data_W0A
#
_chem_comp.id W0A
_chem_comp.name N-[(1H-benzimidazol-2-yl)methyl]butanamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H15 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-09-24
_chem_comp.pdbx_modified_date 2021-01-08
_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 217.267
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code W0A
_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 5RQD
_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
W0A N1 N1 N 0 1 Y N N N N N 14.685 6.166 11.477 -1.512 0.985 0.773 N1 W0A 1
W0A C4 C1 C 0 1 N N N N N N 14.535 8.652 11.249 0.673 1.133 -0.523 C4 W0A 2
W0A C5 C2 C 0 1 Y N N N N N 14.705 7.249 10.717 -0.747 0.674 -0.308 C5 W0A 3
W0A C6 C3 C 0 1 Y N N N N N 14.917 5.111 10.603 -2.737 0.374 0.599 C6 W0A 4
W0A C7 C4 C 0 1 Y N N N N N 15.038 3.748 10.843 -3.905 0.318 1.347 C7 W0A 5
W0A C8 C5 C 0 1 Y N N N N N 15.297 2.909 9.769 -4.982 -0.403 0.878 C8 W0A 6
W0A C10 C6 C 0 1 Y N N N N N 15.303 4.771 8.229 -3.768 -1.024 -1.088 C10 W0A 7
W0A O O1 O 0 1 N N N N N N 16.237 8.983 13.403 3.360 1.322 -0.614 O W0A 8
W0A C3 C7 C 0 1 N N N N N N 15.045 8.774 13.618 2.928 0.294 -0.139 C3 W0A 9
W0A C2 C8 C 0 1 N N N N N N 14.492 8.725 15.021 3.878 -0.769 0.350 C2 W0A 10
W0A C1 C9 C 0 1 N N N N N N 15.389 8.045 15.969 5.319 -0.303 0.132 C1 W0A 11
W0A C C10 C 0 1 N N N N N N 16.086 9.051 16.806 6.284 -1.382 0.628 C W0A 12
W0A N N2 N 0 1 N N N N N N 14.150 8.624 12.644 1.597 0.101 -0.048 N W0A 13
W0A N2 N3 N 0 1 Y N N N N N 14.923 6.973 9.412 -1.419 -0.078 -1.130 N2 W0A 14
W0A C11 C11 C 0 1 Y N N N N N 15.058 5.603 9.306 -2.661 -0.303 -0.630 C11 W0A 15
W0A C9 C12 C 0 1 Y N N N N N 15.426 3.414 8.480 -4.907 -1.071 -0.336 C9 W0A 16
W0A H1 H1 H 0 1 N N N N N N 14.536 6.117 12.465 -1.244 1.533 1.528 H1 W0A 17
W0A H2 H2 H 0 1 N N N N N N 15.486 9.195 11.147 0.841 1.311 -1.585 H2 W0A 18
W0A H3 H3 H 0 1 N N N N N N 13.755 9.167 10.669 0.844 2.056 0.031 H3 W0A 19
W0A H4 H4 H 0 1 N N N N N N 14.933 3.351 11.842 -3.968 0.836 2.293 H4 W0A 20
W0A H5 H5 H 0 1 N N N N N N 15.400 1.847 9.937 -5.891 -0.447 1.459 H5 W0A 21
W0A H6 H6 H 0 1 N N N N N N 15.395 5.165 7.228 -3.720 -1.548 -2.031 H6 W0A 22
W0A H7 H7 H 0 1 N N N N N N 14.329 9.755 15.370 3.710 -0.946 1.412 H7 W0A 23
W0A H8 H8 H 0 1 N N N N N N 13.532 8.189 15.001 3.707 -1.692 -0.204 H8 W0A 24
W0A H9 H9 H 0 1 N N N N N N 14.800 7.377 16.615 5.487 -0.126 -0.930 H9 W0A 25
W0A H10 H10 H 0 1 N N N N N N 16.132 7.455 15.411 5.490 0.620 0.686 H10 W0A 26
W0A H11 H11 H 0 1 N N N N N N 16.756 8.540 17.513 6.116 -1.559 1.691 H11 W0A 27
W0A H12 H12 H 0 1 N N N N N N 16.675 9.719 16.161 6.114 -2.305 0.074 H12 W0A 28
W0A H13 H13 H 0 1 N N N N N N 15.344 9.641 17.364 7.311 -1.049 0.473 H13 W0A 29
W0A H14 H14 H 0 1 N N N N N N 13.188 8.489 12.882 1.251 -0.722 0.333 H14 W0A 30
W0A H16 H16 H 0 1 N N N N N N 15.625 2.738 7.662 -5.760 -1.629 -0.693 H16 W0A 31
#
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
W0A C10 C9 DOUB Y N 1
W0A C10 C11 SING Y N 2
W0A C9 C8 SING Y N 3
W0A C11 N2 SING Y N 4
W0A C11 C6 DOUB Y N 5
W0A N2 C5 DOUB Y N 6
W0A C8 C7 DOUB Y N 7
W0A C6 C7 SING Y N 8
W0A C6 N1 SING Y N 9
W0A C5 C4 SING N N 10
W0A C5 N1 SING Y N 11
