data_L5W
#
_chem_comp.id L5W
_chem_comp.name ~{N}-oxidanylbicyclo[2.2.1]heptane-1-carboxamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H13 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-07-23
_chem_comp.pdbx_modified_date 2020-08-21
_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 155.194
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L5W
_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 6SC1
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
L5W C4 C1 C 0 1 N N N N N N 9.903 39.316 -1.158 2.485 0.477 -0.040 C4 L5W 1
L5W C5 C2 C 0 1 N N N N N N 11.229 38.838 -1.722 2.251 -0.527 -1.209 C5 L5W 2
L5W C6 C3 C 0 1 N N N N N N 10.858 38.231 -3.082 0.732 -0.814 -1.181 C6 L5W 3
L5W C7 C4 C 0 1 N N N N N N 9.189 39.806 -2.425 1.152 1.306 -0.071 C7 L5W 4
L5W N N1 N 0 1 N N N N N N 9.801 38.195 -5.524 -2.173 -0.681 0.034 N L5W 5
L5W C C5 C 0 1 N N N N N N 8.842 38.384 -4.606 -1.288 0.334 -0.015 C L5W 6
L5W O O1 O 0 1 N N N N N N 9.463 38.147 -6.871 -3.563 -0.409 0.017 O L5W 7
L5W C1 C6 C 0 1 N N N N N N 9.355 38.482 -3.184 0.191 0.045 0.003 C1 L5W 8
L5W C2 C7 C 0 1 N N N N N N 8.695 37.494 -2.238 0.731 -0.669 1.280 C2 L5W 9
L5W C3 C8 C 0 1 N N N N N N 9.180 37.981 -0.864 2.267 -0.370 1.251 C3 L5W 10
L5W O1 O2 O 0 1 N N N N N N 7.652 38.452 -4.874 -1.681 1.480 -0.073 O1 L5W 11
L5W H1 H1 H 0 1 N N N N N N 9.954 40.030 -0.323 3.410 1.051 -0.083 H1 L5W 12
L5W H2 H2 H 0 1 N N N N N N 11.682 38.080 -1.066 2.535 -0.076 -2.160 H2 L5W 13
L5W H3 H3 H 0 1 N N N N N N 11.927 39.679 -1.847 2.816 -1.445 -1.041 H3 L5W 14
L5W H4 H4 H 0 1 N N N N N N 11.080 37.154 -3.106 0.270 -0.503 -2.118 H4 L5W 15
L5W H5 H5 H 0 1 N N N N N N 11.397 38.734 -3.898 0.549 -1.873 -1.000 H5 L5W 16
L5W H6 H6 H 0 1 N N N N N N 9.704 40.648 -2.911 1.059 1.962 0.794 H6 L5W 17
L5W H7 H7 H 0 1 N N N N N N 8.136 40.072 -2.250 1.032 1.852 -1.007 H7 L5W 18
L5W H8 H8 H 0 1 N N N N N N 10.754 38.089 -5.241 -1.859 -1.597 0.080 H8 L5W 19
L5W H9 H9 H 0 1 N N N N N N 8.522 38.236 -6.965 -4.119 -1.199 0.055 H9 L5W 20
L5W H10 H10 H 0 1 N N N N N N 7.599 37.542 -2.313 0.267 -0.250 2.174 H10 L5W 21
L5W H11 H11 H 0 1 N N N N N N 9.031 36.466 -2.438 0.547 -1.741 1.223 H11 L5W 22
L5W H12 H12 H 0 1 N N N N N N 8.329 38.141 -0.186 2.817 -1.309 1.187 H12 L5W 23
L5W H13 H13 H 0 1 N N N N N N 9.874 37.254 -0.417 2.576 0.193 2.132 H13 L5W 24
#
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
L5W O N SING N N 1
L5W N C SING N N 2
L5W O1 C DOUB N N 3
L5W C C1 SING N N 4
L5W C1 C6 SING N N 5
L5W C1 C7 SING N N 6
L5W C1 C2 SING N N 7
L5W C6 C5 SING N N 8
L5W C7 C4 SING N N 9
L5W C2 C3 SING N N 10
L5W C5 C4 SING N N 11
L5W C4 C3 SING N N 12
L5W C4 H1 SING N N 13
L5W C5 H2 SING N N 14
L5W C5 H3 SING N N 15
L5W C6 H4 SING N N 16
L5W C6 H5 SING N N 17
L5W C7 H6 SING N N 18
L5W C7 H7 SING N N 19
L5W N H8 SING N N 20
L5W O H9 SING N N 21
L5W C2 H10 SING N N 22
L5W C2 H11 SING N N 23
L5W C3 H12 SING N N 24
L5W C3 H13 SING N N 25
#
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
L5W InChI InChI 1.03 InChI=1S/C8H13NO2/c10-7(9-11)8-3-1-6(5-8)2-4-8/h6,11H,1-5H2,(H,9,10)/t6-,8-
L5W InChIKey InChI 1.03 AHBXSKNCOQIRKT-FKQCQYRASA-N
L5W SMILES_CANONICAL CACTVS 3.385 ONC(=O)C12CCC(CC1)C2
L5W SMILES CACTVS 3.385 ONC(=O)C12CCC(CC1)C2
L5W SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C1CC2(CCC1C2)C(=O)NO
L5W SMILES "OpenEye OEToolkits" 2.0.7 C1CC2(CCC1C2)C(=O)NO
#
_pdbx_chem_comp_identifier.comp_id L5W
_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 ~{N}-oxidanylbicyclo[2.2.1]heptane-1-carboxamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L5W 'Create component' 2019-07-23 EBI
L5W 'Initial release' 2020-08-26 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
