data_CAP
#
_chem_comp.id CAP
_chem_comp.name 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
_chem_comp.type SACCHARIDE
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H14 O13 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 356.115
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CAP
_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 ?
_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
CAP C1 C1 C 0 1 N N N N N N 5.085 2.200 30.258 -0.397 -0.118 -2.323 C1 CAP 1
CAP C2 C2 C 0 1 N N R N N N 5.331 2.960 31.548 0.375 0.374 -1.097 C2 CAP 2
CAP C3 C3 C 0 1 N N R N N N 3.964 3.140 32.318 -0.234 -0.232 0.167 C3 CAP 3
CAP C4 C4 C 0 1 N N R N N N 3.320 1.862 32.908 0.441 0.371 1.399 C4 CAP 4
CAP C5 C5 C 0 1 N N N N N N 2.580 2.047 34.249 -0.261 -0.127 2.663 C5 CAP 5
CAP C C C 0 1 N N N N N N 6.424 2.278 32.437 1.818 -0.046 -1.211 C CAP 6
CAP O1 O1 O 0 1 N N N N N N 6.229 2.244 29.415 0.172 0.448 -3.504 O1 CAP 7
CAP O2 O2 O 0 1 N N N N N N 5.794 4.230 31.064 0.298 1.799 -1.027 O2 CAP 8
CAP O3 O3 O 0 1 N N N N N N 4.064 4.086 33.371 -1.634 0.051 0.204 O3 CAP 9
CAP O4 O4 O 0 1 N N N N N N 2.375 1.437 31.958 1.814 -0.022 1.431 O4 CAP 10
CAP O5 O5 O 0 1 N N N N N N 1.856 0.850 34.574 0.369 0.436 3.814 O5 CAP 11
CAP O6 O6 O 0 1 N N N N N N 6.627 1.068 32.374 2.691 0.788 -1.229 O6 CAP 12
CAP O7 O7 O 0 1 N N N N N N 7.123 2.967 33.188 2.133 -1.348 -1.291 O7 CAP 13
CAP P1 P1 P 0 1 N N N N N N 6.131 1.428 28.039 -0.684 -0.109 -4.748 P1 CAP 14
CAP P2 P2 P 0 1 N N N N N N 0.236 0.863 34.631 -0.417 -0.128 5.100 P2 CAP 15
CAP O1P O1P O 0 1 N N N N N N 5.086 2.107 27.244 -2.098 0.302 -4.597 O1P CAP 16
CAP O2P O2P O 0 1 N N N N N N 5.974 0.002 28.368 -0.094 0.492 -6.120 O2P CAP 17
CAP O3P O3P O 0 1 N N N N N N 7.571 1.669 27.406 -0.594 -1.716 -4.784 O3P CAP 18
CAP O4P O4P O 0 1 N N N N N N -0.254 1.567 33.431 -0.328 -1.605 5.123 O4P CAP 19
CAP O5P O5P O 0 1 N N N N N N -0.187 -0.535 34.877 0.245 0.470 6.440 O5P CAP 20
CAP O6P O6P O 0 1 N N N N N N -0.019 1.766 35.931 -1.962 0.315 5.022 O6P CAP 21
CAP H11 1H1 H 0 1 N N N N N N 4.758 1.152 30.453 -0.338 -1.205 -2.376 H11 CAP 22
CAP H12 2H1 H 0 1 N N N N N N 4.172 2.566 29.732 -1.440 0.186 -2.241 H12 CAP 23
CAP H3 H3 H 0 1 N N N N N N 3.257 3.534 31.602 -0.083 -1.311 0.162 H3 CAP 24
CAP H4 H4 H 0 1 N N N N N N 4.078 1.100 33.024 0.376 1.458 1.353 H4 CAP 25
CAP H51 1H5 H 0 1 N N N N N N 3.269 2.355 35.069 -1.309 0.173 2.639 H51 CAP 26
CAP H52 2H5 H 0 1 N N N N N N 1.921 2.946 34.244 -0.197 -1.214 2.710 H52 CAP 27
CAP HO2 HO2 H 0 1 N N N N N N 6.720 4.347 31.282 -0.630 2.022 -0.878 HO2 CAP 28
CAP HO3 HO3 H 0 1 N N N N N N 4.671 3.764 34.043 -1.724 1.014 0.208 HO3 CAP 29
CAP HO4 HO4 H 0 1 N N N N N N 1.787 2.163 31.737 1.826 -0.988 1.472 HO4 CAP 30
CAP HO7 HO7 H 0 1 N N N N N N 7.786 2.553 33.727 3.059 -1.618 -1.364 HO7 CAP 31
CAP HOP2 2HOP H 0 0 N N N N N N 5.915 -0.481 27.552 -0.634 0.134 -6.837 HOP2 CAP 32
CAP HOP3 3HOP H 0 0 N N N N N N 7.512 1.185 26.590 0.340 -1.941 -4.883 HOP3 CAP 33
CAP HOP5 5HOP H 0 0 N N N N N N -1.136 -0.527 34.910 -0.254 0.108 7.185 HOP5 CAP 34
CAP HOP6 6HOP H 0 0 N N N N N N -0.968 1.773 35.964 -1.976 1.281 5.009 HOP6 CAP 35
