data_SYG
#
_chem_comp.id SYG
_chem_comp.name 2-[(1~{S})-1-azanylpropyl]phenol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H13 N O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-03-13
_chem_comp.pdbx_modified_date 2020-05-29
_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 151.206
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SYG
_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 5R09
_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
SYG C4 C1 C 0 1 Y N N N N N 14.711 25.661 -22.367 -0.824 1.413 0.071 C4 SYG 1
SYG C5 C2 C 0 1 Y N N N N N 15.044 24.693 -23.286 -2.184 1.450 0.312 C5 SYG 2
SYG C6 C3 C 0 1 Y N N N N N 14.081 24.103 -24.047 -2.920 0.279 0.316 C6 SYG 3
SYG C7 C4 C 0 1 Y N N N N N 12.769 24.485 -23.913 -2.297 -0.931 0.080 C7 SYG 4
SYG C8 C5 C 0 1 Y N N N N N 12.436 25.509 -23.058 -0.931 -0.971 -0.162 C8 SYG 5
SYG O O1 O 0 1 N N N N N N 11.185 26.016 -23.053 -0.316 -2.160 -0.395 O SYG 6
SYG C3 C6 C 0 1 Y N N N N N 13.408 26.117 -22.272 -0.195 0.205 -0.166 C3 SYG 7
SYG C2 C7 C 0 1 N N S N N N 13.080 27.389 -21.526 1.287 0.166 -0.434 C2 SYG 8
SYG N N1 N 0 1 N N N N N N 12.790 28.509 -22.470 1.742 1.496 -0.862 N SYG 9
SYG C1 C8 C 0 1 N N N N N N 11.904 27.105 -20.589 2.026 -0.240 0.843 C1 SYG 10
SYG C C9 C 0 1 N N N N N N 12.331 26.526 -19.261 3.517 -0.400 0.540 C SYG 11
SYG H1 H1 H 0 1 N N N N N N 15.471 26.067 -21.716 -0.252 2.329 0.064 H1 SYG 12
SYG H2 H2 H 0 1 N N N N N N 16.076 24.399 -23.405 -2.674 2.395 0.497 H2 SYG 13
SYG H3 H3 H 0 1 N N N N N N 14.349 23.334 -24.756 -3.983 0.310 0.505 H3 SYG 14
SYG H4 H4 H 0 1 N N N N N N 11.999 23.981 -24.479 -2.872 -1.845 0.084 H4 SYG 15
SYG H5 H5 H 0 1 N N N N N N 11.127 26.711 -22.408 -0.288 -2.412 -1.328 H5 SYG 16
SYG H6 H6 H 0 1 N N N N N N 13.949 27.665 -20.911 1.495 -0.559 -1.220 H6 SYG 17
SYG H7 H7 H 0 1 N N N N N N 12.577 29.337 -21.951 1.561 2.187 -0.149 H7 SYG 18
SYG H8 H8 H 0 1 N N N N N N 13.590 28.674 -23.047 2.720 1.481 -1.110 H8 SYG 19
SYG H10 H10 H 0 1 N N N N N N 11.368 28.048 -20.404 1.891 0.531 1.601 H10 SYG 20
SYG H11 H11 H 0 1 N N N N N N 11.229 26.390 -21.082 1.626 -1.185 1.209 H11 SYG 21
SYG H12 H12 H 0 1 N N N N N N 11.443 26.346 -18.637 3.652 -1.171 -0.219 H12 SYG 22
SYG H13 H13 H 0 1 N N N N N N 12.861 25.577 -19.428 3.917 0.545 0.173 H13 SYG 23
SYG H14 H14 H 0 1 N N N N N N 13.000 27.234 -18.751 4.044 -0.690 1.449 H14 SYG 24
#
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
SYG C6 C7 DOUB Y N 1
SYG C6 C5 SING Y N 2
SYG C7 C8 SING Y N 3
SYG C5 C4 DOUB Y N 4
SYG C8 O SING N N 5
SYG C8 C3 DOUB Y N 6
SYG N C2 SING N N 7
SYG C4 C3 SING Y N 8
SYG C3 C2 SING N N 9
SYG C2 C1 SING N N 10
SYG C1 C SING N N 11
SYG C4 H1 SING N N 12
SYG C5 H2 SING N N 13
SYG C6 H3 SING N N 14
SYG C7 H4 SING N N 15
SYG O H5 SING N N 16
SYG C2 H6 SING N N 17
SYG N H7 SING N N 18
SYG N H8 SING N N 19
SYG C1 H10 SING N N 20
SYG C1 H11 SING N N 21
SYG C H12 SING N N 22
SYG C H13 SING N N 23
SYG C H14 SING N N 24
#
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
SYG InChI InChI 1.03 InChI=1S/C9H13NO/c1-2-8(10)7-5-3-4-6-9(7)11/h3-6,8,11H,2,10H2,1H3/t8-/m0/s1
SYG InChIKey InChI 1.03 SJYRIEHMQRIBEN-QMMMGPOBSA-N
SYG SMILES_CANONICAL CACTVS 3.385 CC[C@H](N)c1ccccc1O
SYG SMILES CACTVS 3.385 CC[CH](N)c1ccccc1O
SYG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CC[C@@H](c1ccccc1O)N
SYG SMILES "OpenEye OEToolkits" 2.0.6 CCC(c1ccccc1O)N
#
_pdbx_chem_comp_identifier.comp_id SYG
