data_SDM
#
_chem_comp.id SDM
_chem_comp.name 4-ethoxy-1-benzothiophene-2-carboximidamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H12 N2 O S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-12-15
_chem_comp.pdbx_modified_date 2024-09-16
_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 220.291
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SDM
_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 8BZ0
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_chem_comp.pdbx_pcm ?
#
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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
SDM C1 C1 C 0 1 Y N N N N N 20.197 18.051 -7.202 -1.898 0.373 0.003 C1 SDM 1
SDM C2 C2 C 0 1 Y N N N N N 20.279 19.084 -8.100 -0.625 0.775 0.003 C2 SDM 2
SDM C3 C3 C 0 1 Y N N N N N 19.949 20.375 -7.538 0.335 -0.250 0.002 C3 SDM 3
SDM C4 C4 C 0 1 Y N N N N N 19.942 21.676 -8.078 1.750 -0.144 0.000 C4 SDM 4
SDM C5 C5 C 0 1 N N N N N N 19.605 22.348 -10.450 3.765 1.117 -0.001 C5 SDM 5
SDM C7 C6 C 0 1 Y N N N N N 19.613 22.778 -7.298 2.531 -1.276 -0.002 C7 SDM 6
SDM C9 C7 C 0 1 Y N N N N N 19.280 21.358 -5.389 0.576 -2.661 -0.001 C9 SDM 7
SDM N N1 N 0 1 N N N N N N 20.106 15.868 -6.362 -2.884 2.569 0.000 N SDM 8
SDM C C8 C 0 1 N N N N N N 20.489 16.636 -7.387 -3.062 1.276 -0.001 C SDM 9
SDM O O1 O 0 1 N N N N N N 20.395 21.767 -9.379 2.336 1.082 0.000 O SDM 10
SDM C10 C9 C 0 1 Y N N N N N 19.608 20.252 -6.176 -0.240 -1.526 0.001 C10 SDM 11
SDM C6 C10 C 0 1 N N N N N N 18.273 22.820 -9.955 4.239 2.572 -0.000 C6 SDM 12
SDM C8 C11 C 0 1 Y N N N N N 19.287 22.615 -5.961 1.945 -2.534 -0.003 C8 SDM 13
SDM N1 N2 N 0 1 N N N N N N 21.026 16.071 -8.394 -4.339 0.755 -0.006 N1 SDM 14
SDM S S1 S 0 1 Y N N N N N 19.692 18.600 -5.630 -1.994 -1.379 0.002 S SDM 15
SDM H2 H1 H 0 1 N N N N N N 20.564 18.946 -9.133 -0.352 1.820 0.003 H2 SDM 16
SDM H3 H2 H 0 1 N N N N N N 19.448 21.589 -11.231 4.142 0.613 0.888 H3 SDM 17
SDM H4 H3 H 0 1 N N N N N N 20.152 23.203 -10.875 4.140 0.613 -0.891 H4 SDM 18
SDM H8 H4 H 0 1 N N N N N N 19.611 23.765 -7.736 3.607 -1.186 -0.002 H8 SDM 19
SDM H10 H5 H 0 1 N N N N N N 19.024 21.232 -4.347 0.128 -3.644 -0.001 H10 SDM 20
SDM H H6 H 0 1 N N N N N N 19.678 16.402 -5.633 -1.986 2.936 0.004 H SDM 21
SDM H5 H7 H 0 1 N N N N N N 17.703 23.253 -10.790 5.328 2.600 -0.001 H5 SDM 22
SDM H6 H8 H 0 1 N N N N N N 17.716 21.970 -9.533 3.862 3.078 -0.890 H6 SDM 23
SDM H7 H9 H 0 1 N N N N N N 18.421 23.584 -9.177 3.863 3.076 0.890 H7 SDM 24
SDM H9 H10 H 0 1 N N N N N N 19.036 23.478 -5.362 2.567 -3.417 -0.004 H9 SDM 25
SDM H12 H11 H 0 1 N N N N N N 21.151 15.079 -8.403 -4.471 -0.206 -0.006 H12 SDM 26
SDM H11 H12 H 0 1 N N N N N N 21.323 16.619 -9.176 -5.106 1.349 -0.008 H11 SDM 27
#
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
