data_BMA
#
_chem_comp.id BMA
_chem_comp.name beta-D-mannopyranose
_chem_comp.type "D-saccharide, beta linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H12 O6"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "beta-D-mannose; D-mannose; mannose"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 180.156
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code BMA
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1CF5
_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 BMA beta-D-mannose PDB ?
2 BMA D-mannose PDB ?
3 BMA mannose 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
BMA C1 C1 C 0 1 N N R N N N 27.913 -0.014 -0.918 -1.442 -0.578 -0.504 C1 BMA 1
BMA C2 C2 C 0 1 N N S N N N 28.289 1.181 -0.018 -0.493 -0.194 -1.642 C2 BMA 2
BMA C3 C3 C 0 1 N N S N N N 29.844 1.264 -0.063 0.945 -0.515 -1.223 C3 BMA 3
BMA C4 C4 C 0 1 N N S N N N 30.565 -0.137 -0.527 1.227 0.168 0.119 C4 BMA 4
BMA C5 C5 C 0 1 N N R N N N 29.687 -1.504 -0.194 0.149 -0.244 1.124 C5 BMA 5
BMA C6 C6 C 0 1 N N N N N N 29.877 -2.207 1.231 0.442 0.405 2.478 C6 BMA 6
BMA O1 O1 O 0 1 N Y N N N N 26.518 -0.013 -1.109 -2.789 -0.311 -0.899 O1 BMA 7
BMA O2 O2 O 0 1 N N N N N N 27.730 1.125 1.374 -0.614 1.202 -1.915 O2 BMA 8
BMA O3 O3 O 0 1 N N N N N N 30.418 1.690 1.173 1.853 -0.027 -2.213 O3 BMA 9
BMA O4 O4 O 0 1 N N N N N N 30.854 -0.128 -1.954 2.510 -0.235 0.601 O4 BMA 10
BMA O5 O5 O 0 1 N N N N N N 28.253 -1.252 -0.293 -1.130 0.181 0.661 O5 BMA 11
BMA O6 O6 O 0 1 N N N N N N 30.472 -3.557 1.147 -0.561 0.018 3.419 O6 BMA 12
BMA H1 H1 H 0 1 N N N N N N 28.466 0.085 -1.880 -1.333 -1.640 -0.284 H1 BMA 13
BMA H2 H2 H 0 1 N N N N N N 27.818 2.114 -0.405 -0.748 -0.763 -2.537 H2 BMA 14
BMA H3 H3 H 0 1 N N N N N N 30.043 2.037 -0.841 1.063 -1.593 -1.118 H3 BMA 15
BMA H4 H4 H 0 1 N N N N N N 31.501 -0.179 0.077 1.211 1.250 -0.011 H4 BMA 16
BMA H5 H5 H 0 1 N N N N N N 30.101 -2.195 -0.964 0.152 -1.328 1.234 H5 BMA 17
BMA H61 H61 H 0 1 N N N N N N 30.469 -1.556 1.916 0.439 1.489 2.369 H61 BMA 18
BMA H62 H62 H 0 1 N N N N N N 28.912 -2.234 1.789 1.418 0.078 2.835 H62 BMA 19
BMA HO1 HO1 H 0 1 N Y N N N N 26.286 -0.749 -1.663 -3.354 -0.570 -0.159 HO1 BMA 20
BMA HO2 HO2 H 0 1 N Y N N N N 27.961 1.861 1.928 -1.534 1.360 -2.167 HO2 BMA 21
BMA HO3 HO3 H 0 1 N Y N N N N 31.366 1.740 1.145 1.630 -0.474 -3.041 HO3 BMA 22
BMA HO4 HO4 H 0 1 N Y N N N N 31.271 -0.938 -2.222 3.157 0.035 -0.064 HO4 BMA 23
BMA HO6 HO6 H 0 1 N Y N N N N 30.584 -3.974 1.992 -0.340 0.447 4.256 HO6 BMA 24
#
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
BMA C1 C2 SING N N 1
BMA C1 O1 SING N N 2
BMA C1 O5 SING N N 3
BMA C1 H1 SING N N 4
BMA C2 C3 SING N N 5
BMA C2 O2 SING N N 6
BMA C2 H2 SING N N 7
BMA C3 C4 SING N N 8
BMA C3 O3 SING N N 9
BMA C3 H3 SING N N 10
BMA C4 C5 SING N N 11
BMA C4 O4 SING N N 12
