data_RM4
#
_chem_comp.id RM4
_chem_comp.name beta-L-rhamnopyranose
_chem_comp.type "L-saccharide, beta linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H12 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "beta-L-rhamnose; 6-deoxy-beta-L-mannopyranose; L-rhamnose; rhamnose"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-10-22
_chem_comp.pdbx_modified_date 2020-07-17
_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 164.156
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RM4
_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 2QLX
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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 RM4 beta-L-rhamnose PDB ?
2 RM4 6-deoxy-beta-L-mannopyranose PDB ?
3 RM4 L-rhamnose PDB ?
4 RM4 rhamnose PDB ?
#
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
RM4 C1 C1 C 0 1 N N S N N N 3.551 17.760 14.612 1.474 -0.452 -0.600 C1 RM4 1
RM4 C2 C2 C 0 1 N N R N N N 2.040 17.600 14.432 1.056 0.961 -0.183 C2 RM4 2
RM4 C3 C3 C 0 1 N N R N N N 1.816 16.620 13.268 -0.422 1.169 -0.525 C3 RM4 3
RM4 C4 C4 C 0 1 N N R N N N 2.641 15.323 13.415 -1.254 0.087 0.170 C4 RM4 4
RM4 C5 C5 C 0 1 N N S N N N 4.098 15.622 13.736 -0.747 -1.291 -0.261 C5 RM4 5
RM4 C6 C6 C 0 1 N N N N N N 4.806 14.324 14.108 -1.533 -2.378 0.476 C6 RM4 6
RM4 O1 O1 O 0 1 N Y N N N N 3.773 18.674 15.662 2.837 -0.674 -0.233 O1 RM4 7
RM4 O2 O2 O 0 1 N N N N N N 1.415 17.262 15.682 1.247 1.119 1.224 O2 RM4 8
RM4 O3 O3 O 0 1 N N N N N N 0.422 16.328 13.063 -0.840 2.459 -0.073 O3 RM4 9
RM4 O4 O4 O 0 1 N N N N N N 2.570 14.500 12.224 -2.627 0.228 -0.200 O4 RM4 10
RM4 O5 O5 O 0 1 N N N N N N 4.210 16.509 14.848 0.641 -1.408 0.059 O5 RM4 11
RM4 H1 H1 H 0 1 N N N N N N 3.987 18.147 13.679 1.366 -0.559 -1.680 H1 RM4 12
RM4 H2 H2 H 0 1 N N N N N N 1.542 18.539 14.150 1.661 1.692 -0.717 H2 RM4 13
RM4 H3 H3 H 0 1 N N N N N N 2.183 17.135 12.368 -0.560 1.098 -1.604 H3 RM4 14
RM4 H4 H4 H 0 1 N N N N N N 2.197 14.766 14.253 -1.155 0.190 1.251 H4 RM4 15
RM4 H5 H5 H 0 1 N N N N N N 4.551 16.088 12.848 -0.884 -1.409 -1.336 H5 RM4 16
RM4 H61 H6 H 0 1 N N N N N N 4.977 13.726 13.201 -2.592 -2.288 0.233 H61 RM4 17
RM4 H62 H6A H 0 1 N N N N N N 5.772 14.556 14.581 -1.172 -3.359 0.169 H62 RM4 18
RM4 H63 H6B H 0 1 N N N N N N 4.181 13.754 14.811 -1.396 -2.260 1.551 H63 RM4 19
RM4 HO1 HO1 H 0 1 N Y N N N N 3.823 18.204 16.486 3.170 -1.551 -0.467 HO1 RM4 20
RM4 HO2 HO2 H 0 1 N Y N N N N 2.078 17.187 16.358 2.161 0.995 1.513 HO2 RM4 21
RM4 HO3 HO3 H 0 1 N Y N N N N -0.016 16.264 13.904 -0.350 3.192 -0.468 HO3 RM4 22
RM4 HO4 HO4 H 0 1 N Y N N N N 2.554 15.057 11.454 -3.213 -0.426 0.205 HO4 RM4 23
#
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
RM4 C2 C1 SING N N 1
RM4 C1 O5 SING N N 2
RM4 C1 O1 SING N N 3
RM4 C1 H1 SING N N 4
RM4 C3 C2 SING N N 5
RM4 C2 O2 SING N N 6
RM4 C2 H2 SING N N 7
RM4 O3 C3 SING N N 8
