data_OR6
#
_chem_comp.id OR6
_chem_comp.name "(2~{S})-2-butyl-3-methylidene-butanedioic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H14 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-02-09
_chem_comp.pdbx_modified_date 2024-01-05
_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 186.205
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code OR6
_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 8I52
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
OR6 C1 C1 C 0 1 N N N N N N -1.718 23.333 35.405 -1.545 0.362 0.802 C1 OR6 1
OR6 O1 O1 O 0 1 N N N N N N -0.478 20.473 34.401 -1.146 -1.927 -0.451 O1 OR6 2
OR6 C2 C2 C 0 1 N N S N N N -2.121 21.864 35.291 -0.155 -0.219 0.835 C2 OR6 3
OR6 O2 O2 O 0 1 N N N N N N -0.265 20.865 36.459 1.005 -2.216 -0.037 O2 OR6 4
OR6 C3 C3 C 0 1 N N N N N N -2.520 24.224 36.093 -2.206 0.570 1.938 C3 OR6 5
OR6 C4 C4 C 0 1 N N N N N N -0.408 23.692 34.811 -2.168 0.706 -0.484 C4 OR6 6
OR6 O3 O3 O 0 1 N N N N N N -0.016 22.900 33.811 -3.287 1.179 -0.510 O3 OR6 7
OR6 C5 C5 C 0 1 N N N N N N -0.826 21.024 35.360 -0.135 -1.517 0.068 C5 OR6 8
OR6 O4 O4 O 0 1 N N N N N N 0.255 24.716 35.381 -1.498 0.495 -1.635 O4 OR6 9
OR6 C6 C6 C 0 1 N N N N N N -3.067 21.383 36.383 0.825 0.766 0.195 C6 OR6 10
OR6 C7 C7 C 0 1 N N N N N N -3.587 19.973 36.040 2.252 0.233 0.339 C7 OR6 11
OR6 C8 C8 C 0 1 N N N N N N -4.342 19.386 37.214 3.232 1.218 -0.301 C8 OR6 12
OR6 C9 C9 C 0 1 N N N N N N -4.642 17.951 36.919 4.659 0.684 -0.156 C9 OR6 13
OR6 H2 H2 H 0 1 N N N N N N -2.594 21.700 34.312 0.138 -0.403 1.868 H2 OR6 14
OR6 H3 H3 H 0 1 N N N N N N 0.451 20.249 36.363 0.969 -3.042 -0.539 H3 OR6 15
OR6 H4 H4 H 0 1 N N N N N N -3.436 23.883 36.553 -3.202 0.987 1.915 H4 OR6 16
OR6 H5 H5 H 0 1 N N N N N N -2.231 25.262 36.171 -1.747 0.322 2.884 H5 OR6 17
OR6 H7 H7 H 0 1 N N N N N N 1.100 24.821 34.959 -1.949 0.737 -2.455 H7 OR6 18
OR6 H8 H8 H 0 1 N N N N N N -2.530 21.351 37.343 0.586 0.882 -0.862 H8 OR6 19
OR6 H9 H9 H 0 1 N N N N N N -3.917 22.077 36.461 0.746 1.732 0.693 H9 OR6 20
OR6 H10 H10 H 0 1 N N N N N N -4.260 20.037 35.172 2.491 0.117 1.396 H10 OR6 21
OR6 H11 H11 H 0 1 N N N N N N -2.734 19.322 35.796 2.330 -0.734 -0.159 H11 OR6 22
OR6 H12 H12 H 0 1 N N N N N N -3.727 19.457 38.123 2.992 1.334 -1.358 H12 OR6 23
OR6 H13 H13 H 0 1 N N N N N N -5.282 19.938 37.364 3.153 2.184 0.198 H13 OR6 24
OR6 H14 H14 H 0 1 N N N N N N -5.191 17.510 37.764 4.898 0.569 0.901 H14 OR6 25
OR6 H15 H15 H 0 1 N N N N N N -5.255 17.884 36.008 4.737 -0.282 -0.655 H15 OR6 26
OR6 H16 H16 H 0 1 N N N N N N -3.700 17.403 36.768 5.357 1.386 -0.612 H16 OR6 27
#
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
OR6 O3 C4 DOUB N N 1
OR6 O1 C5 DOUB N N 2
OR6 C4 O4 SING N N 3
OR6 C4 C1 SING N N 4
OR6 C2 C5 SING N N 5
OR6 C2 C1 SING N N 6
OR6 C2 C6 SING N N 7
OR6 C5 O2 SING N N 8
OR6 C1 C3 DOUB N N 9
OR6 C7 C6 SING N N 10
OR6 C7 C8 SING N N 11
OR6 C9 C8 SING N N 12
OR6 C2 H2 SING N N 13
OR6 O2 H3 SING N N 14
OR6 C3 H4 SING N N 15
OR6 C3 H5 SING N N 16
OR6 O4 H7 SING N N 17
OR6 C6 H8 SING N N 18
OR6 C6 H9 SING N N 19
OR6 C7 H10 SING N N 20
OR6 C7 H11 SING N N 21
OR6 C8 H12 SING N N 22
OR6 C8 H13 SING N N 23
OR6 C9 H14 SING N N 24
OR6 C9 H15 SING N N 25
OR6 C9 H16 SING N N 26
#
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
OR6 InChI InChI 1.06 "InChI=1S/C9H14O4/c1-3-4-5-7(9(12)13)6(2)8(10)11/h7H,2-5H2,1H3,(H,10,11)(H,12,13)/t7-/m0/s1"
OR6 InChIKey InChI 1.06 ULDVOPUXMRCBDH-ZETCQYMHSA-N
OR6 SMILES_CANONICAL CACTVS 3.385 "CCCC[C@H](C(O)=O)C(=C)C(O)=O"
