data_SGU
#
_chem_comp.id SGU
_chem_comp.name (5S)-5-methyloxolane-2,2-diol
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H10 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-07-01
_chem_comp.pdbx_modified_date 2023-01-06
_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 118.131
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SGU
_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 8DJF
_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
SGU C02 C1 C 0 1 N N N N N N 17.787 7.284 -10.032 -0.935 0.060 0.013 C02 SGU 1
SGU C04 C2 C 0 1 N N N N N N 19.049 8.125 -9.891 -0.469 -1.403 -0.147 C04 SGU 2
SGU C05 C3 C 0 1 N N N N N N 18.773 8.989 -8.658 1.055 -1.296 0.132 C05 SGU 3
SGU C06 C4 C 0 1 N N S N N N 17.739 8.191 -7.850 1.366 0.101 -0.462 C06 SGU 4
SGU C07 C5 C 0 1 N N N N N N 18.248 7.556 -6.568 2.610 0.696 0.200 C07 SGU 5
SGU O01 O1 O 0 1 N N N N N N 18.080 6.014 -10.536 -1.483 0.254 1.318 O01 SGU 6
SGU O03 O2 O 0 1 N N N N N N 16.870 7.886 -10.837 -1.918 0.367 -0.978 O03 SGU 7
SGU O08 O3 O 0 1 N N N N N N 17.236 7.170 -8.751 0.211 0.901 -0.163 O08 SGU 8
SGU H042 H1 H 0 0 N N N N N N 19.931 7.486 -9.733 -0.954 -2.047 0.586 H042 SGU 9
SGU H041 H2 H 0 0 N N N N N N 19.205 8.751 -10.782 -0.653 -1.760 -1.161 H041 SGU 10
SGU H052 H3 H 0 0 N N N N N N 19.693 9.137 -8.073 1.261 -1.322 1.202 H052 SGU 11
SGU H051 H4 H 0 0 N N N N N N 18.365 9.967 -8.953 1.606 -2.077 -0.391 H051 SGU 12
SGU H061 H5 H 0 0 N N N N N N 16.916 8.873 -7.589 1.509 0.030 -1.540 H061 SGU 13
SGU H071 H6 H 0 0 N N N N N N 18.626 8.340 -5.895 3.462 0.038 0.029 H071 SGU 14
SGU H072 H7 H 0 0 N N N N N N 17.427 7.015 -6.076 2.816 1.677 -0.227 H072 SGU 15
SGU H073 H8 H 0 0 N N N N N N 19.060 6.853 -6.805 2.438 0.795 1.272 H073 SGU 16
SGU H011 H9 H 0 0 N N N N N N 18.720 5.591 -9.976 -1.795 1.154 1.484 H011 SGU 17
SGU H031 H10 H 0 0 N N N N N N 16.668 8.750 -10.497 -2.253 1.273 -0.932 H031 SGU 18
#
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
SGU O03 C02 SING N N 1
SGU O01 C02 SING N N 2
SGU C02 C04 SING N N 3
SGU C02 O08 SING N N 4
SGU C04 C05 SING N N 5
SGU O08 C06 SING N N 6
SGU C05 C06 SING N N 7
SGU C06 C07 SING N N 8
SGU C04 H042 SING N N 9
SGU C04 H041 SING N N 10
SGU C05 H052 SING N N 11
SGU C05 H051 SING N N 12
SGU C06 H061 SING N N 13
SGU C07 H071 SING N N 14
SGU C07 H072 SING N N 15
SGU C07 H073 SING N N 16
SGU O01 H011 SING N N 17
SGU O03 H031 SING N N 18
#
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
SGU SMILES ACDLabs 12.01 CC1CCC(O)(O)O1
SGU InChI InChI 1.06 InChI=1S/C5H10O3/c1-4-2-3-5(6,7)8-4/h4,6-7H,2-3H2,1H3/t4-/m0/s1
SGU InChIKey InChI 1.06 MGKWNPVXYGZJRN-BYPYZUCNSA-N
SGU SMILES_CANONICAL CACTVS 3.385 C[C@H]1CCC(O)(O)O1
SGU SMILES CACTVS 3.385 C[CH]1CCC(O)(O)O1
SGU SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@H]1CCC(O1)(O)O
SGU SMILES "OpenEye OEToolkits" 2.0.7 CC1CCC(O1)(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
SGU "SYSTEMATIC NAME" ACDLabs 12.01 (5S)-5-methyloxolane-2,2-diol
