data_ARM
#
_chem_comp.id ARM
_chem_comp.name DEOXY-METHYL-ARGININE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C7 H16 N4 O'
_chem_comp.mon_nstd_parent_comp_id ARG
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-09-27
_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 172.228
_chem_comp.one_letter_code R
_chem_comp.three_letter_code ARM
_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 N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
ARM N N N 0 1 N N N Y Y N 36.058 12.234 144.106 -1.785 0.227 2.296 N ARM 1
ARM CA CA C 0 1 N N S Y N N 35.029 11.848 145.069 -0.456 -0.397 2.296 CA ARM 2
ARM CB CB C 0 1 N N N N N N 33.713 11.590 144.335 0.324 0.064 1.064 CB ARM 3
ARM CG CG C 0 1 N N N N N N 33.206 12.816 143.626 -0.431 -0.343 -0.201 CG ARM 4
ARM CD CD C 0 1 N N N N N N 32.095 12.508 142.647 0.349 0.119 -1.432 CD ARM 5
ARM NE NE N 0 1 N N N N N N 31.558 13.746 142.088 -0.374 -0.271 -2.645 NE ARM 6
ARM CZ CZ C 0 1 N N N N N N 30.531 13.822 141.244 0.138 0.039 -3.882 CZ ARM 7
ARM NH1 NH1 N 0 1 N N N N N N 29.909 12.721 140.836 1.269 0.681 -3.976 NH1 ARM 8
ARM NH2 NH2 N 0 1 N N N N N N 30.101 15.014 140.831 -0.540 -0.327 -5.020 NH2 ARM 9
ARM C C C 0 1 N N N Y N Y 35.352 10.622 145.984 0.288 0.004 3.543 C ARM 10
ARM O O O 0 1 N N N Y N Y 34.482 10.679 147.158 0.070 1.075 4.057 O ARM 11
ARM CM CM C 0 1 N N N N N N 36.819 10.601 146.514 1.304 -0.929 4.148 CM ARM 12
ARM H 1HN H 0 1 N N N Y Y N 36.936 12.406 144.595 -2.204 0.017 1.403 H ARM 13
ARM H2 2HN H 0 1 N Y N Y Y N 35.772 13.030 143.535 -1.636 1.225 2.320 H2 ARM 14
ARM HA HA H 0 1 N N N Y N N 34.966 12.715 145.766 -0.564 -1.482 2.271 HA ARM 15
ARM HB2 1HB H 0 1 N N N N N N 33.805 10.728 143.633 0.433 1.149 1.089 HB2 ARM 16
ARM HB3 2HB H 0 1 N N N N N N 32.941 11.175 145.025 1.311 -0.399 1.064 HB3 ARM 17
ARM HG2 1HG H 0 1 N N N N N N 32.890 13.597 144.355 -0.539 -1.427 -0.225 HG2 ARM 18
ARM HG3 2HG H 0 1 N N N N N N 34.039 13.361 143.125 -1.417 0.120 -0.201 HG3 ARM 19
ARM HD2 1HD H 0 1 N N N N N N 32.425 11.800 141.851 0.458 1.203 -1.408 HD2 ARM 20
ARM HD3 2HD H 0 1 N N N N N N 31.297 11.878 143.106 1.336 -0.344 -1.433 HD3 ARM 21
ARM HE HNE H 0 1 N N N N N N 32.338 14.230 141.644 -1.215 -0.749 -2.575 HE ARM 22