RM4 C3 C4 SING N N 9
RM4 C3 H3 SING N N 10
RM4 O4 C4 SING N N 11
RM4 C4 C5 SING N N 12
RM4 C4 H4 SING N N 13
RM4 C5 C6 SING N N 14
RM4 C5 O5 SING N N 15
RM4 C5 H5 SING N N 16
RM4 C6 H61 SING N N 17
RM4 C6 H62 SING N N 18
RM4 C6 H63 SING N N 19
RM4 O1 HO1 SING N N 20
RM4 O2 HO2 SING N N 21
RM4 O3 HO3 SING N N 22
RM4 O4 HO4 SING N N 23
#
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
RM4 SMILES ACDLabs 10.04 OC1C(O)C(OC(O)C1O)C
RM4 SMILES_CANONICAL CACTVS 3.341 C[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@H]1O
RM4 SMILES CACTVS 3.341 C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
RM4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O)O)O)O
RM4 SMILES "OpenEye OEToolkits" 1.5.0 CC1C(C(C(C(O1)O)O)O)O
RM4 InChI InChI 1.03 InChI=1S/C6H12O5/c1-2-3(7)4(8)5(9)6(10)11-2/h2-10H,1H3/t2-,3-,4+,5+,6-/m0/s1
RM4 InChIKey InChI 1.03 SHZGCJCMOBCMKK-YJRYQGEOSA-N
#
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
RM4 "SYSTEMATIC NAME" ACDLabs 10.04 6-deoxy-beta-L-mannopyranose
RM4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2S,3R,4R,5R,6S)-6-methyloxane-2,3,4,5-tetrol
RM4 "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 LRhapb
RM4 "COMMON NAME" GMML 1.0 b-L-rhamnopyranose
RM4 "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-L-Rhap
RM4 "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Rha
#
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
RM4 "CARBOHYDRATE ISOMER" L PDB ?
RM4 "CARBOHYDRATE RING" pyranose PDB ?
RM4 "CARBOHYDRATE ANOMER" beta PDB ?
RM4 "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RM4 'Create component' 2008-10-22 RCSB
RM4 'Modify descriptor' 2011-06-04 RCSB
RM4 'Other modification' 2019-08-12 RCSB
RM4 'Other modification' 2019-12-19 RCSB
RM4 'Other modification' 2020-07-03 RCSB
RM4 'Modify name' 2020-07-17 RCSB
RM4 'Modify synonyms' 2020-07-17 RCSB
RM4 'Modify atom id' 2020-07-17 RCSB
RM4 'Modify component atom id' 2020-07-17 RCSB
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
RM4 beta-L-rhamnose wwPDB ?
RM4 6-deoxy-beta-L-mannopyranose wwPDB ?
RM4 L-rhamnose wwPDB ?
RM4 rhamnose wwPDB ?
#
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
RM4 C1 C 5.104 1.268 1
RM4 C2 C 5.104 -0.233 2
RM4 C3 C 6.404 -0.983 3
RM4 C4 C 7.702 -0.233 4
RM4 C5 C 7.702 1.268 5
RM4 C6 C 9.002 2.018 6
RM4 O1 O 3.805 2.018 7
RM4 O2 O 3.805 -0.983 8
RM4 O3 O 6.404 -2.482 9
RM4 O4 O 9.002 -0.983 10
RM4 O5 O 6.404 2.018 11
#
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
RM4 C2 C1 SINGLE NONE 1
RM4 C1 O5 SINGLE NONE 2
RM4 C1 O1 SINGLE BEGINWEDGE 3
RM4 C3 C2 SINGLE NONE 4
RM4 C2 O2 SINGLE BEGINWEDGE 5
RM4 C3 O3 SINGLE BEGINWEDGE 6
RM4 C3 C4 SINGLE NONE 7
RM4 C4 O4 SINGLE BEGINDASH 8
RM4 C4 C5 SINGLE NONE 9
RM4 C5 C6 SINGLE BEGINWEDGE 10
RM4 C5 O5 SINGLE NONE 11
#
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
RM4 MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
