data_ONP
#
_chem_comp.id ONP
_chem_comp.name "O-NITROPHENYL AMINOETHYLDIPHOSPHATE BERYLLIUM TRIFLUORIDE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H11 Be F3 N2 O9 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge -1
_chem_comp.pdbx_initial_date 1999-09-22
_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 407.136
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ONP
_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 Y
_chem_comp.pdbx_model_coordinates_db_code 1D0Y
_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
ONP BE BE BE -1 0 N N N N N N 32.542 58.180 23.043 ? ? ? BE ONP 1
ONP F1 F1 F 0 1 N N N N N N 31.308 57.337 23.218 ? ? ? F1 ONP 2
ONP F2 F2 F 0 1 N N N N N N 32.254 59.185 21.977 ? ? ? F2 ONP 3
ONP F3 F3 F 0 1 N N N N N N 33.019 58.888 24.293 ? ? ? F3 ONP 4
ONP PB PB P 0 1 N N R N N N 34.066 56.671 21.068 ? ? ? PB ONP 5
ONP OB1 OB1 O 0 1 N N N N N N 33.608 55.266 20.852 ? ? ? OB1 ONP 6
ONP OB2 OB2 O 0 1 N N N N N N 33.632 57.631 19.956 ? ? ? OB2 ONP 7
ONP OB3 OB3 O 0 1 N N N N N N 33.701 57.206 22.543 ? ? ? OB3 ONP 8
ONP OA3 OA3 O 0 1 N N N N N N 35.679 56.651 21.048 ? ? ? OA3 ONP 9
ONP PA PA P 0 1 N N R N N N 36.684 57.351 20.065 ? ? ? PA ONP 10
ONP OA1 OA1 O 0 1 N N N N N N 36.300 57.065 18.573 ? ? ? OA1 ONP 11
ONP OA2 OA2 O 0 1 N N N N N N 36.685 58.802 20.370 ? ? ? OA2 ONP 12
ONP OE2 OE2 O 0 1 N N N N N N 38.152 56.718 20.250 ? ? ? OE2 ONP 13
ONP NA3 NA3 N 0 1 N N N N N N 40.708 56.057 20.405 ? ? ? NA3 ONP 14
ONP CA2 CA2 C 0 1 N N N N N N 40.202 56.901 21.450 ? ? ? CA2 ONP 15
ONP CA1 CA1 C 0 1 N N N N N N 38.707 56.703 21.549 ? ? ? CA1 ONP 16
ONP C1 C1 C 0 1 Y N N N N N 42.119 56.108 20.355 ? ? ? C1 ONP 17
ONP C6 C6 C 0 1 Y N N N N N 42.794 56.819 21.291 ? ? ? C6 ONP 18
ONP C5 C5 C 0 1 Y N N N N N 44.209 56.863 21.248 ? ? ? C5 ONP 19
ONP C4 C4 C 0 1 Y N N N N N 44.934 56.178 20.283 ? ? ? C4 ONP 20
ONP C3 C3 C 0 1 Y N N N N N 44.222 55.390 19.357 ? ? ? C3 ONP 21
ONP C2 C2 C 0 1 Y N N N N N 42.832 55.373 19.394 ? ? ? C2 ONP 22
ONP N2 N2 N 1 1 N N N N N N 42.065 54.563 18.427 ? ? ? N2 ONP 23
ONP O2A O2A O 0 1 N N N N N N 42.737 53.883 17.657 ? ? ? O2A ONP 24
ONP O2B O2B O -1 1 N N N N N N 40.788 54.606 18.518 ? ? ? O2B ONP 25
ONP HOB2 2HOB H 0 0 N N N N N N 33.923 58.524 20.093 ? ? ? HOB2 ONP 26
ONP HOA2 2HOA H 0 0 N N N N N N 36.907 57.488 17.978 ? ? ? HOA2 ONP 27
ONP HNA1 1HNA H 0 0 N N N N N N 40.290 56.283 19.502 ? ? ? HNA1 ONP 28
ONP HA21 1HA2 H 0 0 N N N N N N 40.720 56.733 22.422 ? ? ? HA21 ONP 29
ONP HA22 2HA2 H 0 0 N N N N N N 40.482 57.970 21.308 ? ? ? HA22 ONP 30
ONP HA11 1HA1 H 0 0 N N N N N N 38.224 57.447 22.224 ? ? ? HA11 ONP 31
ONP HA12 2HA1 H 0 0 N N N N N N 38.438 55.780 22.114 ? ? ? HA12 ONP 32
ONP H6 H6 H 0 1 N N N N N N 42.209 57.345 22.064 ? ? ? H6 ONP 33
ONP H5 H5 H 0 1 N N N N N N 44.767 57.453 21.994 ? ? ? H5 ONP 34
ONP H4 H4 H 0 1 N N N N N N 46.033 56.256 20.253 ? ? ? H4 ONP 35
ONP H3 H3 H 0 1 N N N N N N 44.753 54.785 18.602 ? ? ? H3 ONP 36
#
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
ONP BE F1 SING N N 1
ONP BE F2 SING N N 2
ONP BE F3 SING N N 3
ONP BE OB3 SING N N 4
ONP PB OB1 DOUB N N 5
ONP PB OB2 SING N N 6
ONP PB OB3 SING N N 7
ONP PB OA3 SING N N 8
ONP OB2 HOB2 SING N N 9
ONP OA3 PA SING N N 10
ONP PA OA1 SING N N 11
ONP PA OA2 DOUB N N 12
