data_L2Y
#
_chem_comp.id L2Y
_chem_comp.name '(S)-N-[(1E)-1-(diethylamino)ethylidene]-P-methylphosphonamidic fluoride'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C7 H16 F N2 O P'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 'A-230 (Nerve agent)'
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-02-01
_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 194.187
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L2Y
_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 6NTO
_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
L2Y C01 C1 C 0 1 N N N N N N 4.006 -50.164 -30.864 3.380 -1.207 0.858 C01 L2Y 1
L2Y C02 C2 C 0 1 N N N N N N 3.920 -51.480 -30.093 2.899 -0.879 -0.558 C02 L2Y 2
L2Y C04 C3 C 0 1 N N N N N N 1.677 -52.123 -30.618 2.109 1.531 -0.636 C04 L2Y 3
L2Y C05 C4 C 0 1 N N N N N N 1.243 -52.493 -29.202 2.399 2.135 0.739 C05 L2Y 4
L2Y C06 C5 C 0 1 N N N N N N 3.379 -53.804 -30.460 0.525 -0.313 -0.289 C06 L2Y 5
L2Y C07 C6 C 0 1 N N N N N N 4.883 -53.918 -30.214 0.210 -1.785 -0.220 C07 L2Y 6
L2Y C11 C7 C 0 1 N N N N N N 4.628 -56.986 -32.065 -3.101 1.438 -0.406 C11 L2Y 7
L2Y N03 N1 N 0 1 N N N N N N 3.083 -52.425 -30.816 1.815 0.103 -0.490 N03 L2Y 8
L2Y N08 N2 N 0 1 N N N N N N 3.022 -54.610 -31.615 -0.423 0.558 -0.160 N08 L2Y 9
L2Y O12 O1 O 0 1 N N N N N N 2.905 -56.676 -29.773 -2.230 -1.070 -0.922 O12 L2Y 10
L2Y P09 P1 P 0 1 N N S N N N 3.056 -56.293 -31.357 -1.977 0.060 -0.001 P09 L2Y 11
L2Y F1 F1 F 0 1 N Y N N N N 1.937 -56.609 -32.135 -2.246 -0.433 1.572 F1 L2Y 12
L2Y H1 H1 H 0 1 N N N N N N 4.640 -49.455 -30.311 3.743 -0.298 1.337 H1 L2Y 13
L2Y H2 H2 H 0 1 N N N N N N 4.442 -50.349 -31.857 2.553 -1.617 1.436 H2 L2Y 14
L2Y H3 H3 H 0 1 N N N N N N 2.997 -49.740 -30.980 4.187 -1.938 0.807 H3 L2Y 15
L2Y H4 H4 H 0 1 N N N N N N 4.929 -51.901 -29.977 3.726 -0.468 -1.137 H4 L2Y 16
L2Y H5 H5 H 0 1 N N N N N N 3.485 -51.293 -29.100 2.536 -1.789 -1.037 H5 L2Y 17
L2Y H6 H6 H 0 1 N N N N N N 1.512 -51.047 -30.777 1.252 2.035 -1.082 H6 L2Y 18
L2Y H7 H7 H 0 1 N N N N N N 1.079 -52.697 -31.341 2.980 1.658 -1.280 H7 L2Y 19
L2Y H8 H8 H 0 1 N N N N N N 0.177 -52.257 -29.071 3.257 1.631 1.184 H8 L2Y 20
L2Y H9 H9 H 0 1 N N N N N N 1.403 -53.569 -29.039 2.618 3.198 0.630 H9 L2Y 21
L2Y H10 H10 H 0 1 N N N N N N 1.837 -51.920 -28.475 1.528 2.009 1.382 H10 L2Y 22
L2Y H12 H12 H 0 1 N N N N N N 5.159 -53.310 -29.340 1.092 -2.329 0.119 H12 L2Y 23
L2Y H13 H13 H 0 1 N N N N N N 5.145 -54.970 -30.026 -0.609 -1.949 0.481 H13 L2Y 24
L2Y H14 H14 H 0 1 N N N N N N 5.428 -53.557 -31.099 -0.080 -2.142 -1.208 H14 L2Y 25
L2Y H15 H15 H 0 1 N N N N N N 4.656 -58.073 -31.902 -2.926 1.760 -1.432 H15 L2Y 26
