data_1OV
#
_chem_comp.id 1OV
_chem_comp.name "[(1R)-1-amino-4-carbamimidamidobutyl]phosphonic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H15 N4 O3 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-04-15
_chem_comp.pdbx_modified_date 2013-06-07
_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 210.171
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 1OV
_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 4K5M
_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
1OV N1 N1 N 0 1 N N N N N N 13.733 9.461 17.657 4.569 0.899 0.705 N1 1OV 1
1OV C1 C1 C 0 1 N N N N N N 12.913 10.402 17.997 4.183 -0.156 0.042 C1 1OV 2
1OV N2 N2 N 0 1 N N N N N N 11.943 10.270 18.957 5.096 -1.126 -0.296 N2 1OV 3
1OV N3 N3 N 0 1 N N N N N N 13.015 11.564 17.306 2.864 -0.297 -0.318 N3 1OV 4
1OV C2 C2 C 0 1 N N N N N N 12.099 11.907 16.239 1.891 0.738 0.043 C2 1OV 5
1OV C3 C3 C 0 1 N N N N N N 12.727 12.717 15.109 0.507 0.339 -0.473 C3 1OV 6
1OV C4 C4 C 0 1 N N N N N N 12.731 11.771 13.854 -0.508 1.419 -0.096 C4 1OV 7
1OV C5 C5 C 0 1 N N R N N N 12.563 12.633 12.574 -1.893 1.020 -0.612 C5 1OV 8
1OV N4 N4 N 0 1 N N N N N N 11.129 12.832 12.132 -2.868 2.057 -0.250 N4 1OV 9
1OV P P P 0 1 N N N N N N 13.404 11.775 11.213 -2.386 -0.567 0.138 P 1OV 10
1OV O1 O1 O 0 1 N N N N N N 13.133 12.679 9.974 -2.315 -0.459 1.612 O1 1OV 11
1OV O3 O3 O 0 1 N N N N N N 14.954 11.560 11.448 -3.894 -0.921 -0.301 O3 1OV 12
1OV O2 O2 O 0 1 N N N N N N 12.515 10.483 10.880 -1.393 -1.730 -0.364 O2 1OV 13
1OV H1 H1 H 0 1 N N N N N N 13.577 8.622 18.178 5.499 0.998 0.959 H1 1OV 14
1OV H2 H2 H 0 1 N N N N N N 11.836 9.403 19.444 6.027 -1.027 -0.042 H2 1OV 15
1OV H3 H3 H 0 1 N N N N N N 11.342 11.040 19.170 4.809 -1.911 -0.789 H3 1OV 16
1OV H4 H4 H 0 1 N N N N N N 13.746 12.204 17.541 2.577 -1.081 -0.811 H4 1OV 17
1OV H5 H5 H 0 1 N N N N N N 11.275 12.496 16.668 1.858 0.843 1.128 H5 1OV 18
1OV H6 H6 H 0 1 N N N N N N 11.700 10.974 15.814 2.187 1.686 -0.405 H6 1OV 19
1OV H7 H7 H 0 1 N N N N N N 13.755 13.009 15.372 0.540 0.234 -1.557 H7 1OV 20
1OV H8 H8 H 0 1 N N N N N N 12.130 13.619 14.907 0.212 -0.610 -0.024 H8 1OV 21
1OV H9 H9 H 0 1 N N N N N N 11.899 11.055 13.929 -0.541 1.524 0.989 H9 1OV 22
1OV H10 H10 H 0 1 N N N N N N 13.684 11.223 13.808 -0.213 2.368 -0.544 H10 1OV 23
1OV H11 H11 H 0 1 N N N N N N 13.066 13.603 12.704 -1.860 0.915 -1.696 H11 1OV 24
1OV H12 H12 H 0 1 N N N N N N 10.620 13.304 12.852 -2.917 2.174 0.751 H12 1OV 25