#
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
CAP C1 C2 SING N N 1
CAP C1 O1 SING N N 2
CAP C1 H11 SING N N 3
CAP C1 H12 SING N N 4
CAP C2 C3 SING N N 5
CAP C2 C SING N N 6
CAP C2 O2 SING N N 7
CAP C3 C4 SING N N 8
CAP C3 O3 SING N N 9
CAP C3 H3 SING N N 10
CAP C4 C5 SING N N 11
CAP C4 O4 SING N N 12
CAP C4 H4 SING N N 13
CAP C5 O5 SING N N 14
CAP C5 H51 SING N N 15
CAP C5 H52 SING N N 16
CAP C O6 DOUB N N 17
CAP C O7 SING N N 18
CAP O1 P1 SING N N 19
CAP O2 HO2 SING N N 20
CAP O3 HO3 SING N N 21
CAP O4 HO4 SING N N 22
CAP O5 P2 SING N N 23
CAP O7 HO7 SING N N 24
CAP P1 O1P DOUB N N 25
CAP P1 O2P SING N N 26
CAP P1 O3P SING N N 27
CAP P2 O4P DOUB N N 28
CAP P2 O5P SING N N 29
CAP P2 O6P SING N N 30
CAP O2P HOP2 SING N N 31
CAP O3P HOP3 SING N N 32
CAP O5P HOP5 SING N N 33
CAP O6P HOP6 SING N N 34
#
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
CAP SMILES ACDLabs 10.04 O=P(O)(O)OCC(O)C(O)C(O)(C(=O)O)COP(=O)(O)O
CAP SMILES_CANONICAL CACTVS 3.341 O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@](O)(CO[P](O)(O)=O)C(O)=O
CAP SMILES CACTVS 3.341 O[CH](CO[P](O)(O)=O)[CH](O)[C](O)(CO[P](O)(O)=O)C(O)=O
CAP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@H]([C@H]([C@](COP(=O)(O)O)(C(=O)O)O)O)O)OP(=O)(O)O
CAP SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(C(COP(=O)(O)O)(C(=O)O)O)O)O)OP(=O)(O)O
CAP InChI InChI 1.03 InChI=1S/C6H14O13P2/c7-3(1-18-20(12,13)14)4(8)6(11,5(9)10)2-19-21(15,16)17/h3-4,7-8,11H,1-2H2,(H,9,10)(H2,12,13,14)(H2,15,16,17)/t3-,4-,6-/m1/s1
CAP InChIKey InChI 1.03 ITHCSGCUQDMYAI-ZMIZWQJLSA-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
CAP "SYSTEMATIC NAME" ACDLabs 10.04 "5-O-phosphono-2-C-[(phosphonooxy)methyl]-D-ribonic acid"
CAP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3R,4R)-2,3,4-trihydroxy-5-phosphonooxy-2-(phosphonooxymethyl)pentanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CAP 'Create component' 1999-07-08 RCSB
CAP 'Modify descriptor' 2011-06-04 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
CAP C1 C 7.354 0.475 1
CAP C2 C 8.104 -0.824 2
CAP C3 C 9.403 -0.073 3
CAP C4 C 10.703 -0.824 4
CAP C5 C 12.002 -0.073 5
CAP C C 6.805 -1.573 6
CAP O1 O 5.854 0.475 7
CAP O2 O 8.854 -2.123 8
CAP O3 O 9.403 1.427 9
CAP O4 O 10.703 -2.324 10
CAP O5 O 13.301 -0.824 11
CAP O6 O 5.506 -0.824 12
CAP O7 O 6.805 -3.074 13
CAP P1 P 5.104 1.774 14
CAP P2 P 14.600 -0.073 15
CAP O1P O 4.354 3.074 16
CAP O2P O 3.805 1.024 17
CAP O3P O 6.404 2.525 18
CAP O4P O 15.899 0.676 19
CAP O5P O 15.350 -1.373 20
CAP O6P O 13.850 1.226 21
#
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
CAP C1 C2 SINGLE NONE 1
CAP C1 O1 SINGLE NONE 2
CAP C2 C3 SINGLE NONE 3
CAP C2 C SINGLE NONE 4
CAP C2 O2 SINGLE BEGINDASH 5
CAP C3 C4 SINGLE NONE 6
CAP C3 O3 SINGLE BEGINDASH 7
CAP C4 C5 SINGLE NONE 8
CAP C4 O4 SINGLE BEGINWEDGE 9
CAP C5 O5 SINGLE NONE 10
CAP C O6 DOUBLE NONE 11
CAP C O7 SINGLE NONE 12
CAP O1 P1 SINGLE NONE 13
CAP O5 P2 SINGLE NONE 14
CAP P1 O1P DOUBLE NONE 15
CAP P1 O2P SINGLE NONE 16
CAP P1 O3P SINGLE NONE 17
CAP P2 O4P DOUBLE NONE 18
CAP P2 O5P SINGLE NONE 19
CAP P2 O6P SINGLE NONE 20
#
_pdbe_chem_comp_substructure.comp_id CAP
