data_E01
#
_chem_comp.id E01
_chem_comp.name "(1r,1'S,3'S,5'S,7'S)-spiro[cyclohexane-1,2'-tricyclo[3.3.1.1~3,7~]decan]-4-amine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H25 N"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-11-20
_chem_comp.pdbx_modified_date 2018-09-14
_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 219.366
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code E01
_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 6BMZ
_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
E01 C1 C1 C 0 1 N N N N N N -20.964 -18.779 -23.309 -3.102 0.001 -0.201 C1 E01 1
E01 C2 C2 C 0 1 N N N N N N -19.984 -19.656 -22.582 -2.269 -1.249 0.091 C2 E01 2
E01 C3 C3 C 0 1 N N N N N N -19.687 -20.936 -23.379 -1.021 -1.248 -0.794 C3 E01 3
E01 C4 C4 C 0 1 N N N N N N -20.888 -21.886 -23.590 -0.188 0.001 -0.500 C4 E01 4
E01 C5 C5 C 0 1 N N N N N N -22.108 -20.946 -23.580 -1.021 1.250 -0.792 C5 E01 5
E01 C6 C6 C 0 1 N N N N N N -21.827 -19.590 -24.233 -2.269 1.250 0.094 C6 E01 6
E01 C14 C7 C 0 1 N N N N N N -22.281 -23.615 -22.406 1.893 1.250 -1.091 C14 E01 7
E01 C15 C8 C 0 1 N N N N N N -21.998 -23.754 -24.875 1.064 1.248 1.266 C15 E01 8
E01 C12 C9 C 0 1 N N N N N N -22.178 -24.543 -23.599 2.312 1.249 0.381 C12 E01 9
E01 C11 C10 C 0 1 N N N N N N -20.772 -22.880 -24.771 0.231 -0.001 0.972 C11 E01 10
E01 C10 C11 C 0 1 N N N N N N -19.577 -23.764 -24.559 1.064 -1.250 1.264 C10 E01 11
E01 C7 C12 C 0 1 N N N N N N -21.040 -22.760 -22.303 1.060 0.001 -1.385 C7 E01 12
E01 C8 C13 C 0 1 N N N N N N -19.891 -23.710 -22.109 1.893 -1.248 -1.093 C8 E01 13
E01 C9 C14 C 0 1 N N N N N N -19.750 -24.601 -23.317 2.312 -1.250 0.379 C9 E01 14
E01 C13 C15 C 0 1 N N N N N N -20.990 -25.443 -23.433 3.145 -0.001 0.673 C13 E01 15
E01 N1 N1 N 0 1 N N N N N N -20.246 -17.799 -24.074 -4.300 0.000 0.650 N1 E01 16
E01 H1 H1 H 0 1 N N N N N N -21.607 -18.277 -22.571 -3.401 0.002 -1.249 H1 E01 17
E01 H2B H2 H 0 1 N N N N N N -20.406 -19.932 -21.604 -1.971 -1.250 1.140 H2B E01 18
E01 H2A H3 H 0 1 N N N N N N -19.047 -19.100 -22.433 -2.863 -2.138 -0.118 H2A E01 19
E01 H3B H4 H 0 1 N N N N N N -18.904 -21.494 -22.844 -0.428 -2.138 -0.586 H3B E01 20
E01 H3A H5 H 0 1 N N N N N N -19.313 -20.638 -24.370 -1.320 -1.247 -1.842 H3A E01 21
E01 H5B H6 H 0 1 N N N N N N -22.410 -20.776 -22.536 -0.427 2.140 -0.582 H5B E01 22
E01 H5A H7 H 0 1 N N N N N N -22.930 -21.433 -24.125 -1.319 1.251 -1.840 H5A E01 23
E01 H6B H8 H 0 1 N N N N N N -21.305 -19.741 -25.189 -2.862 2.140 -0.114 H6B E01 24
E01 H6A H9 H 0 1 N N N N N N -22.775 -19.062 -24.412 -1.970 1.249 1.142 H6A E01 25
E01 H14A H10 H 0 0 N N N N N N -23.161 -22.966 -22.525 1.300 2.140 -1.299 H14A E01 26
E01 H14B H11 H 0 0 N N N N N N -22.388 -24.213 -21.489 2.782 1.250 -1.722 H14B E01 27
