data_RAH
#
_chem_comp.id RAH
_chem_comp.name "[(2~{S},3~{S},4~{S},5~{R})-3,4,5-tris(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]methanesulfonic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H13 O11 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "6-deoxy-6-sulfo-D-fructose 1-phosphate"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-09-22
_chem_comp.pdbx_modified_date 2021-04-09
_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 324.200
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RAH
_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 7AGK
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
RAH C1 C1 C 0 1 N N S N N N 18.434 16.530 79.266 1.720 -0.731 0.330 C1 RAH 1
RAH C2 C2 C 0 1 N N S N N N 19.503 15.526 79.641 1.710 -2.274 0.190 C2 RAH 2
RAH C3 C3 C 0 1 N N S N N N 19.393 14.523 78.502 0.188 -2.569 0.282 C3 RAH 3
RAH C4 C4 C 0 1 N N R N N N 18.946 15.379 77.299 -0.427 -1.334 -0.410 C4 RAH 4
RAH C5 C5 C 0 1 N N N N N N 17.706 14.779 76.674 -1.692 -0.899 0.333 C5 RAH 5
RAH C6 C6 C 0 1 N N N N N N 18.579 17.861 79.958 2.977 -0.147 -0.318 C6 RAH 6
RAH S1 S1 S 0 1 N N N N N N 17.223 18.982 79.774 3.040 1.640 -0.013 S1 RAH 7
RAH O2 O1 O 0 1 N N N N N N 19.975 15.505 76.356 -0.744 -1.646 -1.768 O2 RAH 8
RAH O3 O2 O 0 1 N N N N N N 17.351 15.342 75.384 -2.250 0.250 -0.308 O3 RAH 9
RAH O4 O3 O 0 1 N N N N N N 15.594 15.588 73.596 -3.432 1.349 1.633 O4 RAH 10
RAH O5 O4 O 0 1 N N N N N N 15.273 13.912 75.466 -3.849 2.306 -0.665 O5 RAH 11
RAH O6 O5 O 0 1 N N N N N N 17.013 13.442 73.696 -4.840 -0.023 0.049 O6 RAH 12
RAH O7 O6 O 0 1 N N N N N N 20.576 13.803 78.242 -0.141 -3.768 -0.421 O7 RAH 13
RAH O8 O7 O 0 1 N N N N N N 19.222 15.010 80.935 2.421 -2.893 1.265 O8 RAH 14
RAH O9 O8 O 0 1 N N N N N N 16.080 18.185 80.127 3.267 1.903 1.365 O9 RAH 15
RAH O10 O9 O 0 1 N N N N N N 17.522 20.153 80.546 4.320 2.097 -0.699 O10 RAH 16
RAH O11 O10 O 0 1 N N N N N N 17.146 19.335 78.268 2.005 2.304 -0.725 O11 RAH 17
RAH O1 O11 O 0 1 N N N N N N 18.616 16.641 77.841 0.547 -0.284 -0.367 O1 RAH 18
RAH P1 P1 P 0 1 N N N N N N 16.256 14.528 74.483 -3.589 0.979 0.209 P1 RAH 19
RAH H1 H1 H 0 1 N N N N N N 17.444 16.107 79.492 1.669 -0.446 1.381 H1 RAH 20
RAH H2 H2 H 0 1 N N N N N N 20.491 16.008 79.614 2.113 -2.584 -0.774 H2 RAH 21
RAH H3 H3 H 0 1 N N N N N N 18.579 13.823 78.740 -0.133 -2.631 1.322 H3 RAH 22
RAH H4 H4 H 0 1 N N N N N N 16.863 14.938 77.362 -2.419 -1.711 0.320 H4 RAH 23
RAH H5 H5 H 0 1 N N N N N N 17.874 13.700 76.544 -1.441 -0.653 1.365 H5 RAH 24
RAH H6 H6 H 0 1 N N N N N N 18.713 17.669 81.033 3.861 -0.620 0.112 H6 RAH 25
RAH H7 H7 H 0 1 N N N N N N 19.478 18.352 79.558 2.952 -0.332 -1.392 H7 RAH 26
RAH H8 H8 H 0 1 N N N N N N 20.741 15.883 76.771 -1.129 -0.909 -2.261 H8 RAH 27
RAH H9 H9 H 0 1 N N N N N N 14.416 14.305 75.346 -4.642 2.796 -0.409 H9 RAH 28
RAH H10 H10 H 0 1 N N N N N N 16.941 13.616 72.765 -5.002 -0.307 -0.860 H10 RAH 29
RAH H11 H11 H 0 1 N N N N N N 20.811 13.293 79.008 0.292 -4.560 -0.075 H11 RAH 30
RAH H12 H12 H 0 1 N N N N N N 19.315 15.702 81.579 2.440 -3.859 1.218 H12 RAH 31
RAH H13 H13 H 0 1 N N N N N N 17.610 20.901 79.967 4.491 3.046 -0.620 H13 RAH 32
