data_S8V
#
_chem_comp.id S8V
_chem_comp.name ~{N}-[[(3~{S})-oxolan-3-yl]methyl]cyclopropanamine
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H15 N O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-03-05
_chem_comp.pdbx_modified_date 2020-04-17
_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 141.211
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code S8V
_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 5R8P
_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
S8V C4 C1 C 0 1 N N S N N N 38.628 4.377 73.581 -1.111 0.479 -0.476 C4 S8V 1
S8V C5 C2 C 0 1 N N N N N N 38.375 4.832 72.131 -2.307 1.187 0.207 C5 S8V 2
S8V C6 C3 C 0 1 N N N N N N 39.747 5.186 71.591 -3.428 0.123 0.083 C6 S8V 3
S8V C7 C4 C 0 1 N N N N N N 40.159 4.492 73.784 -1.476 -1.018 -0.419 C7 S8V 4
S8V N N1 N 0 1 N N N N N N 38.185 2.684 75.268 1.305 0.087 -0.383 N S8V 5
S8V C C5 C 0 1 N N N N N N 38.163 2.947 73.810 0.181 0.744 0.299 C S8V 6
S8V O O1 O 0 1 N N N N N N 40.736 4.925 72.590 -2.730 -1.126 0.276 O S8V 7
S8V C1 C6 C 0 1 N N N N N N 37.988 1.277 75.587 2.565 0.321 0.334 C1 S8V 8
S8V C2 C7 C 0 1 N N N N N N 38.891 0.674 76.672 3.862 0.243 -0.474 C2 S8V 9
S8V C3 C8 C 0 1 N N N N N N 39.148 0.361 75.202 3.508 -0.871 0.513 C3 S8V 10
S8V H1 H1 H 0 1 N N N N N N 38.112 5.055 74.277 -1.010 0.808 -1.510 H1 S8V 11
S8V H2 H2 H 0 1 N N N N N N 37.712 5.710 72.110 -2.087 1.400 1.253 H2 S8V 12
S8V H3 H3 H 0 1 N N N N N N 39.958 4.578 70.699 -4.180 0.266 0.859 H3 S8V 13
S8V H4 H4 H 0 1 N N N N N N 40.571 3.510 74.060 -1.577 -1.413 -1.430 H4 S8V 14
S8V H5 H5 H 0 1 N N N N N N 40.373 5.217 74.583 -0.703 -1.567 0.118 H5 S8V 15
S8V H6 H6 H 0 1 N N N N N N 39.070 2.974 75.632 1.131 -0.900 -0.497 H6 S8V 16
S8V H8 H8 H 0 1 N N N N N N 37.141 2.821 73.424 0.363 1.818 0.345 H8 S8V 17
S8V H9 H9 H 0 1 N N N N N N 38.838 2.248 73.295 0.088 0.347 1.309 H9 S8V 18
S8V H10 H10 H 0 1 N N N N N N 36.974 0.859 75.499 2.518 1.052 1.141 H10 S8V 19
S8V H11 H11 H 0 1 N N N N N N 38.501 -0.107 77.341 3.780 0.018 -1.538 H11 S8V 20
S8V H12 H12 H 0 1 N N N N N N 39.589 1.318 77.228 4.669 0.923 -0.198 H12 S8V 21
S8V H13 H13 H 0 1 N N N N N N 38.945 -0.647 74.812 4.081 -0.924 1.439 H13 S8V 22
S8V H14 H14 H 0 1 N N N N N N 40.033 0.778 74.699 3.192 -1.828 0.099 H14 S8V 23
S8V H15 H15 H 0 1 N N N N N N 37.925 4.019 71.543 -2.575 2.099 -0.327 H15 S8V 24
S8V H16 H16 H 0 1 N N N N N N 39.771 6.252 71.322 -3.884 0.159 -0.906 H16 S8V 25
#
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
S8V C6 C5 SING N N 1
S8V C6 O SING N N 2
S8V C5 C4 SING N N 3
S8V O C7 SING N N 4
S8V C4 C7 SING N N 5
S8V C4 C SING N N 6
S8V C N SING N N 7
S8V C3 C1 SING N N 8
S8V C3 C2 SING N N 9
S8V N C1 SING N N 10
S8V C1 C2 SING N N 11
S8V C4 H1 SING N N 12
S8V C5 H2 SING N N 13
S8V C6 H3 SING N N 14
S8V C7 H4 SING N N 15
S8V C7 H5 SING N N 16
S8V N H6 SING N N 17
S8V C H8 SING N N 18
S8V C H9 SING N N 19
S8V C1 H10 SING N N 20
S8V C2 H11 SING N N 21
S8V C2 H12 SING N N 22
S8V C3 H13 SING N N 23
S8V C3 H14 SING N N 24
S8V C5 H15 SING N N 25
S8V C6 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
S8V InChI InChI 1.03 InChI=1S/C8H15NO/c1-2-8(1)9-5-7-3-4-10-6-7/h7-9H,1-6H2/t7-/m0/s1
S8V InChIKey InChI 1.03 XTBAPHZUOIOBDQ-ZETCQYMHSA-N
S8V SMILES_CANONICAL CACTVS 3.385 C1C[C@@H](CNC2CC2)CO1
S8V SMILES CACTVS 3.385 C1C[CH](CNC2CC2)CO1
S8V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C1COC[C@@H]1CNC2CC2
S8V SMILES "OpenEye OEToolkits" 2.0.6 C1CC1NCC2CCOC2
#
_pdbx_chem_comp_identifier.comp_id S8V
_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 ~{N}-[[(3~{S})-oxolan-3-yl]methyl]cyclopropanamine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
