data_L4O
#
_chem_comp.id L4O
_chem_comp.name "tert-butyl (1S,4S)-2,5-diazabicyclo[2.2.1]heptane-2-carboxylate"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H18 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-02-28
_chem_comp.pdbx_modified_date 2022-09-30
_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 198.262
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L4O
_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 7U3E
_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
L4O C11 C1 C 0 1 N N N N N N -16.679 0.247 -28.325 -2.921 -0.145 1.248 C11 L4O 1
L4O C10 C2 C 0 1 N N S N N N -17.540 0.480 -27.069 -2.943 1.096 0.285 C10 L4O 2
L4O C12 C3 C 0 1 N N S N N N -16.363 -1.222 -27.860 -1.952 -0.981 0.338 C12 L4O 3
L4O C13 C4 C 0 1 N N N N N N -15.730 -0.894 -26.479 -2.716 -0.882 -1.019 C13 L4O 4
L4O C01 C5 C 0 1 N N N N N N -18.332 -5.983 -28.075 3.015 -0.707 -1.272 C01 L4O 5
L4O C02 C6 C 0 1 N N N N N N -17.108 -5.462 -27.299 2.808 0.227 -0.078 C02 L4O 6
L4O C03 C7 C 0 1 N N N N N N -15.858 -6.172 -27.883 3.181 -0.505 1.213 C03 L4O 7
L4O C04 C8 C 0 1 N N N N N N -17.200 -5.806 -25.797 3.695 1.464 -0.237 C04 L4O 8
L4O C06 C9 C 0 1 N N N N N N -17.969 -3.118 -27.283 0.499 -0.341 0.123 C06 L4O 9
L4O C09 C10 C 0 1 N N N N N N -18.555 -0.685 -27.245 -1.409 1.320 0.114 C09 L4O 10
L4O N08 N1 N 0 1 N N N N N N -17.740 -1.802 -27.828 -0.811 -0.031 0.185 N08 L4O 11
L4O N14 N2 N 0 1 N N N N N N -16.616 0.196 -25.937 -3.363 0.453 -0.999 N14 L4O 12
L4O O05 O1 O 0 1 N N N N N N -16.980 -4.031 -27.493 1.416 0.635 -0.018 O05 L4O 13
L4O O07 O2 O 0 1 N N N N N N -18.986 -3.400 -26.645 0.852 -1.501 0.193 O07 L4O 14
L4O H1 H1 H 0 1 N N N N N N -15.793 0.896 -28.385 -2.479 0.090 2.217 H1 L4O 15
L4O H2 H2 H 0 1 N N N N N N -17.241 0.305 -29.269 -3.901 -0.610 1.348 H2 L4O 16
L4O H3 H3 H 0 1 N N N N N N -18.014 1.472 -27.035 -3.534 1.953 0.609 H3 L4O 17
L4O H4 H4 H 0 1 N N N N N N -15.672 -1.744 -28.538 -1.699 -1.982 0.688 H4 L4O 18
L4O H5 H5 H 0 1 N N N N N N -15.743 -1.775 -25.821 -2.017 -0.952 -1.852 H5 L4O 19
L4O H6 H6 H 0 1 N N N N N N -14.695 -0.539 -26.595 -3.469 -1.666 -1.088 H6 L4O 20
L4O H7 H7 H 0 1 N N N N N N -19.243 -5.502 -27.690 4.061 -1.013 -1.316 H7 L4O 21
L4O H8 H8 H 0 1 N N N N N N -18.217 -5.747 -29.143 2.384 -1.588 -1.158 H8 L4O 22
L4O H9 H9 H 0 1 N N N N N N -18.411 -7.073 -27.947 2.750 -0.185 -2.191 H9 L4O 23
L4O H10 H10 H 0 1 N N N N N N -14.958 -5.826 -27.353 4.226 -0.811 1.168 H10 L4O 24
L4O H11 H11 H 0 1 N N N N N N -15.962 -7.260 -27.757 3.033 0.161 2.064 H11 L4O 25
L4O H12 H12 H 0 1 N N N N N N -15.768 -5.934 -28.953 2.549 -1.386 1.327 H12 L4O 26
L4O H13 H13 H 0 1 N N N N N N -16.311 -5.419 -25.277 3.429 1.985 -1.157 H13 L4O 27
L4O H14 H14 H 0 1 N N N N N N -18.104 -5.346 -25.370 3.547 2.129 0.613 H14 L4O 28
L4O H15 H15 H 0 1 N N N N N N -17.251 -6.898 -25.673 4.740 1.158 -0.282 H15 L4O 29
L4O H16 H16 H 0 1 N N N N N N -19.366 -0.395 -27.930 -1.199 1.777 -0.853 H16 L4O 30
L4O H17 H17 H 0 1 N N N N N N -18.982 -0.979 -26.275 -1.026 1.947 0.919 H17 L4O 31