RM4 pyranose F1 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-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
RM4 C1 S1 1
RM4 C2 S1 1
RM4 C3 S1 1
RM4 C4 S1 1
RM4 C5 S1 1
RM4 O5 S1 1
RM4 C4 F1 1
RM4 C5 F1 1
RM4 O5 F1 1
RM4 C1 F1 1
RM4 C2 F1 1
RM4 C3 F1 1
RM4 O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RM4
_pdbe_chem_comp_rdkit_properties.exactmw 164.068
_pdbe_chem_comp_rdkit_properties.amw 164.157
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_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 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 81.055
_pdbe_chem_comp_rdkit_properties.tpsa 90.150
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.194
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.574
_pdbe_chem_comp_rdkit_properties.chi0v 5.041
_pdbe_chem_comp_rdkit_properties.chi1v 2.475
_pdbe_chem_comp_rdkit_properties.chi2v 0.999
_pdbe_chem_comp_rdkit_properties.chi3v 0.999
_pdbe_chem_comp_rdkit_properties.chi4v 0.484
_pdbe_chem_comp_rdkit_properties.chi0n 17.041
_pdbe_chem_comp_rdkit_properties.chi1n 8.108
_pdbe_chem_comp_rdkit_properties.chi2n 0.999
_pdbe_chem_comp_rdkit_properties.chi3n 0.999
_pdbe_chem_comp_rdkit_properties.chi4n 0.484
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.200
_pdbe_chem_comp_rdkit_properties.kappa1 1.995
_pdbe_chem_comp_rdkit_properties.kappa2 3.040
_pdbe_chem_comp_rdkit_properties.kappa3 1.521
_pdbe_chem_comp_rdkit_properties.Phi 0.551
#
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
RM4 UniChem PDBe RM4
RM4 UniChem 'KEGG LIGAND' C02338
RM4 UniChem ChEBI 27586
RM4 UniChem ZINC ZINC000003861281
RM4 UniChem fdasrs V3MX976UUR
RM4 UniChem MetaboLights MTBLC27586
RM4 UniChem BRENDA 179009
RM4 UniChem BRENDA 81690
RM4 UniChem Rhea 27586
RM4 UniChem Nikkaji J822.122G
RM4 UniChem eMolecules 2723861
RM4 UniChem SureChEMBL SCHEMBL1974227
RM4 UniChem 'PubChem TPHARMA' 15147052
RM4 UniChem PubChem 439730
RM4 UniChem NMRShiftDB 70103211
#
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
RM4 C1 -0.171 1.667 -0.156 ETKDGv3 1
RM4 C2 -1.410 0.781 -0.385 ETKDGv3 2
RM4 C3 -0.968 -0.568 -0.980 ETKDGv3 3
RM4 C4 0.155 -1.189 -0.128 ETKDGv3 4
RM4 C5 1.270 -0.144 0.112 ETKDGv3 5
RM4 C6 2.355 -0.711 1.029 ETKDGv3 6
RM4 O1 -0.572 2.884 0.412 ETKDGv3 7
RM4 O2 -2.083 0.564 0.831 ETKDGv3 8
RM4 O3 -2.057 -1.452 -1.042 ETKDGv3 9
RM4 O4 0.690 -2.305 -0.793 ETKDGv3 10
RM4 O5 0.739 1.022 0.719 ETKDGv3 11
RM4 H1 0.310 1.885 -1.141 ETKDGv3 12
RM4 H2 -2.089 1.281 -1.115 ETKDGv3 13
RM4 H3 -0.571 -0.394 -2.008 ETKDGv3 14
RM4 H4 -0.262 -1.497 0.861 ETKDGv3 15
RM4 H5 1.761 0.110 -0.857 ETKDGv3 16
RM4 H61 3.140 0.056 1.198 ETKDGv3 17
RM4 H62 1.923 -0.998 2.011 ETKDGv3 18
RM4 H63 2.832 -1.601 0.567 ETKDGv3 19
RM4 HO1 0.238 3.455 0.452 ETKDGv3 20
RM4 HO2 -2.661 1.356 0.987 ETKDGv3 21
RM4 HO3 -2.636 -1.141 -1.787 ETKDGv3 22
RM4 HO4 0.067 -3.062 -0.634 ETKDGv3 23
#