data_EU0
#
_chem_comp.id EU0
_chem_comp.name 1-[(2~{S})-3-methyl-1-oxidanylidene-butan-2-yl]guanidine
_chem_comp.type "L-peptide linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C6 H14 N3 O2"
_chem_comp.mon_nstd_parent_comp_id VAL
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2022-01-13
_chem_comp.pdbx_modified_date 2023-11-03
_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 160.194
_chem_comp.one_letter_code V
_chem_comp.three_letter_code EU0
_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 7QS6
_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
EU0 NT1 N N 1 1 N N N N N N -14.962 0.973 -12.606 -2.189 0.596 -1.023 N EU0 1
EU0 CT CT C 0 1 N N N N N N -15.505 1.932 -11.943 -2.050 -0.384 -0.131 CT EU0 2
EU0 NT2 NT2 N 0 1 N N N N N N -16.063 2.880 -12.600 -3.126 -1.011 0.342 NT2 EU0 3
EU0 N NE N 0 1 N N N Y Y N -15.494 1.991 -10.651 -0.803 -0.746 0.299 NE EU0 4
EU0 CA CA C 0 1 N N S Y N N -15.119 0.912 -9.694 0.380 -0.056 -0.221 CA EU0 5
EU0 CB CB C 0 1 N N N N N N -14.258 1.475 -8.531 0.628 1.215 0.593 CB EU0 6
EU0 CG1 CG1 C 0 1 N N N N N N -13.662 0.354 -7.663 1.864 1.936 0.050 CG1 EU0 7
EU0 CG2 CG2 C 0 1 N N N N N N -13.078 2.343 -9.014 -0.588 2.136 0.484 CG2 EU0 8
EU0 C C C 0 1 N N N Y N Y -16.349 0.128 -9.173 1.579 -0.964 -0.114 C EU0 9
EU0 O O O 0 1 N N N Y N Y -17.338 0.755 -8.787 1.457 -2.073 0.350 O EU0 10
EU0 HT12 H2 H 0 1 N N N N N N -14.504 0.227 -12.122 -1.405 1.052 -1.367 H2 EU0 11
EU0 HT22 HT22 H 0 0 N N N N N N -16.480 3.648 -12.113 -4.010 -0.755 0.037 HT22 EU0 12
EU0 HT21 HT21 H 0 0 N N N N N N -16.082 2.852 -13.599 -3.025 -1.725 0.991 HT21 EU0 13
EU0 H HE H 0 1 N N N Y Y N -15.770 2.863 -10.247 -0.702 -1.459 0.948 HE EU0 14
EU0 HA HA H 0 1 N N N Y N N -14.489 0.192 -10.237 0.217 0.208 -1.266 HA EU0 15
EU0 HB HB H 0 1 N N N N N N -14.906 2.097 -7.896 0.792 0.951 1.638 HB EU0 16
EU0 HG11 HG11 H 0 0 N N N N N N -13.062 0.796 -6.854 1.701 2.200 -0.995 HG11 EU0 17
EU0 HG13 HG13 H 0 0 N N N N N N -14.476 -0.246 -7.230 2.041 2.841 0.630 HG13 EU0 18
EU0 HG12 HG12 H 0 0 N N N N N N -13.022 -0.290 -8.284 2.731 1.279 0.128 HG12 EU0 19
EU0 HG23 HG23 H 0 0 N N N N N N -12.511 2.709 -8.145 -1.468 1.623 0.871 HG23 EU0 20
EU0 HG22 HG22 H 0 0 N N N N N N -12.418 1.740 -9.655 -0.411 3.042 1.064 HG22 EU0 21
EU0 HG21 HG21 H 0 0 N N N N N N -13.463 3.199 -9.587 -0.752 2.400 -0.561 HG21 EU0 22
EU0 OXT OXT O 0 1 N Y N Y N Y -16.340 -0.952 -9.148 2.781 -0.540 -0.533 OXT EU0 23
EU0 HXT H1 H 0 1 N Y N Y N Y -17.167 -1.268 -8.803 3.520 -1.157 -0.444 H1 EU0 24
EU0 HT11 H3 H 0 1 N N N N N N -14.998 0.973 -13.605 -3.073 0.850 -1.331 H3 EU0 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
EU0 NT1 CT DOUB N N 1
EU0 NT2 CT SING N N 2
EU0 CT N SING N N 3
EU0 N CA SING N N 4
EU0 CA C SING N N 5
EU0 CA CB SING N N 6
EU0 C O DOUB N N 7
EU0 CG2 CB SING N N 8
EU0 CB CG1 SING N N 9
EU0 NT1 HT12 SING N N 10
EU0 NT2 HT22 SING N N 11
EU0 NT2 HT21 SING N N 12
EU0 N H SING N N 13
EU0 CA HA SING N N 14
EU0 CB HB SING N N 15
EU0 CG1 HG11 SING N N 16
EU0 CG1 HG13 SING N N 17
EU0 CG1 HG12 SING N N 18
EU0 CG2 HG23 SING N N 19
EU0 CG2 HG22 SING N N 20
EU0 CG2 HG21 SING N N 21
EU0 C OXT SING N N 22
EU0 OXT HXT SING N N 23
EU0 HT11 NT1 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
EU0 InChI InChI 1.06 InChI=1S/C6H13N3O2/c1-3(2)4(5(10)11)9-6(7)8/h3-4H,1-2H3,(H,10,11)(H4,7,8,9)/p+1/t4-/m0/s1
EU0 InChIKey InChI 1.06 KRDSZDZVHLBUMZ-BYPYZUCNSA-O
EU0 SMILES_CANONICAL CACTVS 3.385 CC(C)[C@H](NC(N)=[NH2+])C(O)=O
EU0 SMILES CACTVS 3.385 CC(C)[CH](NC(N)=[NH2+])C(O)=O