L4O H18 H18 H 0 1 N N N N N N -16.082 1.007 -25.699 -4.367 0.368 -1.050 H18 L4O 32
#
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
L4O C11 C12 SING N N 1
L4O C11 C10 SING N N 2
L4O C01 C02 SING N N 3
L4O C03 C02 SING N N 4
L4O C12 N08 SING N N 5
L4O C12 C13 SING N N 6
L4O N08 C06 SING N N 7
L4O N08 C09 SING N N 8
L4O O05 C02 SING N N 9
L4O O05 C06 SING N N 10
L4O C02 C04 SING N N 11
L4O C06 O07 DOUB N N 12
L4O C09 C10 SING N N 13
L4O C10 N14 SING N N 14
L4O C13 N14 SING N N 15
L4O C11 H1 SING N N 16
L4O C11 H2 SING N N 17
L4O C10 H3 SING N N 18
L4O C12 H4 SING N N 19
L4O C13 H5 SING N N 20
L4O C13 H6 SING N N 21
L4O C01 H7 SING N N 22
L4O C01 H8 SING N N 23
L4O C01 H9 SING N N 24
L4O C03 H10 SING N N 25
L4O C03 H11 SING N N 26
L4O C03 H12 SING N N 27
L4O C04 H13 SING N N 28
L4O C04 H14 SING N N 29
L4O C04 H15 SING N N 30
L4O C09 H16 SING N N 31
L4O C09 H17 SING N N 32
L4O N14 H18 SING N N 33
#
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
L4O SMILES ACDLabs 12.01 CC(C)(C)OC(=O)N1CC2CC1CN2
L4O InChI InChI 1.03 InChI=1S/C10H18N2O2/c1-10(2,3)14-9(13)12-6-7-4-8(12)5-11-7/h7-8,11H,4-6H2,1-3H3/t7-,8-/m0/s1
L4O InChIKey InChI 1.03 UXAWXZDXVOYLII-YUMQZZPRSA-N
L4O SMILES_CANONICAL CACTVS 3.385 CC(C)(C)OC(=O)N1C[C@@H]2C[C@H]1CN2
L4O SMILES CACTVS 3.385 CC(C)(C)OC(=O)N1C[CH]2C[CH]1CN2
L4O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(C)(C)OC(=O)N1C[C@@H]2C[C@H]1CN2
L4O SMILES "OpenEye OEToolkits" 2.0.7 CC(C)(C)OC(=O)N1CC2CC1CN2
#
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
L4O "SYSTEMATIC NAME" ACDLabs 12.01 "tert-butyl (1S,4S)-2,5-diazabicyclo[2.2.1]heptane-2-carboxylate"
L4O "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{tert}-butyl (1~{S},4~{S})-2,5-diazabicyclo[2.2.1]heptane-2-carboxylate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L4O 'Create component' 2022-02-28 RCSB
L4O 'Initial release' 2022-10-05 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
L4O C11 C 2.189 1.603 1
L4O C10 C 1.906 2.592 2
L4O C12 C 1.903 0.613 3
L4O C13 C 3.402 0.613 4
L4O C01 C -2.790 -1.189 5
L4O C02 C -1.936 -2.430 6
L4O C03 C -3.440 -2.545 7
L4O C04 C -1.829 -3.924 8
L4O C06 C -0.799 -0.085 9
L4O C09 C 0.418 2.362 10
L4O N08 N 0.417 0.846 11
L4O N14 N 3.404 2.590 12
L4O O05 O -0.671 -1.573 13
L4O O07 O -2.174 0.528 14
#
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
L4O C11 C12 SINGLE NONE 1
L4O C11 C10 SINGLE NONE 2
L4O C01 C02 SINGLE NONE 3
L4O C03 C02 SINGLE NONE 4
L4O C12 N08 SINGLE NONE 5
L4O C12 C13 SINGLE NONE 6
L4O N08 C06 SINGLE NONE 7
L4O N08 C09 SINGLE NONE 8
L4O O05 C02 SINGLE NONE 9
L4O O05 C06 SINGLE NONE 10
L4O C02 C04 SINGLE NONE 11
L4O C06 O07 DOUBLE NONE 12
L4O C09 C10 SINGLE NONE 13
L4O C10 N14 SINGLE NONE 14
L4O C13 N14 SINGLE NONE 15
#
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
L4O MurckoScaffold S1 scaffold 'C1N[C@@H]2CN[C@H]1C2' InChI=1S/C5H10N2/c1-4-2-6-5(1)3-7-4/h4-7H,1-3H2/t4-,5-/m0/s1 UKHJNJFJCGBKSF-WHFBIAKZSA-N
L4O piperazine F1 fragment C1CNCCN1 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2 GLUUGHFHXGJENI-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
