data_SJ2
#
_chem_comp.id SJ2
_chem_comp.name ~{N}-[(2~{S})-5-carbamimidamido-1-oxidanyl-pentan-2-yl]-~{N}-methyl-ethanamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H20 N4 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-11-16
_chem_comp.pdbx_modified_date 2021-11-26
_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 216.281
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SJ2
_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 7AZ7
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
SJ2 C1 C1 C 0 1 N N N N N N 2.629 16.228 26.206 2.325 -0.037 -1.657 C1 SJ2 1
SJ2 C2 C2 C 0 1 N N N N N N 3.598 18.231 27.273 2.424 1.612 0.135 C2 SJ2 2
SJ2 C3 C3 C 0 1 N N N N N N 4.151 18.918 28.491 2.840 2.641 -0.885 C3 SJ2 3
SJ2 O4 O1 O 0 1 N N N N N N 3.575 18.856 26.219 2.306 1.926 1.300 O4 SJ2 4
SJ2 O O2 O 0 1 N N N N N N 4.250 14.937 30.251 2.786 -2.477 -0.488 O SJ2 5
SJ2 N N1 N 0 1 N N N N N N 3.164 16.949 27.371 2.182 0.343 -0.249 N SJ2 6
SJ2 CA C4 C 0 1 N N S N N N 3.157 16.266 28.694 1.777 -0.658 0.742 CA SJ2 7
SJ2 C C5 C 0 1 N N N N N N 4.208 15.196 28.920 2.801 -1.794 0.767 C SJ2 8
SJ2 CB C6 C 0 1 N N N N N N 1.749 15.740 28.987 0.403 -1.218 0.370 CB SJ2 9
SJ2 CG C7 C 0 1 N N N N N N 0.867 16.890 29.464 -0.644 -0.106 0.465 CG SJ2 10
SJ2 CD C8 C 0 1 N N N N N N -0.518 16.525 29.775 -2.018 -0.666 0.093 CD SJ2 11
SJ2 NE N2 N 0 1 N N N N N N -1.295 16.477 30.761 -3.020 0.398 0.185 NE SJ2 12
SJ2 CZ C9 C 0 1 N N N N N N -2.132 17.246 31.465 -4.337 0.130 -0.106 CZ SJ2 13
SJ2 NH1 N3 N 0 1 N N N N N N -3.164 16.691 32.158 -5.278 1.129 -0.020 NH1 SJ2 14
SJ2 NH2 N4 N 0 1 N N N N N N -2.039 18.589 31.579 -4.693 -1.072 -0.464 NH2 SJ2 15
SJ2 H1 H1 H 0 1 N N N N N N 2.338 15.211 26.506 3.346 -0.368 -1.842 H1 SJ2 16
SJ2 H2 H2 H 0 1 N N N N N N 1.749 16.762 25.817 1.633 -0.847 -1.886 H2 SJ2 17
SJ2 H3 H3 H 0 1 N N N N N N 3.400 16.173 25.423 2.101 0.822 -2.289 H3 SJ2 18
SJ2 H4 H4 H 0 1 N N N N N N 4.467 19.938 28.226 2.062 2.738 -1.642 H4 SJ2 19
SJ2 H5 H5 H 0 1 N N N N N N 3.375 18.966 29.269 2.989 3.601 -0.391 H5 SJ2 20
SJ2 H6 H6 H 0 1 N N N N N N 5.015 18.353 28.870 3.770 2.327 -1.358 H6 SJ2 21
SJ2 H7 H7 H 0 1 N N N N N N 4.902 14.268 30.423 3.412 -3.212 -0.543 H7 SJ2 22
SJ2 H8 H8 H 0 1 N N N N N N 3.350 17.045 29.446 1.725 -0.193 1.727 H8 SJ2 23
SJ2 H9 H9 H 0 1 N N N N N N 3.939 14.283 28.369 2.549 -2.493 1.565 H9 SJ2 24
SJ2 H10 H10 H 0 1 N N N N N N 5.189 15.556 28.577 3.795 -1.383 0.945 H10 SJ2 25
SJ2 H11 H11 H 0 1 N N N N N N 1.322 15.305 28.071 0.432 -1.603 -0.650 H11 SJ2 26
SJ2 H12 H12 H 0 1 N N N N N N 1.801 14.969 29.769 0.141 -2.024 1.055 H12 SJ2 27
SJ2 H13 H13 H 0 1 N N N N N N 1.320 17.312 30.373 -0.673 0.279 1.485 H13 SJ2 28
SJ2 H14 H14 H 0 1 N N N N N N 0.848 17.655 28.674 -0.382 0.700 -0.220 H14 SJ2 29
SJ2 H15 H15 H 0 1 N N N N N N -1.077 17.176 29.086 -1.989 -1.051 -0.927 H15 SJ2 30
