data_AHM
#
_chem_comp.id AHM
_chem_comp.name 2,5-anhydro-1,6-di-O-phosphono-D-mannitol
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H14 O11 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 2,5-ANHYDROMANNITOL-1,6-DIPHOSPHATE
_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 324.116
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AHM
_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 1FBF
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id AHM
_pdbx_chem_comp_synonyms.name 2,5-ANHYDROMANNITOL-1,6-DIPHOSPHATE
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
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
AHM P1 P1 P 0 1 N N N N N N 40.586 89.032 26.093 -1.181 -0.098 -4.059 P1 AHM 1
AHM O1P O1P O 0 1 N N N N N N 41.669 90.045 26.166 -0.907 -1.541 -4.243 O1P AHM 2
AHM O2P O2P O 0 1 N N N N N N 40.938 87.606 25.800 -2.743 0.188 -4.321 O2P AHM 3
AHM O3P O3P O 0 1 N N N N N N 39.786 89.127 27.470 -0.296 0.752 -5.101 O3P AHM 4
AHM O1 O1 O 0 1 N N N N N N 39.507 89.428 24.983 -0.801 0.332 -2.555 O1 AHM 5
AHM C1 C1 C 0 1 N N N N N N 38.645 90.553 25.151 0.590 0.054 -2.385 C1 AHM 6
AHM C2 C2 C 0 1 N N R N N N 37.235 90.055 25.405 1.018 0.443 -0.969 C2 AHM 7
AHM C3 C3 C 0 1 N N S N N N 36.137 90.796 24.641 2.508 0.086 -0.736 C3 AHM 8
AHM O3 O3 O 0 1 N N N N N N 36.051 90.291 23.330 3.365 1.145 -1.169 O3 AHM 9
AHM C4 C4 C 0 1 N N S N N N 34.910 90.551 25.529 2.539 -0.062 0.808 C4 AHM 10
AHM O4 O4 O 0 1 N N N N N N 33.909 91.572 25.497 3.570 -0.965 1.212 O4 AHM 11
AHM C5 C5 C 0 1 N N R N N N 35.525 90.470 26.951 1.142 -0.646 1.109 C5 AHM 12
AHM O5 O5 O 0 1 N N N N N N 36.931 90.288 26.772 0.292 -0.329 0.000 O5 AHM 13
AHM C6 C6 C 0 1 N N N N N N 34.952 89.340 27.757 0.583 -0.021 2.389 C6 AHM 14
AHM O6 O6 O 0 1 N N N N N N 34.188 89.903 28.822 -0.709 -0.566 2.660 O6 AHM 15
AHM P2 P2 P 0 1 N N N N N N 32.753 89.271 29.248 -1.234 0.131 4.013 P2 AHM 16
AHM O4P O4P O 0 1 N N N N N N 32.896 87.756 29.230 -1.314 1.596 3.813 O4P AHM 17
AHM O5P O5P O 0 1 N N N N N N 31.708 89.760 28.254 -2.694 -0.439 4.379 O5P AHM 18
AHM O6P O6P O 0 1 N N N N N N 32.546 89.866 30.627 -0.214 -0.191 5.215 O6P AHM 19
AHM HOP2 HOP2 H 0 0 N N N N N N 40.245 86.958 25.753 -2.928 -0.082 -5.231 HOP2 AHM 20
AHM HOP3 HOP3 H 0 0 N N N N N N 39.093 88.479 27.423 -0.504 1.684 -4.948 HOP3 AHM 21
AHM H11 H11 H 0 1 N N N N N N 38.698 91.262 24.292 1.167 0.629 -3.110 H11 AHM 22
AHM H12 H12 H 0 1 N N N N N N 39.001 91.247 25.947 0.769 -1.009 -2.540 H12 AHM 23
AHM H2 H2 H 0 1 N N N N N N 37.238 88.988 25.082 0.855 1.507 -0.804 H2 AHM 24
