data_DYD
#
_chem_comp.id DYD
_chem_comp.name (2S,5S)-hexane-2,5-diol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H14 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-11-15
_chem_comp.pdbx_modified_date 2018-01-19
_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 118.174
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DYD
_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 6BMM
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
DYD C01 C1 C 0 1 N N N N N N -17.877 -13.881 -29.958 -3.052 0.782 -0.431 C01 DYD 1
DYD C02 C2 C 0 1 N N S N N N -16.465 -14.158 -30.466 -1.911 -0.230 -0.305 C02 DYD 2
DYD C03 C3 C 0 1 N N N N N N -15.764 -15.251 -29.662 -0.572 0.508 -0.305 C03 DYD 3
DYD C04 C4 C 0 1 N N N N N N -14.328 -15.471 -30.126 0.572 -0.509 -0.304 C04 DYD 4
DYD C05 C5 C 0 1 N N S N N N -13.500 -16.261 -29.117 1.911 0.230 -0.305 C05 DYD 5
DYD C06 C6 C 0 1 N N N N N N -12.005 -15.994 -29.272 3.052 -0.783 -0.430 C06 DYD 6
DYD O07 O1 O 0 1 N N N N N N -13.725 -17.626 -29.336 2.054 0.960 0.915 O07 DYD 7
DYD O08 O2 O 0 1 N N N N N N -16.553 -14.582 -31.798 -2.054 -0.958 0.917 O08 DYD 8
DYD H1 H1 H 0 1 N N N N N N -17.832 -13.546 -28.911 -4.006 0.256 -0.431 H1 DYD 9
DYD H2 H2 H 0 1 N N N N N N -18.341 -13.097 -30.574 -3.018 1.474 0.410 H2 DYD 10
DYD H3 H3 H 0 1 N N N N N N -18.477 -14.801 -30.023 -2.943 1.337 -1.363 H3 DYD 11
DYD H4 H4 H 0 1 N N N N N N -15.875 -13.232 -30.394 -1.945 -0.923 -1.146 H4 DYD 12
DYD H5 H5 H 0 1 N N N N N N -15.754 -14.960 -28.601 -0.501 1.133 -1.196 H5 DYD 13
DYD H6 H6 H 0 1 N N N N N N -16.323 -16.191 -29.779 -0.501 1.135 0.584 H6 DYD 14
DYD H7 H7 H 0 1 N N N N N N -14.346 -16.024 -31.077 0.501 -1.133 0.586 H7 DYD 15
DYD H8 H8 H 0 1 N N N N N N -13.854 -14.491 -30.281 0.501 -1.135 -1.194 H8 DYD 16
DYD H9 H9 H 0 1 N N N N N N -13.809 -15.975 -28.101 1.945 0.920 -1.148 H9 DYD 17
DYD H10 H10 H 0 1 N N N N N N -11.448 -16.582 -28.528 2.943 -1.339 -1.361 H10 DYD 18
DYD H11 H11 H 0 1 N N N N N N -11.684 -16.284 -30.283 4.006 -0.257 -0.430 H11 DYD 19
DYD H12 H12 H 0 1 N N N N N N -11.806 -14.923 -29.117 3.018 -1.474 0.413 H12 DYD 20
DYD H13 H13 H 0 1 N N N N N N -13.216 -18.135 -28.715 2.882 1.453 0.984 H13 DYD 21
DYD H14 H14 H 0 1 N N N N N N -15.682 -14.760 -32.132 -2.882 -1.451 0.987 H14 DYD 22
#
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
DYD O08 C02 SING N N 1
DYD C02 C01 SING N N 2
DYD C02 C03 SING N N 3
DYD C04 C03 SING N N 4
DYD C04 C05 SING N N 5
DYD O07 C05 SING N N 6
DYD C06 C05 SING N N 7
DYD C01 H1 SING N N 8
DYD C01 H2 SING N N 9
DYD C01 H3 SING N N 10
DYD C02 H4 SING N N 11
DYD C03 H5 SING N N 12
DYD C03 H6 SING N N 13
DYD C04 H7 SING N N 14
DYD C04 H8 SING N N 15
DYD C05 H9 SING N N 16
DYD C06 H10 SING N N 17
DYD C06 H11 SING N N 18
DYD C06 H12 SING N N 19
DYD O07 H13 SING N N 20
DYD O08 H14 SING N N 21
#
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
DYD SMILES ACDLabs 12.01 CC(CCC(C)O)O
DYD InChI InChI 1.03 InChI=1S/C6H14O2/c1-5(7)3-4-6(2)8/h5-8H,3-4H2,1-2H3/t5-,6-/m0/s1
DYD InChIKey InChI 1.03 OHMBHFSEKCCCBW-WDSKDSINSA-N
DYD SMILES_CANONICAL CACTVS 3.385 C[C@H](O)CC[C@H](C)O
DYD SMILES CACTVS 3.385 C[CH](O)CC[CH](C)O
DYD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C[C@@H](CC[C@H](C)O)O
DYD SMILES "OpenEye OEToolkits" 2.0.6 CC(CCC(C)O)O