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-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
CAP O1 F1 1
CAP P1 F1 1
CAP O1P F1 1
CAP O2P F1 1
CAP O3P F1 1
CAP O5 F1 2
CAP P2 F1 2
CAP O4P F1 2
CAP O5P F1 2
CAP O6P F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id CAP
_pdbe_chem_comp_rdkit_properties.exactmw 355.991
_pdbe_chem_comp_rdkit_properties.amw 356.113
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 13
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 16
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 13
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 15
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 136.769
_pdbe_chem_comp_rdkit_properties.tpsa 231.510
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.257
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.591
_pdbe_chem_comp_rdkit_properties.chi0v 10.991
_pdbe_chem_comp_rdkit_properties.chi1v 7.061
_pdbe_chem_comp_rdkit_properties.chi2v 1.995
_pdbe_chem_comp_rdkit_properties.chi3v 1.995
_pdbe_chem_comp_rdkit_properties.chi4v 1.040
_pdbe_chem_comp_rdkit_properties.chi0n 23.202
_pdbe_chem_comp_rdkit_properties.chi1n 10.405
_pdbe_chem_comp_rdkit_properties.chi2n 1.365
_pdbe_chem_comp_rdkit_properties.chi3n 1.365
_pdbe_chem_comp_rdkit_properties.chi4n 0.604
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.430
_pdbe_chem_comp_rdkit_properties.kappa1 6.991
_pdbe_chem_comp_rdkit_properties.kappa2 7.221
_pdbe_chem_comp_rdkit_properties.kappa3 7.401
_pdbe_chem_comp_rdkit_properties.Phi 2.404
#
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
CAP UniChem PDBe CAP
CAP UniChem ChEBI 41351
CAP UniChem SureChEMBL SCHEMBL65098
CAP UniChem Nikkaji J985.969A
CAP UniChem 'EPA CompTox Dashboard' DTXSID90181857
CAP UniChem ACTor 27442-42-8
CAP UniChem PubChem 122210
#
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
CAP C1 -2.158 -0.367 0.282 ETKDGv3 1
CAP C2 -0.965 0.587 0.548 ETKDGv3 2
CAP C3 0.251 -0.209 1.159 ETKDGv3 3
CAP C4 0.968 -1.216 0.195 ETKDGv3 4
CAP C5 2.169 -0.626 -0.568 ETKDGv3 5
CAP C -0.581 1.304 -0.737 ETKDGv3 6
CAP O1 -3.271 0.381 -0.158 ETKDGv3 7
CAP O2 -1.428 1.527 1.495 ETKDGv3 8
CAP O3 1.180 0.642 1.788 ETKDGv3 9
CAP O4 1.414 -2.333 0.923 ETKDGv3 10
CAP O5 3.251 -0.423 0.314 ETKDGv3 11
CAP O6 -0.696 0.727 -1.853 ETKDGv3 12
CAP O7 -0.049 2.591 -0.691 ETKDGv3 13
CAP P1 -4.559 -0.692 -0.474 ETKDGv3 14
CAP P2 4.508 0.341 -0.547 ETKDGv3 15
CAP O1P -4.210 -1.587 -1.642 ETKDGv3 16
CAP O2P -5.938 0.207 -0.862 ETKDGv3 17
CAP O3P -4.882 -1.641 0.892 ETKDGv3 18
CAP O4P 5.704 0.491 0.365 ETKDGv3 19
CAP O5P 4.945 -0.594 -1.890 ETKDGv3 20
CAP O6P 4.002 1.875 -1.058 ETKDGv3 21
CAP H11 -2.408 -0.890 1.234 ETKDGv3 22
CAP H12 -1.883 -1.130 -0.477 ETKDGv3 23
CAP H3 -0.184 -0.819 1.982 ETKDGv3 24
CAP H4 0.255 -1.568 -0.581 ETKDGv3 25
CAP H51 1.865 0.320 -1.064 ETKDGv3 26
CAP H52 2.460 -1.356 -1.357 ETKDGv3 27
CAP HO2 -0.717 2.197 1.668 ETKDGv3 28
CAP HO3 1.452 1.336 1.134 ETKDGv3 29
CAP HO4 0.620 -2.905 1.092 ETKDGv3 30
CAP HO7 0.232 3.068 -1.539 ETKDGv3 31
CAP HOP2 -6.105 0.768 -0.063 ETKDGv3 32
CAP HOP3 -5.679 -2.174 0.646 ETKDGv3 33
CAP HOP5 5.660 -0.077 -2.339 ETKDGv3 34
CAP HOP6 4.773 2.244 -1.558 ETKDGv3 35
#