L5W C4 C -0.080 -2.271 1
L5W C5 C -1.572 -2.041 2
L5W C6 C -1.569 -0.521 3
L5W C7 C 0.200 -1.284 4
L5W N N 1.063 2.125 5
L5W C C -0.196 1.262 6
L5W O O 0.955 3.639 7
L5W C1 C -0.085 -0.302 8
L5W C2 C 1.405 -0.280 9
L5W C3 C 1.423 -2.259 10
L5W O1 O -1.545 1.933 11
#
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
L5W O N SINGLE NONE 1
L5W N C SINGLE NONE 2
L5W O1 C DOUBLE NONE 3
L5W C1 C SINGLE BEGINDASH 4
L5W C1 C6 SINGLE NONE 5
L5W C1 C7 SINGLE NONE 6
L5W C1 C2 SINGLE NONE 7
L5W C6 C5 SINGLE NONE 8
L5W C7 C4 SINGLE NONE 9
L5W C2 C3 SINGLE NONE 10
L5W C5 C4 SINGLE NONE 11
L5W C4 C3 SINGLE 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
L5W MurckoScaffold S1 scaffold C1CC2CCC1C2 InChI=1S/C7H12/c1-2-7-4-3-6(1)5-7/h6-7H,1-5H2 UMRZSTCPUPJPOJ-UHFFFAOYSA-N
L5W amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
L5W cyclohexane F2 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
L5W cyclopentane F3 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-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
L5W C4 S1 1
L5W C5 S1 1
L5W C6 S1 1
L5W C7 S1 1
L5W C1 S1 1
L5W C2 S1 1
L5W C3 S1 1
L5W N F1 1
L5W C F1 1
L5W O1 F1 1
L5W C1 F1 1
L5W C4 F2 1
L5W C5 F2 1
L5W C6 F2 1
L5W C1 F2 1
L5W C2 F2 1
L5W C3 F2 1
L5W C4 F3 1
L5W C7 F3 1
L5W C1 F3 1
L5W C6 F3 1
L5W C5 F3 1
L5W C4 F3 2
L5W C7 F3 2
L5W C1 F3 2
L5W C2 F3 2
L5W C3 F3 2
#
_pdbe_chem_comp_rdkit_properties.comp_id L5W
_pdbe_chem_comp_rdkit_properties.exactmw 155.095
_pdbe_chem_comp_rdkit_properties.amw 155.197
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.875
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_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 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 84.151
_pdbe_chem_comp_rdkit_properties.tpsa 49.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.072
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.937
_pdbe_chem_comp_rdkit_properties.chi0v 5.264
_pdbe_chem_comp_rdkit_properties.chi1v 2.860
_pdbe_chem_comp_rdkit_properties.chi2v 1.466
_pdbe_chem_comp_rdkit_properties.chi3v 1.466
_pdbe_chem_comp_rdkit_properties.chi4v 0.916
_pdbe_chem_comp_rdkit_properties.chi0n 18.264
_pdbe_chem_comp_rdkit_properties.chi1n 9.216
_pdbe_chem_comp_rdkit_properties.chi2n 1.466
_pdbe_chem_comp_rdkit_properties.chi3n 1.466
_pdbe_chem_comp_rdkit_properties.chi4n 0.916
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.570
_pdbe_chem_comp_rdkit_properties.kappa1 1.554
_pdbe_chem_comp_rdkit_properties.kappa2 2.206
_pdbe_chem_comp_rdkit_properties.kappa3 0.872
_pdbe_chem_comp_rdkit_properties.Phi 0.312
#
_pdbe_chem_comp_external_mappings.comp_id L5W
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id L5W
#
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
L5W C4 -1.839 -0.174 -0.717 ETKDGv3 1
L5W C5 -1.777 1.194 -0.012 ETKDGv3 2
L5W C6 -0.282 1.342 0.317 ETKDGv3 3
L5W C7 -0.532 -0.194 -1.475 ETKDGv3 4
L5W N 2.695 0.300 0.627 ETKDGv3 5
L5W C 1.805 0.098 -0.474 ETKDGv3 6
L5W O 4.033 0.368 0.428 ETKDGv3 7
L5W C1 0.316 0.033 -0.239 ETKDGv3 8
L5W C2 -0.119 -1.139 0.663 ETKDGv3 9
L5W C3 -1.615 -1.279 0.333 ETKDGv3 10
L5W O1 2.271 -0.025 -1.639 ETKDGv3 11
L5W H1 -2.744 -0.321 -1.345 ETKDGv3 12
L5W H2 -2.105 1.999 -0.706 ETKDGv3 13
L5W H3 -2.406 1.222 0.904 ETKDGv3 14
L5W H4 -0.112 1.448 1.411 ETKDGv3 15
L5W H5 0.142 2.227 -0.207 ETKDGv3 16
L5W H6 -0.336 -1.174 -1.971 ETKDGv3 17
L5W H7 -0.454 0.630 -2.222 ETKDGv3 18
L5W H8 2.317 0.418 1.594 ETKDGv3 19
L5W H9 4.354 -0.563 0.538 ETKDGv3 20
L5W H10 0.043 -0.921 1.742 ETKDGv3 21
L5W H11 0.423 -2.073 0.392 ETKDGv3 22
L5W H12 -2.252 -1.137 1.233 ETKDGv3 23
L5W H13 -1.825 -2.278 -0.110 ETKDGv3 24
#