data_DAR
#
_chem_comp.id DAR
_chem_comp.name D-ARGININE
_chem_comp.type "D-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C6 H15 N4 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 1999-07-08
_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 175.209
_chem_comp.one_letter_code R
_chem_comp.three_letter_code DAR
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag Y
_chem_comp.pdbx_model_coordinates_db_code 1CZQ
_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
DAR N N N 0 1 N N N Y Y N 17.418 -6.202 32.216 -2.318 1.786 -0.308 N DAR 1
DAR CA CA C 0 1 N N R Y N N 18.673 -6.893 32.489 -2.260 0.486 0.373 CA DAR 2
DAR CB CB C 0 1 N N N N N N 18.480 -8.408 32.369 -1.023 -0.282 -0.099 CB DAR 3
DAR CG CG C 0 1 N N N N N N 18.169 -8.847 30.969 0.238 0.463 0.342 CG DAR 4
DAR CD CD C 0 1 N N N N N N 19.397 -8.762 30.070 1.475 -0.305 -0.130 CD DAR 5
DAR NE NE N 0 1 N N N N N N 19.715 -7.408 29.607 2.683 0.409 0.292 NE DAR 6
DAR CZ CZ C 0 1 N N N N N N 20.121 -7.134 28.370 3.917 -0.093 -0.019 CZ DAR 7
DAR NH1 NH1 N 0 1 N N N N N N 20.248 -8.118 27.481 4.020 -1.229 -0.705 NH1 DAR 8
DAR NH2 NH2 N 1 1 N N N N N N 20.409 -5.891 28.015 5.015 0.556 0.365 NH2 DAR 9
DAR C C C 0 1 N N N Y N Y 19.313 -6.582 33.833 -3.499 -0.308 0.047 C DAR 10
DAR O O O 0 1 N N N Y N Y 19.994 -7.423 34.421 -3.870 -1.327 0.838 O DAR 11
DAR OXT OXT O 0 1 N Y N Y N Y 19.100 -5.379 34.342 -4.157 -0.028 -0.926 OXT DAR 12
DAR H H H 0 1 N N N Y Y N 17.546 -5.193 32.295 -2.371 1.593 -1.297 H DAR 13
DAR H2 HN2 H 0 1 N Y N Y Y N 16.660 -6.537 32.811 -3.196 2.210 -0.048 H2 DAR 14
DAR HA HA H 0 1 N N N Y N N 19.378 -6.505 31.717 -2.201 0.642 1.450 HA DAR 15
DAR HB2 1HB H 0 1 N N N N N N 19.363 -8.955 32.771 -1.027 -1.281 0.338 HB2 DAR 16
DAR HB3 2HB H 0 1 N N N N N N 17.702 -8.768 33.082 -1.037 -0.361 -1.186 HB3 DAR 17
DAR HG2 1HG H 0 1 N N N N N N 17.721 -9.868 30.951 0.242 1.462 -0.095 HG2 DAR 18
DAR HG3 2HG H 0 1 N N N N N N 17.311 -8.275 30.543 0.253 0.542 1.429 HG3 DAR 19
DAR HD2 1HD H 0 1 N N N N N N 20.280 -9.218 30.574 1.471 -1.303 0.307 HD2 DAR 20
DAR HD3 2HD H 0 1 N N N N N N 19.293 -9.455 29.202 1.461 -0.383 -1.217 HD3 DAR 21
DAR HE HNE H 0 1 N N N N N N 20.411 -7.025 30.246 2.608 1.236 0.793 HE DAR 22
DAR HH11 1HH1 H 0 0 N N N N N N 20.559 -7.907 26.532 3.221 -1.701 -0.985 HH11 DAR 23
DAR HH12 2HH1 H 0 0 N N N N N N 19.362 -8.621 27.426 4.896 -1.584 -0.926 HH12 DAR 24
DAR HH21 1HH2 H 0 0 N N N N N N 20.311 -5.137 28.695 5.890 0.200 0.145 HH21 DAR 25
DAR HH22 2HH2 H 0 0 N N N N N N 20.720 -5.680 27.066 4.940 1.384 0.865 HH22 DAR 26
DAR HXT HXT H 0 1 N Y N Y N Y 19.499 -5.184 35.181 ? ? ? HXT DAR 27
#
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
DAR N CA SING N N 1
DAR N H SING N N 2
DAR N H2 SING N N 3
DAR CA CB SING N N 4
DAR CA C SING N N 5
DAR CA HA SING N N 6
DAR CB CG SING N N 7
DAR CB HB2 SING N N 8
DAR CB HB3 SING N N 9
DAR CG CD SING N N 10
DAR CG HG2 SING N N 11
DAR CG HG3 SING N N 12
DAR CD NE SING N N 13
DAR CD HD2 SING N N 14
DAR CD HD3 SING N N 15
DAR NE CZ SING N N 16
DAR NE HE SING N N 17
DAR CZ NH1 SING N N 18
DAR CZ NH2 DOUB N N 19
DAR NH1 HH11 SING N N 20
DAR NH1 HH12 SING N N 21
DAR NH2 HH21 SING N N 22
DAR NH2 HH22 SING N N 23
DAR C O DOUB N N 24
DAR C OXT SING N N 25
DAR OXT HXT SING N N 26
#
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
DAR SMILES ACDLabs 10.04 O=C(O)C(N)CCCN\C(=[NH2+])N
DAR SMILES_CANONICAL CACTVS 3.341 N[C@H](CCCNC(N)=[NH2+])C(O)=O
DAR SMILES CACTVS 3.341 N[CH](CCCNC(N)=[NH2+])C(O)=O
DAR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C(C[C@H](C(=O)O)N)CNC(=[NH2+])N
DAR SMILES "OpenEye OEToolkits" 1.5.0 C(CC(C(=O)O)N)CNC(=[NH2+])N
DAR InChI InChI 1.03 InChI=1S/C6H14N4O2/c7-4(5(11)12)2-1-3-10-6(8)9/h4H,1-3,7H2,(H,11,12)(H4,8,9,10)/p+1/t4-/m1/s1