AHM H3 H3 H 0 1 N N N N N N 36.293 91.888 24.481 2.769 -0.851 -1.226 H3 AHM 25
AHM HO3 HO3 H 0 1 N N N N N N 35.369 90.751 22.855 4.268 0.882 -0.946 HO3 AHM 26
AHM H4 H4 H 0 1 N N N N N N 34.362 89.644 25.181 2.666 0.907 1.289 H4 AHM 27
AHM HO4 HO4 H 0 1 N N N N N N 33.149 91.420 26.047 4.408 -0.583 0.916 HO4 AHM 28
AHM H5 H5 H 0 1 N N N N N N 35.293 91.401 27.519 1.210 -1.727 1.226 H5 AHM 29
AHM H61 H61 H 0 1 N N N N N N 35.731 88.627 28.115 1.251 -0.238 3.222 H61 AHM 30
AHM H62 H62 H 0 1 N N N N N N 34.366 88.622 27.138 0.502 1.058 2.261 H62 AHM 31
AHM HOP5 HOP5 H 0 0 N N N N N N 30.869 89.391 28.503 -2.971 0.003 5.193 HOP5 AHM 32
AHM HOP6 HOP6 H 0 0 N N N N N N 31.707 89.497 30.876 -0.191 -1.153 5.312 HOP6 AHM 33
#
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
AHM P1 O1P DOUB N N 1
AHM P1 O2P SING N N 2
AHM P1 O3P SING N N 3
AHM P1 O1 SING N N 4
AHM O2P HOP2 SING N N 5
AHM O3P HOP3 SING N N 6
AHM O1 C1 SING N N 7
AHM C1 C2 SING N N 8
AHM C1 H11 SING N N 9
AHM C1 H12 SING N N 10
AHM C2 C3 SING N N 11
AHM C2 O5 SING N N 12
AHM C2 H2 SING N N 13
AHM C3 O3 SING N N 14
AHM C3 C4 SING N N 15
AHM C3 H3 SING N N 16
AHM O3 HO3 SING N N 17
AHM C4 O4 SING N N 18
AHM C4 C5 SING N N 19
AHM C4 H4 SING N N 20
AHM O4 HO4 SING N N 21
AHM C5 O5 SING N N 22
AHM C5 C6 SING N N 23
AHM C5 H5 SING N N 24
AHM C6 O6 SING N N 25
AHM C6 H61 SING N N 26
AHM C6 H62 SING N N 27
AHM O6 P2 SING N N 28
AHM P2 O4P DOUB N N 29
AHM P2 O5P SING N N 30
AHM P2 O6P SING N N 31
AHM O5P HOP5 SING N N 32
AHM O6P HOP6 SING N N 33
#
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
AHM SMILES ACDLabs 10.04 O=P(OCC1OC(C(O)C1O)COP(=O)(O)O)(O)O
AHM SMILES_CANONICAL CACTVS 3.341 O[C@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@@H]1CO[P](O)(O)=O
AHM SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1CO[P](O)(O)=O
AHM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@@H]1[C@H]([C@@H]([C@H](O1)COP(=O)(O)O)O)O)OP(=O)(O)O
AHM SMILES "OpenEye OEToolkits" 1.5.0 C(C1C(C(C(O1)COP(=O)(O)O)O)O)OP(=O)(O)O
AHM InChI InChI 1.03 InChI=1S/C6H14O11P2/c7-5-3(1-15-18(9,10)11)17-4(6(5)8)2-16-19(12,13)14/h3-8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,4-,5-,6-/m1/s1
AHM InChIKey InChI 1.03 WSMBXSQDFPTODV-KVTDHHQDSA-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
AHM "SYSTEMATIC NAME" ACDLabs 10.04 2,5-anhydro-1,6-di-O-phosphono-D-mannitol
AHM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]methyl dihydrogen phosphate"
#
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
AHM "CARBOHYDRATE ISOMER" D PDB ?
