data_PHY
#
_chem_comp.id PHY
_chem_comp.name "1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H15 N O7 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 275.133
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PHY
_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 1IOW
_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
PHY C1 C1 C 0 1 N N S N N N 31.843 18.868 74.134 2.055 0.058 -1.092 C1 PHY 1
PHY C2 C2 C 0 1 N N N N N N 31.662 18.571 75.466 2.311 1.566 -1.064 C2 PHY 2
PHY "C1'" "C1'" C 0 1 N N N N N N 30.247 17.183 72.961 0.744 0.063 1.580 "C1'" PHY 3
PHY "C2'" "C2'" C 0 1 N N R N N N 29.775 15.857 72.331 -0.547 -0.248 2.338 "C2'" PHY 4
PHY "C3'" "C3'" C 0 1 N N N N N N 28.353 15.980 71.710 -1.687 0.603 1.777 "C3'" PHY 5
PHY C C C 0 1 N N N N N N 29.899 14.649 73.335 -0.359 0.063 3.800 C PHY 6
PHY O1 O1 O 0 1 N N N N N N 30.421 13.659 72.872 0.698 0.491 4.195 O1 PHY 7
PHY O2 O2 O 0 1 N N N N N N 29.627 14.818 74.571 -1.367 -0.134 4.664 O2 PHY 8
PHY N1 N1 N 0 1 N N N N N N 32.882 19.725 73.967 3.179 -0.640 -0.454 N1 PHY 9
PHY P1 P1 P 0 1 N N R N N N 31.684 17.674 73.141 0.516 -0.314 -0.188 P1 PHY 10
PHY O1P O1P O 0 1 N N N N N N 32.558 16.525 73.515 0.185 -1.747 -0.348 O1P PHY 11
PHY O2P O2P O 0 1 N N N N N N 32.264 18.021 71.809 -0.683 0.582 -0.779 O2P PHY 12
PHY P2 P2 P 0 1 N N N N N N 31.970 19.091 70.745 -0.955 0.066 -2.279 P2 PHY 13
PHY O3P O3P O 0 1 N N N N N N 30.701 19.574 71.213 -0.999 -1.412 -2.292 O3P PHY 14
PHY O4P O4P O 0 1 N N N N N N 31.873 18.677 69.354 -2.362 0.649 -2.800 O4P PHY 15
PHY O5P O5P O 0 1 N N N N N N 32.990 20.130 70.990 0.227 0.576 -3.245 O5P PHY 16
PHY H1 H1 H 0 1 N N N N N N 30.957 19.449 73.787 1.959 -0.275 -2.125 H1 PHY 17
PHY H21 1H2 H 0 1 N N N N N N 30.808 17.866 75.603 3.231 1.788 -1.605 H21 PHY 18
PHY H22 2H2 H 0 1 N N N N N N 32.596 18.181 75.932 1.477 2.084 -1.538 H22 PHY 19
PHY H23 3H2 H 0 1 N N N N N N 31.538 19.492 76.080 2.406 1.899 -0.031 H23 PHY 20
PHY "H1'1" "1H1'" H 0 0 N N N N N N 29.717 17.990 72.402 1.556 -0.543 1.979 "H1'1" PHY 21
PHY "H1'2" "2H1'" H 0 0 N N N N N N 29.784 17.219 73.974 0.988 1.119 1.697 "H1'2" PHY 22
PHY "H2'" "H2'" H 0 1 N N N N N N 30.466 15.631 71.485 -0.791 -1.304 2.220 "H2'" PHY 23
PHY "H3'1" "1H3'" H 0 0 N N N N N N 28.011 15.021 71.254 -1.443 1.659 1.895 "H3'1" PHY 24
PHY "H3'2" "2H3'" H 0 0 N N N N N N 27.616 16.357 72.457 -1.823 0.377 0.719 "H3'2" PHY 25
PHY "H3'3" "3H3'" H 0 0 N N N N N N 28.303 16.817 70.975 -2.607 0.381 2.317 "H3'3" PHY 26
PHY HO2 HO2 H 0 1 N N N N N N 29.701 14.089 75.176 -1.247 0.065 5.602 HO2 PHY 27
PHY HN11 1HN1 H 0 0 N N N N N N 33.016 19.945 72.980 3.229 -0.302 0.494 HN11 PHY 28
PHY HN12 2HN1 H 0 0 N N N N N N 33.737 19.368 74.393 2.922 -1.615 -0.402 HN12 PHY 29
PHY HO4P PHO4 H 0 0 N N N N N N 31.691 19.338 68.696 -2.486 0.317 -3.700 HO4P PHY 30