SJ2 H16 H16 H 0 1 N N N N N N -0.558 15.487 29.413 -2.280 -1.472 0.778 H16 SJ2 31
SJ2 H17 H17 H 0 1 N N N N N N -1.284 15.555 31.149 -2.755 1.293 0.451 H17 SJ2 32
SJ2 H18 H18 H 0 1 N N N N N N -3.777 17.272 32.694 -5.012 2.023 0.246 H18 SJ2 33
SJ2 H19 H19 H 0 1 N N N N N N -3.310 15.702 32.131 -6.207 0.939 -0.225 H19 SJ2 34
SJ2 H20 H20 H 0 1 N N N N N N -2.756 18.966 32.165 -5.622 -1.262 -0.669 H20 SJ2 35
#
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
SJ2 C1 N SING N N 1
SJ2 O4 C2 DOUB N N 2
SJ2 C2 N SING N N 3
SJ2 C2 C3 SING N N 4
SJ2 N CA SING N N 5
SJ2 CA C SING N N 6
SJ2 CA CB SING N N 7
SJ2 C O SING N N 8
SJ2 CB CG SING N N 9
SJ2 CG CD SING N N 10
SJ2 CD NE SING N N 11
SJ2 NE CZ SING N N 12
SJ2 CZ NH2 DOUB N N 13
SJ2 CZ NH1 SING N N 14
SJ2 C1 H1 SING N N 15
SJ2 C1 H2 SING N N 16
SJ2 C1 H3 SING N N 17
SJ2 C3 H4 SING N N 18
SJ2 C3 H5 SING N N 19
SJ2 C3 H6 SING N N 20
SJ2 O H7 SING N N 21
SJ2 CA H8 SING N N 22
SJ2 C H9 SING N N 23
SJ2 C H10 SING N N 24
SJ2 CB H11 SING N N 25
SJ2 CB H12 SING N N 26
SJ2 CG H13 SING N N 27
SJ2 CG H14 SING N N 28
SJ2 CD H15 SING N N 29
SJ2 CD H16 SING N N 30
SJ2 NE H17 SING N N 31
SJ2 NH1 H18 SING N N 32
SJ2 NH1 H19 SING N N 33
SJ2 NH2 H20 SING N N 34
#
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
SJ2 InChI InChI 1.03 InChI=1S/C9H20N4O2/c1-7(15)13(2)8(6-14)4-3-5-12-9(10)11/h8,14H,3-6H2,1-2H3,(H4,10,11,12)/t8-/m0/s1
SJ2 InChIKey InChI 1.03 FVJAWAIBRGBBJT-QMMMGPOBSA-N
SJ2 SMILES_CANONICAL CACTVS 3.385 CN([C@H](CO)CCCNC(N)=N)C(C)=O
SJ2 SMILES CACTVS 3.385 CN([CH](CO)CCCNC(N)=N)C(C)=O
SJ2 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NCCC[C@@H](CO)N(C)C(=O)C"
SJ2 SMILES "OpenEye OEToolkits" 2.0.7 CC(=O)N(C)C(CCCNC(=N)N)CO
#
_pdbx_chem_comp_identifier.comp_id SJ2
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier ~{N}-[(2~{S})-5-carbamimidamido-1-oxidanyl-pentan-2-yl]-~{N}-methyl-ethanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SJ2 'Create component' 2020-11-16 PDBE
SJ2 'Initial release' 2021-12-01 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
SJ2 C1 C 12.899 2.482 1
SJ2 C2 C 14.198 0.233 2
SJ2 C3 C 15.497 0.983 3
SJ2 O4 O 14.198 -1.268 4
SJ2 O O 10.301 -2.018 5
SJ2 N N 12.899 0.983 6
SJ2 CA C 11.600 0.233 7
SJ2 C C 11.600 -1.268 8
SJ2 CB C 10.301 0.983 9
SJ2 CG C 9.002 0.233 10
SJ2 CD C 7.702 0.983 11
SJ2 NE N 6.404 0.233 12
SJ2 CZ C 5.104 0.983 13
SJ2 NH1 N 5.104 2.482 14
SJ2 NH2 N 3.805 0.233 15
SJ2 H20 H 3.805 -1.267 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
SJ2 C1 N SINGLE NONE 1
SJ2 O4 C2 DOUBLE NONE 2
SJ2 C2 N SINGLE NONE 3
SJ2 C2 C3 SINGLE NONE 4
SJ2 N CA SINGLE NONE 5
SJ2 CA C SINGLE BEGINDASH 6
SJ2 CA CB SINGLE NONE 7
SJ2 C O SINGLE NONE 8
SJ2 CB CG SINGLE NONE 9
SJ2 CG CD SINGLE NONE 10
SJ2 CD NE SINGLE NONE 11
SJ2 NE CZ SINGLE ENDUPRIGHT 12
SJ2 CZ NH2 DOUBLE NONE 13
SJ2 CZ NH1 SINGLE ENDUPRIGHT 14
#
_pdbe_chem_comp_substructure.comp_id SJ2