#
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
RAH O4 P1 DOUB N N 1
RAH O6 P1 SING N N 2
RAH P1 O3 SING N N 3
RAH P1 O5 SING N N 4
RAH O3 C5 SING N N 5
RAH O2 C4 SING N N 6
RAH C5 C4 SING N N 7
RAH C4 O1 SING N N 8
RAH C4 C3 SING N N 9
RAH O1 C1 SING N N 10
RAH O7 C3 SING N N 11
RAH O11 S1 DOUB N N 12
RAH C3 C2 SING N N 13
RAH C1 C2 SING N N 14
RAH C1 C6 SING N N 15
RAH C2 O8 SING N N 16
RAH S1 C6 SING N N 17
RAH S1 O9 DOUB N N 18
RAH S1 O10 SING N N 19
RAH C1 H1 SING N N 20
RAH C2 H2 SING N N 21
RAH C3 H3 SING N N 22
RAH C5 H4 SING N N 23
RAH C5 H5 SING N N 24
RAH C6 H6 SING N N 25
RAH C6 H7 SING N N 26
RAH O2 H8 SING N N 27
RAH O5 H9 SING N N 28
RAH O6 H10 SING N N 29
RAH O7 H11 SING N N 30
RAH O8 H12 SING N N 31
RAH O10 H13 SING N N 32
#
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
RAH InChI InChI 1.03 InChI=1S/C6H13O11PS/c7-4-3(1-19(13,14)15)17-6(9,5(4)8)2-16-18(10,11)12/h3-5,7-9H,1-2H2,(H2,10,11,12)(H,13,14,15)/t3-,4-,5+,6-/m1/s1
RAH InChIKey InChI 1.03 IZVMCURFIBVEOJ-ARQDHWQXSA-N
RAH SMILES_CANONICAL CACTVS 3.385 O[C@H]1[C@H](O)[C@@](O)(CO[P](O)(O)=O)O[C@@H]1C[S](O)(=O)=O
RAH SMILES CACTVS 3.385 O[CH]1[CH](O)[C](O)(CO[P](O)(O)=O)O[CH]1C[S](O)(=O)=O
RAH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C([C@@H]1[C@H]([C@@H]([C@](O1)(COP(=O)(O)O)O)O)O)S(=O)(=O)O
RAH SMILES "OpenEye OEToolkits" 2.0.7 C(C1C(C(C(O1)(COP(=O)(O)O)O)O)O)S(=O)(=O)O
#
_pdbx_chem_comp_identifier.comp_id RAH
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
"[(2~{S},3~{S},4~{S},5~{R})-3,4,5-tris(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]methanesulfonic acid"
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id RAH
_pdbx_chem_comp_synonyms.name "6-deoxy-6-sulfo-D-fructose 1-phosphate"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RAH 'Create component' 2020-09-22 PDBE
RAH 'Initial release' 2021-04-14 RCSB
#
_pdbe_chem_comp_synonyms.comp_id RAH
_pdbe_chem_comp_synonyms.name '6-deoxy-6-sulfo-D-fructose 1-phosphate'
_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
RAH C1 C 7.081 -1.622 1
RAH C2 C 5.581 -1.622 2
RAH C3 C 5.118 -0.195 3
RAH C4 C 6.331 0.686 4
RAH C5 C 7.213 1.900 5
RAH C6 C 7.963 -2.835 6
RAH S1 S 9.455 -2.679 7
RAH O2 O 5.449 1.900 8
RAH O3 O 8.705 1.743 9
RAH O4 O 10.468 4.170 10
RAH O5 O 8.373 3.838 11
RAH O6 O 10.800 2.075 12
RAH O7 O 3.691 0.268 13
RAH O8 O 4.699 -2.835 14
RAH O9 O 9.612 -4.170 15
RAH O10 O 9.298 -1.187 16
RAH O11 O 10.946 -2.522 17
RAH O1 O 7.545 -0.195 18
RAH P1 P 9.586 2.957 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
RAH O4 P1 DOUBLE NONE 1
RAH O6 P1 SINGLE NONE 2
RAH P1 O3 SINGLE NONE 3
RAH P1 O5 SINGLE NONE 4
RAH O3 C5 SINGLE NONE 5
RAH C4 O2 SINGLE BEGINDASH 6
RAH C5 C4 SINGLE NONE 7
RAH C4 O1 SINGLE NONE 8
RAH C4 C3 SINGLE NONE 9
RAH O1 C1 SINGLE NONE 10
RAH C3 O7 SINGLE BEGINDASH 11
RAH O11 S1 DOUBLE NONE 12
RAH C3 C2 SINGLE NONE 13
RAH C1 C2 SINGLE NONE 14
RAH C1 C6 SINGLE BEGINDASH 15
RAH C2 O8 SINGLE BEGINWEDGE 16
RAH S1 C6 SINGLE NONE 17
RAH S1 O9 DOUBLE NONE 18
RAH S1 O10 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
RAH MurckoScaffold S1 scaffold C1CCOC1 InChI=1S/C4H8O/c1-2-4-5-3-1/h1-4H2 WYURNTSHIVDZCO-UHFFFAOYSA-N