E01 H15A H12 H 0 0 N N N N N N -22.883 -23.122 -25.041 1.363 1.247 2.314 H15A E01 28
E01 H15B H13 H 0 0 N N N N N N -21.880 -24.449 -25.720 0.471 2.138 1.058 H15B E01 29
E01 H12 H14 H 0 1 N N N N N N -23.093 -25.149 -23.670 2.906 2.138 0.590 H12 E01 30
E01 H11 H15 H 0 1 N N N N N N -20.648 -22.312 -25.705 -0.658 -0.001 1.603 H11 E01 31
E01 H10B H16 H 0 0 N N N N N N -19.459 -24.427 -25.429 1.362 -1.251 2.312 H10B E01 32
E01 H10A H17 H 0 0 N N N N N N -18.679 -23.138 -24.451 0.470 -2.140 1.054 H10A E01 33
E01 H7 H18 H 0 1 N N N N N N -21.122 -22.096 -21.430 0.762 0.002 -2.434 H7 E01 34
E01 H8A H19 H 0 1 N N N N N N -20.077 -24.329 -21.219 1.299 -2.138 -1.303 H8A E01 35
E01 H8B H20 H 0 1 N N N N N N -18.963 -23.136 -21.969 2.782 -1.248 -1.724 H8B E01 36
E01 H9 H21 H 0 1 N N N N N N -18.874 -25.254 -23.190 2.905 -2.140 0.586 H9 E01 37
E01 H13A H22 H 0 0 N N N N N N -21.111 -26.049 -22.523 4.034 -0.001 0.042 H13A E01 38
E01 H13B H23 H 0 0 N N N N N N -20.905 -26.106 -24.306 3.444 -0.002 1.721 H13B E01 39
E01 H1B H24 H 0 1 N N N N N N -19.669 -17.256 -23.464 -4.868 0.816 0.475 H1B E01 40
E01 H1A H25 H 0 1 N N N N N N -19.673 -18.260 -24.751 -4.835 -0.846 0.521 H1A E01 41
#
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
E01 C15 C11 SING N N 1
E01 C15 C12 SING N N 2
E01 C11 C10 SING N N 3
E01 C11 C4 SING N N 4
E01 C10 C9 SING N N 5
E01 C6 C5 SING N N 6
E01 C6 C1 SING N N 7
E01 N1 C1 SING N N 8
E01 C12 C13 SING N N 9
E01 C12 C14 SING N N 10
E01 C4 C5 SING N N 11
E01 C4 C3 SING N N 12
E01 C4 C7 SING N N 13
E01 C13 C9 SING N N 14
E01 C3 C2 SING N N 15
E01 C9 C8 SING N N 16
E01 C1 C2 SING N N 17
E01 C14 C7 SING N N 18
E01 C7 C8 SING N N 19
E01 C1 H1 SING N N 20
E01 C2 H2B SING N N 21
E01 C2 H2A SING N N 22
E01 C3 H3B SING N N 23
E01 C3 H3A SING N N 24
E01 C5 H5B SING N N 25
E01 C5 H5A SING N N 26
E01 C6 H6B SING N N 27
E01 C6 H6A SING N N 28
E01 C14 H14A SING N N 29
E01 C14 H14B SING N N 30
E01 C15 H15A SING N N 31
E01 C15 H15B SING N N 32
E01 C12 H12 SING N N 33
E01 C11 H11 SING N N 34
E01 C10 H10B SING N N 35
E01 C10 H10A SING N N 36
E01 C7 H7 SING N N 37
E01 C8 H8A SING N N 38
E01 C8 H8B SING N N 39
E01 C9 H9 SING N N 40
E01 C13 H13A SING N N 41
E01 C13 H13B SING N N 42
E01 N1 H1B SING N N 43
E01 N1 H1A SING N N 44
#
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
E01 SMILES ACDLabs 12.01 C1(CCC2(CC1)C3CC4CC2CC(C3)C4)N
E01 InChI InChI 1.03 InChI=1S/C15H25N/c16-14-1-3-15(4-2-14)12-6-10-5-11(8-12)9-13(15)7-10/h10-14H,1-9,16H2/t10-,11+,12-,13+,14-,15-
E01 InChIKey InChI 1.03 VNTMIVFMVGTSHV-RLUXGHLOSA-N
E01 SMILES_CANONICAL CACTVS 3.385 NC1CCC2(CC1)C3CC4CC(C3)CC2C4
E01 SMILES CACTVS 3.385 NC1CCC2(CC1)C3CC4CC(C3)CC2C4
E01 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C1CC2(CCC1N)C3CC4CC(C3)CC2C4
