data_XPS
#
_chem_comp.id XPS
_chem_comp.name 6-deoxy-6-(methylamino)-D-galactitol
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H17 N O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-12-23
_chem_comp.pdbx_modified_date 2021-09-17
_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 195.214
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code XPS
_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 7L2V
_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
XPS C1 C1 C 0 1 N N R N N N 133.061 131.700 104.886 -0.993 -0.490 0.137 C1 XPS 1
XPS C2 C2 C 0 1 N N R N N N 135.179 132.242 103.625 1.497 -0.440 -0.064 C2 XPS 2
XPS C3 C3 C 0 1 N N S N N N 131.917 132.540 105.452 -2.265 0.360 0.125 C3 XPS 3
XPS C4 C4 C 0 1 N N N N N N 136.264 133.308 103.492 2.722 0.472 -0.152 C4 XPS 4
XPS C5 C5 C 0 1 N N N N N N 131.258 133.337 104.329 -3.490 -0.552 0.213 C5 XPS 5
XPS C6 C6 C 0 1 N N N N N N 136.784 134.431 101.471 5.135 0.497 -0.349 C6 XPS 6
XPS N N1 N 0 1 N N N N N N 136.914 133.182 102.200 3.936 -0.347 -0.261 N XPS 7
XPS C C7 C 0 1 N N S N N N 134.349 132.525 104.875 0.225 0.410 -0.076 C XPS 8
XPS O O1 O 0 1 N N N N N N 135.108 132.225 106.013 0.290 1.380 0.972 O XPS 9
XPS O1 O2 O 0 1 N N N N N N 132.728 131.271 103.595 -1.058 -1.459 -0.911 O1 XPS 10
XPS O2 O3 O 0 1 N N N N N N 135.777 130.981 103.735 1.553 -1.196 1.147 O2 XPS 11
XPS O3 O4 O 0 1 N N N N N N 132.408 133.424 106.421 -2.320 1.117 -1.086 O3 XPS 12
XPS O4 O5 O 0 1 N N N N N N 131.272 132.579 103.150 -4.671 0.245 0.319 O4 XPS 13
XPS H1 H1 H 0 1 N N N N N N 133.212 130.832 105.545 -0.905 -0.999 1.097 H1 XPS 14
XPS H2 H2 H 0 1 N N N N N N 134.523 132.287 102.743 1.488 -1.120 -0.916 H2 XPS 15
XPS H3 H3 H 0 1 N N N N N N 131.168 131.865 105.892 -2.256 1.040 0.978 H3 XPS 16
XPS H4 H4 H 0 1 N N N N N N 137.008 133.175 104.291 2.635 1.112 -1.030 H4 XPS 17
XPS H5 H5 H 0 1 N N N N N N 135.809 134.306 103.577 2.780 1.090 0.743 H5 XPS 18
XPS H6 H6 H 0 1 N N N N N N 131.812 134.274 104.170 -3.548 -1.170 -0.682 H6 XPS 19
XPS H7 H7 H 0 1 N N N N N N 130.218 133.568 104.604 -3.403 -1.192 1.092 H7 XPS 20
XPS H8 H8 H 0 1 N N N N N N 137.276 134.337 100.492 5.210 1.115 0.546 H8 XPS 21
XPS H9 H9 H 0 1 N N N N N N 135.718 134.661 101.325 6.019 -0.135 -0.428 H9 XPS 22
XPS H10 H10 H 0 1 N N N N N N 137.259 135.241 102.044 5.065 1.138 -1.228 H10 XPS 23
XPS H11 H11 H 0 1 N N N N N N 136.482 132.445 101.680 3.878 -0.976 -1.048 H11 XPS 24
XPS H13 H13 H 0 1 N N N N N N 134.076 133.591 104.874 0.137 0.919 -1.036 H13 XPS 25
XPS H14 H14 H 0 1 N N N N N N 134.594 132.400 106.792 0.370 0.998 1.857 H14 XPS 26
XPS H15 H15 H 0 1 N N N N N N 131.927 130.762 103.627 -1.138 -1.077 -1.796 H15 XPS 27