BMA C4 H4 SING N N 13
BMA C5 C6 SING N N 14
BMA C5 O5 SING N N 15
BMA C5 H5 SING N N 16
BMA C6 O6 SING N N 17
BMA C6 H61 SING N N 18
BMA C6 H62 SING N N 19
BMA O1 HO1 SING N N 20
BMA O2 HO2 SING N N 21
BMA O3 HO3 SING N N 22
BMA O4 HO4 SING N N 23
BMA O6 HO6 SING N N 24
#
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
BMA SMILES ACDLabs 10.04 OC1C(O)C(OC(O)C1O)CO
BMA SMILES_CANONICAL CACTVS 3.341 OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O
BMA SMILES CACTVS 3.341 OC[CH]1O[CH](O)[CH](O)[CH](O)[CH]1O
BMA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H]1[C@H]([C@@H]([C@@H]([C@@H](O1)O)O)O)O)O
BMA SMILES "OpenEye OEToolkits" 1.5.0 C(C1C(C(C(C(O1)O)O)O)O)O
BMA InChI InChI 1.03 InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5+,6-/m1/s1
BMA InChIKey InChI 1.03 WQZGKKKJIJFFOK-RWOPYEJCSA-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
BMA "SYSTEMATIC NAME" ACDLabs 10.04 beta-D-mannopyranose
BMA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2R,3S,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
BMA "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DManpb
BMA "COMMON NAME" GMML 1.0 b-D-mannopyranose
BMA "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-Manp
BMA "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Man
#
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
BMA "CARBOHYDRATE ISOMER" D PDB ?
BMA "CARBOHYDRATE RING" pyranose PDB ?
BMA "CARBOHYDRATE ANOMER" beta PDB ?
BMA "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
BMA 'Create component' 1999-07-08 RCSB
BMA 'Modify descriptor' 2011-06-04 RCSB
BMA 'Other modification' 2019-08-12 RCSB
BMA 'Other modification' 2019-12-19 RCSB
BMA 'Other modification' 2020-07-03 RCSB
BMA 'Modify name' 2020-07-17 RCSB
BMA 'Modify synonyms' 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
BMA beta-D-mannose wwPDB ?
BMA D-mannose wwPDB ?
BMA mannose 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
BMA C1 C 7.702 0.750 1
BMA C2 C 7.702 -0.750 2
BMA C3 C 6.404 -1.500 3
BMA C4 C 5.104 -0.750 4
BMA C5 C 5.104 0.750 5
BMA C6 C 3.805 1.500 6
BMA O1 O 9.002 1.500 7
BMA O2 O 9.002 -1.500 8
BMA O3 O 6.404 -3.000 9
BMA O4 O 3.805 -1.500 10
BMA O5 O 6.404 1.500 11
BMA O6 O 3.805 3.000 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
BMA C1 C2 SINGLE NONE 1
BMA C1 O1 SINGLE BEGINWEDGE 2
BMA C1 O5 SINGLE NONE 3
BMA C2 C3 SINGLE NONE 4
BMA C2 O2 SINGLE BEGINWEDGE 5
BMA C3 C4 SINGLE NONE 6
BMA C3 O3 SINGLE BEGINWEDGE 7
BMA C4 C5 SINGLE NONE 8
BMA C4 O4 SINGLE BEGINDASH 9
BMA C5 C6 SINGLE BEGINWEDGE 10
BMA C5 O5 SINGLE NONE 11
BMA C6 O6 SINGLE NONE 12
#
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
BMA MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
BMA 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
BMA C1 S1 1
BMA C2 S1 1
BMA C3 S1 1
