data_SVD
#
_chem_comp.id SVD
_chem_comp.name (5~{R})-5-~{tert}-butyl-2-methyl-1-oxidanyl-pyrazolidin-3-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H16 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-03-11
_chem_comp.pdbx_modified_date 2020-07-17
_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 172.225
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SVD
_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 5RA3
_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
SVD N1 N1 N 0 1 N N N N N N 36.453 129.014 21.182 -0.394 -1.092 0.098 N1 SVD 1
SVD C4 C1 C 0 1 N N R N N N 35.111 128.197 21.133 0.667 -0.309 0.773 C4 SVD 2
SVD C5 C2 C 0 1 N N N N N N 35.518 126.999 22.011 -0.116 0.932 1.265 C5 SVD 3
SVD C6 C3 C 0 1 N N N N N N 36.334 127.640 23.094 -1.293 0.969 0.307 C6 SVD 4
SVD C7 C4 C 0 1 N N N N N N 37.589 129.758 23.379 -2.347 -0.541 -1.349 C7 SVD 5
SVD N N2 N 0 1 N N N N N N 36.814 128.799 22.591 -1.354 -0.219 -0.322 N SVD 6
SVD C C5 C 0 1 N N N N N N 33.873 126.446 19.770 1.152 0.916 -1.349 C SVD 7
SVD O O1 O 0 1 N N N N N N 36.508 127.243 24.234 -2.046 1.905 0.138 O SVD 8
SVD C1 C6 C 0 1 N N N N N N 34.507 127.844 19.746 1.764 0.092 -0.215 C1 SVD 9
SVD C2 C7 C 0 1 N N N N N N 33.411 128.882 19.476 2.822 0.928 0.508 C2 SVD 10
SVD C3 C8 C 0 1 N N N N N N 35.521 127.896 18.594 2.415 -1.166 -0.793 C3 SVD 11
SVD O1 O2 O 0 1 N N N N N N 36.329 130.314 20.868 -0.957 -2.098 0.998 O1 SVD 12
SVD H1 H1 H 0 1 N N N N N N 34.356 128.775 21.686 1.086 -0.864 1.613 H1 SVD 13
SVD H2 H2 H 0 1 N N N N N N 34.633 126.495 22.428 -0.456 0.795 2.291 H2 SVD 14
SVD H3 H3 H 0 1 N N N N N N 36.117 126.275 21.440 0.488 1.834 1.172 H3 SVD 15
SVD H4 H4 H 0 1 N N N N N N 37.726 129.369 24.399 -3.230 -0.973 -0.878 H4 SVD 16
SVD H5 H5 H 0 1 N N N N N N 38.572 129.909 22.909 -2.627 0.368 -1.882 H5 SVD 17
SVD H6 H6 H 0 1 N N N N N N 37.051 130.717 23.422 -1.923 -1.259 -2.052 H6 SVD 18
SVD H7 H7 H 0 1 N N N N N N 33.142 126.388 20.590 0.688 1.813 -0.938 H7 SVD 19
SVD H8 H8 H 0 1 N N N N N N 33.365 126.257 18.813 1.933 1.202 -2.054 H8 SVD 20
SVD H9 H9 H 0 1 N N N N N N 34.657 125.690 19.924 0.398 0.321 -1.865 H9 SVD 21
SVD H10 H10 H 0 1 N N N N N N 32.674 128.859 20.293 2.358 1.824 0.920 H10 SVD 22
SVD H11 H11 H 0 1 N N N N N N 33.861 129.884 19.417 3.258 0.340 1.317 H11 SVD 23
SVD H12 H12 H 0 1 N N N N N N 32.911 128.648 18.525 3.603 1.214 -0.196 H12 SVD 24
SVD H13 H13 H 0 1 N N N N N N 36.316 127.157 18.771 3.197 -0.880 -1.497 H13 SVD 25
SVD H14 H14 H 0 1 N N N N N N 35.011 127.667 17.647 2.852 -1.753 0.015 H14 SVD 26
SVD H15 H15 H 0 1 N N N N N N 35.962 128.902 18.539 1.662 -1.761 -1.309 H15 SVD 27
SVD H16 H16 H 0 1 N N N N N N 37.179 130.735 20.921 -1.658 -2.633 0.601 H16 SVD 28
#
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
SVD C3 C1 SING N N 1
SVD C2 C1 SING N N 2
SVD C1 C SING N N 3
SVD C1 C4 SING N N 4
SVD O1 N1 SING N N 5
SVD C4 N1 SING N N 6
SVD C4 C5 SING N N 7
SVD N1 N SING N N 8
SVD C5 C6 SING N N 9
SVD N C6 SING N N 10
SVD N C7 SING N N 11
SVD C6 O DOUB N N 12
SVD C4 H1 SING N N 13
SVD C5 H2 SING N N 14
SVD C5 H3 SING N N 15
SVD C7 H4 SING N N 16
SVD C7 H5 SING N N 17
SVD C7 H6 SING N N 18
SVD C H7 SING N N 19
SVD C H8 SING N N 20
SVD C H9 SING N N 21
SVD C2 H10 SING N N 22
SVD C2 H11 SING N N 23
SVD C2 H12 SING N N 24
SVD C3 H13 SING N N 25
SVD C3 H14 SING N N 26
SVD C3 H15 SING N N 27
SVD O1 H16 SING N N 28
#
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
SVD InChI InChI 1.03 InChI=1S/C8H16N2O2/c1-8(2,3)6-5-7(11)9(4)10(6)12/h6,12H,5H2,1-4H3/t6-/m1/s1
SVD InChIKey InChI 1.03 WSOJYUWEGFKKBH-ZCFIWIBFSA-N
SVD SMILES_CANONICAL CACTVS 3.385 CN1N(O)[C@H](CC1=O)C(C)(C)C
SVD SMILES CACTVS 3.385 CN1N(O)[CH](CC1=O)C(C)(C)C
