data_RTK
#
_chem_comp.id RTK
_chem_comp.name trimethyl(3-oxidanylphosphonoylpropyl)azanium
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H17 N O2 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2013-03-27
_chem_comp.pdbx_modified_date 2014-09-05
_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 166.178
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RTK
_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 4BGK
_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
RTK O7 O7 O 0 1 N N N N N N 20.695 26.519 88.161 2.559 -1.412 0.288 O7 RTK 1
RTK P5 P5 P 0 1 N N N N N N 21.561 27.681 87.773 2.506 -0.048 -0.284 P5 RTK 2
RTK O4 O4 O 0 1 N N N N N N 22.995 27.271 87.495 3.817 0.772 0.163 O4 RTK 3
RTK C6 C6 C 0 1 N N N N N N 21.433 28.926 89.080 1.016 0.809 0.325 C6 RTK 4
RTK C3 C3 C 0 1 N N N N N N 22.392 30.091 88.853 -0.230 0.029 -0.099 C3 RTK 5
RTK C2 C2 C 0 1 N N N N N N 21.937 30.920 87.661 -1.480 0.748 0.412 C2 RTK 6
RTK N1 N1 N 1 1 N N N N N N 22.700 32.178 87.437 -2.676 -0.001 0.004 N1 RTK 7
RTK C28 C28 C 0 1 N N N N N N 24.122 31.936 87.090 -2.624 -1.355 0.571 C28 RTK 8
RTK C9 C9 C 0 1 N N N N N N 22.627 33.090 88.603 -3.876 0.690 0.495 C9 RTK 9
RTK C8 C8 C 0 1 N N N N N N 22.042 32.819 86.277 -2.725 -0.085 -1.462 C8 RTK 10
RTK H4 H4 H 0 1 N N N N N N 23.087 26.334 87.620 4.649 0.373 -0.128 H4 RTK 11
RTK H5 H5 H 0 1 N N N N N N 21.024 28.290 86.608 2.459 -0.130 -1.701 H5 RTK 12
RTK H61C H61C H 0 0 N N N N N N 20.403 29.312 89.103 1.053 0.872 1.413 H61C RTK 13
RTK H62C H62C H 0 0 N N N N N N 21.669 28.454 90.045 0.978 1.813 -0.096 H62C RTK 14
RTK H31C H31C H 0 0 N N N N N N 22.412 30.726 89.751 -0.266 -0.034 -1.187 H31C RTK 15
RTK H32C H32C H 0 0 N N N N N N 23.401 29.699 88.659 -0.191 -0.976 0.322 H32C RTK 16
RTK H21C H21C H 0 0 N N N N N N 22.032 30.299 86.758 -1.444 0.811 1.499 H21C RTK 17
RTK H22C H22C H 0 0 N N N N N N 20.881 31.185 87.814 -1.519 1.753 -0.009 H22C RTK 18
RTK H281 H281 H 0 0 N N N N N N 24.632 32.899 86.937 -2.587 -1.292 1.659 H281 RTK 19
RTK H282 H282 H 0 0 N N N N N N 24.611 31.388 87.909 -3.511 -1.910 0.269 H282 RTK 20
RTK H283 H283 H 0 0 N N N N N N 24.178 31.341 86.167 -1.733 -1.867 0.207 H283 RTK 21
RTK H91C H91C H 0 0 N N N N N N 23.203 34.003 88.392 -3.915 1.694 0.074 H91C RTK 22
RTK H92C H92C H 0 0 N N N N N N 21.577 33.356 88.795 -4.764 0.134 0.192 H92C RTK 23
RTK H93C H93C H 0 0 N N N N N N 23.046 32.588 89.488 -3.840 0.753 1.582 H93C RTK 24
RTK H81C H81C H 0 0 N N N N N N 22.551 33.766 86.043 -1.834 -0.597 -1.826 H81C RTK 25
RTK H82C H82C H 0 0 N N N N N N 22.098 32.148 85.407 -3.613 -0.641 -1.764 H82C RTK 26
RTK H83C H83C H 0 0 N N N N N N 20.988 33.019 86.518 -2.764 0.919 -1.883 H83C RTK 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
RTK O7 P5 DOUB N N 1
RTK P5 O4 SING N N 2
RTK P5 C6 SING N N 3
RTK P5 H5 SING N N 4
RTK C6 C3 SING N N 5
RTK C3 C2 SING N N 6
RTK C2 N1 SING N N 7
RTK N1 C28 SING N N 8
RTK N1 C9 SING N N 9
RTK N1 C8 SING N N 10
RTK O4 H4 SING N N 11
RTK C6 H61C SING N N 12
RTK C6 H62C SING N N 13
RTK C3 H31C SING N N 14
RTK C3 H32C SING N N 15
RTK C2 H21C SING N N 16
RTK C2 H22C SING N N 17
RTK C28 H281 SING N N 18
RTK C28 H282 SING N N 19
RTK C28 H283 SING N N 20
RTK C9 H91C SING N N 21
RTK C9 H92C SING N N 22
RTK C9 H93C SING N N 23
RTK C8 H81C SING N N 24
RTK C8 H82C SING N N 25
RTK C8 H83C 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
RTK SMILES ACDLabs 12.01 O=P(O)CCC[N+](C)(C)C
RTK InChI InChI 1.03 InChI=1S/C6H16NO2P/c1-7(2,3)5-4-6-10(8)9/h10H,4-6H2,1-3H3/p+1
RTK InChIKey InChI 1.03 WOSBPQBJRYGKCZ-UHFFFAOYSA-O
