data_G2B
#
_chem_comp.id G2B
_chem_comp.name 1-[(2~{R},3~{S})-2-azanyl-3-oxidanyl-butyl]urea
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H13 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-08-22
_chem_comp.pdbx_modified_date 2020-07-03
_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 147.176
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code G2B
_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 6HF8
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
G2B N1 N1 N 0 1 N N N N N N -7.734 52.986 13.378 1.023 1.762 0.374 N1 G2B 1
G2B C2 C1 C 0 1 N N N N N N -9.639 54.494 13.760 -0.157 -0.371 0.143 C2 G2B 2
G2B N2 N2 N 0 1 N N N N N N -8.681 55.448 14.264 -1.350 0.384 -0.249 N2 G2B 3
G2B CA C2 C 0 1 N N R N N N -9.052 53.423 12.900 1.095 0.425 -0.230 CA G2B 4
G2B C C3 C 0 1 N N N N N N -9.005 56.703 14.460 -2.576 -0.126 -0.016 C G2B 5
G2B O O1 O 0 1 N N N N N N -10.063 57.185 14.069 -2.692 -1.212 0.518 O G2B 6
G2B CB C4 C 0 1 N N S N N N -10.165 52.399 13.085 2.336 -0.303 0.289 CB G2B 7
G2B CG C5 C 0 1 N N N N N N -11.455 52.755 12.350 3.589 0.493 -0.084 CG G2B 8
G2B OG1 O2 O 0 1 N N N N N N -10.387 52.361 14.514 2.406 -1.604 -0.299 OG1 G2B 9
G2B H1 H1 H 0 1 N N N N N N -7.064 53.712 13.220 0.248 2.288 -0.002 H1 G2B 10
G2B H2 H2 H 0 1 N N N N N N -7.784 52.786 14.356 0.966 1.702 1.379 H2 G2B 11
G2B H4 H4 H 0 1 N N N N N N -10.388 55.039 13.167 -0.172 -0.541 1.219 H4 G2B 12
G2B H5 H5 H 0 1 N N N N N N -10.131 54.014 14.619 -0.147 -1.329 -0.377 H5 G2B 13
G2B H6 H6 H 0 1 N N N N N N -7.750 55.145 14.468 -1.258 1.250 -0.675 H6 G2B 14
G2B H7 H7 H 0 1 N N N N N N -9.004 53.749 11.851 1.156 0.519 -1.315 H7 G2B 15
G2B H9 H9 H 0 1 N N N N N N -9.812 51.419 12.732 2.275 -0.397 1.373 H9 G2B 16
G2B H10 H10 H 0 1 N N N N N N -12.208 51.973 12.530 3.535 1.485 0.364 H10 G2B 17
G2B H11 H11 H 0 1 N N N N N N -11.833 53.720 12.719 4.473 -0.026 0.286 H11 G2B 18
G2B H12 H12 H 0 1 N N N N N N -11.254 52.829 11.271 3.649 0.586 -1.168 H12 G2B 19
G2B H13 H13 H 0 1 N N N N N N -9.576 52.138 14.955 2.463 -1.597 -1.264 H13 G2B 20
G2B N3 N3 N 0 1 N Y N N N N -8.085 57.327 15.193 -3.674 0.568 -0.377 N3 G2B 21
G2B H3 H3 H 0 1 N N N N N N -8.228 58.276 15.473 -3.581 1.435 -0.803 H3 G2B 22
G2B H8 H8 H 0 1 N N N N N N -7.251 56.846 15.463 -4.556 0.202 -0.209 H8 G2B 23
#
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
G2B CG CB SING N N 1
G2B CA CB SING N N 2
G2B CA N1 SING N N 3
G2B CA C2 SING N N 4
G2B CB OG1 SING N N 5
G2B C2 N2 SING N N 6
G2B O C DOUB N N 7
G2B N2 C SING N N 8
G2B N1 H1 SING N N 9
G2B N1 H2 SING N N 10
G2B C2 H4 SING N N 11
G2B C2 H5 SING N N 12
G2B N2 H6 SING N N 13
G2B CA H7 SING N N 14
G2B CB H9 SING N N 15
G2B CG H10 SING N N 16
G2B CG H11 SING N N 17
G2B CG H12 SING N N 18
G2B OG1 H13 SING N N 19
G2B C N3 SING N N 20
G2B N3 H3 SING N N 21
G2B N3 H8 SING N N 22
#
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
G2B InChI InChI 1.03 InChI=1S/C5H13N3O2/c1-3(9)4(6)2-8-5(7)10/h3-4,9H,2,6H2,1H3,(H3,7,8,10)/t3-,4+/m0/s1
G2B InChIKey InChI 1.03 DMDDGYOTJFLDRR-IUYQGCFVSA-N
G2B SMILES_CANONICAL CACTVS 3.385 C[C@H](O)[C@H](N)CNC(N)=O
