data_L1M
#
_chem_comp.id L1M
_chem_comp.name "ethyl (R)-N-[(1E)-1-(diethylamino)ethylidene]phosphonamidate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H19 N2 O2 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-01-31
_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 206.222
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code L1M
_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 6NTG
_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
L1M C10 C1 C 0 1 N N N N N N 9.521 44.929 31.582 -3.590 -0.325 -0.262 C10 L1M 1
L1M C13 C2 C 0 1 N N N N N N 7.406 42.955 33.256 -2.270 2.707 -0.556 C13 L1M 2
L1M C01 C3 C 0 1 N N N N N N 6.817 40.397 25.684 4.922 1.155 0.426 C01 L1M 3
L1M C02 C4 C 0 1 N N N N N N 8.031 41.002 26.381 4.006 0.025 -0.049 C02 L1M 4
L1M C07 C5 C 0 1 N N N N N N 8.270 43.279 30.136 -1.134 -0.322 -0.238 C07 L1M 5
L1M C08 C6 C 0 1 N N N N N N 9.444 43.285 29.160 -1.156 -1.714 -0.815 C08 L1M 6
L1M C11 C7 C 0 1 N N N N N N 9.173 46.404 31.379 -4.047 -1.105 0.973 C11 L1M 7
L1M C12 C8 C 0 1 N N N N N N 7.247 44.113 32.273 -2.289 1.684 0.581 C12 L1M 8
L1M N06 N1 N 0 1 N N N N N N 7.234 42.590 29.966 -0.005 0.257 0.011 N06 L1M 9
L1M N09 N2 N 0 1 N N N N N N 8.350 44.107 31.328 -2.310 0.331 0.021 N09 L1M 10
L1M O03 O1 O 0 1 N N N N N N 7.561 41.999 27.226 2.642 0.422 0.103 O03 L1M 11
L1M O05 O2 O 0 1 N N N N N N 7.430 40.252 29.103 1.459 -1.773 0.492 O05 L1M 12
L1M P04 P1 P 0 1 N N R N N N 6.889 41.541 28.661 1.403 -0.524 -0.300 P04 L1M 13
L1M H1 H1 H 0 1 N N N N N N 9.859 44.773 32.617 -3.469 -1.010 -1.100 H1 L1M 14
L1M H2 H2 H 0 1 N N N N N N 10.325 44.644 30.887 -4.336 0.429 -0.513 H2 L1M 15
L1M H3 H3 H 0 1 N N N N N N 6.569 42.962 33.970 -1.381 2.553 -1.168 H3 L1M 16
L1M H4 H4 H 0 1 N N N N N N 7.409 42.003 32.704 -3.161 2.583 -1.172 H4 L1M 17
L1M H5 H5 H 0 1 N N N N N N 8.355 43.065 33.802 -2.254 3.714 -0.140 H5 L1M 18
L1M H6 H6 H 0 1 N N N N N N 7.145 39.599 25.002 4.736 2.049 -0.169 H6 L1M 19
L1M H7 H7 H 0 1 N N N N N N 6.133 39.978 26.437 4.721 1.368 1.476 H7 L1M 20
L1M H8 H8 H 0 1 N N N N N N 6.296 41.178 25.111 5.963 0.852 0.310 H8 L1M 21
L1M H9 H9 H 0 1 N N N N N N 8.556 40.230 26.963 4.208 -0.188 -1.099 H9 L1M 22
L1M H10 H10 H 0 1 N N N N N N 8.719 41.431 25.637 4.193 -0.869 0.545 H10 L1M 23
L1M H11 H11 H 0 1 N N N N N N 10.226 43.965 29.530 -1.153 -1.657 -1.903 H11 L1M 24
L1M H12 H12 H 0 1 N N N N N N 9.854 42.268 29.074 -0.276 -2.261 -0.477 H12 L1M 25
L1M H13 H13 H 0 1 N N N N N N 9.098 43.626 28.173 -2.056 -2.231 -0.481 H13 L1M 26
L1M H14 H14 H 0 1 N N N N N N 10.063 47.021 31.573 -3.300 -1.858 1.224 H14 L1M 27
L1M H15 H15 H 0 1 N N N N N N 8.835 46.562 30.344 -4.168 -0.419 1.812 H15 L1M 28
L1M H16 H16 H 0 1 N N N N N N 8.370 46.690 32.074 -4.999 -1.592 0.762 H16 L1M 29
L1M H17 H17 H 0 1 N N N N N N 7.244 45.064 32.826 -1.398 1.809 1.197 H17 L1M 30
L1M H18 H18 H 0 1 N N N N N N 6.298 44.003 31.728 -3.178 1.838 1.193 H18 L1M 31
L1M H19 H19 H 0 1 N N N N N N 5.479 41.480 28.506 1.476 -0.836 -1.683 H19 L1M 32
#
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
L1M C01 C02 SING N N 1
L1M C02 O03 SING N N 2
L1M O03 P04 SING N N 3
L1M P04 O05 DOUB N N 4
L1M P04 N06 SING N N 5
L1M C08 C07 SING N N 6
L1M N06 C07 DOUB N N 7
L1M C07 N09 SING N N 8
L1M N09 C10 SING N N 9
L1M N09 C12 SING N N 10
L1M C11 C10 SING N N 11
L1M C12 C13 SING N N 12
L1M C10 H1 SING N N 13
L1M C10 H2 SING N N 14
L1M C13 H3 SING N N 15
L1M C13 H4 SING N N 16
L1M C13 H5 SING N N 17
L1M C01 H6 SING N N 18
L1M C01 H7 SING N N 19
L1M C01 H8 SING N N 20
L1M C02 H9 SING N N 21
L1M C02 H10 SING N N 22
L1M C08 H11 SING N N 23
L1M C08 H12 SING N N 24
L1M C08 H13 SING N N 25
L1M C11 H14 SING N N 26
L1M C11 H15 SING N N 27
L1M C11 H16 SING N N 28
L1M C12 H17 SING N N 29
L1M C12 H18 SING N N 30
L1M P04 H19 SING N N 31
#
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
L1M SMILES ACDLabs 12.01 "C(C)N(/C(C)=N/P(OCC)=O)CC"
L1M InChI InChI 1.03 "InChI=1S/C8H19N2O2P/c1-5-10(6-2)8(4)9-13(11)12-7-3/h13H,5-7H2,1-4H3/b9-8+"
L1M InChIKey InChI 1.03 OJNAFPOCQGTUIK-CMDGGOBGSA-N
L1M SMILES_CANONICAL CACTVS 3.385 "CCO[P@@H](=O)N=C(C)N(CC)CC"
L1M SMILES CACTVS 3.385 "CCO[PH](=O)N=C(C)N(CC)CC"
L1M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCN(CC)/C(=N/[P@H](=O)OCC)/C"
L1M SMILES "OpenEye OEToolkits" 2.0.7 "CCN(CC)C(=NP(=O)OCC)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
L1M "SYSTEMATIC NAME" ACDLabs 12.01 "ethyl (R)-N-[(1E)-1-(diethylamino)ethylidene]phosphonamidate"
L1M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}'-ethoxyphosphonoyl-~{N},~{N}-diethyl-ethanimidamide"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
L1M "Create component" 2019-01-31 RCSB
L1M "Initial release" 2020-07-01 RCSB
L1M "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id L1M
_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 P04
_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 ?
#