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
DYD "SYSTEMATIC NAME" ACDLabs 12.01 (2S,5S)-hexane-2,5-diol
DYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 (2~{S},5~{S})-hexane-2,5-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
DYD 'Create component' 2017-11-15 RCSB
DYD 'Initial release' 2018-01-24 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
DYD C01 C 10.301 -0.375 1
DYD C02 C 9.002 0.375 2
DYD C03 C 7.702 -0.375 3
DYD C04 C 6.404 0.375 4
DYD C05 C 5.104 -0.375 5
DYD C06 C 5.104 -1.875 6
DYD O07 O 3.805 0.375 7
DYD O08 O 9.002 1.875 8
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
DYD O08 C02 SINGLE NONE 1
DYD C02 C01 SINGLE BEGINWEDGE 2
DYD C02 C03 SINGLE NONE 3
DYD C04 C03 SINGLE NONE 4
DYD C04 C05 SINGLE NONE 5
DYD O07 C05 SINGLE NONE 6
DYD C05 C06 SINGLE BEGINDASH 7
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id DYD
_pdbe_chem_comp_rdkit_properties.exactmw 118.099
_pdbe_chem_comp_rdkit_properties.amw 118.176
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 69.995
_pdbe_chem_comp_rdkit_properties.tpsa 40.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.528
_pdbe_chem_comp_rdkit_properties.CrippenMR 32.596
_pdbe_chem_comp_rdkit_properties.chi0v 3.816
_pdbe_chem_comp_rdkit_properties.chi1v 1.658
_pdbe_chem_comp_rdkit_properties.chi2v 0.290
_pdbe_chem_comp_rdkit_properties.chi3v 0.290
_pdbe_chem_comp_rdkit_properties.chi4v 0.114
_pdbe_chem_comp_rdkit_properties.chi0n 17.816
_pdbe_chem_comp_rdkit_properties.chi1n 8.475
_pdbe_chem_comp_rdkit_properties.chi2n 0.290
_pdbe_chem_comp_rdkit_properties.chi3n 0.290
_pdbe_chem_comp_rdkit_properties.chi4n 0.114
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.080
_pdbe_chem_comp_rdkit_properties.kappa1 0.867
_pdbe_chem_comp_rdkit_properties.kappa2 3.866
_pdbe_chem_comp_rdkit_properties.kappa3 5.920
_pdbe_chem_comp_rdkit_properties.Phi 0.419
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
DYD UniChem PDBe DYD
DYD UniChem ZINC ZINC000000388717
DYD UniChem eMolecules 504380
DYD UniChem 'PubChem TPHARMA' 16153778
DYD UniChem ACTor 34338-96-0
DYD UniChem Nikkaji J808.181F
DYD UniChem 'EPA CompTox Dashboard' DTXSID10426191
DYD UniChem BRENDA 194816
DYD UniChem BRENDA 39166
DYD UniChem ChemicalBook CB4390062
DYD UniChem SureChEMBL SCHEMBL789937
DYD UniChem 'PubChem TPHARMA' 16178086
DYD UniChem PubChem 6950288
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
DYD C01 -2.637 0.359 -0.464 ETKDGv3 1
DYD C02 -1.791 -0.164 0.704 ETKDGv3 2
DYD C03 -0.328 0.310 0.616 ETKDGv3 3
DYD C04 0.437 -0.336 -0.557 ETKDGv3 4
DYD C05 1.947 -0.010 -0.583 ETKDGv3 5
DYD C06 2.725 -0.650 0.578 ETKDGv3 6
DYD O07 2.172 1.376 -0.653 ETKDGv3 7
DYD O08 -2.337 0.296 1.913 ETKDGv3 8
DYD H1 -2.306 -0.089 -1.423 ETKDGv3 9
DYD H2 -3.701 0.080 -0.312 ETKDGv3 10
DYD H3 -2.569 1.466 -0.531 ETKDGv3 11
DYD H4 -1.807 -1.279 0.691 ETKDGv3 12
DYD H5 0.171 0.039 1.570 ETKDGv3 13
DYD H6 -0.305 1.417 0.522 ETKDGv3 14
DYD H7 0.309 -1.440 -0.522 ETKDGv3 15
DYD H8 0.001 0.020 -1.514 ETKDGv3 16
DYD H9 2.352 -0.455 -1.518 ETKDGv3 17
DYD H10 2.449 -0.196 1.552 ETKDGv3 18
DYD H11 2.528 -1.742 0.617 ETKDGv3 19
DYD H12 3.814 -0.496 0.422 ETKDGv3 20
DYD H13 2.012 1.760 0.248 ETKDGv3 21
DYD H14 -3.136 -0.263 2.101 ETKDGv3 22
#