data_XIF
#
_chem_comp.id XIF
_chem_comp.name PIPERIDINE-3,4-DIOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H11 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "XYLOSE-DERIVED ISOFAGOMINE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-08-17
_chem_comp.pdbx_modified_date 2021-03-01
_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 117.146
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XIF
_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 1FH8
_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
XIF N1 N1 N 0 1 N N N N N N -65.007 20.466 54.473 1.876 -0.615 -0.321 N1 XIF 1
XIF C2 C2 C 0 1 N N N N N N -65.952 19.943 55.511 0.723 -1.403 0.131 C2 XIF 2
XIF C3 C3 C 0 1 N N R N N N -65.079 19.582 56.760 -0.571 -0.711 -0.303 C3 XIF 3
XIF O3 O3 O 0 1 N N N N N N -65.880 19.061 57.814 -1.694 -1.467 0.155 O3 XIF 4
XIF C4 C4 C 0 1 N N R N N N -63.976 18.583 56.335 -0.621 0.695 0.301 C4 XIF 5
XIF O4 O4 O 0 1 N N N N N N -63.206 18.275 57.489 -1.799 1.366 -0.148 O4 XIF 6
XIF C5 C5 C 0 1 N N N N N N -63.118 19.178 55.202 0.616 1.478 -0.147 C5 XIF 7
XIF C6 C6 C 0 1 N N N N N N -64.045 19.472 54.061 1.876 0.723 0.283 C6 XIF 8
XIF HN1 HN1 H 0 1 N N N N N N -65.534 20.755 53.674 2.741 -1.098 -0.130 HN1 XIF 9
XIF H21 H21 H 0 1 N N N N N N -66.693 20.713 55.774 0.768 -2.399 -0.309 H21 XIF 10
XIF H22 H22 H 0 1 N N N N N N -66.470 19.048 55.137 0.743 -1.485 1.218 H22 XIF 11
XIF H3 H3 H 0 1 N N N N N N -64.585 20.505 57.098 -0.599 -0.642 -1.391 H3 XIF 12
XIF HO3 HO3 H 0 1 N N N N N N -65.328 18.851 58.558 -1.725 -2.371 -0.187 HO3 XIF 13
XIF H4 H4 H 0 1 N N N N N N -64.464 17.673 55.957 -0.633 0.623 1.389 H4 XIF 14
XIF HO4 HO4 H 0 1 N N N N N N -62.519 17.661 57.257 -1.896 2.265 0.197 HO4 XIF 15
XIF H51 H51 H 0 1 N N N N N N -62.632 20.104 55.542 0.608 1.583 -1.232 H51 XIF 16
XIF H52 H52 H 0 1 N N N N N N -62.351 18.455 54.889 0.609 2.466 0.314 H52 XIF 17
XIF H61 H61 H 0 1 N N N N N N -64.570 18.551 53.768 1.891 0.631 1.369 H61 XIF 18
XIF H62 H62 H 0 1 N N N N N N -63.467 19.852 53.206 2.759 1.271 -0.047 H62 XIF 19
#
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
XIF N1 C2 SING N N 1
XIF N1 C6 SING N N 2
XIF N1 HN1 SING N N 3
XIF C2 C3 SING N N 4
XIF C2 H21 SING N N 5
XIF C2 H22 SING N N 6
XIF C3 O3 SING N N 7
XIF C3 C4 SING N N 8
XIF C3 H3 SING N N 9
XIF O3 HO3 SING N N 10
XIF C4 O4 SING N N 11
XIF C4 C5 SING N N 12
XIF C4 H4 SING N N 13
XIF O4 HO4 SING N N 14
XIF C5 C6 SING N N 15
XIF C5 H51 SING N N 16
XIF C5 H52 SING N N 17
XIF C6 H61 SING N N 18
XIF C6 H62 SING N N 19
#
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
XIF SMILES ACDLabs 12.01 OC1CCNCC1O
XIF InChI InChI 1.03 InChI=1S/C5H11NO2/c7-4-1-2-6-3-5(4)8/h4-8H,1-3H2/t4-,5-/m1/s1
XIF InChIKey InChI 1.03 IZXWMVPZODQBRB-RFZPGFLSSA-N
XIF SMILES_CANONICAL CACTVS 3.370 O[C@@H]1CCNC[C@H]1O
XIF SMILES CACTVS 3.370 O[CH]1CCNC[CH]1O
XIF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C1CNC[C@H]([C@@H]1O)O
XIF SMILES "OpenEye OEToolkits" 1.7.6 C1CNCC(C1O)O
#
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
XIF "SYSTEMATIC NAME" ACDLabs 12.01 (3R,4R)-piperidine-3,4-diol
XIF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 (3R,4R)-piperidine-3,4-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XIF 'Create component' 2000-08-17 RCSB
