data_PON
#
_chem_comp.id PON
_chem_comp.name "IMIDO DIPHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "H3 N O6 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge -2
_chem_comp.pdbx_initial_date 2000-08-04
_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 174.974
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PON
_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 1FFW
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
PON P1 P1 P 0 1 N N N N N N -3.045 3.442 30.044 1.269 0.008 -0.063 P1 PON 1
PON O1 O1 O 0 1 N N N N N N -2.405 2.086 29.942 1.421 1.445 0.485 O1 PON 2
PON O2 O2 O 0 1 N N N N N N -4.492 3.551 30.403 2.599 -0.402 -0.872 O2 PON 3
PON O3 O3 O 0 1 N N N N N N -2.715 4.290 28.741 -0.001 -0.057 -1.050 O3 PON 4
PON O4 O4 O -1 1 N N N N N N -2.302 4.218 31.215 1.058 -0.972 1.113 O4 PON 5
PON P2 P2 P 0 1 N N S N N N -2.134 5.403 27.829 -1.315 -0.034 -0.121 P2 PON 6
PON O5 O5 O 0 1 N N N N N N -2.510 5.214 26.415 -1.335 1.322 0.747 O5 PON 7
PON O6 O6 O -1 1 N N N N N N -0.601 5.364 27.834 -1.295 -1.304 0.869 O6 PON 8
PON N7 N7 N 0 1 N N N N N N -2.516 6.767 28.290 -2.584 -0.095 -1.015 N7 PON 9
PON HO2 HO2 H 0 1 N N N N N N -4.896 4.408 30.467 3.334 -0.350 -0.246 HO2 PON 10
PON HO5 HO5 H 0 1 N N N N N N -2.154 5.895 25.856 -1.347 2.056 0.118 HO5 PON 11
PON H7 H7 H 0 1 N N N N N N -1.837 7.460 27.974 -3.465 -0.090 -0.609 H7 PON 12
#
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
PON P1 O1 DOUB N N 1
PON P1 O2 SING N N 2
PON P1 O3 SING N N 3
PON P1 O4 SING N N 4
PON O2 HO2 SING N N 5
PON O3 P2 SING N N 6
PON P2 O5 SING N N 7
PON P2 O6 SING N N 8
PON P2 N7 DOUB N N 9
PON O5 HO5 SING N N 10
PON N7 H7 SING N N 11
#
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
PON SMILES_CANONICAL CACTVS 3.341 O[P@@]([O-])(=N)O[P](O)([O-])=O
PON SMILES CACTVS 3.341 O[P]([O-])(=N)O[P](O)([O-])=O
PON SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 N=[P@@](O)([O-])O[P@](=O)(O)[O-]
PON SMILES "OpenEye OEToolkits" 1.5.0 N=P(O)([O-])OP(=O)(O)[O-]
PON InChI InChI 1.03 InChI=1S/H4NO6P2/c1-8(2,3)7-9(4,5)6/h(H4-,1,2,3,4,5,6)/q-1/p-1
PON InChIKey InChI 1.03 VYBCVOULKDXKCH-UHFFFAOYSA-M
#
_pdbx_chem_comp_identifier.comp_id PON
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.5.0
_pdbx_chem_comp_identifier.identifier "(hydroxy-oxido-phosphinimyl) hydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
PON 'Create component' 2000-08-04 RCSB
PON '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
PON P1 P 5.104 -0.403 1
PON O1 O 3.805 -1.153 2
PON O2 O 5.854 -1.702 3
PON O3 O 6.404 0.347 4
PON O4 O 4.354 0.896 5
PON P2 P 7.702 -0.403 6
PON O5 O 9.002 -1.153 7
PON O6 O 8.453 0.896 8
PON N7 N 6.952 -1.702 9
#
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
PON P1 O1 DOUBLE NONE 1
PON P1 O2 SINGLE BEGINDASH 2
PON P1 O3 SINGLE NONE 3
PON P1 O4 SINGLE NONE 4
PON O3 P2 SINGLE NONE 5
PON P2 O5 SINGLE BEGINWEDGE 6
PON P2 O6 SINGLE NONE 7
PON P2 N7 DOUBLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id PON
_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
PON O2 F1 1
PON P1 F1 1
PON O1 F1 1
PON O3 F1 1
PON O4 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PON
_pdbe_chem_comp_rdkit_properties.exactmw 174.945
_pdbe_chem_comp_rdkit_properties.amw 174.973
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 12
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 54.700
_pdbe_chem_comp_rdkit_properties.tpsa 136.730
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.659
_pdbe_chem_comp_rdkit_properties.CrippenMR 22.769
_pdbe_chem_comp_rdkit_properties.chi0v 5.580
_pdbe_chem_comp_rdkit_properties.chi1v 4.434
_pdbe_chem_comp_rdkit_properties.chi2v 1.829
_pdbe_chem_comp_rdkit_properties.chi3v 1.829
_pdbe_chem_comp_rdkit_properties.chi4v 1.137
_pdbe_chem_comp_rdkit_properties.chi0n 6.791
_pdbe_chem_comp_rdkit_properties.chi1n 2.742
_pdbe_chem_comp_rdkit_properties.chi2n 0.203
_pdbe_chem_comp_rdkit_properties.chi3n 0.203
_pdbe_chem_comp_rdkit_properties.chi4n 0.126
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.260
_pdbe_chem_comp_rdkit_properties.kappa1 4.983
_pdbe_chem_comp_rdkit_properties.kappa2 2.476
_pdbe_chem_comp_rdkit_properties.kappa3 8.260
_pdbe_chem_comp_rdkit_properties.Phi 1.371
#
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
PON UniChem PDBe PON
PON UniChem PubChem 3316608
#
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
PON P1 1.588 0.419 -0.231 ETKDGv3 1
PON O1 1.824 0.064 -1.682 ETKDGv3 2
PON O2 1.606 -0.988 0.712 ETKDGv3 3
PON O3 0.112 1.249 -0.064 ETKDGv3 4
PON O4 2.836 1.435 0.289 ETKDGv3 5
PON P2 -1.143 0.134 -0.346 ETKDGv3 6
PON O5 -1.209 -0.997 0.912 ETKDGv3 7
PON O6 -0.919 -0.667 -1.821 ETKDGv3 8
PON N7 -2.508 0.916 -0.399 ETKDGv3 9
PON HO2 2.515 -1.363 0.590 ETKDGv3 10
PON HO5 -1.881 -1.663 0.619 ETKDGv3 11
PON H7 -2.822 1.461 0.416 ETKDGv3 12
#