C10 VBL 10 
VBL C12 C11 C 0 1 N N N N N N 20.921 39.619 21.263 6.917  0.615  -0.197 C12 VBL 11 
VBL C11 C12 C 0 1 N N N N N N 19.856 39.028 20.337 5.654  -0.192 -0.504 C11 VBL 12 
VBL C   C13 C 0 1 N N N N N N 19.764 39.759 18.986 4.422  0.607  -0.074 C   VBL 13 
VBL O   O1  O 0 1 N N N N N N 25.465 39.891 17.198 -0.562 1.001  1.439  O   VBL 14 
VBL O1  O2  O 0 1 N N N N N N 22.945 37.121 16.480 -0.472 -2.285 0.233  O1  VBL 15 
VBL H1  H1  H 0 1 N N N N N N 23.190 38.882 18.052 0.656  -0.485 -1.312 H1  VBL 16 
VBL H2  H2  H 0 1 N N N N N N 24.129 41.235 16.336 -0.559 1.540  -0.556 H2  VBL 17 
VBL H3  H3  H 0 1 N N N N N N 23.156 41.924 18.506 -1.800 -0.521 -1.282 H3  VBL 18 
VBL H4  H4  H 0 1 N N N N N N 24.171 40.712 19.360 -1.893 -1.023 0.423  H4  VBL 19 
VBL H5  H5  H 0 1 N N N N N N 26.111 42.084 18.030 -3.102 1.070  0.975  H5  VBL 20 
VBL H6  H6  H 0 1 N N N N N N 24.894 43.390 18.225 -3.009 1.573  -0.730 H6  VBL 21 
VBL H7  H7  H 0 1 N N N N N N 24.877 43.079 20.651 -4.294 -0.441 -1.394 H7  VBL 22 
VBL H8  H8  H 0 1 N N N N N N 25.967 41.658 20.512 -4.387 -0.944 0.311  H8  VBL 23 
VBL H9  H9  H 0 1 N N N N N N 27.827 42.984 19.929 -5.596 1.150  0.863  H9  VBL 24 
VBL H10 H10 H 0 1 N N N N N N 27.012 43.895 21.245 -5.503 1.653  -0.842 H10 VBL 25 
VBL H11 H11 H 0 1 N N N N N N 27.803 45.405 19.465 -7.702 0.623  -0.336 H11 VBL 26 
VBL H12 H12 H 0 1 N N N N N N 26.826 44.508 18.255 -6.789 -0.361 -1.506 H12 VBL 27 
VBL H13 H13 H 0 1 N N N N N N 26.010 45.418 19.571 -6.882 -0.864 0.199  H13 VBL 28 
VBL H14 H14 H 0 1 N N N N N N 19.950 38.723 17.110 3.189  -1.144 0.165  H14 VBL 29 
VBL H15 H15 H 0 1 N N N N N N 21.188 38.284 18.335 3.107  -0.401 -1.451 H15 VBL 30 
VBL H16 H16 H 0 1 N N N N N N 21.663 41.014 17.804 1.896  1.542  -0.496 H16 VBL 31 
VBL H17 H17 H 0 1 N N N N N N 21.280 40.304 16.199 1.979  0.799  1.120  H17 VBL 32 
VBL H18 H18 H 0 1 N N N N N N 24.253 38.512 15.551 1.567  -2.034 0.444  H18 VBL 33 
VBL H19 H19 H 0 1 N N N N N N 22.515 38.717 15.148 0.563  -1.199 1.653  H19 VBL 34 
VBL H20 H20 H 0 1 N N N N N N 20.939 39.057 22.208 7.795  0.046  -0.503 H20 VBL 35 
VBL H21 H21 H 0 1 N N N N N N 21.906 39.552 20.778 6.887  1.559  -0.742 H21 VBL 36 
VBL H22 H22 H 0 1 N N N N N N 20.684 40.673 21.468 6.969  0.815  0.873  H22 VBL 37 
VBL H23 H23 H 0 1 N N N N N N 18.879 39.094 20.839 5.602  -0.392 -1.574 H23 VBL 38 
VBL H24 H24 H 0 1 N N N N N N 20.101 37.972 20.149 5.684  -1.135 0.042  H24 VBL 39 
VBL H25 H25 H 0 1 N N N N N N 20.099 40.797 19.127 4.392  1.550  -0.619 H25 VBL 40 
VBL H26 H26 H 0 1 N N N N N N 18.714 39.754 18.657 4.474  0.807  0.997  H26 VBL 41 
VBL H27 H27 H 0 1 N N N N N N 26.171 40.526 17.237 -0.572 0.246  2.043  H27 VBL 42 