RTK SMILES_CANONICAL CACTVS 3.385 C[N+](C)(C)CCC[PH](O)=O
RTK SMILES CACTVS 3.385 C[N+](C)(C)CCC[PH](O)=O
RTK SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 C[N+](C)(C)CCCP(=O)O
RTK SMILES "OpenEye OEToolkits" 1.9.2 C[N+](C)(C)CCCP(=O)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
RTK "SYSTEMATIC NAME" ACDLabs 12.01 3-[(R)-hydroxy(oxido)-lambda~5~-phosphanyl]-N,N,N-trimethylpropan-1-aminium
RTK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 trimethyl(3-oxidanylphosphonoylpropyl)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
RTK 'Create component' 2013-03-27 EBI
RTK 'Initial release' 2014-03-12 RCSB
RTK 'Modify descriptor' 2014-09-05 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
RTK O7 O -2.859 1.388 1
RTK P5 P -2.858 -0.112 2
RTK O4 O -4.156 -0.863 3
RTK C6 C -1.558 -0.861 4
RTK C3 C -0.260 -0.110 5
RTK C2 C 1.040 -0.859 6
RTK N1 N 2.338 -0.108 7
RTK C28 C 1.587 1.190 8
RTK C9 C 3.087 1.192 9
RTK C8 C 3.638 -0.857 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
RTK O7 P5 DOUBLE NONE 1
RTK P5 O4 SINGLE BEGINWEDGE 2
RTK P5 C6 SINGLE NONE 3
RTK C6 C3 SINGLE NONE 4
RTK C3 C2 SINGLE NONE 5
RTK C2 N1 SINGLE NONE 6
RTK N1 C28 SINGLE NONE 7
RTK N1 C9 SINGLE NONE 8
RTK N1 C8 SINGLE NONE 9
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id RTK
_pdbe_chem_comp_rdkit_properties.exactmw 166.099
_pdbe_chem_comp_rdkit_properties.amw 166.181
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 86.967
_pdbe_chem_comp_rdkit_properties.tpsa 37.300
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.550
_pdbe_chem_comp_rdkit_properties.CrippenMR 43.604
_pdbe_chem_comp_rdkit_properties.chi0v 5.605
_pdbe_chem_comp_rdkit_properties.chi1v 3.161
_pdbe_chem_comp_rdkit_properties.chi2v 0.665
_pdbe_chem_comp_rdkit_properties.chi3v 0.665
_pdbe_chem_comp_rdkit_properties.chi4v 0.296
_pdbe_chem_comp_rdkit_properties.chi0n 21.711
_pdbe_chem_comp_rdkit_properties.chi1n 10.339
_pdbe_chem_comp_rdkit_properties.chi2n 0.371
_pdbe_chem_comp_rdkit_properties.chi3n 0.371
_pdbe_chem_comp_rdkit_properties.chi4n 0.154
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.150
_pdbe_chem_comp_rdkit_properties.kappa1 1.243
_pdbe_chem_comp_rdkit_properties.kappa2 4.117
_pdbe_chem_comp_rdkit_properties.kappa3 8.150
_pdbe_chem_comp_rdkit_properties.Phi 0.512
#
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
RTK UniChem PDBe RTK
RTK UniChem ZINC ZINC000098209378
RTK UniChem BRENDA 224215
#
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
RTK O7 4.779 -0.806 1.179 ETKDGv3 1
RTK P5 3.632 -0.706 0.200 ETKDGv3 2
RTK O4 3.987 0.475 -0.958 ETKDGv3 3
RTK C6 2.112 -0.259 1.095 ETKDGv3 4
RTK C3 0.917 -0.206 0.140 ETKDGv3 5
RTK C2 -0.379 0.146 0.907 ETKDGv3 6
RTK N1 -1.613 0.229 0.067 ETKDGv3 7
RTK C28 -2.749 0.571 0.957 ETKDGv3 8
RTK C9 -1.495 1.290 -0.963 ETKDGv3 9
RTK C8 -1.909 -1.068 -0.587 ETKDGv3 10
RTK H4 3.420 0.245 -1.736 ETKDGv3 11
RTK H5 3.454 -1.952 -0.433 ETKDGv3 12
RTK H61C 2.261 0.732 1.576 ETKDGv3 13
RTK H62C 1.933 -1.019 1.886 ETKDGv3 14
RTK H31C 1.126 0.562 -0.633 ETKDGv3 15
RTK H32C 0.819 -1.198 -0.347 ETKDGv3 16
RTK H21C -0.520 -0.618 1.706 ETKDGv3 17
RTK H22C -0.213 1.118 1.428 ETKDGv3 18
RTK H281 -3.703 0.648 0.388 ETKDGv3 19
RTK H282 -2.889 -0.205 1.744 ETKDGv3 20
RTK H283 -2.581 1.547 1.465 ETKDGv3 21
RTK H91C -0.761 1.017 -1.751 ETKDGv3 22
RTK H92C -1.178 2.255 -0.508 ETKDGv3 23
RTK H93C -2.467 1.456 -1.479 ETKDGv3 24
RTK H81C -1.168 -1.306 -1.381 ETKDGv3 25
RTK H82C -2.906 -1.049 -1.082 ETKDGv3 26
RTK H83C -1.909 -1.899 0.154 ETKDGv3 27
#