L4O C11 S1 1
L4O C10 S1 1
L4O C12 S1 1
L4O C13 S1 1
L4O C09 S1 1
L4O N08 S1 1
L4O N14 S1 1
L4O N08 F1 1
L4O C12 F1 1
L4O C13 F1 1
L4O N14 F1 1
L4O C10 F1 1
L4O C09 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id L4O
_pdbe_chem_comp_rdkit_properties.exactmw 198.137
_pdbe_chem_comp_rdkit_properties.amw 198.266
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 0
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.900
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 109.944
_pdbe_chem_comp_rdkit_properties.tpsa 41.570
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.968
_pdbe_chem_comp_rdkit_properties.CrippenMR 53.136
_pdbe_chem_comp_rdkit_properties.chi0v 6.711
_pdbe_chem_comp_rdkit_properties.chi1v 3.480
_pdbe_chem_comp_rdkit_properties.chi2v 1.375
_pdbe_chem_comp_rdkit_properties.chi3v 1.375
_pdbe_chem_comp_rdkit_properties.chi4v 0.911
_pdbe_chem_comp_rdkit_properties.chi0n 24.711
_pdbe_chem_comp_rdkit_properties.chi1n 12.428
_pdbe_chem_comp_rdkit_properties.chi2n 1.375
_pdbe_chem_comp_rdkit_properties.chi3n 1.375
_pdbe_chem_comp_rdkit_properties.chi4n 0.911
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.770
_pdbe_chem_comp_rdkit_properties.kappa1 1.905
_pdbe_chem_comp_rdkit_properties.kappa2 3.121
_pdbe_chem_comp_rdkit_properties.kappa3 1.846
_pdbe_chem_comp_rdkit_properties.Phi 0.425
#
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
L4O UniChem PDBe L4O
L4O UniChem ZINC ZINC000000403198
L4O UniChem eMolecules 512214
L4O UniChem SureChEMBL SCHEMBL71827
L4O UniChem 'PubChem TPHARMA' 16623184
L4O UniChem ACTor 113451-59-5
L4O UniChem Nikkaji J2.815.643J
L4O UniChem 'EPA CompTox Dashboard' DTXSID90467966
L4O UniChem PubChem 11521263
#
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
L4O C11 2.934 1.479 -0.486 ETKDGv3 1
L4O C10 3.424 0.068 -0.735 ETKDGv3 2
L4O C12 1.496 1.088 -0.690 ETKDGv3 3
L4O C13 1.591 0.455 -2.083 ETKDGv3 4
L4O C01 -3.385 0.801 0.174 ETKDGv3 5
L4O C02 -2.425 -0.239 0.772 ETKDGv3 6
L4O C03 -2.763 -1.623 0.186 ETKDGv3 7
L4O C04 -2.587 -0.243 2.304 ETKDGv3 8
L4O C06 0.092 -0.520 0.734 ETKDGv3 9
L4O C09 2.614 -0.720 0.307 ETKDGv3 10
L4O N08 1.342 -0.006 0.265 ETKDGv3 11
L4O N14 2.878 -0.267 -2.062 ETKDGv3 12
L4O O05 -1.094 0.153 0.405 ETKDGv3 13
L4O O07 0.073 -1.567 1.437 ETKDGv3 14
L4O H1 3.307 2.210 -1.240 ETKDGv3 15
L4O H2 3.141 1.841 0.548 ETKDGv3 16
L4O H3 4.525 -0.070 -0.664 ETKDGv3 17
L4O H4 0.754 1.906 -0.571 ETKDGv3 18
L4O H5 1.580 1.241 -2.873 ETKDGv3 19
L4O H6 0.754 -0.255 -2.259 ETKDGv3 20
L4O H7 -3.153 1.812 0.572 ETKDGv3 21
L4O H8 -4.441 0.557 0.420 ETKDGv3 22
L4O H9 -3.278 0.833 -0.932 ETKDGv3 23
L4O H10 -3.832 -1.871 0.360 ETKDGv3 24
L4O H11 -2.152 -2.422 0.655 ETKDGv3 25
L4O H12 -2.570 -1.633 -0.908 ETKDGv3 26
L4O H13 -1.978 -1.042 2.774 ETKDGv3 27
L4O H14 -3.648 -0.419 2.584 ETKDGv3 28
L4O H15 -2.266 0.734 2.725 ETKDGv3 29
L4O H16 3.066 -0.644 1.320 ETKDGv3 30
L4O H17 2.490 -1.784 0.007 ETKDGv3 31
L4O H18 3.509 0.148 -2.788 ETKDGv3 32
#