AHM "CARBOHYDRATE RING" furanose 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
AHM 'Create component' 1999-07-08 RCSB
AHM 'Modify descriptor' 2011-06-04 RCSB
AHM 'Other modification' 2020-07-03 RCSB
AHM 'Modify name' 2020-07-17 RCSB
AHM 'Modify synonyms' 2020-07-17 RCSB
AHM 'Modify internal type' 2020-07-17 RCSB
AHM 'Modify linking type' 2020-07-17 RCSB
#
_pdbe_chem_comp_synonyms.comp_id AHM
_pdbe_chem_comp_synonyms.name 2,5-ANHYDROMANNITOL-1,6-DIPHOSPHATE
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
AHM P1 P 4.620 -1.707 1
AHM O1P O 3.193 -2.171 2
AHM O2P O 5.083 -3.134 3
AHM O3P O 4.156 -0.281 4
AHM O1 O 6.046 -1.244 5
AHM C1 C 6.358 0.224 6
AHM C2 C 7.785 0.687 7
AHM C3 C 8.248 2.114 8
AHM O3 O 7.367 3.327 9
AHM C4 C 9.748 2.114 10
AHM O4 O 10.630 3.327 11
AHM C5 C 10.212 0.687 12
AHM O5 O 8.998 -0.195 13
AHM C6 C 11.639 0.224 14
AHM O6 O 11.950 -1.244 15
AHM P2 P 13.377 -1.707 16
AHM O4P O 14.804 -2.171 17
AHM O5P O 12.914 -3.134 18
AHM O6P O 13.841 -0.281 19
#
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
AHM P1 O1P DOUBLE NONE 1
AHM P1 O2P SINGLE NONE 2
AHM P1 O3P SINGLE NONE 3
AHM P1 O1 SINGLE NONE 4
AHM O1 C1 SINGLE NONE 5
AHM C2 C1 SINGLE BEGINDASH 6
AHM C2 C3 SINGLE NONE 7
AHM C2 O5 SINGLE NONE 8
AHM C3 O3 SINGLE BEGINWEDGE 9
AHM C3 C4 SINGLE NONE 10
AHM C4 O4 SINGLE BEGINDASH 11
AHM C4 C5 SINGLE NONE 12
AHM C5 O5 SINGLE NONE 13
AHM C5 C6 SINGLE BEGINWEDGE 14
AHM C6 O6 SINGLE NONE 15
AHM O6 P2 SINGLE NONE 16
AHM P2 O4P DOUBLE NONE 17
AHM P2 O5P SINGLE NONE 18
AHM P2 O6P SINGLE NONE 19
#
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
AHM MurckoScaffold S1 scaffold C1CCOC1 InChI=1S/C4H8O/c1-2-4-5-3-1/h1-4H2 WYURNTSHIVDZCO-UHFFFAOYSA-N
AHM phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
AHM ribose F2 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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
AHM C2 S1 1
AHM C3 S1 1
AHM C4 S1 1
AHM C5 S1 1
AHM O5 S1 1
AHM O2P F1 1
AHM P1 F1 1
AHM O1P F1 1
AHM O3P F1 1
AHM O1 F1 1
AHM O6 F1 2
AHM P2 F1 2
AHM O4P F1 2
AHM O5P F1 2
AHM O6P F1 2
AHM C3 F2 1
AHM C4 F2 1
AHM C5 F2 1
AHM O5 F2 1
AHM C2 F2 1
AHM C6 F2 1
AHM O6 F2 1
AHM O4 F2 1
AHM O3 F2 1
AHM C4 F2 2
AHM C3 F2 2
AHM C2 F2 2
AHM O5 F2 2
AHM C5 F2 2
AHM C1 F2 2
AHM O1 F2 2
AHM O3 F2 2
AHM O4 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id AHM
_pdbe_chem_comp_rdkit_properties.exactmw 324.001
_pdbe_chem_comp_rdkit_properties.amw 324.115
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 11
