Docking pose detail

Molecular metrics status: done

Cached molecular metrics are available for this pose.

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

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.593 kcal/mol/HA) ✓ Good fit quality (FQ -6.02) ✗ Very high strain energy (31.6 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-21.333

kcal/mol

-0.593

kcal/mol/HA

Fit Quality

-6.02

FQ (Leeson)

HAC

heavy atoms

489

LogP

2.27

cLogP

Strain ΔE

31.6 kcal/mol

SASA buried

computing…

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: strong

Ligand efficiency: excellent

Geometry reliability: low

Reason: geometry warning, clashes, protein contact clashes, strain 31.6 kcal/mol

Interaction summary

Collapsible panels

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

Final rank	55.10182626462225	Score	-21.3332
Inter norm	-0.622591	Intra norm	0.0300025
Top1000	no	Excluded	no
Contacts	18	H-bonds	0
Artifact reason	geometry warning; 16 clashes; 8 protein contact clashes
Residues	A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49;A:VAL87

Protein summary

225 residues

Protein target	T03	Atoms	3428
Residues	225	Chains	2
Residue summary	LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

Native ligand reference

★ reference

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

Name	3CL9	Contacts	20
Pose	Open native pose	H-bonds	9
IFP residues	A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87
Current overlap	14	Native recall	0.70
Jaccard	0.58	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

No hydrogen bonds detected for this pose.

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	RMSD	Excluded
1704	4.7944941951523905	-0.698908	-25.3389	1	21	17	0.85	-	no	Open
1697	5.184889223389343	-0.582627	-20.7978	0	19	15	0.75	-	no	Open
1702	5.810964759701129	-0.605718	-20.7231	1	17	16	0.80	-	no	Open
1699	55.10182626462225	-0.622591	-21.3332	0	18	14	0.70	-	no	Current
1698	55.340791026813044	-0.507098	-17.2117	0	17	13	0.65	-	no	Open
1703	55.98808808332293	-0.672463	-19.4215	0	18	15	0.75	-	yes	Open
1701	57.5980901399089	-0.668796	-22.711	1	16	14	0.70	-	yes	Open
1700	58.17180302868122	-0.697056	-17.6094	0	19	16	0.80	-	yes	Open

Molecular metrics

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

✓ Metrics available

Scoring & efficiency

Docking score -21.333kcal/mol

Ligand efficiency (LE) -0.5926kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.023

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 36HA

Physicochemical properties

Molecular weight 488.8Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.27

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 31.60kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy 240.36kcal/mol

Minimised FF energy 208.76kcal/mol

SASA & burial (FreeSASA)

not yet run

SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.

OSA_Lib_241