Docking pose detail

Molecular metrics status: queued

Pose metrics recompute is queued in the background.

Metrics cached · SASA missing

py3Dmol interaction viewer

Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.

Strict H-bonds Permissive H-bonds

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: strong

Ligand efficiency: weak

Geometry reliability: low

Reason: geometry warning, clashes, protein contact clashes

Interaction summary

Collapsible panels

H-bonds 2 Hydrophobic 24 π–π 2 Clashes 8 Severe clashes 0

Final rank	5.595804383431705	Score	-25.4199
Inter norm	-0.746918	Intra norm	0.0598929
Top1000	no	Excluded	no
Contacts	18	H-bonds	2
Artifact reason	geometry warning; 17 clashes; 8 protein contact clashes; moderate strain Δ 18.0
Residues	A:NDP301;B:ALA32;B:ARG48;B:ASP52;B:ILE45;B:LEU94;B:MET53;B:PHE56;B:PHE91;B:PRO88;B:SER86;B:TRP47;B:TYR162;B:VAL156;B:VAL30;B:VAL31;B:VAL49;B:VAL87

Protein summary

511 residues

Protein target	T09	Atoms	8170
Residues	511	Chains	2
Residue summary	LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	3CL9	Contacts	21
Pose	Open native pose	H-bonds	9
IFP residues	A:NDP301; B:ALA32; B:ARG97; B:ASP52; B:GLY157; B:ILE45; B:LEU94; B:LYS57; B:MET53; B:PHE55; B:PHE56; B:PHE91; B:PRO88; B:SER86; B:THR180; B:THR83; B:TYR162; B:VAL156; B:VAL30; B:VAL31; B:VAL87
Current overlap	15	Native recall	0.71
Jaccard	0.62	RMSD	-
H-bond strict	0	Strict recall	0.00
H-bond same residue+role	0	Role recall	0.00
H-bond same residue	0	Residue recall	0.00

Hydrogen bonds

Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

Hydrophobic contacts

Clashes

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	Contacts	Native overlap	Native recall	HB role recall	RMSD	Excluded
540	5.595804383431705	-0.746918	-25.4199	2	18	15	0.71	0.00	-	no	Current
541	6.213368125786769	-0.64062	-16.9109	0	17	15	0.71	0.00	-	no	Open
549	7.522371415632253	-0.67329	-23.9723	3	19	15	0.71	0.00	-	no	Open
553	7.52813639249333	-0.646711	-17.9557	1	18	17	0.81	0.17	-	no	Open
550	6.629529269040337	-0.590538	-21.0884	0	19	17	0.81	0.00	-	yes	Open
543	9.024657323951638	-0.618332	-20.5006	1	16	12	0.57	0.00	-	yes	Open
548	9.293884475259304	-0.689173	-25.2034	0	20	19	0.90	0.00	-	yes	Open
551	9.375625065586323	-0.59031	-17.7886	0	21	18	0.86	0.00	-	yes	Open
547	9.510819956806936	-0.675505	-19.8171	0	21	18	0.86	0.00	-	yes	Open
544	10.669188232996438	-0.651693	-16.5248	0	21	19	0.90	0.00	-	yes	Open
545	10.93242242824422	-0.589413	-18.713	0	18	14	0.67	0.00	-	yes	Open
546	58.04468069669457	-0.515593	-18.7441	3	10	6	0.29	0.33	-	yes	Open
552	58.68892250638533	-0.574481	-15.7719	0	18	17	0.81	0.00	-	yes	Open
542	58.909788394937856	-0.776775	-26.3117	5	17	12	0.57	0.17	-	yes	Open

Molecular metrics

FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

⚠ Not yet computed

Molecular metrics have not been computed for this pose yet. This page now reads only cached values; use a background recompute when you want fresh metrics without slowing the UI.

KB_Leish_188