1OV H13 H13 H 0 1 N N N N N N 11.111 13.381 11.297 -2.652 2.931 -0.706 H13 1OV 26
1OV H15 H15 H 0 1 N N N N N N 15.444 12.028 10.782 -4.015 -1.007 -1.257 H15 1OV 27
1OV H16 H16 H 0 1 N N N N N N 12.075 10.607 10.047 -1.597 -2.604 -0.004 H16 1OV 28
#
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
1OV O1 P DOUB N N 1
1OV O2 P SING N N 2
1OV P O3 SING N N 3
1OV P C5 SING N N 4
1OV N4 C5 SING N N 5
1OV C5 C4 SING N N 6
1OV C4 C3 SING N N 7
1OV C3 C2 SING N N 8
1OV C2 N3 SING N N 9
1OV N3 C1 SING N N 10
1OV N1 C1 DOUB N N 11
1OV C1 N2 SING N N 12
1OV N1 H1 SING N N 13
1OV N2 H2 SING N N 14
1OV N2 H3 SING N N 15
1OV N3 H4 SING N N 16
1OV C2 H5 SING N N 17
1OV C2 H6 SING N N 18
1OV C3 H7 SING N N 19
1OV C3 H8 SING N N 20
1OV C4 H9 SING N N 21
1OV C4 H10 SING N N 22
1OV C5 H11 SING N N 23
1OV N4 H12 SING N N 24
1OV N4 H13 SING N N 25
1OV O3 H15 SING N N 26
1OV O2 H16 SING N N 27
#
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
1OV SMILES ACDLabs 12.01 O=P(O)(O)C(N)CCCNC(=[N@H])N
1OV InChI InChI 1.03 InChI=1S/C5H15N4O3P/c6-4(13(10,11)12)2-1-3-9-5(7)8/h4H,1-3,6H2,(H4,7,8,9)(H2,10,11,12)/t4-/m1/s1
1OV InChIKey InChI 1.03 MMEPWCMDQUSOLC-SCSAIBSYSA-N
1OV SMILES_CANONICAL CACTVS 3.370 N[C@@H](CCCNC(N)=N)[P](O)(O)=O
1OV SMILES CACTVS 3.370 N[CH](CCCNC(N)=N)[P](O)(O)=O
1OV SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[H]/N=C(/N)\NCCC[C@H](N)P(=O)(O)O"
1OV SMILES "OpenEye OEToolkits" 1.7.6 C(CC(N)P(=O)(O)O)CNC(=N)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
1OV "SYSTEMATIC NAME" ACDLabs 12.01 "[(1R)-1-amino-4-carbamimidamidobutyl]phosphonic acid"
1OV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(1R)-1-azanyl-4-carbamimidamido-butyl]phosphonic 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
1OV 'Create component' 2013-04-15 RCSB
1OV 'Initial release' 2013-06-12 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
1OV N1 N 10.301 3.934 1
1OV C1 C 9.002 3.184 2
1OV N2 N 7.702 3.934 3
1OV N3 N 9.002 1.685 4
1OV C2 C 7.702 0.934 5
1OV C3 C 7.702 -0.566 6
1OV C4 C 6.404 -1.315 7
1OV C5 C 6.404 -2.816 8
1OV N4 N 7.702 -3.566 9
1OV P P 5.104 -3.566 10
1OV O1 O 3.805 -4.316 11
1OV O3 O 5.854 -4.864 12
1OV O2 O 4.354 -2.267 13
1OV H1 H 10.301 5.434 14
#
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
1OV O1 P DOUBLE NONE 1
1OV O2 P SINGLE NONE 2
1OV P O3 SINGLE NONE 3
1OV P C5 SINGLE NONE 4
1OV C5 N4 SINGLE BEGINDASH 5
1OV C5 C4 SINGLE NONE 6
1OV C4 C3 SINGLE NONE 7
1OV C3 C2 SINGLE NONE 8
1OV C2 N3 SINGLE NONE 9