OR6 SMILES CACTVS 3.385 "CCCC[CH](C(O)=O)C(=C)C(O)=O"
OR6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCCC[C@@H](C(=C)C(=O)O)C(=O)O"
OR6 SMILES "OpenEye OEToolkits" 2.0.7 "CCCCC(C(=C)C(=O)O)C(=O)O"
#
_pdbx_chem_comp_identifier.comp_id OR6
_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})-2-butyl-3-methylidene-butanedioic 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
OR6 'Create component' 2023-02-09 PDBJ
OR6 'Initial release' 2024-01-10 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
OR6 C1 C 7.702 1.875 1
OR6 O1 O 3.805 1.125 2
OR6 C2 C 6.404 1.125 3
OR6 O2 O 5.104 3.375 4
OR6 C3 C 7.702 3.375 5
OR6 C4 C 9.002 1.125 6
OR6 O3 O 10.301 1.875 7
OR6 C5 C 5.104 1.875 8
OR6 O4 O 9.002 -0.375 9
OR6 C6 C 6.404 -0.375 10
OR6 C7 C 5.104 -1.125 11
OR6 C8 C 5.104 -2.625 12
OR6 C9 C 3.805 -3.375 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
OR6 O3 C4 DOUBLE NONE 1
OR6 O1 C5 DOUBLE NONE 2
OR6 C4 O4 SINGLE NONE 3
OR6 C4 C1 SINGLE NONE 4
OR6 C2 C5 SINGLE NONE 5
OR6 C2 C1 SINGLE NONE 6
OR6 C2 C6 SINGLE BEGINDASH 7
OR6 C5 O2 SINGLE NONE 8
OR6 C1 C3 DOUBLE NONE 9
OR6 C7 C6 SINGLE NONE 10
OR6 C7 C8 SINGLE NONE 11
OR6 C9 C8 SINGLE NONE 12
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id OR6
_pdbe_chem_comp_rdkit_properties.exactmw 186.089
_pdbe_chem_comp_rdkit_properties.amw 186.207
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 96.724
_pdbe_chem_comp_rdkit_properties.tpsa 74.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.518
_pdbe_chem_comp_rdkit_properties.CrippenMR 47.427
_pdbe_chem_comp_rdkit_properties.chi0v 6.133
_pdbe_chem_comp_rdkit_properties.chi1v 2.816
_pdbe_chem_comp_rdkit_properties.chi2v 0.908
_pdbe_chem_comp_rdkit_properties.chi3v 0.908
_pdbe_chem_comp_rdkit_properties.chi4v 0.411
_pdbe_chem_comp_rdkit_properties.chi0n 20.133
_pdbe_chem_comp_rdkit_properties.chi1n 9.633
_pdbe_chem_comp_rdkit_properties.chi2n 0.908
_pdbe_chem_comp_rdkit_properties.chi3n 0.908
_pdbe_chem_comp_rdkit_properties.chi4n 0.411
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.320
_pdbe_chem_comp_rdkit_properties.kappa1 2.187
_pdbe_chem_comp_rdkit_properties.kappa2 5.347
_pdbe_chem_comp_rdkit_properties.kappa3 3.734
_pdbe_chem_comp_rdkit_properties.Phi 0.900
#
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
OR6 UniChem ChEMBL CHEMBL3359155
OR6 UniChem PDBe OR6
OR6 UniChem ZINC ZINC000034202661
OR6 UniChem PubChem 118723291
OR6 UniChem NMRShiftDB 80020760
#
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
OR6 C1 1.739 0.203 0.364 ETKDGv3 1
OR6 O1 -0.410 -2.617 -0.657 ETKDGv3 2
OR6 C2 1.008 -0.666 -0.657 ETKDGv3 3
OR6 O2 1.233 -2.603 0.938 ETKDGv3 4
OR6 C3 1.301 0.306 1.630 ETKDGv3 5
OR6 C4 2.905 1.010 -0.078 ETKDGv3 6
OR6 O3 3.559 1.703 0.748 ETKDGv3 7
OR6 C5 0.539 -1.996 -0.106 ETKDGv3 8
OR6 O4 3.286 1.012 -1.417 ETKDGv3 9
OR6 C6 -0.089 0.127 -1.419 ETKDGv3 10
OR6 C7 -1.154 0.841 -0.560 ETKDGv3 11
OR6 C8 -2.155 -0.119 0.098 ETKDGv3 12
OR6 C9 -3.279 0.648 0.789 ETKDGv3 13
OR6 H2 1.752 -0.958 -1.429 ETKDGv3 14
OR6 H3 0.953 -3.511 1.290 ETKDGv3 15
OR6 H4 0.429 -0.236 1.970 ETKDGv3 16
OR6 H5 1.796 0.942 2.351 ETKDGv3 17
OR6 H7 4.078 1.560 -1.732 ETKDGv3 18
OR6 H8 -0.591 -0.533 -2.159 ETKDGv3 19
OR6 H9 0.424 0.911 -2.018 ETKDGv3 20
OR6 H10 -1.719 1.521 -1.234 ETKDGv3 21
OR6 H11 -0.675 1.483 0.208 ETKDGv3 22
OR6 H12 -2.599 -0.787 -0.672 ETKDGv3 23
OR6 H13 -1.645 -0.742 0.860 ETKDGv3 24
OR6 H14 -2.863 1.314 1.575 ETKDGv3 25
OR6 H15 -3.842 1.257 0.051 ETKDGv3 26
OR6 H16 -3.980 -0.069 1.266 ETKDGv3 27
#