ARM HH1 HN1 H 0 1 N N N N N N 28.938 12.711 141.149 1.630 0.900 -4.849 HH1 ARM 23
ARM HH21 1HN2 H 0 0 N N N N N N 29.314 15.072 140.184 -0.178 -0.108 -5.892 HH21 ARM 24
ARM HH22 2HN2 H 0 0 N N N N N N 30.889 15.521 140.428 -1.381 -0.805 -4.949 HH22 ARM 25
ARM HM1 1HM H 0 1 N N N N N N 37.049 9.726 147.166 1.735 -0.470 5.038 HM1 ARM 26
ARM HM2 2HM H 0 1 N N N N N N 37.543 10.661 145.668 0.818 -1.866 4.422 HM2 ARM 27
ARM HM3 3HM H 0 1 N N N N N N 37.061 11.555 147.036 2.093 -1.127 3.423 HM3 ARM 28
#
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
ARM N CA SING N N 1
ARM N H SING N N 2
ARM N H2 SING N N 3
ARM CA CB SING N N 4
ARM CA C SING N N 5
ARM CA HA SING N N 6
ARM CB CG SING N N 7
ARM CB HB2 SING N N 8
ARM CB HB3 SING N N 9
ARM CG CD SING N N 10
ARM CG HG2 SING N N 11
ARM CG HG3 SING N N 12
ARM CD NE SING N N 13
ARM CD HD2 SING N N 14
ARM CD HD3 SING N N 15
ARM NE CZ SING N N 16
ARM NE HE SING N N 17
ARM CZ NH1 DOUB N N 18
ARM CZ NH2 SING N N 19
ARM NH1 HH1 SING N N 20
ARM NH2 HH21 SING N N 21
ARM NH2 HH22 SING N N 22
ARM C O DOUB N N 23
ARM C CM SING N N 24
ARM CM HM1 SING N N 25
ARM CM HM2 SING N N 26
ARM CM HM3 SING N N 27
#
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
ARM SMILES ACDLabs 10.04 'O=C(C)C(N)CCCNC(=[N@H])N'
ARM SMILES_CANONICAL CACTVS 3.341 'CC(=O)[C@@H](N)CCCNC(N)=N'
ARM SMILES CACTVS 3.341 'CC(=O)[CH](N)CCCNC(N)=N'
ARM SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'CC(=O)[C@H](CCCNC(=N)N)N'
ARM SMILES 'OpenEye OEToolkits' 1.5.0 'CC(=O)C(CCCNC(=N)N)N'
ARM InChI InChI 1.03 'InChI=1S/C7H16N4O/c1-5(12)6(8)3-2-4-11-7(9)10/h6H,2-4,8H2,1H3,(H4,9,10,11)/t6-/m0/s1'
ARM InChIKey InChI 1.03 GCCQNSQKSSOQIR-LURJTMIESA-N
#
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
ARM 'SYSTEMATIC NAME' ACDLabs 10.04 '1-[(4S)-4-amino-5-oxohexyl]guanidine'
ARM 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '1-[(4S)-4-amino-5-oxo-hexyl]guanidine'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ARM 'Create component' 1999-07-08 RCSB
ARM 'Modify descriptor' 2011-06-04 RCSB
ARM 'Modify backbone' 2023-11-03 PDBE
ARM 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 ARM ARG Dehydroxylation 'Named protein modification' 'Amino-acid backbone' C-terminal ? ? ? ?