DAR InChIKey InChI 1.03 ODKSFYDXXFIFQN-SCSAIBSYSA-O
#
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
DAR "SYSTEMATIC NAME" ACDLabs 10.04 amino{[(4R)-4-amino-4-carboxybutyl]amino}methaniminium
DAR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[amino-[[(4R)-4-amino-5-hydroxy-5-oxo-pentyl]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
DAR 'Create component' 1999-07-08 RCSB
DAR 'Modify descriptor' 2011-06-04 RCSB
DAR '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
DAR N N 3.805 3.465 1
DAR CA C 5.104 2.715 2
DAR CB C 5.104 1.215 3
DAR CG C 6.404 0.465 4
DAR CD C 6.404 -1.035 5
DAR NE N 7.702 -1.785 6
DAR CZ C 7.702 -3.285 7
DAR NH1 N 9.002 -4.035 8
DAR NH2 N 6.404 -4.035 9
DAR C C 6.404 3.465 10
DAR O O 7.702 2.715 11
DAR OXT O 6.404 4.965 12
#
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
DAR CA N SINGLE BEGINWEDGE 1
DAR CA CB SINGLE NONE 2
DAR CA C SINGLE NONE 3
DAR CB CG SINGLE NONE 4
DAR CG CD SINGLE NONE 5
DAR CD NE SINGLE NONE 6
DAR NE CZ SINGLE NONE 7
DAR CZ NH1 SINGLE NONE 8
DAR CZ NH2 DOUBLE NONE 9
DAR C O DOUBLE NONE 10
DAR C OXT SINGLE NONE 11
#
_pdbe_chem_comp_substructure.comp_id DAR
_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
DAR O F1 1
DAR C F1 1
DAR CA F1 1
DAR N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DAR
_pdbe_chem_comp_rdkit_properties.exactmw 175.119
_pdbe_chem_comp_rdkit_properties.amw 175.212
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_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 92.002
_pdbe_chem_comp_rdkit_properties.tpsa 126.960
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.158
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.968
_pdbe_chem_comp_rdkit_properties.chi0v 5.605
_pdbe_chem_comp_rdkit_properties.chi1v 2.526
_pdbe_chem_comp_rdkit_properties.chi2v 0.586
_pdbe_chem_comp_rdkit_properties.chi3v 0.586
_pdbe_chem_comp_rdkit_properties.chi4v 0.216
_pdbe_chem_comp_rdkit_properties.chi0n 20.605
_pdbe_chem_comp_rdkit_properties.chi1n 9.565
_pdbe_chem_comp_rdkit_properties.chi2n 0.586
_pdbe_chem_comp_rdkit_properties.chi3n 0.586
_pdbe_chem_comp_rdkit_properties.chi4n 0.216
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.300
_pdbe_chem_comp_rdkit_properties.kappa1 1.650
_pdbe_chem_comp_rdkit_properties.kappa2 5.363
_pdbe_chem_comp_rdkit_properties.kappa3 5.482
_pdbe_chem_comp_rdkit_properties.Phi 0.738
#
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
DAR UniChem PDBe DAR
DAR UniChem ChEBI 32689
DAR UniChem PubChem 1549104
DAR UniChem PubChem 17753939
DAR UniChem Recon 'arg_D'
DAR UniChem MetaboLights MTBLC32689
DAR UniChem Rhea 32689
DAR UniChem PubChem 59667378
#
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
DAR N 3.043 -1.537 1.284 ETKDGv3 1
DAR CA 2.456 -0.219 1.042 ETKDGv3 2
DAR CB 1.138 -0.369 0.257 ETKDGv3 3
DAR CG 0.390 0.969 0.115 ETKDGv3 4
DAR CD -0.949 0.802 -0.617 ETKDGv3 5
DAR NE -1.937 0.106 0.212 ETKDGv3 6
DAR CZ -3.264 -0.221 -0.240 ETKDGv3 7
DAR NH1 -4.142 -0.930 0.639 ETKDGv3 8
DAR NH2 -3.679 0.118 -1.426 ETKDGv3 9
DAR C 3.437 0.630 0.281 ETKDGv3 10
DAR O 3.763 1.766 0.719 ETKDGv3 11
DAR OXT 3.976 0.168 -0.917 ETKDGv3 12
DAR H 2.388 -2.086 1.888 ETKDGv3 13
DAR H2 3.914 -1.411 1.851 ETKDGv3 14
DAR HA 2.238 0.262 2.024 ETKDGv3 15
DAR HB2 1.348 -0.790 -0.752 ETKDGv3 16
DAR HB3 0.487 -1.092 0.792 ETKDGv3 17
DAR HG2 0.212 1.417 1.117 ETKDGv3 18
DAR HG3 1.015 1.678 -0.469 ETKDGv3 19
DAR HD2 -0.786 0.238 -1.562 ETKDGv3 20
DAR HD3 -1.339 1.811 -0.872 ETKDGv3 21
DAR HE -1.683 -0.163 1.190 ETKDGv3 22
DAR HH11 -3.824 -1.210 1.593 ETKDGv3 23
DAR HH12 -5.111 -1.182 0.343 ETKDGv3 24
DAR HH21 -3.079 0.640 -2.100 ETKDGv3 25
DAR HH22 -4.645 -0.127 -1.739 ETKDGv3 26
DAR HXT 4.632 0.732 -1.443 ETKDGv3 27
#