VBL H28 H28 H 0 1 N N N N N N 23.031 36.481 15.783 -0.547 -3.106 0.738  H28 VBL 43 
# 
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 
VBL C10 O1  SING N N 1  
VBL C10 C3  SING N N 2  
VBL C3  C4  SING N N 3  
VBL C3  C2  SING N N 4  
VBL O   C4  SING N N 5  
VBL C4  C5  SING N N 6  
VBL C2  C1  SING N N 7  
VBL C1  C   SING N N 8  
VBL C5  C6  SING N N 9  
VBL C6  C7  SING N N 10 
VBL C   C11 SING N N 11 
VBL C9  C8  SING N N 12 
VBL C7  C8  SING N N 13 
VBL C11 C12 SING N N 14 
VBL C3  H1  SING N N 15 
VBL C4  H2  SING N N 16 
VBL C5  H3  SING N N 17 
VBL C5  H4  SING N N 18 
VBL C6  H5  SING N N 19 
VBL C6  H6  SING N N 20 
VBL C7  H7  SING N N 21 
VBL C7  H8  SING N N 22 
VBL C8  H9  SING N N 23 
VBL C8  H10 SING N N 24 
VBL C9  H11 SING N N 25 
VBL C9  H12 SING N N 26 
VBL C9  H13 SING N N 27 
VBL C1  H14 SING N N 28 
VBL C1  H15 SING N N 29 
VBL C2  H16 SING N N 30 
VBL C2  H17 SING N N 31 
VBL C10 H18 SING N N 32 
VBL C10 H19 SING N N 33 
VBL C12 H20 SING N N 34 
VBL C12 H21 SING N N 35 
VBL C12 H22 SING N N 36 
VBL C11 H23 SING N N 37 
VBL C11 H24 SING N N 38 
VBL C   H25 SING N N 39 
VBL C   H26 SING N N 40 
VBL O   H27 SING N N 41 
VBL O1  H28 SING N N 42 
# 
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 
VBL InChI            InChI                1.06  "InChI=1S/C13H28O2/c1-3-5-7-9-12(11-14)13(15)10-8-6-4-2/h12-15H,3-11H2,1-2H3/t12-,13+/m0/s1" 
VBL InChIKey         InChI                1.06  BPTAAAKIMVUYQK-QWHCGFSZSA-N                                                                  
VBL SMILES_CANONICAL CACTVS               3.385 "CCCCC[C@@H](O)[C@H](CO)CCCCC"                                                               
VBL SMILES           CACTVS               3.385 "CCCCC[CH](O)[CH](CO)CCCCC"                                                                  
VBL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCCC[C@@H](CO)[C@@H](CCCCC)O"                                                              
VBL SMILES           "OpenEye OEToolkits" 2.0.7 "CCCCCC(CO)C(CCCCC)O"                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           VBL 
_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})-2-pentyloctane-1,3-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 
VBL "Create component" 2023-09-11 PDBE 
VBL "Modify PCM"       2024-09-27 PDBE 
VBL "Initial release"  2025-02-12 RCSB 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            VBL 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           Lipid/lipid-like 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C10 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