G2B SMILES CACTVS 3.385 C[CH](O)[CH](N)CNC(N)=O
G2B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C[C@@H]([C@@H](CNC(=O)N)N)O
G2B SMILES "OpenEye OEToolkits" 2.0.6 CC(C(CNC(=O)N)N)O
#
_pdbx_chem_comp_identifier.comp_id G2B
_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 1-[(2~{R},3~{S})-2-azanyl-3-oxidanyl-butyl]urea
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
G2B 'Create component' 2018-08-22 EBI
G2B 'Initial release' 2020-07-08 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
G2B N1 N 9.002 -1.643 1
G2B C2 C 7.702 0.608 2
G2B N2 N 6.404 -0.142 3
G2B CA C 9.002 -0.142 4
G2B C C 5.104 0.608 5
G2B O O 5.104 2.107 6
G2B CB C 10.301 0.608 7
G2B CG C 11.600 -0.142 8
G2B OG1 O 10.301 2.107 9
G2B N3 N 3.805 -0.142 10
#
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
G2B CB CG SINGLE BEGINWEDGE 1
G2B CA CB SINGLE NONE 2
G2B CA N1 SINGLE BEGINDASH 3
G2B CA C2 SINGLE NONE 4
G2B CB OG1 SINGLE NONE 5
G2B C2 N2 SINGLE NONE 6
G2B O C DOUBLE NONE 7
G2B N2 C SINGLE NONE 8
G2B C N3 SINGLE NONE 9
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id G2B
_pdbe_chem_comp_rdkit_properties.exactmw 147.101
_pdbe_chem_comp_rdkit_properties.amw 147.178
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 78.026
_pdbe_chem_comp_rdkit_properties.tpsa 101.370
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.637
_pdbe_chem_comp_rdkit_properties.CrippenMR 37.242
_pdbe_chem_comp_rdkit_properties.chi0v 4.658
_pdbe_chem_comp_rdkit_properties.chi1v 2.053
_pdbe_chem_comp_rdkit_properties.chi2v 0.473
_pdbe_chem_comp_rdkit_properties.chi3v 0.473
_pdbe_chem_comp_rdkit_properties.chi4v 0.152
_pdbe_chem_comp_rdkit_properties.chi0n 17.658
_pdbe_chem_comp_rdkit_properties.chi1n 8.197
_pdbe_chem_comp_rdkit_properties.chi2n 0.473
_pdbe_chem_comp_rdkit_properties.chi3n 0.473
_pdbe_chem_comp_rdkit_properties.chi4n 0.152
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.810
_pdbe_chem_comp_rdkit_properties.kappa1 1.373
_pdbe_chem_comp_rdkit_properties.kappa2 4.077
_pdbe_chem_comp_rdkit_properties.kappa3 4.107
_pdbe_chem_comp_rdkit_properties.Phi 0.560
#
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
G2B UniChem PDBe G2B
G2B UniChem PubChem 146681109
#
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
G2B N1 -0.529 -0.778 1.329 ETKDGv3 1
G2B C2 0.307 -1.218 -0.953 ETKDGv3 2
G2B N2 1.484 -0.356 -0.837 ETKDGv3 3
G2B CA -0.870 -0.697 -0.096 ETKDGv3 4
G2B C 2.490 -0.533 0.169 ETKDGv3 5
G2B O 2.436 -1.512 0.962 ETKDGv3 6
G2B CB -1.260 0.754 -0.487 ETKDGv3 7
G2B CG -2.529 1.226 0.236 ETKDGv3 8
G2B OG1 -1.480 0.821 -1.874 ETKDGv3 9
G2B H1 -0.220 -1.755 1.542 ETKDGv3 10
G2B H2 -1.401 -0.651 1.890 ETKDGv3 11
G2B H4 -0.003 -1.262 -2.019 ETKDGv3 12
G2B H5 0.564 -2.261 -0.665 ETKDGv3 13
G2B H6 1.589 0.431 -1.517 ETKDGv3 14
G2B H7 -1.741 -1.364 -0.295 ETKDGv3 15
G2B H9 -0.425 1.436 -0.203 ETKDGv3 16
G2B H10 -2.846 2.212 -0.165 ETKDGv3 17
G2B H11 -2.341 1.353 1.322 ETKDGv3 18
G2B H12 -3.357 0.501 0.085 ETKDGv3 19
G2B H13 -1.366 1.772 -2.139 ETKDGv3 20
G2B N3 3.566 0.397 0.272 ETKDGv3 21
G2B H3 4.304 0.271 1.001 ETKDGv3 22
G2B H8 3.627 1.213 -0.376 ETKDGv3 23
#