E01 SMILES "OpenEye OEToolkits" 2.0.6 C1CC2(CCC1N)C3CC4CC(C3)CC2C4
#
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
E01 "SYSTEMATIC NAME" ACDLabs 12.01 "(1r,1'S,3'S,5'S,7'S)-spiro[cyclohexane-1,2'-tricyclo[3.3.1.1~3,7~]decan]-4-amine"
E01 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "spiro[adamantane-2,4'-cyclohexane]-1'-amine"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
E01 'Create component' 2017-11-20 RCSB
E01 'Initial release' 2018-09-19 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
E01 C1 C 5.871 -4.770 1
E01 C2 C 7.160 -4.003 2
E01 C3 C 7.140 -2.503 3
E01 C4 C 5.831 -1.770 4
E01 C5 C 4.542 -2.537 5
E01 C6 C 4.562 -4.037 6
E01 C14 C 4.473 0.513 7
E01 C15 C 6.764 1.046 8
E01 C12 C 5.510 1.770 9
E01 C11 C 6.764 -0.402 10
E01 C10 C 5.510 -0.857 11
E01 C7 C 4.473 -1.055 12
E01 C8 C 3.000 -1.127 13
E01 C9 C 4.255 -0.402 14
E01 C13 C 4.255 1.046 15
E01 N1 N 5.891 -6.270 16
#
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
E01 C15 C11 SINGLE NONE 1
E01 C15 C12 SINGLE NONE 2
E01 C11 C10 SINGLE NONE 3
E01 C11 C4 SINGLE NONE 4
E01 C10 C9 SINGLE NONE 5
E01 C6 C5 SINGLE NONE 6
E01 C6 C1 SINGLE NONE 7
E01 C1 N1 SINGLE BEGINWEDGE 8
E01 C12 C13 SINGLE NONE 9
E01 C12 C14 SINGLE NONE 10
E01 C4 C5 SINGLE NONE 11
E01 C4 C3 SINGLE NONE 12
E01 C4 C7 SINGLE NONE 13
E01 C13 C9 SINGLE NONE 14
E01 C3 C2 SINGLE NONE 15
E01 C9 C8 SINGLE NONE 16
E01 C1 C2 SINGLE NONE 17
E01 C14 C7 SINGLE NONE 18
E01 C7 C8 SINGLE NONE 19
#
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
E01 MurckoScaffold S1 scaffold 'C1CCC2(CC1)[C@H]1C[C@@H]3C[C@@H](C[C@H]2C3)C1' InChI=1S/C15H24/c1-2-4-15(5-3-1)13-7-11-6-12(9-13)10-14(15)8-11/h11-14H,1-10H2/t11-,12+,13-,14+ DNHVRYKLQJXVAE-KPWCQOOUSA-N
E01 cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-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
E01 C1 S1 1
E01 C2 S1 1
E01 C3 S1 1
E01 C4 S1 1
E01 C5 S1 1
E01 C6 S1 1
E01 C14 S1 1
E01 C15 S1 1
E01 C12 S1 1
E01 C11 S1 1
E01 C10 S1 1
E01 C7 S1 1
E01 C8 S1 1
E01 C9 S1 1
E01 C13 S1 1
E01 C1 F1 1
E01 C6 F1 1
E01 C5 F1 1
E01 C4 F1 1
E01 C3 F1 1
E01 C2 F1 1
E01 C4 F1 2
E01 C11 F1 2
E01 C15 F1 2
E01 C12 F1 2
E01 C14 F1 2
E01 C7 F1 2
E01 C4 F1 3
E01 C11 F1 3
E01 C10 F1 3
E01 C9 F1 3
E01 C8 F1 3
E01 C7 F1 3
E01 C14 F1 4
E01 C12 F1 4
E01 C13 F1 4
E01 C9 F1 4
E01 C8 F1 4
E01 C7 F1 4
E01 C15 F1 5
E01 C11 F1 5
E01 C10 F1 5
E01 C9 F1 5
E01 C13 F1 5
E01 C12 F1 5
#
_pdbe_chem_comp_rdkit_properties.comp_id E01
_pdbe_chem_comp_rdkit_properties.exactmw 219.199
_pdbe_chem_comp_rdkit_properties.amw 219.372
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 41
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 1
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 5
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 5