EU0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC(C)[C@@H](C(=O)O)NC(=[NH2+])N
EU0 SMILES "OpenEye OEToolkits" 2.0.7 CC(C)C(C(=O)O)NC(=[NH2+])N
#
_pdbx_chem_comp_identifier.comp_id EU0
_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
"[azanyl-[[(2~{S})-3-methyl-1-oxidanyl-1-oxidanylidene-butan-2-yl]amino]methylidene]azanium"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
EU0 'Create component' 2022-01-13 PDBE
EU0 'Modify charge' 2022-01-21 PDBE
EU0 'Modify descriptor' 2022-08-22 RCSB
EU0 'Initial release' 2023-05-10 RCSB
EU0 'Modify backbone' 2023-11-03 PDBE
#
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
EU0 NT1 N 3.465 1.562 1
EU0 CT C 4.965 1.562 2
EU0 NT2 N 5.715 2.861 3
EU0 N N 5.715 0.263 4
EU0 CA C 7.014 -0.487 5
EU0 CB C 7.014 -1.987 6
EU0 CG1 C 8.313 -2.737 7
EU0 CG2 C 5.715 -2.737 8
EU0 C C 8.313 0.263 9
EU0 O O 9.612 -0.487 10
EU0 OXT O 8.313 1.763 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
EU0 NT1 CT DOUBLE NONE 1
EU0 NT2 CT SINGLE NONE 2
EU0 CT N SINGLE NONE 3
EU0 CA N SINGLE BEGINDASH 4
EU0 CA C SINGLE NONE 5
EU0 CA CB SINGLE NONE 6
EU0 C O DOUBLE NONE 7
EU0 CG2 CB SINGLE NONE 8
EU0 CB CG1 SINGLE NONE 9
EU0 C OXT SINGLE NONE 10
#
_pdbe_chem_comp_substructure.comp_id EU0
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys LYIIBVSRGJSHAV-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
EU0 O F1 1
EU0 C F1 1
EU0 CA F1 1
EU0 N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id EU0
_pdbe_chem_comp_rdkit_properties.exactmw 160.108
_pdbe_chem_comp_rdkit_properties.amw 160.197
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 85.141
_pdbe_chem_comp_rdkit_properties.tpsa 100.940
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.241
_pdbe_chem_comp_rdkit_properties.CrippenMR 40.517
_pdbe_chem_comp_rdkit_properties.chi0v 5.158
_pdbe_chem_comp_rdkit_properties.chi1v 2.303
_pdbe_chem_comp_rdkit_properties.chi2v 0.642
_pdbe_chem_comp_rdkit_properties.chi3v 0.642
_pdbe_chem_comp_rdkit_properties.chi4v 0.304
_pdbe_chem_comp_rdkit_properties.chi0n 19.158
_pdbe_chem_comp_rdkit_properties.chi1n 8.947
_pdbe_chem_comp_rdkit_properties.chi2n 0.642
_pdbe_chem_comp_rdkit_properties.chi3n 0.642
_pdbe_chem_comp_rdkit_properties.chi4n 0.304
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.260
_pdbe_chem_comp_rdkit_properties.kappa1 1.439
_pdbe_chem_comp_rdkit_properties.kappa2 3.799
_pdbe_chem_comp_rdkit_properties.kappa3 3.442
_pdbe_chem_comp_rdkit_properties.Phi 0.497
#
_pdbe_chem_comp_external_mappings.comp_id EU0
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id EU0
#
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
EU0 NT1 2.103 0.253 1.094 ETKDGv3 1
EU0 CT 2.067 -0.334 -0.066 ETKDGv3 2
EU0 NT2 3.137 -1.207 -0.440 ETKDGv3 3
EU0 N 0.994 -0.111 -1.007 ETKDGv3 4
EU0 CA -0.344 0.443 -0.728 ETKDGv3 5
EU0 CB -1.064 -0.300 0.441 ETKDGv3 6
EU0 CG1 -2.503 0.205 0.641 ETKDGv3 7
EU0 CG2 -1.096 -1.816 0.186 ETKDGv3 8
EU0 C -0.292 1.947 -0.579 ETKDGv3 9
EU0 O 0.791 2.540 -0.325 ETKDGv3 10
EU0 HT12 1.379 0.929 1.411 ETKDGv3 11
EU0 HT22 3.129 -1.688 -1.367 ETKDGv3 12
EU0 HT21 3.938 -1.385 0.206 ETKDGv3 13
EU0 H 1.146 -0.472 -1.977 ETKDGv3 14
EU0 HA -0.961 0.265 -1.638 ETKDGv3 15
EU0 HB -0.530 -0.134 1.396 ETKDGv3 16
EU0 HG11 -3.075 0.158 -0.311 ETKDGv3 17
EU0 HG13 -2.501 1.249 1.018 ETKDGv3 18
EU0 HG12 -3.029 -0.411 1.402 ETKDGv3 19
EU0 HG23 -1.621 -2.042 -0.767 ETKDGv3 20
EU0 HG22 -0.067 -2.229 0.134 ETKDGv3 21
EU0 HG21 -1.620 -2.338 1.015 ETKDGv3 22
EU0 OXT -1.446 2.697 -0.784 ETKDGv3 23
EU0 HXT -1.430 3.707 -0.707 ETKDGv3 24
EU0 HT11 2.894 0.075 1.752 ETKDGv3 25
#