L2Y H16 H16 H 0 1 N N N N N N 4.668 -56.776 -33.144 -4.134 1.107 -0.300 H16 L2Y 27
L2Y H17 H17 H 0 1 N N N N N N 5.491 -56.518 -31.569 -2.914 2.270 0.273 H17 L2Y 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
L2Y C11 P09 SING N N 1
L2Y N08 P09 SING N N 2
L2Y N08 C06 DOUB N N 3
L2Y P09 O12 DOUB N N 4
L2Y C01 C02 SING N N 5
L2Y N03 C04 SING N N 6
L2Y N03 C06 SING N N 7
L2Y N03 C02 SING N N 8
L2Y C04 C05 SING N N 9
L2Y C06 C07 SING N N 10
L2Y P09 F1 SING N N 11
L2Y C01 H1 SING N N 12
L2Y C01 H2 SING N N 13
L2Y C01 H3 SING N N 14
L2Y C02 H4 SING N N 15
L2Y C02 H5 SING N N 16
L2Y C04 H6 SING N N 17
L2Y C04 H7 SING N N 18
L2Y C05 H8 SING N N 19
L2Y C05 H9 SING N N 20
L2Y C05 H10 SING N N 21
L2Y C07 H12 SING N N 22
L2Y C07 H13 SING N N 23
L2Y C07 H14 SING N N 24
L2Y C11 H15 SING N N 25
L2Y C11 H16 SING N N 26
L2Y C11 H17 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
L2Y SMILES ACDLabs 12.01 'CCN(CC)C(\C)=N\P(C)(=O)F'
L2Y InChI InChI 1.03 'InChI=1S/C7H16FN2OP/c1-5-10(6-2)7(3)9-12(4,8)11/h5-6H2,1-4H3/b9-7+/t12-/m0/s1'
L2Y InChIKey InChI 1.03 OUJDIWHRYQBZSR-CRALRDPISA-N
L2Y SMILES_CANONICAL CACTVS 3.385 'CCN(CC)C(C)=N[P@](C)(F)=O'
L2Y SMILES CACTVS 3.385 'CCN(CC)C(C)=N[P](C)(F)=O'
L2Y SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'CCN(CC)/C(=N/[P@](=O)(C)F)/C'
L2Y SMILES 'OpenEye OEToolkits' 2.0.7 'CCN(CC)C(=NP(=O)(C)F)C'
#
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
L2Y 'SYSTEMATIC NAME' ACDLabs 12.01 '(S)-N-[(1E)-1-(diethylamino)ethylidene]-P-methylphosphonamidic fluoride'
L2Y 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.7 "~{N},~{N}-diethyl-~{N}'-[fluoranyl(methyl)phosphoryl]ethanimidamide"
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id L2Y
_pdbx_chem_comp_synonyms.name 'A-230 (Nerve agent)'
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L2Y 'Create component' 2019-02-01 RCSB
L2Y 'Modify synonyms' 2019-05-02 RCSB
L2Y 'Modify synonyms' 2020-06-05 PDBE
L2Y 'Initial release' 2020-07-01 RCSB
L2Y 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id L2Y
_pdbx_chem_comp_pcm.modified_residue_id SER
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom P09
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_synonyms.comp_id L2Y
_pdbe_chem_comp_synonyms.name 'A-230 (Nerve agent)'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
L2Y C01 C 9.495 2.250 1
L2Y C02 C 8.196 1.500 2
L2Y C04 C 9.495 -0.750 3
L2Y C05 C 10.794 0.000 4
L2Y C06 C 6.897 -0.750 5
L2Y C07 C 6.897 -2.250 6
L2Y C11 C 3.000 -1.500 7
L2Y N03 N 8.196 0.000 8
L2Y N08 N 5.598 0.000 9
L2Y O12 O 5.049 -2.049 10
L2Y P09 P 4.299 -0.750 11
L2Y F1 F 3.549 0.549 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
L2Y P09 C11 SINGLE BEGINDASH 1