PHY HO5P PHO5 H 0 0 N N N N N N 32.808 20.791 70.332 0.221 1.542 -3.208 HO5P PHY 31
#
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
PHY C1 C2 SING N N 1
PHY C1 N1 SING N N 2
PHY C1 P1 SING N N 3
PHY C1 H1 SING N N 4
PHY C2 H21 SING N N 5
PHY C2 H22 SING N N 6
PHY C2 H23 SING N N 7
PHY "C1'" "C2'" SING N N 8
PHY "C1'" P1 SING N N 9
PHY "C1'" "H1'1" SING N N 10
PHY "C1'" "H1'2" SING N N 11
PHY "C2'" "C3'" SING N N 12
PHY "C2'" C SING N N 13
PHY "C2'" "H2'" SING N N 14
PHY "C3'" "H3'1" SING N N 15
PHY "C3'" "H3'2" SING N N 16
PHY "C3'" "H3'3" SING N N 17
PHY C O1 DOUB N N 18
PHY C O2 SING N N 19
PHY O2 HO2 SING N N 20
PHY N1 HN11 SING N N 21
PHY N1 HN12 SING N N 22
PHY P1 O1P DOUB N N 23
PHY P1 O2P SING N N 24
PHY O2P P2 SING N N 25
PHY P2 O3P DOUB N N 26
PHY P2 O4P SING N N 27
PHY P2 O5P SING N N 28
PHY O4P HO4P SING N N 29
PHY O5P HO5P SING N N 30
#
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
PHY SMILES ACDLabs 10.04 O=P(OP(=O)(O)O)(C(N)C)CC(C(=O)O)C
PHY SMILES_CANONICAL CACTVS 3.341 C[C@@H](N)[P@@](=O)(C[C@H](C)C(O)=O)O[P](O)(O)=O
PHY SMILES CACTVS 3.341 C[CH](N)[P](=O)(C[CH](C)C(O)=O)O[P](O)(O)=O
PHY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@@H](C[P@](=O)([C@@H](C)N)OP(=O)(O)O)C(=O)O
PHY SMILES "OpenEye OEToolkits" 1.5.0 CC(CP(=O)(C(C)N)OP(=O)(O)O)C(=O)O
PHY InChI InChI 1.03 InChI=1S/C6H15NO7P2/c1-4(6(8)9)3-15(10,5(2)7)14-16(11,12)13/h4-5H,3,7H2,1-2H3,(H,8,9)(H2,11,12,13)/t4-,5-,15+/m0/s1
PHY InChIKey InChI 1.03 BAIYWTZQRMCJBV-DKDXWZAISA-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
PHY "SYSTEMATIC NAME" ACDLabs 10.04 "(2R)-3-[(R)-[(1S)-1-aminoethyl](phosphonooxy)phosphoryl]-2-methylpropanoic acid"
PHY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-3-[[(1S)-1-aminoethyl]-phosphonooxy-phosphoryl]-2-methyl-propanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PHY 'Create component' 1999-07-08 EBI
PHY 'Modify descriptor' 2011-06-04 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
PHY C1 C 5.104 -2.626 1
PHY C2 C 3.805 -1.876 2
PHY "C1'" C 5.654 -0.577 3
PHY "C2'" C 6.404 0.722 4
PHY "C3'" C 7.904 0.722 5
PHY C C 5.654 2.021 6
PHY O1 O 6.404 3.320 7
PHY O2 O 4.154 2.021 8
PHY N1 N 5.104 -4.126 9
PHY P1 P 6.404 -1.876 10
PHY O1P O 7.154 -3.175 11
PHY O2P O 7.702 -1.126 12
PHY P2 P 9.002 -1.876 13
PHY O3P O 10.301 -2.626 14
PHY O4P O 9.752 -0.577 15
PHY O5P O 8.252 -3.175 16
#
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
PHY C1 C2 SINGLE BEGINDASH 1
PHY C1 N1 SINGLE NONE 2
PHY C1 P1 SINGLE NONE 3
PHY "C1'" "C2'" SINGLE NONE 4
PHY P1 "C1'" SINGLE BEGINDASH 5
PHY "C2'" "C3'" SINGLE BEGINWEDGE 6
PHY "C2'" C SINGLE NONE 7
PHY C O1 DOUBLE NONE 8
PHY C O2 SINGLE NONE 9
PHY P1 O1P DOUBLE NONE 10
PHY P1 O2P SINGLE NONE 11
PHY O2P P2 SINGLE NONE 12
PHY P2 O3P DOUBLE NONE 13
PHY P2 O4P SINGLE NONE 14