BMA C4 S1 1
BMA C5 S1 1
BMA O5 S1 1
BMA C4 F1 1
BMA C5 F1 1
BMA O5 F1 1
BMA C1 F1 1
BMA C2 F1 1
BMA C3 F1 1
BMA O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id BMA
_pdbe_chem_comp_rdkit_properties.exactmw 180.063
_pdbe_chem_comp_rdkit_properties.amw 180.156
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_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 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 85.936
_pdbe_chem_comp_rdkit_properties.tpsa 110.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.221
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.986
_pdbe_chem_comp_rdkit_properties.chi0v 5.449
_pdbe_chem_comp_rdkit_properties.chi1v 2.679
_pdbe_chem_comp_rdkit_properties.chi2v 1.092
_pdbe_chem_comp_rdkit_properties.chi3v 1.092
_pdbe_chem_comp_rdkit_properties.chi4v 0.552
_pdbe_chem_comp_rdkit_properties.chi0n 17.449
_pdbe_chem_comp_rdkit_properties.chi1n 8.220
_pdbe_chem_comp_rdkit_properties.chi2n 1.092
_pdbe_chem_comp_rdkit_properties.chi3n 1.092
_pdbe_chem_comp_rdkit_properties.chi4n 0.552
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.240
_pdbe_chem_comp_rdkit_properties.kappa1 2.412
_pdbe_chem_comp_rdkit_properties.kappa2 3.649
_pdbe_chem_comp_rdkit_properties.kappa3 1.582
_pdbe_chem_comp_rdkit_properties.Phi 0.733
#
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
BMA UniChem PDBe BMA
BMA UniChem 'KEGG LIGAND' C02209
BMA UniChem 'KEGG LIGAND' C17207
BMA UniChem ChEBI 28563
BMA UniChem ZINC ZINC000003830679
BMA UniChem fdasrs CUO87O37MT
BMA UniChem SureChEMBL SCHEMBL396651
BMA UniChem PubChem 439680
BMA UniChem NMRShiftDB 60024413
BMA UniChem Nikkaji J15.394J
BMA UniChem MetaboLights MTBLC28563
BMA UniChem BRENDA 225418
BMA UniChem BRENDA 5686
BMA UniChem BRENDA 6731
BMA UniChem Rhea 28563
BMA UniChem 'PubChem TPHARMA' 15147314
BMA UniChem ACTor 7322-31-8
#
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
BMA C1 -0.944 1.151 0.744 ETKDGv3 1
BMA C2 -1.865 0.119 0.038 ETKDGv3 2
BMA C3 -1.097 -1.163 -0.358 ETKDGv3 3
BMA C4 0.381 -0.843 -0.605 ETKDGv3 4
BMA C5 0.993 -0.242 0.693 ETKDGv3 5
BMA C6 2.266 0.574 0.405 ETKDGv3 6
BMA O1 -0.384 2.062 -0.173 ETKDGv3 7
BMA O2 -2.468 0.696 -1.094 ETKDGv3 8
BMA O3 -1.674 -1.741 -1.503 ETKDGv3 9
BMA O4 1.062 -2.021 -0.959 ETKDGv3 10
BMA O5 0.079 0.512 1.490 ETKDGv3 11
BMA O6 2.783 1.113 1.592 ETKDGv3 12
BMA H1 -1.570 1.716 1.474 ETKDGv3 13
BMA H2 -2.664 -0.190 0.754 ETKDGv3 14
BMA H3 -1.163 -1.881 0.496 ETKDGv3 15
BMA H4 0.441 -0.108 -1.444 ETKDGv3 16
BMA H5 1.306 -1.103 1.325 ETKDGv3 17
BMA H61 2.043 1.407 -0.292 ETKDGv3 18
BMA H62 3.032 -0.069 -0.084 ETKDGv3 19
BMA HO1 -1.056 2.776 -0.327 ETKDGv3 20
BMA HO2 -3.168 1.317 -0.760 ETKDGv3 21
BMA HO3 -1.431 -2.703 -1.498 ETKDGv3 22
BMA HO4 1.882 -1.745 -1.445 ETKDGv3 23
BMA HO6 3.217 0.365 2.079 ETKDGv3 24
#