W0A C4 N SING N N 12
W0A N C3 SING N N 13
W0A O C3 DOUB N N 14
W0A C3 C2 SING N N 15
W0A C2 C1 SING N N 16
W0A C1 C SING N N 17
W0A N1 H1 SING N N 18
W0A C4 H2 SING N N 19
W0A C4 H3 SING N N 20
W0A C7 H4 SING N N 21
W0A C8 H5 SING N N 22
W0A C10 H6 SING N N 23
W0A C2 H7 SING N N 24
W0A C2 H8 SING N N 25
W0A C1 H9 SING N N 26
W0A C1 H10 SING N N 27
W0A C H11 SING N N 28
W0A C H12 SING N N 29
W0A C H13 SING N N 30
W0A N H14 SING N N 31
W0A C9 H16 SING N N 32
#
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
W0A SMILES ACDLabs 12.01 n1c(CNC(=O)CCC)nc2c1cccc2
W0A InChI InChI 1.03 InChI=1S/C12H15N3O/c1-2-5-12(16)13-8-11-14-9-6-3-4-7-10(9)15-11/h3-4,6-7H,2,5,8H2,1H3,(H,13,16)(H,14,15)
W0A InChIKey InChI 1.03 MXDONONSXPZRMO-UHFFFAOYSA-N
W0A SMILES_CANONICAL CACTVS 3.385 CCCC(=O)NCc1[nH]c2ccccc2n1
W0A SMILES CACTVS 3.385 CCCC(=O)NCc1[nH]c2ccccc2n1
W0A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CCCC(=O)NCc1[nH]c2ccccc2n1
W0A SMILES "OpenEye OEToolkits" 2.0.7 CCCC(=O)NCc1[nH]c2ccccc2n1
#
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
W0A "SYSTEMATIC NAME" ACDLabs 12.01 N-[(1H-benzimidazol-2-yl)methyl]butanamide
W0A "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-(1~{H}-benzimidazol-2-ylmethyl)butanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
W0A 'Create component' 2020-09-24 RCSB
W0A 'Initial release' 2021-01-13 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
W0A N1 N 7.018 -0.304 1
W0A C4 C 9.393 0.903 2
W0A C5 C 7.893 0.903 3
W0A C6 C 5.598 0.153 4
W0A C7 C 4.299 -0.597 5
W0A C8 C 3.000 0.153 6
W0A C10 C 4.299 2.403 7
W0A O O 12.393 0.903 8
W0A C3 C 11.643 -0.396 9
W0A C2 C 12.393 -1.695 10
W0A C1 C 13.893 -1.695 11
W0A C C 14.643 -2.994 12
W0A N N 10.143 -0.396 13
W0A N2 N 7.018 2.110 14
W0A C11 C 5.598 1.653 15
W0A C9 C 3.000 1.653 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
W0A C10 C9 DOUBLE NONE 1
W0A C10 C11 SINGLE NONE 2
W0A C9 C8 SINGLE NONE 3
W0A C11 N2 SINGLE NONE 4
W0A C11 C6 DOUBLE NONE 5
W0A N2 C5 DOUBLE NONE 6
W0A C8 C7 DOUBLE NONE 7
W0A C6 C7 SINGLE NONE 8
W0A C6 N1 SINGLE NONE 9
W0A C5 C4 SINGLE NONE 10
W0A C5 N1 SINGLE NONE 11
W0A C4 N SINGLE NONE 12
W0A N C3 SINGLE NONE 13
W0A O C3 DOUBLE NONE 14
W0A C3 C2 SINGLE NONE 15
W0A C2 C1 SINGLE NONE 16
W0A C1 C SINGLE NONE 17
#
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
W0A MurckoScaffold S1 scaffold 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
W0A amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
W0A benzimidazole F2 fragment 'c1ccc2[nH]cnc2c1' InChI=1S/C7H6N2/c1-2-4-7-6(3-1)8-5-9-7/h1-5H,(H,8,9) HYZJCKYKOHLVJF-UHFFFAOYSA-N
W0A imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
W0A phenyl F4 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
W0A Z1203191681 F5 fragment 'CC(=O)NCc1ncc[nH]1' InChI=1S/C6H9N3O/c1-5(10)9-4-6-7-2-3-8-6/h2-3H,4H2,1H3,(H,7,8)(H,9,10) SXKAQLCLHGQXHB-UHFFFAOYSA-N
W0A Z26781952 F6 fragment 'CCCC(=O)NCc1nc2ccccc2[nH]1' InChI=1S/C12H15N3O/c1-2-5-12(16)13-8-11-14-9-6-3-4-7-10(9)15-11/h3-4,6-7H,2,5,8H2,1H3,(H,13,16)(H,14,15) MXDONONSXPZRMO-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
W0A N1 S1 1
W0A C5 S1 1
W0A C6 S1 1
W0A C7 S1 1
W0A C8 S1 1
W0A C10 S1 1
W0A N2 S1 1
W0A C11 S1 1