1OV N3 C1 SINGLE ENDDOWNRIGHT 10
1OV N1 C1 DOUBLE NONE 11
1OV C1 N2 SINGLE ENDDOWNRIGHT 12
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id 1OV
_pdbe_chem_comp_rdkit_properties.exactmw 210.088
_pdbe_chem_comp_rdkit_properties.amw 210.174
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.800
_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 97.762
_pdbe_chem_comp_rdkit_properties.tpsa 145.450
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.288
_pdbe_chem_comp_rdkit_properties.CrippenMR 49.170
_pdbe_chem_comp_rdkit_properties.chi0v 6.855
_pdbe_chem_comp_rdkit_properties.chi1v 4.182
_pdbe_chem_comp_rdkit_properties.chi2v 1.276
_pdbe_chem_comp_rdkit_properties.chi3v 1.276
_pdbe_chem_comp_rdkit_properties.chi4v 0.423
_pdbe_chem_comp_rdkit_properties.chi0n 20.961
_pdbe_chem_comp_rdkit_properties.chi1n 9.639
_pdbe_chem_comp_rdkit_properties.chi2n 0.646
_pdbe_chem_comp_rdkit_properties.chi3n 0.646
_pdbe_chem_comp_rdkit_properties.chi4n 0.230
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.620
_pdbe_chem_comp_rdkit_properties.kappa1 2.304
_pdbe_chem_comp_rdkit_properties.kappa2 5.184
_pdbe_chem_comp_rdkit_properties.kappa3 6.533
_pdbe_chem_comp_rdkit_properties.Phi 0.919
#
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
1OV UniChem PDBe 1OV
1OV UniChem ZINC ZINC000025964403
1OV UniChem PubChem 71563402
#
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
1OV N1 3.037 0.812 -1.705 ETKDGv3 1
1OV C1 3.575 0.279 -0.653 ETKDGv3 2
1OV N2 4.889 0.670 -0.245 ETKDGv3 3
1OV N3 2.864 -0.712 0.103 ETKDGv3 4
1OV C2 1.508 -1.149 -0.228 ETKDGv3 5
1OV C3 0.484 -0.094 0.201 ETKDGv3 6
1OV C4 -0.947 -0.557 -0.108 ETKDGv3 7
1OV C5 -1.987 0.506 0.284 ETKDGv3 8
1OV N4 -1.980 0.721 1.732 ETKDGv3 9
1OV P -3.658 0.008 -0.280 ETKDGv3 10
1OV O1 -3.662 -0.151 -1.784 ETKDGv3 11
1OV O3 -4.777 1.200 0.156 ETKDGv3 12
1OV O2 -4.102 -1.456 0.445 ETKDGv3 13
1OV H1 3.537 1.532 -2.273 ETKDGv3 14
1OV H2 5.427 1.386 -0.783 ETKDGv3 15
1OV H3 5.328 0.244 0.600 ETKDGv3 16
1OV H4 3.353 -1.181 0.898 ETKDGv3 17
1OV H5 1.432 -1.348 -1.320 ETKDGv3 18
1OV H6 1.295 -2.101 0.306 ETKDGv3 19
1OV H7 0.685 0.859 -0.334 ETKDGv3 20
1OV H8 0.592 0.087 1.293 ETKDGv3 21
1OV H9 -1.155 -1.504 0.436 ETKDGv3 22
1OV H10 -1.027 -0.759 -1.199 ETKDGv3 23
1OV H11 -1.732 1.462 -0.224 ETKDGv3 24
1OV H12 -2.336 -0.139 2.211 ETKDGv3 25
1OV H13 -2.639 1.501 1.957 ETKDGv3 26
1OV H15 -4.447 2.028 -0.275 ETKDGv3 27
1OV H16 -3.556 -2.145 -0.011 ETKDGv3 28
#