_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 1
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 4
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 134.405
_pdbe_chem_comp_rdkit_properties.tpsa 26.020
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.330
_pdbe_chem_comp_rdkit_properties.CrippenMR 65.921
_pdbe_chem_comp_rdkit_properties.chi0v 7.947
_pdbe_chem_comp_rdkit_properties.chi1v 4.724
_pdbe_chem_comp_rdkit_properties.chi2v 2.737
_pdbe_chem_comp_rdkit_properties.chi3v 2.737
_pdbe_chem_comp_rdkit_properties.chi4v 1.993
_pdbe_chem_comp_rdkit_properties.chi0n 32.947
_pdbe_chem_comp_rdkit_properties.chi1n 17.118
_pdbe_chem_comp_rdkit_properties.chi2n 2.737
_pdbe_chem_comp_rdkit_properties.chi3n 2.737
_pdbe_chem_comp_rdkit_properties.chi4n 1.993
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.040
_pdbe_chem_comp_rdkit_properties.kappa1 1.848
_pdbe_chem_comp_rdkit_properties.kappa2 3.248
_pdbe_chem_comp_rdkit_properties.kappa3 1.213
_pdbe_chem_comp_rdkit_properties.Phi 0.375
#
_pdbe_chem_comp_external_mappings.comp_id E01
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id E01
#
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
E01 C1 3.268 -0.281 -0.052 ETKDGv3 1
E01 C2 2.331 -1.309 -0.696 ETKDGv3 2
E01 C3 1.064 -1.511 0.149 ETKDGv3 3
E01 C4 0.251 -0.188 0.380 ETKDGv3 4
E01 C5 1.261 0.822 1.033 ETKDGv3 5
E01 C6 2.529 1.044 0.195 ETKDGv3 6
E01 C14 -1.379 -0.653 -1.567 ETKDGv3 7
E01 C15 -1.945 -1.488 0.762 ETKDGv3 8
E01 C12 -2.521 -0.945 -0.566 ETKDGv3 9
E01 C11 -0.948 -0.459 1.365 ETKDGv3 10
E01 C10 -1.749 0.843 1.644 ETKDGv3 11
E01 C7 -0.385 0.371 -0.953 ETKDGv3 12
E01 C8 -1.182 1.677 -0.684 ETKDGv3 13
E01 C9 -2.323 1.401 0.322 ETKDGv3 14
E01 C13 -3.290 0.363 -0.285 ETKDGv3 15
E01 N1 4.443 -0.078 -0.901 ETKDGv3 16
E01 H1 3.611 -0.685 0.928 ETKDGv3 17
E01 H2B 2.058 -0.996 -1.726 ETKDGv3 18
E01 H2A 2.864 -2.282 -0.777 ETKDGv3 19
E01 H3B 0.473 -2.307 -0.337 ETKDGv3 20
E01 H3A 1.367 -1.927 1.136 ETKDGv3 21
E01 H5B 0.821 1.816 1.226 ETKDGv3 22
E01 H5A 1.567 0.435 2.030 ETKDGv3 23
E01 H6B 2.269 1.533 -0.768 ETKDGv3 24
E01 H6A 3.202 1.737 0.746 ETKDGv3 25
E01 H14A -1.809 -0.238 -2.505 ETKDGv3 26
E01 H14B -0.873 -1.591 -1.868 ETKDGv3 27
E01 H15A -1.475 -2.479 0.608 ETKDGv3 28
E01 H15B -2.776 -1.665 1.480 ETKDGv3 29
E01 H12 -3.215 -1.695 -1.004 ETKDGv3 30
E01 H11 -0.564 -0.857 2.330 ETKDGv3 31
E01 H10B -2.584 0.623 2.346 ETKDGv3 32
E01 H10A -1.131 1.607 2.156 ETKDGv3 33
E01 H7 0.397 0.590 -1.707 ETKDGv3 34
E01 H8A -0.528 2.493 -0.321 ETKDGv3 35
E01 H8B -1.615 2.051 -1.638 ETKDGv3 36
E01 H9 -2.875 2.345 0.526 ETKDGv3 37
E01 H13A -3.732 0.757 -1.226 ETKDGv3 38
E01 H13B -4.132 0.168 0.417 ETKDGv3 39
E01 H1B 4.154 0.393 -1.790 ETKDGv3 40
E01 H1A 5.104 0.566 -0.409 ETKDGv3 41
#