L2Y N08 P09 SINGLE ENDDOWNRIGHT 2
L2Y N08 C06 DOUBLE NONE 3
L2Y P09 O12 DOUBLE NONE 4
L2Y C01 C02 SINGLE NONE 5
L2Y N03 C04 SINGLE NONE 6
L2Y N03 C06 SINGLE ENDDOWNRIGHT 7
L2Y N03 C02 SINGLE NONE 8
L2Y C04 C05 SINGLE NONE 9
L2Y C06 C07 SINGLE ENDDOWNRIGHT 10
L2Y P09 F1 SINGLE NONE 11
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id L2Y
_pdbe_chem_comp_rdkit_properties.exactmw 194.098
_pdbe_chem_comp_rdkit_properties.amw 194.190
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_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 0.857
_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 95.697
_pdbe_chem_comp_rdkit_properties.tpsa 32.670
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.539
_pdbe_chem_comp_rdkit_properties.CrippenMR 50.669
_pdbe_chem_comp_rdkit_properties.chi0v 6.522
_pdbe_chem_comp_rdkit_properties.chi1v 3.970
_pdbe_chem_comp_rdkit_properties.chi2v 1.105
_pdbe_chem_comp_rdkit_properties.chi3v 1.105
_pdbe_chem_comp_rdkit_properties.chi4v 0.634
_pdbe_chem_comp_rdkit_properties.chi0n 21.628
_pdbe_chem_comp_rdkit_properties.chi1n 10.420
_pdbe_chem_comp_rdkit_properties.chi2n 0.659
_pdbe_chem_comp_rdkit_properties.chi3n 0.659
_pdbe_chem_comp_rdkit_properties.chi4n 0.300
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.370
_pdbe_chem_comp_rdkit_properties.kappa1 1.853
_pdbe_chem_comp_rdkit_properties.kappa2 4.606
_pdbe_chem_comp_rdkit_properties.kappa3 4.496
_pdbe_chem_comp_rdkit_properties.Phi 0.711
#
_pdbe_chem_comp_external_mappings.comp_id L2Y
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 146672928
#
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
L2Y C01 -2.527 -1.362 -0.466 ETKDGv3 1
L2Y C02 -2.297 -0.295 0.602 ETKDGv3 2
L2Y C04 -1.111 1.863 -0.015 ETKDGv3 3
L2Y C05 -1.469 2.026 -1.489 ETKDGv3 4
L2Y C06 0.233 -0.228 0.378 ETKDGv3 5
L2Y C07 0.495 -1.299 1.409 ETKDGv3 6
L2Y C11 3.867 0.090 0.465 ETKDGv3 7
L2Y N03 -1.047 0.441 0.352 ETKDGv3 8
L2Y N08 1.108 0.068 -0.543 ETKDGv3 9
L2Y O12 2.660 -2.130 -0.584 ETKDGv3 10
L2Y P09 2.713 -0.627 -0.740 ETKDGv3 11
L2Y F1 3.268 -0.261 -2.277 ETKDGv3 12
L2Y H1 -1.729 -2.131 -0.429 ETKDGv3 13
L2Y H2 -2.540 -0.899 -1.475 ETKDGv3 14
L2Y H3 -3.504 -1.860 -0.289 ETKDGv3 15
L2Y H4 -3.166 0.399 0.589 ETKDGv3 16
L2Y H5 -2.278 -0.764 1.607 ETKDGv3 17
L2Y H6 -1.869 2.383 0.609 ETKDGv3 18
L2Y H7 -0.135 2.358 0.182 ETKDGv3 19
L2Y H8 -0.733 1.493 -2.127 ETKDGv3 20
L2Y H9 -2.484 1.622 -1.685 ETKDGv3 21
L2Y H10 -1.459 3.104 -1.757 ETKDGv3 22
L2Y H12 1.536 -1.257 1.780 ETKDGv3 23
L2Y H13 0.301 -2.299 0.971 ETKDGv3 24
L2Y H14 -0.155 -1.156 2.295 ETKDGv3 25
L2Y H15 3.896 1.191 0.335 ETKDGv3 26
L2Y H16 4.881 -0.325 0.296 ETKDGv3 27
L2Y H17 3.544 -0.147 1.498 ETKDGv3 28
#