_pdbe_chem_comp_substructure.substructure_name amide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles CC(N)=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys DLFVBJFMPXGRIB-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
SJ2 N F1 1
SJ2 C2 F1 1
SJ2 O4 F1 1
SJ2 C3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SJ2
_pdbe_chem_comp_rdkit_properties.exactmw 216.159
_pdbe_chem_comp_rdkit_properties.amw 216.285
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.778
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 118.368
_pdbe_chem_comp_rdkit_properties.tpsa 102.440
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.911
_pdbe_chem_comp_rdkit_properties.CrippenMR 58.469
_pdbe_chem_comp_rdkit_properties.chi0v 7.105
_pdbe_chem_comp_rdkit_properties.chi1v 3.223
_pdbe_chem_comp_rdkit_properties.chi2v 0.916
_pdbe_chem_comp_rdkit_properties.chi3v 0.916
_pdbe_chem_comp_rdkit_properties.chi4v 0.394
_pdbe_chem_comp_rdkit_properties.chi0n 27.105
_pdbe_chem_comp_rdkit_properties.chi1n 12.921
_pdbe_chem_comp_rdkit_properties.chi2n 0.916
_pdbe_chem_comp_rdkit_properties.chi3n 0.916
_pdbe_chem_comp_rdkit_properties.chi4n 0.394
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.300
_pdbe_chem_comp_rdkit_properties.kappa1 2.066
_pdbe_chem_comp_rdkit_properties.kappa2 7.053
_pdbe_chem_comp_rdkit_properties.kappa3 5.899
_pdbe_chem_comp_rdkit_properties.Phi 0.972
#
_pdbe_chem_comp_external_mappings.comp_id SJ2
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id SJ2
#
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
SJ2 C1 -3.264 -0.151 -1.724 ETKDGv3 1
SJ2 C2 -3.678 -0.718 0.671 ETKDGv3 2
SJ2 C3 -3.176 -1.021 2.052 ETKDGv3 3
SJ2 O4 -4.855 -1.064 0.376 ETKDGv3 4
SJ2 O -0.755 2.913 0.245 ETKDGv3 5
SJ2 N -2.862 -0.043 -0.314 ETKDGv3 6
SJ2 CA -1.613 0.659 0.057 ETKDGv3 7
SJ2 C -1.614 2.097 -0.505 ETKDGv3 8
SJ2 CB -0.394 -0.170 -0.409 ETKDGv3 9
SJ2 CG 0.932 0.318 0.194 ETKDGv3 10
SJ2 CD 2.080 -0.635 -0.155 ETKDGv3 11
SJ2 NE 3.344 -0.157 0.407 ETKDGv3 12
SJ2 CZ 4.574 -0.871 0.221 ETKDGv3 13
SJ2 NH1 5.782 -0.361 0.792 ETKDGv3 14
SJ2 NH2 4.594 -1.973 -0.461 ETKDGv3 15
SJ2 H1 -2.514 0.299 -2.404 ETKDGv3 16
SJ2 H2 -4.233 0.370 -1.877 ETKDGv3 17
SJ2 H3 -3.375 -1.221 -2.002 ETKDGv3 18
SJ2 H4 -3.187 -0.098 2.667 ETKDGv3 19
SJ2 H5 -3.825 -1.779 2.541 ETKDGv3 20
SJ2 H6 -2.145 -1.430 2.003 ETKDGv3 21
SJ2 H7 -0.792 3.812 -0.174 ETKDGv3 22
SJ2 H8 -1.558 0.758 1.161 ETKDGv3 23
SJ2 H9 -1.299 2.103 -1.572 ETKDGv3 24
SJ2 H10 -2.645 2.513 -0.441 ETKDGv3 25
SJ2 H11 -0.321 -0.156 -1.518 ETKDGv3 26
SJ2 H12 -0.555 -1.227 -0.099 ETKDGv3 27
SJ2 H13 0.839 0.383 1.300 ETKDGv3 28
SJ2 H14 1.175 1.325 -0.206 ETKDGv3 29
SJ2 H15 1.859 -1.646 0.252 ETKDGv3 30
SJ2 H16 2.177 -0.707 -1.261 ETKDGv3 31
SJ2 H17 3.365 0.728 0.962 ETKDGv3 32
SJ2 H18 5.773 0.527 1.342 ETKDGv3 33
SJ2 H19 6.688 -0.864 0.669 ETKDGv3 34
SJ2 H20 5.476 -2.511 -0.610 ETKDGv3 35
#