XPS H16 H16 H 0 1 N N N N N N 135.103 130.317 103.818 1.564 -0.655 1.949 H16 XPS 28
XPS H17 H17 H 0 1 N N N N N N 132.819 132.931 107.121 -2.332 0.575 -1.887 H17 XPS 29
XPS H18 H18 H 0 1 N N N N N N 130.862 133.074 102.450 -5.488 -0.269 0.380 H18 XPS 30
#
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
XPS C6 N SING N N 1
XPS N C4 SING N N 2
XPS O4 C5 SING N N 3
XPS C4 C2 SING N N 4
XPS O1 C1 SING N N 5
XPS C2 O2 SING N N 6
XPS C2 C SING N N 7
XPS C5 C3 SING N N 8
XPS C C1 SING N N 9
XPS C O SING N N 10
XPS C1 C3 SING N N 11
XPS C3 O3 SING N N 12
XPS C1 H1 SING N N 13
XPS C2 H2 SING N N 14
XPS C3 H3 SING N N 15
XPS C4 H4 SING N N 16
XPS C4 H5 SING N N 17
XPS C5 H6 SING N N 18
XPS C5 H7 SING N N 19
XPS C6 H8 SING N N 20
XPS C6 H9 SING N N 21
XPS C6 H10 SING N N 22
XPS N H11 SING N N 23
XPS C H13 SING N N 24
XPS O H14 SING N N 25
XPS O1 H15 SING N N 26
XPS O2 H16 SING N N 27
XPS O3 H17 SING N N 28
XPS O4 H18 SING N N 29
#
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
XPS SMILES ACDLabs 12.01 C(C(O)CO)(C(C(O)CNC)O)O
XPS InChI InChI 1.03 InChI=1S/C7H17NO5/c1-8-2-4(10)6(12)7(13)5(11)3-9/h4-13H,2-3H2,1H3/t4-,5+,6+,7-/m1/s1
XPS InChIKey InChI 1.03 MBBZMMPHUWSWHV-JRTVQGFMSA-N
XPS SMILES_CANONICAL CACTVS 3.385 CNC[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)CO
XPS SMILES CACTVS 3.385 CNC[CH](O)[CH](O)[CH](O)[CH](O)CO
XPS SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CNC[C@H]([C@@H]([C@@H]([C@H](CO)O)O)O)O
XPS SMILES "OpenEye OEToolkits" 2.0.7 CNCC(C(C(C(CO)O)O)O)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
XPS "SYSTEMATIC NAME" ACDLabs 12.01 6-deoxy-6-(methylamino)-D-galactitol
XPS "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 (2~{S},3~{R},4~{S},5~{R})-6-(methylamino)hexane-1,2,3,4,5-pentol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
XPS 'Create component' 2020-12-23 RCSB
XPS 'Initial release' 2021-09-22 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
XPS C1 C 9.495 0.375 1
XPS C2 C 6.897 0.375 2
XPS C3 C 10.794 -0.375 3
XPS C4 C 5.598 -0.375 4
XPS C5 C 12.093 0.375 5
XPS C6 C 3.000 -0.375 6
XPS N N 4.299 0.375 7
XPS C C 8.196 -0.375 8
XPS O O 8.196 -1.875 9
XPS O1 O 9.495 1.875 10
XPS O2 O 6.897 1.875 11
XPS O3 O 10.794 -1.875 12
XPS O4 O 13.392 -0.375 13
#
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
XPS C6 N SINGLE NONE 1
XPS N C4 SINGLE NONE 2
XPS O4 C5 SINGLE NONE 3
XPS C4 C2 SINGLE NONE 4
XPS C1 O1 SINGLE BEGINDASH 5
XPS C2 O2 SINGLE BEGINWEDGE 6
XPS C2 C SINGLE NONE 7
XPS C5 C3 SINGLE NONE 8
XPS C C1 SINGLE NONE 9
XPS C O SINGLE BEGINWEDGE 10
XPS C1 C3 SINGLE NONE 11