SVD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CC(C)(C)[C@H]1CC(=O)N(N1O)C
SVD SMILES "OpenEye OEToolkits" 2.0.6 CC(C)(C)C1CC(=O)N(N1O)C
#
_pdbx_chem_comp_identifier.comp_id SVD
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier (5~{R})-5-~{tert}-butyl-2-methyl-1-oxidanyl-pyrazolidin-3-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SVD 'Create component' 2020-03-11 RCSB
SVD 'Initial release' 2020-07-22 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
SVD N1 N 7.067 -0.778 1
SVD C4 C 5.853 0.103 2
SVD C5 C 6.317 1.530 3
SVD C6 C 7.817 1.530 4
SVD C7 C 9.707 -0.360 5
SVD N N 8.280 0.103 6
SVD C C 4.890 -1.787 7
SVD O O 8.698 2.743 8
SVD C1 C 4.427 -0.360 9
SVD C2 C 3.963 1.066 10
SVD C3 C 3.000 -0.824 11
SVD O1 O 7.067 -2.278 12
#
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
SVD C3 C1 SINGLE NONE 1
SVD C2 C1 SINGLE NONE 2
SVD C1 C SINGLE NONE 3
SVD C4 C1 SINGLE BEGINWEDGE 4
SVD O1 N1 SINGLE NONE 5
SVD C4 N1 SINGLE NONE 6
SVD C4 C5 SINGLE NONE 7
SVD N1 N SINGLE NONE 8
SVD C5 C6 SINGLE NONE 9
SVD N C6 SINGLE NONE 10
SVD N C7 SINGLE NONE 11
SVD C6 O DOUBLE NONE 12
#
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
SVD MurckoScaffold S1 scaffold O=C1CCNN1 InChI=1S/C3H6N2O/c6-3-1-2-4-5-3/h4H,1-2H2,(H,5,6) NDGRWYRVNANFNB-UHFFFAOYSA-N
SVD amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-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
SVD N1 S1 1
SVD C4 S1 1
SVD C5 S1 1
SVD C6 S1 1
SVD N S1 1
SVD O S1 1
SVD N F1 1
SVD C6 F1 1
SVD O F1 1
SVD C5 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SVD
_pdbe_chem_comp_rdkit_properties.exactmw 172.121
_pdbe_chem_comp_rdkit_properties.amw 172.228
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.875
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 95.254
_pdbe_chem_comp_rdkit_properties.tpsa 43.780
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.869
_pdbe_chem_comp_rdkit_properties.CrippenMR 44.256
_pdbe_chem_comp_rdkit_properties.chi0v 5.711
_pdbe_chem_comp_rdkit_properties.chi1v 2.758
_pdbe_chem_comp_rdkit_properties.chi2v 1.146
_pdbe_chem_comp_rdkit_properties.chi3v 1.146
_pdbe_chem_comp_rdkit_properties.chi4v 0.622
_pdbe_chem_comp_rdkit_properties.chi0n 21.711
_pdbe_chem_comp_rdkit_properties.chi1n 10.666
_pdbe_chem_comp_rdkit_properties.chi2n 1.146
_pdbe_chem_comp_rdkit_properties.chi3n 1.146
_pdbe_chem_comp_rdkit_properties.chi4n 0.622
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.639
_pdbe_chem_comp_rdkit_properties.kappa2 2.709
_pdbe_chem_comp_rdkit_properties.kappa3 1.445
_pdbe_chem_comp_rdkit_properties.Phi 0.370
#
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
SVD UniChem PDBe SVD
SVD UniChem PubChem 146676940
#
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
SVD N1 0.952 0.889 -0.188 ETKDGv3 1
SVD C4 -0.029 0.103 0.613 ETKDGv3 2
SVD C5 0.614 -1.271 0.967 ETKDGv3 3
SVD C6 1.900 -1.193 0.276 ETKDGv3 4
SVD C7 3.182 0.386 -1.234 ETKDGv3 5
SVD N 2.054 0.043 -0.375 ETKDGv3 6
SVD C -2.439 -0.755 0.699 ETKDGv3 7
SVD O 2.765 -2.109 0.256 ETKDGv3 8
SVD C1 -1.395 0.008 -0.150 ETKDGv3 9
SVD C2 -1.938 1.435 -0.392 ETKDGv3 10
SVD C3 -1.237 -0.692 -1.519 ETKDGv3 11
SVD O1 1.380 1.939 0.560 ETKDGv3 12
SVD H1 -0.232 0.620 1.582 ETKDGv3 13
SVD H2 0.782 -1.361 2.062 ETKDGv3 14
SVD H3 0.050 -2.152 0.603 ETKDGv3 15
SVD H4 4.118 0.385 -0.638 ETKDGv3 16
SVD H5 3.266 -0.357 -2.055 ETKDGv3 17
SVD H6 3.035 1.394 -1.676 ETKDGv3 18
SVD H7 -2.542 -0.290 1.703 ETKDGv3 19
SVD H8 -2.162 -1.820 0.834 ETKDGv3 20
SVD H9 -3.435 -0.735 0.205 ETKDGv3 21
SVD H10 -2.048 1.982 0.570 ETKDGv3 22
SVD H11 -1.256 2.017 -1.048 ETKDGv3 23
SVD H12 -2.933 1.402 -0.886 ETKDGv3 24
SVD H13 -2.206 -0.702 -2.064 ETKDGv3 25
SVD H14 -0.907 -1.744 -1.407 ETKDGv3 26
SVD H15 -0.495 -0.160 -2.153 ETKDGv3 27
SVD H16 1.154 2.739 0.020 ETKDGv3 28
#