SDM C5 C6 SING N N 1
SDM C5 O SING N N 2
SDM O C4 SING N N 3
SDM N1 C SING N N 4
SDM C2 C3 SING Y N 5
SDM C2 C1 DOUB Y N 6
SDM C4 C3 DOUB Y N 7
SDM C4 C7 SING Y N 8
SDM C3 C10 SING Y N 9
SDM C C1 SING N N 10
SDM C N DOUB N N 11
SDM C7 C8 DOUB Y N 12
SDM C1 S SING Y N 13
SDM C10 S SING Y N 14
SDM C10 C9 DOUB Y N 15
SDM C8 C9 SING Y N 16
SDM C2 H2 SING N N 17
SDM C5 H3 SING N N 18
SDM C5 H4 SING N N 19
SDM C7 H8 SING N N 20
SDM C9 H10 SING N N 21
SDM N H SING N N 22
SDM C6 H5 SING N N 23
SDM C6 H6 SING N N 24
SDM C6 H7 SING N N 25
SDM C8 H9 SING N N 26
SDM N1 H12 SING N N 27
SDM N1 H11 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
SDM SMILES ACDLabs 14.52 "N=C(N)c1cc2c(cccc2s1)OCC"
SDM InChI InChI 1.06 "InChI=1S/C11H12N2OS/c1-2-14-8-4-3-5-9-7(8)6-10(15-9)11(12)13/h3-6H,2H2,1H3,(H3,12,13)"
SDM InChIKey InChI 1.06 LOIXMYZGPMLLIW-UHFFFAOYSA-N
SDM SMILES_CANONICAL CACTVS 3.385 "CCOc1cccc2sc(cc12)C(N)=N"
SDM SMILES CACTVS 3.385 "CCOc1cccc2sc(cc12)C(N)=N"
SDM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\c1cc2c(cccc2s1)OCC)/N"
SDM SMILES "OpenEye OEToolkits" 2.0.7 "CCOc1cccc2c1cc(s2)C(=N)N"
#
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
SDM "SYSTEMATIC NAME" ACDLabs 14.52 4-ethoxy-1-benzothiophene-2-carboximidamide
SDM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 4-ethoxy-1-benzothiophene-2-carboximidamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SDM 'Create component' 2022-12-15 PDBE
SDM 'Initial release' 2023-08-02 RCSB
SDM 'Modify formula' 2024-09-16 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
SDM C1 C 7.893 -1.573 1
SDM C2 C 7.018 -0.366 2
SDM C3 C 5.598 -0.823 3
SDM C4 C 4.299 -0.073 4
SDM C5 C 3.000 2.177 5
SDM C7 C 3.000 -0.823 6
SDM C9 C 4.299 -3.073 7
SDM N N 10.143 -0.274 8
SDM C C 9.393 -1.573 9
SDM O O 4.299 1.427 10
SDM C10 C 5.598 -2.323 11
SDM C6 C 3.000 3.677 12
SDM C8 C 3.000 -2.323 13
SDM N1 N 10.143 -2.872 14
SDM S S 7.018 -2.780 15
SDM H H 9.393 1.025 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
SDM C5 C6 SINGLE NONE 1
SDM C5 O SINGLE NONE 2
SDM O C4 SINGLE NONE 3
SDM N1 C SINGLE ENDUPRIGHT 4
SDM C2 C3 SINGLE NONE 5
SDM C2 C1 DOUBLE NONE 6
SDM C4 C3 DOUBLE NONE 7
SDM C4 C7 SINGLE NONE 8
SDM C3 C10 SINGLE NONE 9
SDM C C1 SINGLE ENDUPRIGHT 10
SDM C N DOUBLE NONE 11
SDM C7 C8 DOUBLE NONE 12
SDM C1 S SINGLE NONE 13
SDM C10 S SINGLE NONE 14
SDM C10 C9 DOUBLE NONE 15
SDM C8 C9 SINGLE NONE 16
#
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
SDM MurckoScaffold S1 scaffold c1ccc2sccc2c1 InChI=1S/C8H6S/c1-2-4-8-7(3-1)5-6-9-8/h1-6H FCEHBMOGCRZNNI-UHFFFAOYSA-N
SDM benzothiophen F1 fragment c1ccc2sccc2c1 InChI=1S/C8H6S/c1-2-4-8-7(3-1)5-6-9-8/h1-6H FCEHBMOGCRZNNI-UHFFFAOYSA-N
SDM phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
