data_X9X
#
_chem_comp.id X9X
_chem_comp.name D-allitol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H14 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-10-30
_chem_comp.pdbx_modified_date 2014-11-07
_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 182.172
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code X9X
_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 4WT7
_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
X9X OAA O1 O 0 1 N N N N N N 0.707 15.999 10.119 4.296 0.145 -0.248 OAA X9X 1
X9X CAG C1 C 0 1 N N N N N N 1.279 15.794 11.366 3.079 0.578 0.364 CAG X9X 2
X9X CAI C2 C 0 1 N N R N N N 2.632 15.174 11.371 1.900 -0.175 -0.255 CAI X9X 3
X9X OAC O2 O 0 1 N N N N N N 2.494 14.008 10.646 2.006 -1.565 0.058 OAC X9X 4
X9X CAK C3 C 0 1 N N R N N N 3.634 16.120 10.751 0.590 0.377 0.309 CAK X9X 5
X9X OAE O3 O 0 1 N N N N N N 3.659 17.328 11.469 0.484 1.767 -0.004 OAE X9X 6
X9X CAL C4 C 0 1 N N S N N N 5.013 15.571 10.816 -0.590 -0.377 -0.309 CAL X9X 7
X9X OAF O4 O 0 1 N N N N N N 5.190 15.140 12.128 -0.484 -1.767 0.004 OAF X9X 8
X9X CAJ C5 C 0 1 N N S N N N 5.406 14.500 9.799 -1.900 0.175 0.255 CAJ X9X 9
X9X OAD O5 O 0 1 N N N N N N 4.993 13.245 10.179 -2.006 1.565 -0.058 OAD X9X 10
X9X CAH C6 C 0 1 N N N N N N 4.902 14.622 8.394 -3.079 -0.578 -0.364 CAH X9X 11
X9X OAB O6 O 0 1 N N N N N N 5.623 13.868 7.462 -4.296 -0.145 0.248 OAB X9X 12
X9X H1 H1 H 0 1 N N N N N N -0.149 16.396 10.224 5.087 0.581 0.096 H1 X9X 13
X9X H2 H2 H 0 1 N N N N N N 1.355 16.771 11.866 3.118 0.376 1.434 H2 X9X 14
X9X H3 H3 H 0 1 N N N N N N 0.607 15.139 11.941 2.952 1.649 0.201 H3 X9X 15
X9X H4 H4 H 0 1 N N N N N N 2.932 14.960 12.407 1.913 -0.044 -1.337 H4 X9X 16
X9X H5 H5 H 0 1 N N N N N N 1.857 13.445 11.070 2.001 -1.756 1.006 H5 X9X 17
X9X H6 H6 H 0 1 N N N N N N 3.359 16.299 9.701 0.576 0.246 1.391 H6 X9X 18
X9X H7 H7 H 0 1 N N N N N N 2.795 17.722 11.457 0.489 1.958 -0.952 H7 X9X 19
X9X H8 H8 H 0 1 N N N N N N 5.695 16.417 10.647 -0.576 -0.246 -1.391 H8 X9X 20
X9X H9 H9 H 0 1 N N N N N N 4.935 15.832 12.726 -0.489 -1.958 0.952 H9 X9X 21
X9X H10 H10 H 0 1 N N N N N N 6.505 14.505 9.747 -1.913 0.044 1.337 H10 X9X 22
X9X H11 H11 H 0 1 N N N N N N 5.272 13.076 11.071 -2.001 1.756 -1.006 H11 X9X 23
X9X H12 H12 H 0 1 N N N N N N 4.956 15.680 8.098 -3.118 -0.376 -1.434 H12 X9X 24
X9X H13 H13 H 0 1 N N N N N N 3.854 14.288 8.372 -2.952 -1.649 -0.201 H13 X9X 25
X9X H14 H14 H 0 1 N N N N N N 5.250 13.992 6.597 -5.087 -0.581 -0.096 H14 X9X 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
X9X OAB CAH SING N N 1
X9X CAH CAJ SING N N 2
X9X CAJ OAD SING N N 3
X9X CAJ CAL SING N N 4
X9X OAA CAG SING N N 5
X9X OAC CAI SING N N 6
X9X CAK CAL SING N N 7
X9X CAK CAI SING N N 8
X9X CAK OAE SING N N 9
X9X CAL OAF SING N N 10
X9X CAG CAI SING N N 11
X9X OAA H1 SING N N 12
X9X CAG H2 SING N N 13
X9X CAG H3 SING N N 14
X9X CAI H4 SING N N 15
X9X OAC H5 SING N N 16
X9X CAK H6 SING N N 17
X9X OAE H7 SING N N 18
X9X CAL H8 SING N N 19
X9X OAF H9 SING N N 20
X9X CAJ H10 SING N N 21
X9X OAD H11 SING N N 22
X9X CAH H12 SING N N 23
X9X CAH H13 SING N N 24
X9X OAB H14 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
X9X SMILES ACDLabs 12.01 OC(C(O)CO)C(O)C(O)CO
X9X InChI InChI 1.03 InChI=1S/C6H14O6/c7-1-3(9)5(11)6(12)4(10)2-8/h3-12H,1-2H2/t3-,4+,5-,6+
X9X InChIKey InChI 1.03 FBPFZTCFMRRESA-FBXFSONDSA-N
X9X SMILES_CANONICAL CACTVS 3.385 OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CO
X9X SMILES CACTVS 3.385 OC[CH](O)[CH](O)[CH](O)[CH](O)CO
X9X SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 C([C@H]([C@H]([C@H]([C@H](CO)O)O)O)O)O
X9X SMILES "OpenEye OEToolkits" 1.9.2 C(C(C(C(C(CO)O)O)O)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