XIF 'Modify descriptor' 2011-06-04 RCSB
XIF 'Modify linking type' 2012-12-21 RCSB
XIF 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id XIF
_pdbx_chem_comp_synonyms.name "XYLOSE-DERIVED ISOFAGOMINE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id XIF
_pdbe_chem_comp_synonyms.name 'XYLOSE-DERIVED ISOFAGOMINE'
_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
XIF N1 N 3.000 -1.268 1
XIF C2 C 3.000 0.233 2
XIF C3 C 4.299 0.983 3
XIF O3 O 4.299 2.482 4
XIF C4 C 5.598 0.233 5
XIF O4 O 6.897 0.983 6
XIF C5 C 5.598 -1.268 7
XIF C6 C 4.299 -2.018 8
#
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
XIF N1 C2 SINGLE NONE 1
XIF N1 C6 SINGLE NONE 2
XIF C2 C3 SINGLE NONE 3
XIF C3 O3 SINGLE BEGINWEDGE 4
XIF C3 C4 SINGLE NONE 5
XIF C4 O4 SINGLE BEGINDASH 6
XIF C4 C5 SINGLE NONE 7
XIF C5 C6 SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id XIF
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles C1CCNCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H11N/c1-2-4-6-5-3-1/h6H,1-5H2
_pdbe_chem_comp_substructure.substructure_inchikeys NQRYJNQNLNOLGT-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
XIF N1 S1 1
XIF C2 S1 1
XIF C3 S1 1
XIF C4 S1 1
XIF C5 S1 1
XIF C6 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id XIF
_pdbe_chem_comp_rdkit_properties.exactmw 117.079
_pdbe_chem_comp_rdkit_properties.amw 117.148
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 64.018
_pdbe_chem_comp_rdkit_properties.tpsa 52.490
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.299
_pdbe_chem_comp_rdkit_properties.CrippenMR 29.500
_pdbe_chem_comp_rdkit_properties.chi0v 3.764
_pdbe_chem_comp_rdkit_properties.chi1v 1.855
_pdbe_chem_comp_rdkit_properties.chi2v 0.589
_pdbe_chem_comp_rdkit_properties.chi3v 0.589
_pdbe_chem_comp_rdkit_properties.chi4v 0.265
_pdbe_chem_comp_rdkit_properties.chi0n 14.764
_pdbe_chem_comp_rdkit_properties.chi1n 7.119
_pdbe_chem_comp_rdkit_properties.chi2n 0.589
_pdbe_chem_comp_rdkit_properties.chi3n 0.589
_pdbe_chem_comp_rdkit_properties.chi4n 0.265
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.120
_pdbe_chem_comp_rdkit_properties.kappa1 1.046
_pdbe_chem_comp_rdkit_properties.kappa2 2.437
_pdbe_chem_comp_rdkit_properties.kappa3 1.183
_pdbe_chem_comp_rdkit_properties.Phi 0.319
#
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
XIF UniChem PDBe XIF
XIF UniChem ZINC ZINC000005847923
XIF UniChem SureChEMBL SCHEMBL6104004
XIF UniChem Nikkaji J947.805A
XIF UniChem BRENDA 85276
XIF UniChem 'PubChem TPHARMA' 15686044
XIF UniChem PubChem 445613
#
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
XIF N1 0.595 1.437 0.687 ETKDGv3 1
XIF C2 1.473 0.503 -0.028 ETKDGv3 2
XIF C3 0.849 -0.912 -0.127 ETKDGv3 3
XIF O3 1.303 -1.716 0.932 ETKDGv3 4
XIF C4 -0.695 -0.870 -0.098 ETKDGv3 5
XIF O4 -1.205 -1.995 -0.766 ETKDGv3 6
XIF C5 -1.210 0.415 -0.757 ETKDGv3 7
XIF C6 -0.668 1.671 -0.040 ETKDGv3 8
XIF HN1 0.381 1.043 1.634 ETKDGv3 9
XIF H21 1.671 0.896 -1.050 ETKDGv3 10
XIF H22 2.456 0.457 0.489 ETKDGv3 11
XIF H3 1.173 -1.361 -1.097 ETKDGv3 12
XIF HO3 2.232 -1.988 0.710 ETKDGv3 13
XIF H4 -1.038 -0.882 0.965 ETKDGv3 14
XIF HO4 -2.158 -2.079 -0.500 ETKDGv3 15
XIF H51 -2.322 0.430 -0.741 ETKDGv3 16
XIF H52 -0.889 0.431 -1.823 ETKDGv3 17
XIF H61 -1.434 2.039 0.679 ETKDGv3 18
XIF H62 -0.512 2.480 -0.786 ETKDGv3 19
#