PHY P2 O5P SINGLE NONE 15
#
_pdbe_chem_comp_substructure.comp_id PHY
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-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
PHY O2P F1 1
PHY P2 F1 1
PHY O3P F1 1
PHY O4P F1 1
PHY O5P F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PHY
_pdbe_chem_comp_rdkit_properties.exactmw 275.032
_pdbe_chem_comp_rdkit_properties.amw 275.134
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_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 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 113.938
_pdbe_chem_comp_rdkit_properties.tpsa 147.150
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.399
_pdbe_chem_comp_rdkit_properties.CrippenMR 56.052
_pdbe_chem_comp_rdkit_properties.chi0v 8.988
_pdbe_chem_comp_rdkit_properties.chi1v 6.260
_pdbe_chem_comp_rdkit_properties.chi2v 3.752
_pdbe_chem_comp_rdkit_properties.chi3v 3.752
_pdbe_chem_comp_rdkit_properties.chi4v 2.537
_pdbe_chem_comp_rdkit_properties.chi0n 22.199
_pdbe_chem_comp_rdkit_properties.chi1n 10.294
_pdbe_chem_comp_rdkit_properties.chi2n 0.957
_pdbe_chem_comp_rdkit_properties.chi3n 0.957
_pdbe_chem_comp_rdkit_properties.chi4n 0.446
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.230
_pdbe_chem_comp_rdkit_properties.kappa1 3.882
_pdbe_chem_comp_rdkit_properties.kappa2 5.402
_pdbe_chem_comp_rdkit_properties.kappa3 5.205
_pdbe_chem_comp_rdkit_properties.Phi 1.311
#
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
PHY UniChem PDBe PHY
PHY UniChem ZINC ZINC000001532435
PHY UniChem PubChem 9543432
#
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
PHY C1 -0.898 1.640 -0.045 ETKDGv3 1
PHY C2 -2.360 1.975 -0.359 ETKDGv3 2
PHY "C1'" 1.072 -0.585 0.413 ETKDGv3 3
PHY "C2'" 2.126 -0.301 -0.677 ETKDGv3 4
PHY "C3'" 3.473 -0.923 -0.294 ETKDGv3 5
PHY C 2.307 1.174 -0.905 ETKDGv3 6
PHY O1 2.206 1.648 -2.069 ETKDGv3 7
PHY O2 2.609 2.017 0.161 ETKDGv3 8
PHY N1 -0.513 2.144 1.273 ETKDGv3 9
PHY P1 -0.631 -0.166 -0.115 ETKDGv3 10
PHY O1P -0.859 -0.625 -1.541 ETKDGv3 11
PHY O2P -1.733 -0.885 0.974 ETKDGv3 12
PHY P2 -2.139 -2.438 0.401 ETKDGv3 13
PHY O3P -0.898 -3.248 0.100 ETKDGv3 14
PHY O4P -3.038 -3.235 1.592 ETKDGv3 15
PHY O5P -3.086 -2.305 -0.996 ETKDGv3 16
PHY H1 -0.260 2.121 -0.815 ETKDGv3 17
PHY H21 -3.040 1.507 0.385 ETKDGv3 18
PHY H22 -2.510 3.075 -0.337 ETKDGv3 19
PHY H23 -2.627 1.607 -1.372 ETKDGv3 20
PHY "H1'1" 1.090 -1.667 0.657 ETKDGv3 21
PHY "H1'2" 1.312 -0.034 1.347 ETKDGv3 22
PHY "H2'" 1.797 -0.781 -1.625 ETKDGv3 23
PHY "H3'1" 3.840 -0.505 0.669 ETKDGv3 24
PHY "H3'2" 3.370 -2.024 -0.189 ETKDGv3 25
PHY "H3'3" 4.227 -0.721 -1.084 ETKDGv3 26
PHY HO2 2.734 3.012 0.017 ETKDGv3 27
PHY HN11 -0.594 3.187 1.269 ETKDGv3 28
PHY HN12 -1.180 1.780 1.992 ETKDGv3 29
PHY HO4P -2.467 -3.206 2.401 ETKDGv3 30
PHY HO5P -3.328 -3.237 -1.227 ETKDGv3 31
#