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 11
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 13
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 126.953
_pdbe_chem_comp_rdkit_properties.tpsa 183.210
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.306
_pdbe_chem_comp_rdkit_properties.CrippenMR 56.667
_pdbe_chem_comp_rdkit_properties.chi0v 10.174
_pdbe_chem_comp_rdkit_properties.chi1v 6.857
_pdbe_chem_comp_rdkit_properties.chi2v 1.953
_pdbe_chem_comp_rdkit_properties.chi3v 1.953
_pdbe_chem_comp_rdkit_properties.chi4v 1.119
_pdbe_chem_comp_rdkit_properties.chi0n 22.385
_pdbe_chem_comp_rdkit_properties.chi1n 10.385
_pdbe_chem_comp_rdkit_properties.chi2n 1.323
_pdbe_chem_comp_rdkit_properties.chi3n 1.323
_pdbe_chem_comp_rdkit_properties.chi4n 0.730
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.100
_pdbe_chem_comp_rdkit_properties.kappa1 5.711
_pdbe_chem_comp_rdkit_properties.kappa2 6.250
_pdbe_chem_comp_rdkit_properties.kappa3 5.942
_pdbe_chem_comp_rdkit_properties.Phi 1.879
#
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
AHM UniChem PDBe AHM
AHM UniChem ZINC ZINC000012502591
AHM UniChem PubChem 445556
AHM UniChem Nikkaji J916.067A
AHM UniChem BRENDA 43041
#
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
AHM P1 4.270 1.140 0.949 ETKDGv3 1
AHM O1P 4.664 2.103 2.045 ETKDGv3 2
AHM O2P 5.351 -0.163 0.942 ETKDGv3 3
AHM O3P 4.344 1.938 -0.542 ETKDGv3 4
AHM O1 2.683 0.587 1.240 ETKDGv3 5
AHM C1 2.338 -0.321 0.220 ETKDGv3 6
AHM C2 0.901 -0.808 0.446 ETKDGv3 7
AHM C3 0.466 -1.813 -0.624 ETKDGv3 8
AHM O3 -0.344 -2.810 -0.054 ETKDGv3 9
AHM C4 -0.355 -0.976 -1.569 ETKDGv3 10
AHM O4 0.463 -0.503 -2.609 ETKDGv3 11
AHM C5 -0.824 0.188 -0.691 ETKDGv3 12
AHM O5 0.025 0.299 0.433 ETKDGv3 13
AHM C6 -2.270 -0.003 -0.217 ETKDGv3 14
AHM O6 -2.647 1.103 0.570 ETKDGv3 15
AHM P2 -4.240 0.850 1.127 ETKDGv3 16
AHM O4P -4.279 -0.344 2.055 ETKDGv3 17
AHM O5P -5.287 0.585 -0.176 ETKDGv3 18
AHM O6P -4.749 2.221 1.977 ETKDGv3 19
AHM HOP2 5.206 -0.616 1.810 ETKDGv3 20
AHM HOP3 3.632 2.626 -0.496 ETKDGv3 21
AHM H11 3.015 -1.205 0.243 ETKDGv3 22
AHM H12 2.395 0.167 -0.780 ETKDGv3 23
AHM H2 0.856 -1.283 1.452 ETKDGv3 24
AHM H3 1.327 -2.287 -1.154 ETKDGv3 25
AHM HO3 0.267 -3.448 0.398 ETKDGv3 26
AHM H4 -1.200 -1.568 -1.996 ETKDGv3 27
AHM HO4 -0.145 -0.131 -3.300 ETKDGv3 28
AHM H5 -0.776 1.139 -1.266 ETKDGv3 29
AHM H61 -2.330 -0.947 0.371 ETKDGv3 30
AHM H62 -2.925 -0.079 -1.115 ETKDGv3 31
AHM HOP5 -5.191 1.390 -0.745 ETKDGv3 32
AHM HOP6 -4.639 2.969 1.337 ETKDGv3 33
#