SGU "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 (5~{S})-5-methyloxolane-2,2-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
SGU 'Create component' 2022-07-01 RCSB
SGU 'Initial release' 2023-01-11 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
SGU C02 C 4.807 1.154 1
SGU C04 C 3.593 0.272 2
SGU C05 C 4.057 -1.154 3
SGU C06 C 5.557 -1.154 4
SGU C07 C 6.438 -2.368 5
SGU O01 O 3.925 2.368 6
SGU O03 O 5.688 2.368 7
SGU O08 O 6.020 0.272 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
SGU O03 C02 SINGLE NONE 1
SGU O01 C02 SINGLE NONE 2
SGU C02 C04 SINGLE NONE 3
SGU C02 O08 SINGLE NONE 4
SGU C04 C05 SINGLE NONE 5
SGU O08 C06 SINGLE NONE 6
SGU C05 C06 SINGLE NONE 7
SGU C06 C07 SINGLE BEGINWEDGE 8
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
SGU MurckoScaffold S1 scaffold C1CCOC1 InChI=1S/C4H8O/c1-2-4-5-3-1/h1-4H2 WYURNTSHIVDZCO-UHFFFAOYSA-N
SGU furanose F1 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
SGU C02 S1 1
SGU C04 S1 1
SGU C05 S1 1
SGU C06 S1 1
SGU O08 S1 1
SGU C05 F1 1
SGU C06 F1 1
SGU O08 F1 1
SGU C02 F1 1
SGU C04 F1 1
SGU O03 F1 1
SGU C05 F1 2
SGU C06 F1 2
SGU O08 F1 2
SGU C02 F1 2
SGU C04 F1 2
SGU O01 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id SGU
_pdbe_chem_comp_rdkit_properties.exactmw 118.063
_pdbe_chem_comp_rdkit_properties.amw 118.132
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 62.118
_pdbe_chem_comp_rdkit_properties.tpsa 49.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.176
_pdbe_chem_comp_rdkit_properties.CrippenMR 26.950
_pdbe_chem_comp_rdkit_properties.chi0v 3.725
_pdbe_chem_comp_rdkit_properties.chi1v 1.816
_pdbe_chem_comp_rdkit_properties.chi2v 0.566
_pdbe_chem_comp_rdkit_properties.chi3v 0.566
_pdbe_chem_comp_rdkit_properties.chi4v 0.319
_pdbe_chem_comp_rdkit_properties.chi0n 13.725
_pdbe_chem_comp_rdkit_properties.chi1n 6.633
_pdbe_chem_comp_rdkit_properties.chi2n 0.566
_pdbe_chem_comp_rdkit_properties.chi3n 0.566
_pdbe_chem_comp_rdkit_properties.chi4n 0.319
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.120
_pdbe_chem_comp_rdkit_properties.kappa1 1.167
_pdbe_chem_comp_rdkit_properties.kappa2 1.685
_pdbe_chem_comp_rdkit_properties.kappa3 1.183
_pdbe_chem_comp_rdkit_properties.Phi 0.246
#
_pdbe_chem_comp_external_mappings.comp_id SGU
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id SGU
#
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
SGU C02 -1.366 0.171 0.150 ETKDGv3 1
SGU C04 -0.711 -1.193 -0.013 ETKDGv3 2
SGU C05 0.497 -0.884 -0.841 ETKDGv3 3
SGU C06 0.790 0.573 -0.503 ETKDGv3 4
SGU C07 1.930 0.702 0.508 ETKDGv3 5
SGU O01 -1.999 0.262 1.403 ETKDGv3 6
SGU O03 -2.323 0.347 -0.862 ETKDGv3 7
SGU O08 -0.373 1.172 0.031 ETKDGv3 8
SGU H042 -0.388 -1.599 0.972 ETKDGv3 9
SGU H041 -1.377 -1.930 -0.513 ETKDGv3 10
SGU H052 0.241 -0.975 -1.921 ETKDGv3 11
SGU H051 1.341 -1.572 -0.611 ETKDGv3 12
SGU H061 1.081 1.116 -1.429 ETKDGv3 13
SGU H071 1.676 0.170 1.450 ETKDGv3 14
SGU H072 2.866 0.275 0.089 ETKDGv3 15
SGU H073 2.107 1.773 0.741 ETKDGv3 16
SGU H011 -1.285 0.339 2.089 ETKDGv3 17
SGU H031 -2.706 1.254 -0.739 ETKDGv3 18
#