2 ARM ARG Methylation 'Named protein modification' 'Amino-acid backbone' C-terminal ? ? ? ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
ARM N N 6.404 3.465 1
ARM CA C 7.702 2.715 2
ARM CB C 7.702 1.215 3
ARM CG C 6.404 0.465 4
ARM CD C 6.404 -1.035 5
ARM NE N 5.104 -1.785 6
ARM CZ C 5.104 -3.285 7
ARM NH1 N 3.805 -4.035 8
ARM NH2 N 6.404 -4.035 9
ARM C C 9.002 3.465 10
ARM O O 9.002 4.965 11
ARM CM C 10.301 2.715 12
ARM HH1 H 3.805 -5.535 13
#
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
ARM CA N SINGLE BEGINDASH 1
ARM CA CB SINGLE NONE 2
ARM CA C SINGLE NONE 3
ARM CB CG SINGLE NONE 4
ARM CG CD SINGLE NONE 5
ARM CD NE SINGLE NONE 6
ARM NE CZ SINGLE ENDUPRIGHT 7
ARM CZ NH1 DOUBLE NONE 8
ARM CZ NH2 SINGLE ENDUPRIGHT 9
ARM C O DOUBLE NONE 10
ARM C CM SINGLE NONE 11
#
_pdbe_chem_comp_substructure.comp_id ARM
_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
ARM O F1 1
ARM C F1 1
ARM CA F1 1
ARM N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ARM
_pdbe_chem_comp_rdkit_properties.exactmw 172.132
_pdbe_chem_comp_rdkit_properties.amw 172.232
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.714
_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 94.833
_pdbe_chem_comp_rdkit_properties.tpsa 104.990
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.834
_pdbe_chem_comp_rdkit_properties.CrippenMR 47.807
_pdbe_chem_comp_rdkit_properties.chi0v 5.697
_pdbe_chem_comp_rdkit_properties.chi1v 2.572
_pdbe_chem_comp_rdkit_properties.chi2v 0.608
_pdbe_chem_comp_rdkit_properties.chi3v 0.608
_pdbe_chem_comp_rdkit_properties.chi4v 0.222
_pdbe_chem_comp_rdkit_properties.chi0n 21.697
_pdbe_chem_comp_rdkit_properties.chi1n 10.255
_pdbe_chem_comp_rdkit_properties.chi2n 0.608
_pdbe_chem_comp_rdkit_properties.chi3n 0.608
_pdbe_chem_comp_rdkit_properties.chi4n 0.222
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 1.593
_pdbe_chem_comp_rdkit_properties.kappa2 5.538
_pdbe_chem_comp_rdkit_properties.kappa3 5.667
_pdbe_chem_comp_rdkit_properties.Phi 0.735
#
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
ARM UniChem ZINC ZINC000006363629
ARM UniChem SureChEMBL SCHEMBL8214683
ARM UniChem PubChem 5287607
ARM UniChem BRENDA 246756
#
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
ARM N -0.984 -1.623 1.412 ETKDGv3 1
ARM CA -1.648 -0.440 0.856 ETKDGv3 2
ARM CB -0.663 0.385 0.008 ETKDGv3 3
ARM CG 0.492 0.944 0.854 ETKDGv3 4
ARM CD 1.436 1.823 0.024 ETKDGv3 5
ARM NE 2.088 1.050 -1.034 ETKDGv3 6
ARM CZ 3.149 0.115 -0.785 ETKDGv3 7
ARM NH1 3.615 -0.043 0.414 ETKDGv3 8
ARM NH2 3.698 -0.635 -1.871 ETKDGv3 9
ARM C -2.849 -0.846 0.024 ETKDGv3 10
ARM O -2.694 -1.556 -0.959 ETKDGv3 11
ARM CM -4.235 -0.393 0.379 ETKDGv3 12
ARM H -0.697 -2.263 0.635 ETKDGv3 13
ARM H2 -1.669 -2.141 2.009 ETKDGv3 14
ARM HA -1.987 0.196 1.703 ETKDGv3 15
ARM HB2 -0.254 -0.250 -0.810 ETKDGv3 16
ARM HB3 -1.211 1.235 -0.457 ETKDGv3 17
ARM HG2 0.075 1.563 1.679 ETKDGv3 18
ARM HG3 1.065 0.110 1.313 ETKDGv3 19
ARM HD2 0.857 2.656 -0.431 ETKDGv3 20
ARM HD3 2.206 2.277 0.684 ETKDGv3 21
ARM HE 1.794 1.221 -2.022 ETKDGv3 22
ARM HH1 4.388 -0.715 0.619 ETKDGv3 23
ARM HH21 3.327 -0.512 -2.839 ETKDGv3 24
ARM HH22 4.473 -1.317 -1.714 ETKDGv3 25
ARM HM1 -4.660 0.192 -0.463 ETKDGv3 26
ARM HM2 -4.235 0.244 1.288 ETKDGv3 27
ARM HM3 -4.877 -1.278 0.567 ETKDGv3 28
#