X9X "SYSTEMATIC NAME" ACDLabs 12.01 D-allitol
X9X "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 (2R,3R,4S,5S)-hexane-1,2,3,4,5,6-hexol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
X9X 'Create component' 2014-10-30 RCSB
X9X 'Initial release' 2014-11-12 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
X9X OAA O 3.805 0.375 1
X9X CAG C 5.104 -0.375 2
X9X CAI C 6.404 0.375 3
X9X OAC O 6.404 1.875 4
X9X CAK C 7.702 -0.375 5
X9X OAE O 7.702 -1.875 6
X9X CAL C 9.002 0.375 7
X9X OAF O 9.002 1.875 8
X9X CAJ C 10.301 -0.375 9
X9X OAD O 10.301 -1.875 10
X9X CAH C 11.600 0.375 11
X9X OAB O 12.899 -0.375 12
#
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
X9X OAB CAH SINGLE NONE 1
X9X CAH CAJ SINGLE NONE 2
X9X CAJ OAD SINGLE BEGINDASH 3
X9X CAJ CAL SINGLE NONE 4
X9X OAA CAG SINGLE NONE 5
X9X CAI OAC SINGLE BEGINWEDGE 6
X9X CAK CAL SINGLE NONE 7
X9X CAK CAI SINGLE NONE 8
X9X CAK OAE SINGLE BEGINDASH 9
X9X CAL OAF SINGLE BEGINWEDGE 10
X9X CAG CAI SINGLE NONE 11
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id X9X
_pdbe_chem_comp_rdkit_properties.exactmw 182.079
_pdbe_chem_comp_rdkit_properties.amw 182.172
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 89.519
_pdbe_chem_comp_rdkit_properties.tpsa 121.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.585
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.199
_pdbe_chem_comp_rdkit_properties.chi0v 5.449
_pdbe_chem_comp_rdkit_properties.chi1v 2.475
_pdbe_chem_comp_rdkit_properties.chi2v 0.804
_pdbe_chem_comp_rdkit_properties.chi3v 0.804
_pdbe_chem_comp_rdkit_properties.chi4v 0.299
_pdbe_chem_comp_rdkit_properties.chi0n 19.449
_pdbe_chem_comp_rdkit_properties.chi1n 8.924
_pdbe_chem_comp_rdkit_properties.chi2n 0.804
_pdbe_chem_comp_rdkit_properties.chi3n 0.804
_pdbe_chem_comp_rdkit_properties.chi4n 0.299
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.240
_pdbe_chem_comp_rdkit_properties.kappa1 2.221
_pdbe_chem_comp_rdkit_properties.kappa2 5.413
_pdbe_chem_comp_rdkit_properties.kappa3 3.015
_pdbe_chem_comp_rdkit_properties.Phi 1.002
#
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
X9X UniChem PDBe X9X
X9X UniChem ChEBI 181263
X9X UniChem ZINC ZINC000017836367
X9X UniChem fdasrs B3F996O6JU
X9X UniChem BRENDA 106283
X9X UniChem BRENDA 34649
X9X UniChem BRENDA 627
X9X UniChem 'Probes And Drugs' PD087337
X9X UniChem MedChemExpress HY-N2840
X9X UniChem eMolecules 10476912
X9X UniChem SureChEMBL SCHEMBL15545455
X9X UniChem 'PubChem TPHARMA' 15195197
X9X UniChem PubChem 120700
X9X UniChem NMRShiftDB 70128803
X9X UniChem ACTor 488-44-8
X9X UniChem ACTor 715-48-0
X9X UniChem Nikkaji J12.559H
X9X UniChem 'EPA CompTox Dashboard' DTXSID60197607
X9X UniChem ChemicalBook CB5309494
#
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
X9X OAA 2.791 0.969 -0.948 ETKDGv3 1
X9X CAG 2.785 0.068 0.125 ETKDGv3 2
X9X CAI 1.833 -1.103 -0.159 ETKDGv3 3
X9X OAC 1.844 -1.971 0.947 ETKDGv3 4
X9X CAK 0.378 -0.667 -0.504 ETKDGv3 5
X9X OAE -0.309 -1.757 -1.070 ETKDGv3 6
X9X CAL -0.421 -0.078 0.707 ETKDGv3 7
X9X OAF 0.111 1.149 1.146 ETKDGv3 8
X9X CAJ -1.948 0.055 0.454 ETKDGv3 9
X9X OAD -2.564 0.532 1.624 ETKDGv3 10
X9X CAH -2.323 0.957 -0.743 ETKDGv3 11
X9X OAB -1.997 2.300 -0.502 ETKDGv3 12
X9X H1 3.408 1.702 -0.689 ETKDGv3 13
X9X H2 2.502 0.587 1.065 ETKDGv3 14
X9X H3 3.812 -0.338 0.265 ETKDGv3 15
X9X H4 2.248 -1.630 -1.052 ETKDGv3 16
X9X H5 1.706 -2.891 0.601 ETKDGv3 17
X9X H6 0.438 0.108 -1.296 ETKDGv3 18
X9X H7 -0.435 -2.438 -0.359 ETKDGv3 19
X9X H8 -0.317 -0.793 1.551 ETKDGv3 20
X9X H9 0.262 1.723 0.352 ETKDGv3 21
X9X H10 -2.343 -0.965 0.240 ETKDGv3 22
X9X H11 -3.533 0.332 1.544 ETKDGv3 23
X9X H12 -3.414 0.861 -0.947 ETKDGv3 24
X9X H13 -1.804 0.618 -1.662 ETKDGv3 25
X9X H14 -2.714 2.670 0.077 ETKDGv3 26
#