XPS C3 O3 SINGLE BEGINDASH 12
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id XPS
_pdbe_chem_comp_rdkit_properties.exactmw 195.111
_pdbe_chem_comp_rdkit_properties.amw 195.215
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_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 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_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 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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 100.826
_pdbe_chem_comp_rdkit_properties.tpsa 113.180
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.358
_pdbe_chem_comp_rdkit_properties.CrippenMR 45.040
_pdbe_chem_comp_rdkit_properties.chi0v 5.988
_pdbe_chem_comp_rdkit_properties.chi1v 2.718
_pdbe_chem_comp_rdkit_properties.chi2v 0.869
_pdbe_chem_comp_rdkit_properties.chi3v 0.869
_pdbe_chem_comp_rdkit_properties.chi4v 0.354
_pdbe_chem_comp_rdkit_properties.chi0n 22.988
_pdbe_chem_comp_rdkit_properties.chi1n 10.706
_pdbe_chem_comp_rdkit_properties.chi2n 0.869
_pdbe_chem_comp_rdkit_properties.chi3n 0.869
_pdbe_chem_comp_rdkit_properties.chi4n 0.354
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.240
_pdbe_chem_comp_rdkit_properties.kappa1 2.133
_pdbe_chem_comp_rdkit_properties.kappa2 6.250
_pdbe_chem_comp_rdkit_properties.kappa3 3.988
_pdbe_chem_comp_rdkit_properties.Phi 1.026
#
_pdbe_chem_comp_external_mappings.comp_id XPS
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 56846464
#
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
XPS C1 -1.003 -0.312 0.555 ETKDGv3 1
XPS C2 1.300 0.527 -0.337 ETKDGv3 2
XPS C3 -2.543 -0.109 0.529 ETKDGv3 3
XPS C4 1.985 -0.862 -0.373 ETKDGv3 4
XPS C5 -3.168 -0.471 -0.832 ETKDGv3 5
XPS C6 4.033 -0.222 0.796 ETKDGv3 6
XPS N 3.456 -0.790 -0.425 ETKDGv3 7
XPS C -0.237 0.449 -0.571 ETKDGv3 8
XPS O -0.749 1.750 -0.728 ETKDGv3 9
XPS O1 -0.732 -1.688 0.455 ETKDGv3 10
XPS O2 1.868 1.343 -1.332 ETKDGv3 11
XPS O3 -2.859 1.217 0.873 ETKDGv3 12
XPS O4 -4.566 -0.517 -0.731 ETKDGv3 13
XPS H1 -0.631 0.068 1.537 ETKDGv3 14
XPS H2 1.480 0.973 0.671 ETKDGv3 15
XPS H3 -2.974 -0.796 1.297 ETKDGv3 16
XPS H4 1.636 -1.418 -1.270 ETKDGv3 17
XPS H5 1.691 -1.456 0.517 ETKDGv3 18
XPS H6 -2.814 -1.475 -1.149 ETKDGv3 19
XPS H7 -2.860 0.258 -1.616 ETKDGv3 20
XPS H8 3.833 0.870 0.859 ETKDGv3 21
XPS H9 5.133 -0.369 0.780 ETKDGv3 22
XPS H10 3.632 -0.733 1.698 ETKDGv3 23
XPS H11 3.764 -0.221 -1.247 ETKDGv3 24
XPS H13 -0.408 -0.087 -1.531 ETKDGv3 25
XPS H14 -0.555 2.249 0.109 ETKDGv3 26
XPS H15 -0.888 -2.082 1.353 ETKDGv3 27
XPS H16 1.848 2.277 -0.995 ETKDGv3 28
XPS H17 -3.777 1.211 1.251 ETKDGv3 29
XPS H18 -4.892 0.415 -0.836 ETKDGv3 30
#