SDM thiophen F3 fragment c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-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
SDM C1 S1 1
SDM C2 S1 1
SDM C3 S1 1
SDM C4 S1 1
SDM C7 S1 1
SDM C9 S1 1
SDM C10 S1 1
SDM C8 S1 1
SDM S S1 1
SDM C10 F1 1
SDM C3 F1 1
SDM C2 F1 1
SDM C1 F1 1
SDM S F1 1
SDM C4 F1 1
SDM C7 F1 1
SDM C8 F1 1
SDM C9 F1 1
SDM C3 F2 1
SDM C4 F2 1
SDM C7 F2 1
SDM C8 F2 1
SDM C9 F2 1
SDM C10 F2 1
SDM C1 F3 1
SDM C2 F3 1
SDM C3 F3 1
SDM C10 F3 1
SDM S F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SDM
_pdbe_chem_comp_rdkit_properties.exactmw 220.067
_pdbe_chem_comp_rdkit_properties.amw 220.297
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.182
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 109.021
_pdbe_chem_comp_rdkit_properties.tpsa 59.100
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.639
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.928
_pdbe_chem_comp_rdkit_properties.chi0v 8.027
_pdbe_chem_comp_rdkit_properties.chi1v 4.580
_pdbe_chem_comp_rdkit_properties.chi2v 2.604
_pdbe_chem_comp_rdkit_properties.chi3v 2.604
_pdbe_chem_comp_rdkit_properties.chi4v 1.830
_pdbe_chem_comp_rdkit_properties.chi0n 19.211
_pdbe_chem_comp_rdkit_properties.chi1n 9.605
_pdbe_chem_comp_rdkit_properties.chi2n 1.605
_pdbe_chem_comp_rdkit_properties.chi3n 1.605
_pdbe_chem_comp_rdkit_properties.chi4n 1.033
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.550
_pdbe_chem_comp_rdkit_properties.kappa1 2.980
_pdbe_chem_comp_rdkit_properties.kappa2 3.903
_pdbe_chem_comp_rdkit_properties.kappa3 1.804
_pdbe_chem_comp_rdkit_properties.Phi 0.775
#
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
SDM UniChem PDBe SDM
SDM UniChem PDBe SH9
#
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
SDM C1 -2.536 -0.308 -0.122 ETKDGv3 1
SDM C2 -1.306 0.229 -0.025 ETKDGv3 2
SDM C3 -0.205 -0.761 -0.056 ETKDGv3 3
SDM C4 1.108 -0.501 0.023 ETKDGv3 4
SDM C5 2.914 1.204 0.237 ETKDGv3 5
SDM C7 2.058 -1.657 -0.025 ETKDGv3 6
SDM C9 0.140 -3.179 -0.227 ETKDGv3 7
SDM N -4.933 -0.135 0.102 ETKDGv3 8
SDM C -3.803 0.463 -0.109 ETKDGv3 9
SDM O 1.545 0.825 0.146 ETKDGv3 10
SDM C10 -0.684 -2.133 -0.183 ETKDGv3 11
SDM C6 3.014 2.716 0.360 ETKDGv3 12
SDM C8 1.597 -2.918 -0.143 ETKDGv3 13
SDM N1 -3.808 1.875 -0.342 ETKDGv3 14
SDM S -2.450 -2.103 -0.254 ETKDGv3 15
SDM H2 -1.123 1.288 0.090 ETKDGv3 16
SDM H3 3.376 0.735 1.132 ETKDGv3 17
SDM H4 3.457 0.876 -0.676 ETKDGv3 18
SDM H8 3.126 -1.494 0.035 ETKDGv3 19
SDM H10 -0.241 -4.187 -0.321 ETKDGv3 20
SDM H -5.011 -1.161 0.280 ETKDGv3 21
SDM H5 2.561 3.200 -0.532 ETKDGv3 22
SDM H6 4.081 3.017 0.431 ETKDGv3 23
SDM H7 2.481 3.059 1.271 ETKDGv3 24
SDM H9 2.291 -3.748 -0.177 ETKDGv3 25
SDM H12 -2.948 2.389 -0.632 ETKDGv3 26
SDM H11 -4.702 2.411 -0.285 ETKDGv3 27
#