W0A C9 S1 1
W0A N F1 1
W0A C3 F1 1
W0A O F1 1
W0A C2 F1 1
W0A C6 F2 1
W0A N1 F2 1
W0A C5 F2 1
W0A N2 F2 1
W0A C11 F2 1
W0A C10 F2 1
W0A C9 F2 1
W0A C8 F2 1
W0A C7 F2 1
W0A C6 F3 1
W0A C11 F3 1
W0A N2 F3 1
W0A C5 F3 1
W0A N1 F3 1
W0A C6 F4 1
W0A C11 F4 1
W0A C10 F4 1
W0A C9 F4 1
W0A C8 F4 1
W0A C7 F4 1
W0A C2 F5 1
W0A C3 F5 1
W0A O F5 1
W0A N F5 1
W0A C4 F5 1
W0A C5 F5 1
W0A N2 F5 1
W0A C11 F5 1
W0A C6 F5 1
W0A N1 F5 1
W0A C F6 1
W0A C1 F6 1
W0A C2 F6 1
W0A C3 F6 1
W0A O F6 1
W0A N F6 1
W0A C4 F6 1
W0A C5 F6 1
W0A N2 F6 1
W0A C11 F6 1
W0A C10 F6 1
W0A C9 F6 1
W0A C8 F6 1
W0A C7 F6 1
W0A C6 F6 1
W0A N1 F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id W0A
_pdbe_chem_comp_rdkit_properties.exactmw 217.122
_pdbe_chem_comp_rdkit_properties.amw 217.272
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_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 115.269
_pdbe_chem_comp_rdkit_properties.tpsa 57.780
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.496
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.376
_pdbe_chem_comp_rdkit_properties.chi0v 7.750
_pdbe_chem_comp_rdkit_properties.chi1v 4.046
_pdbe_chem_comp_rdkit_properties.chi2v 1.511
_pdbe_chem_comp_rdkit_properties.chi3v 1.511
_pdbe_chem_comp_rdkit_properties.chi4v 0.930
_pdbe_chem_comp_rdkit_properties.chi0n 22.750
_pdbe_chem_comp_rdkit_properties.chi1n 11.440
_pdbe_chem_comp_rdkit_properties.chi2n 1.511
_pdbe_chem_comp_rdkit_properties.chi3n 1.511
_pdbe_chem_comp_rdkit_properties.chi4n 0.930
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.840
_pdbe_chem_comp_rdkit_properties.kappa1 2.696
_pdbe_chem_comp_rdkit_properties.kappa2 4.788
_pdbe_chem_comp_rdkit_properties.kappa3 2.392
_pdbe_chem_comp_rdkit_properties.Phi 0.807
#
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
W0A UniChem PDBe W0A
W0A UniChem ZINC ZINC000000200671
W0A UniChem eMolecules 2268162
W0A UniChem SureChEMBL SCHEMBL8278816
W0A UniChem PubChem 751089
W0A UniChem Mcule MCULE-2410706457
#
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
W0A N1 2.033 -0.666 1.154 ETKDGv3 1
W0A C4 -0.382 -1.525 0.917 ETKDGv3 2
W0A C5 0.944 -1.130 0.349 ETKDGv3 3
W0A C6 3.000 -0.353 0.172 ETKDGv3 4
W0A C7 4.354 0.190 0.361 ETKDGv3 5
W0A C8 5.095 0.427 -0.737 ETKDGv3 6
W0A C10 3.299 -0.351 -2.239 ETKDGv3 7
W0A O -3.038 -1.597 1.908 ETKDGv3 8
W0A C3 -2.581 -0.471 1.571 ETKDGv3 9
W0A C2 -3.463 0.741 1.666 ETKDGv3 10
W0A C1 -4.378 0.874 0.441 ETKDGv3 11
W0A C -3.602 1.202 -0.834 ETKDGv3 12
W0A N -1.245 -0.355 1.065 ETKDGv3 13
W0A N2 1.181 -1.096 -0.930 ETKDGv3 14
W0A C11 2.513 -0.603 -1.021 ETKDGv3 15
W0A C9 4.544 0.144 -2.097 ETKDGv3 16
W0A H1 2.087 -0.553 2.191 ETKDGv3 17
W0A H2 -0.868 -2.263 0.244 ETKDGv3 18
W0A H3 -0.227 -1.999 1.910 ETKDGv3 19
W0A H4 4.741 0.393 1.351 ETKDGv3 20
W0A H5 6.096 0.827 -0.638 ETKDGv3 21
W0A H6 2.889 -0.557 -3.219 ETKDGv3 22
W0A H7 -2.845 1.657 1.782 ETKDGv3 23
W0A H8 -4.094 0.653 2.576 ETKDGv3 24
W0A H9 -5.105 1.692 0.631 ETKDGv3 25
W0A H10 -4.955 -0.065 0.294 ETKDGv3 26
W0A H11 -4.315 1.364 -1.670 ETKDGv3 27
W0A H12 -2.928 0.363 -1.108 ETKDGv3 28
W0A H13 -3.002 2.126 -0.696 ETKDGv3 29
W0A H14 -0.896 0.591 0.785 ETKDGv3 30
W0A H16 5.149 0.342 -2.972 ETKDGv3 31
#