ONP PA OE2 SING N N 13
ONP OA1 HOA2 SING N N 14
ONP OE2 CA1 SING N N 15
ONP NA3 CA2 SING N N 16
ONP NA3 C1 SING N N 17
ONP NA3 HNA1 SING N N 18
ONP CA2 CA1 SING N N 19
ONP CA2 HA21 SING N N 20
ONP CA2 HA22 SING N N 21
ONP CA1 HA11 SING N N 22
ONP CA1 HA12 SING N N 23
ONP C1 C6 DOUB Y N 24
ONP C1 C2 SING Y N 25
ONP C6 C5 SING Y N 26
ONP C6 H6 SING N N 27
ONP C5 C4 DOUB Y N 28
ONP C5 H5 SING N N 29
ONP C4 C3 SING Y N 30
ONP C4 H4 SING N N 31
ONP C3 C2 DOUB Y N 32
ONP C3 H3 SING N N 33
ONP C2 N2 SING N N 34
ONP N2 O2A DOUB N N 35
ONP N2 O2B SING N N 36
#
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
ONP SMILES_CANONICAL CACTVS 3.341 O[P@](=O)(OCCNc1ccccc1[N+]([O-])=O)O[P@@](O)(=O)O[Be-](F)(F)F
ONP SMILES CACTVS 3.341 O[P](=O)(OCCNc1ccccc1[N+]([O-])=O)O[P](O)(=O)O[Be-](F)(F)F
ONP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[Be-](O[P@@](=O)(O)O[P@](=O)(O)OCCNc1ccccc1[N+](=O)[O-])(F)(F)F"
ONP SMILES "OpenEye OEToolkits" 1.5.0 "[Be-](OP(=O)(O)OP(=O)(O)OCCNc1ccccc1[N+](=O)[O-])(F)(F)F"
ONP InChI InChI 1.03 InChI=1S/C8H12N2O9P2.Be.3FH/c11-10(12)8-4-2-1-3-7(8)9-5-6-18-21(16,17)19-20(13,14)15;;;;/h1-4,9H,5-6H2,(H,16,17)(H2,13,14,15);;3*1H/q;+3;;;/p-4
ONP InChIKey InChI 1.03 REAYVLUAJKGPLT-UHFFFAOYSA-J
#
_pdbx_chem_comp_identifier.comp_id ONP
_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
trifluoro-[hydroxy-[hydroxy-[2-[(2-nitrophenyl)amino]ethoxy]phosphoryl]oxy-phosphoryl]oxy-beryllium
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ONP 'Create component' 1999-09-22 RCSB
ONP '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
ONP BE Be 2.391 6.678 1
ONP F1 F 1.616 7.956 2
ONP F2 F 3.129 7.993 3
ONP F3 F 3.722 5.965 4
ONP PB P 1.358 4.346 5
ONP OB1 O 2.787 4.757 6
ONP OB2 O -0.103 3.950 7
ONP OB3 O 1.096 5.820 8
ONP OA3 O 1.927 2.932 9
ONP PA P 1.317 1.524 10
ONP OA1 O 2.737 1.095 11
ONP OA2 O -0.137 1.954 12
ONP OE2 O 1.038 0.023 13
ONP NA3 N -1.392 -3.023 14
ONP CA2 C -0.178 -2.196 15
ONP CA1 C -0.257 -0.669 16
ONP C1 C -1.328 -4.542 17
ONP C6 C -0.028 -5.292 18
ONP C5 C -0.033 -6.794 19
ONP C4 C -1.332 -7.541 20
ONP C3 C -2.631 -6.790 21
ONP C2 C -2.626 -5.289 22
ONP N2 N -3.925 -4.537 23
ONP O2A O -3.923 -3.037 24
ONP O2B O -5.225 -5.285 25
#
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
ONP BE F1 SINGLE NONE 1
ONP BE F2 SINGLE NONE 2
ONP BE F3 SINGLE NONE 3
ONP BE OB3 SINGLE NONE 4
ONP PB OB1 DOUBLE NONE 5
ONP PB OB2 SINGLE NONE 6
ONP PB OB3 SINGLE NONE 7
ONP PB OA3 SINGLE NONE 8
ONP OA3 PA SINGLE NONE 9
ONP PA OA1 SINGLE NONE 10
ONP PA OA2 DOUBLE NONE 11
ONP PA OE2 SINGLE NONE 12
ONP OE2 CA1 SINGLE NONE 13
ONP NA3 CA2 SINGLE NONE 14
ONP NA3 C1 SINGLE NONE 15
ONP CA2 CA1 SINGLE NONE 16
ONP C1 C6 DOUBLE NONE 17
ONP C1 C2 SINGLE NONE 18
ONP C6 C5 SINGLE NONE 19
ONP C5 C4 DOUBLE NONE 20
ONP C4 C3 SINGLE NONE 21
ONP C3 C2 DOUBLE NONE 22
ONP C2 N2 SINGLE NONE 23
ONP N2 O2A DOUBLE NONE 24
ONP N2 O2B SINGLE NONE 25
#
_pdbe_chem_comp_substructure.comp_id ONP
_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
ONP OB2 F1 1
ONP PB F1 1
ONP OB1 F1 1
ONP OB3 F1 1
ONP OA3 F1 1
ONP OA3 F1 2
ONP PA F1 2
ONP OA2 F1 2
ONP OA1 F1 2
ONP OE2 F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id ONP
#
_pdbe_chem_comp_external_mappings.comp_id ONP
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id ONP
#