RAH furanose F1 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
RAH phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
RAH ribose F3 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
RAH C1 S1 1
RAH C2 S1 1
RAH C3 S1 1
RAH C4 S1 1
RAH O1 S1 1
RAH C2 F1 1
RAH C1 F1 1
RAH O1 F1 1
RAH C4 F1 1
RAH C3 F1 1
RAH O2 F1 1
RAH O3 F2 1
RAH P1 F2 1
RAH O4 F2 1
RAH O6 F2 1
RAH O5 F2 1
RAH C2 F3 1
RAH C3 F3 1
RAH C4 F3 1
RAH O1 F3 1
RAH C1 F3 1
RAH C5 F3 1
RAH O3 F3 1
RAH O7 F3 1
RAH O8 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RAH
_pdbe_chem_comp_rdkit_properties.exactmw 323.992
_pdbe_chem_comp_rdkit_properties.amw 324.200
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 11
_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 11
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_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 125.719
_pdbe_chem_comp_rdkit_properties.tpsa 191.050
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.207
_pdbe_chem_comp_rdkit_properties.CrippenMR 56.248
_pdbe_chem_comp_rdkit_properties.chi0v 10.057
_pdbe_chem_comp_rdkit_properties.chi1v 6.778
_pdbe_chem_comp_rdkit_properties.chi2v 2.217
_pdbe_chem_comp_rdkit_properties.chi3v 2.217
_pdbe_chem_comp_rdkit_properties.chi4v 1.446
_pdbe_chem_comp_rdkit_properties.chi0n 21.346
_pdbe_chem_comp_rdkit_properties.chi1n 9.859
_pdbe_chem_comp_rdkit_properties.chi2n 1.467
_pdbe_chem_comp_rdkit_properties.chi3n 1.467
_pdbe_chem_comp_rdkit_properties.chi4n 0.853
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.140
_pdbe_chem_comp_rdkit_properties.kappa1 5.927
_pdbe_chem_comp_rdkit_properties.kappa2 5.331
_pdbe_chem_comp_rdkit_properties.kappa3 4.717
_pdbe_chem_comp_rdkit_properties.Phi 1.663
#
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
RAH UniChem PDBe RAH
RAH UniChem ZINC ZINC000096095525
RAH UniChem PubChem 155884485
#
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
RAH C1 -1.177 0.601 0.430 ETKDGv3 1
RAH C2 -1.447 -0.690 -0.345 ETKDGv3 2
RAH C3 -0.087 -1.344 -0.349 ETKDGv3 3
RAH C4 0.529 -0.842 0.968 ETKDGv3 4
RAH C5 2.059 -0.675 0.854 ETKDGv3 5
RAH C6 -2.366 1.042 1.299 ETKDGv3 6
RAH S1 -3.785 1.539 0.327 ETKDGv3 7
RAH O2 0.216 -1.709 2.035 ETKDGv3 8
RAH O3 2.362 0.354 -0.061 ETKDGv3 9
RAH O4 4.614 0.946 1.182 ETKDGv3 10
RAH O5 4.756 -0.962 -0.611 ETKDGv3 11
RAH O6 4.435 1.681 -1.319 ETKDGv3 12
RAH O7 -0.143 -2.748 -0.452 ETKDGv3 13
RAH O8 -1.879 -0.411 -1.651 ETKDGv3 14
RAH O9 -3.363 2.473 -0.774 ETKDGv3 15
RAH O10 -4.892 2.318 1.323 ETKDGv3 16
RAH O11 -4.441 0.328 -0.274 ETKDGv3 17
RAH O1 -0.044 0.417 1.257 ETKDGv3 18
RAH P1 4.057 0.512 -0.156 ETKDGv3 19
RAH H1 -0.932 1.419 -0.284 ETKDGv3 20
RAH H2 -2.195 -1.319 0.194 ETKDGv3 21
RAH H3 0.493 -0.954 -1.216 ETKDGv3 22
RAH H4 2.453 -0.422 1.865 ETKDGv3 23
RAH H5 2.499 -1.643 0.521 ETKDGv3 24
RAH H6 -2.054 1.912 1.916 ETKDGv3 25
RAH H7 -2.663 0.226 1.992 ETKDGv3 26
RAH H8 0.763 -2.532 1.940 ETKDGv3 27
RAH H9 5.722 -0.764 -0.707 ETKDGv3 28
RAH H10 3.927 2.486 -1.042 ETKDGv3 29
RAH H11 -0.807 -3.091 0.201 ETKDGv3 30
RAH H12 -2.186 -1.273 -2.035 ETKDGv3 31
RAH H13 -4.422 3.128 1.644 ETKDGv3 32
#