S8V 'Create component' 2020-03-05 RCSB
S8V 'Initial release' 2020-04-22 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
S8V C4 C 4.963 -0.727 1
S8V C5 C 5.427 -2.154 2
S8V C6 C 4.213 -3.035 3
S8V C7 C 3.463 -0.727 4
S8V N N 7.337 0.330 5
S8V C C 5.845 0.487 6
S8V O O 3.000 -2.154 7
S8V C1 C 8.219 1.543 8
S8V C2 C 9.589 2.154 9
S8V C3 C 8.375 3.035 10
#
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
S8V C6 C5 SINGLE NONE 1
S8V C6 O SINGLE NONE 2
S8V C5 C4 SINGLE NONE 3
S8V O C7 SINGLE NONE 4
S8V C4 C7 SINGLE NONE 5
S8V C4 C SINGLE BEGINDASH 6
S8V C N SINGLE NONE 7
S8V C3 C1 SINGLE NONE 8
S8V C3 C2 SINGLE NONE 9
S8V N C1 SINGLE NONE 10
S8V C1 C2 SINGLE NONE 11
#
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
S8V MurckoScaffold S1 scaffold 'C1C[C@@H](CNC2CC2)CO1' InChI=1S/C8H15NO/c1-2-8(1)9-5-7-3-4-10-6-7/h7-9H,1-6H2/t7-/m0/s1 XTBAPHZUOIOBDQ-ZETCQYMHSA-N
S8V cyclopropane F1 fragment C1CC1 InChI=1S/C3H6/c1-2-3-1/h1-3H2 LVZWSLJZHVFIQJ-UHFFFAOYSA-N
S8V Z818727262 F2 fragment C1CC(CNC2CC2)CO1 InChI=1S/C8H15NO/c1-2-8(1)9-5-7-3-4-10-6-7/h7-9H,1-6H2 XTBAPHZUOIOBDQ-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
S8V C4 S1 1
S8V C5 S1 1
S8V C6 S1 1
S8V C7 S1 1
S8V N S1 1
S8V C S1 1
S8V O S1 1
S8V C1 S1 1
S8V C2 S1 1
S8V C3 S1 1
S8V C1 F1 1
S8V C3 F1 1
S8V C2 F1 1
S8V C F2 1
S8V N F2 1
S8V C1 F2 1
S8V C3 F2 1
S8V C2 F2 1
S8V C4 F2 1
S8V C5 F2 1
S8V C6 F2 1
S8V O F2 1
S8V C7 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id S8V
_pdbe_chem_comp_rdkit_properties.exactmw 141.115
_pdbe_chem_comp_rdkit_properties.amw 141.214
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 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 83.078
_pdbe_chem_comp_rdkit_properties.tpsa 21.260
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.775
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.951
_pdbe_chem_comp_rdkit_properties.chi0v 4.855
_pdbe_chem_comp_rdkit_properties.chi1v 2.605
_pdbe_chem_comp_rdkit_properties.chi2v 0.896
_pdbe_chem_comp_rdkit_properties.chi3v 0.896
_pdbe_chem_comp_rdkit_properties.chi4v 0.425
_pdbe_chem_comp_rdkit_properties.chi0n 19.855
_pdbe_chem_comp_rdkit_properties.chi1n 10.053
_pdbe_chem_comp_rdkit_properties.chi2n 0.896
_pdbe_chem_comp_rdkit_properties.chi3n 0.896
_pdbe_chem_comp_rdkit_properties.chi4n 0.425
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.080
_pdbe_chem_comp_rdkit_properties.kappa1 1.175
_pdbe_chem_comp_rdkit_properties.kappa2 2.888
_pdbe_chem_comp_rdkit_properties.kappa3 1.704
_pdbe_chem_comp_rdkit_properties.Phi 0.339
#
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
S8V UniChem PDBe S8V
S8V UniChem ZINC ZINC000022562148
S8V UniChem PubChem 30427697
#
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
S8V C4 -1.326 -0.005 -0.582 ETKDGv3 1
S8V C5 -1.780 0.621 0.708 ETKDGv3 2
S8V C6 -3.275 0.358 0.702 ETKDGv3 3
S8V C7 -2.359 -1.100 -0.787 ETKDGv3 4
S8V N 1.077 0.553 -0.447 ETKDGv3 5
S8V C 0.114 -0.549 -0.535 ETKDGv3 6
S8V O -3.566 -0.706 -0.177 ETKDGv3 7
S8V C1 2.441 0.018 -0.580 ETKDGv3 8
S8V C2 3.517 0.942 -0.029 ETKDGv3 9
S8V C3 3.143 -0.326 0.726 ETKDGv3 10
S8V H1 -1.419 0.738 -1.406 ETKDGv3 11
S8V H2 -1.319 0.116 1.587 ETKDGv3 12
S8V H3 -3.629 0.107 1.724 ETKDGv3 13
S8V H4 -2.527 -1.274 -1.871 ETKDGv3 14
S8V H5 -2.027 -2.057 -0.324 ETKDGv3 15
S8V H6 0.949 1.028 0.478 ETKDGv3 16
S8V H8 0.240 -1.242 0.328 ETKDGv3 17
S8V H9 0.292 -1.126 -1.471 ETKDGv3 18
S8V H10 2.717 -0.537 -1.503 ETKDGv3 19
S8V H11 3.161 1.877 0.455 ETKDGv3 20
S8V H12 4.493 0.879 -0.554 ETKDGv3 21
S8V H13 2.562 -0.150 1.656 ETKDGv3 22
S8V H14 3.892 -1.142 0.639 ETKDGv3 23
S8V H15 -1.555 1.709 0.739 ETKDGv3 24
S8V H16 -3.815 1.265 0.355 ETKDGv3 25
#