_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 2-[(1~{S})-1-azanylpropyl]phenol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SYG 'Create component' 2020-03-13 RCSB
SYG 'Initial release' 2020-06-03 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
SYG C4 C 7.702 -1.125 1
SYG C5 C 7.702 -2.625 2
SYG C6 C 6.404 -3.375 3
SYG C7 C 5.104 -2.625 4
SYG C8 C 5.104 -1.125 5
SYG O O 3.805 -0.375 6
SYG C3 C 6.404 -0.375 7
SYG C2 C 6.404 1.125 8
SYG N N 7.702 1.875 9
SYG C1 C 5.104 1.875 10
SYG C C 5.104 3.375 11
#
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
SYG C6 C7 DOUBLE NONE 1
SYG C6 C5 SINGLE NONE 2
SYG C7 C8 SINGLE NONE 3
SYG C5 C4 DOUBLE NONE 4
SYG C8 O SINGLE NONE 5
SYG C8 C3 DOUBLE NONE 6
SYG C2 N SINGLE BEGINDASH 7
SYG C4 C3 SINGLE NONE 8
SYG C3 C2 SINGLE NONE 9
SYG C2 C1 SINGLE NONE 10
SYG C1 C 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
SYG MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
SYG phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
SYG C4 S1 1
SYG C5 S1 1
SYG C6 S1 1
SYG C7 S1 1
SYG C8 S1 1
SYG C3 S1 1
SYG C4 F1 1
SYG C5 F1 1
SYG C6 F1 1
SYG C7 F1 1
SYG C8 F1 1
SYG C3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SYG
_pdbe_chem_comp_rdkit_properties.exactmw 151.100
_pdbe_chem_comp_rdkit_properties.amw 151.209
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_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 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_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 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 85.128
_pdbe_chem_comp_rdkit_properties.tpsa 46.250
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.285
_pdbe_chem_comp_rdkit_properties.CrippenMR 44.450
_pdbe_chem_comp_rdkit_properties.chi0v 5.355
_pdbe_chem_comp_rdkit_properties.chi1v 2.678
_pdbe_chem_comp_rdkit_properties.chi2v 1.008
_pdbe_chem_comp_rdkit_properties.chi3v 1.008
_pdbe_chem_comp_rdkit_properties.chi4v 0.530
_pdbe_chem_comp_rdkit_properties.chi0n 18.355
_pdbe_chem_comp_rdkit_properties.chi1n 8.980
_pdbe_chem_comp_rdkit_properties.chi2n 1.008
_pdbe_chem_comp_rdkit_properties.chi3n 1.008
_pdbe_chem_comp_rdkit_properties.chi4n 0.530
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.020
_pdbe_chem_comp_rdkit_properties.kappa1 1.524
_pdbe_chem_comp_rdkit_properties.kappa2 3.394
_pdbe_chem_comp_rdkit_properties.kappa3 1.713
_pdbe_chem_comp_rdkit_properties.Phi 0.470
#
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
SYG UniChem PDBe SYG
SYG UniChem ZINC ZINC000022142789
SYG UniChem SureChEMBL SCHEMBL17092611
SYG UniChem PubChem 30046311
SYG UniChem Nikkaji J2.886.995I
#
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
SYG C4 1.363 -1.324 -0.598 ETKDGv3 1
SYG C5 2.657 -1.139 -0.886 ETKDGv3 2
SYG C6 3.321 0.127 -0.528 ETKDGv3 3
SYG C7 2.630 1.096 0.081 ETKDGv3 4
SYG C8 1.195 0.905 0.402 ETKDGv3 5
SYG O 0.493 1.936 1.026 ETKDGv3 6
SYG C3 0.582 -0.261 0.089 ETKDGv3 7
SYG C2 -0.892 -0.504 0.373 ETKDGv3 8
SYG N -1.206 -0.182 1.768 ETKDGv3 9
SYG C1 -1.760 0.325 -0.598 ETKDGv3 10
SYG C -3.231 -0.090 -0.574 ETKDGv3 11
SYG H1 0.889 -2.258 -0.871 ETKDGv3 12
SYG H2 3.219 -1.918 -1.385 ETKDGv3 13
SYG H3 4.368 0.271 -0.762 ETKDGv3 14
SYG H4 3.122 2.025 0.339 ETKDGv3 15
SYG H5 0.943 2.812 1.263 ETKDGv3 16
SYG H6 -1.111 -1.584 0.203 ETKDGv3 17
SYG H7 -0.547 -0.711 2.385 ETKDGv3 18
SYG H8 -2.156 -0.557 1.993 ETKDGv3 19
SYG H10 -1.687 1.406 -0.353 ETKDGv3 20
SYG H11 -1.383 0.184 -1.635 ETKDGv3 21
SYG H12 -3.781 0.460 -1.367 ETKDGv3 22
SYG H13 -3.695 0.159 0.402 ETKDGv3 23
SYG H14 -3.332 -1.179 -0.767 ETKDGv3 24
#