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 ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-0.784 kcal/mol/HA) ✓ Good fit quality (FQ -7.64) ✗ Moderate strain (9.1 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-24.306

kcal/mol

-0.784

kcal/mol/HA

Fit Quality

-7.64

FQ (Leeson)

HAC

heavy atoms

420

LogP

5.65

cLogP

Strain ΔE

9.1 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

Interaction summary

Collapsible panels

H-bonds 1 Hydrophobic 24 π–π 2 Clashes 10 Severe clashes 0

Final rank	6.019914115663894	Score	-24.3058
Inter norm	-0.815569	Intra norm	0.0315115
Top1000	no	Excluded	no
Contacts	20	H-bonds	1
Artifact reason	geometry warning; 19 clashes; 10 protein contact clashes
Residues	A:ALA32;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:THR180;A:THR83;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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	18	Native recall	0.90
Jaccard	0.82	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	RMSD	Excluded
2832	4.501030450910017	-0.884852	-27.6653	1	18	0	0.00	-	no	Open
1883	4.988317998919972	-0.833854	-25.7642	2	17	1	0.05	-	no	Open
2750	6.019914115663894	-0.815569	-24.3058	1	20	18	0.90	-	no	Current
1405	6.072926978953465	-1.07349	-31.6975	4	22	0	0.00	-	no	Open
3545	6.546849881890731	-0.678561	-20.3581	1	14	0	0.00	-	no	Open
2086	6.641414636785736	-0.662632	-20.132	3	14	0	0.00	-	no	Open
1512	7.453163605326336	-1.03103	-30.8386	2	15	0	0.00	-	no	Open
1760	8.396671088178499	-0.811786	-23.1787	3	20	0	0.00	-	no	Open

Molecular metrics

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

✓ Metrics available

Scoring & efficiency

Docking score -24.306kcal/mol

Ligand efficiency (LE) -0.7841kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.639

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

Heavy atom count 31HA

Physicochemical properties

Molecular weight 420.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 5.65

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 9.10kcal/mol

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

Docked FF energy 98.43kcal/mol

Minimised FF energy 89.33kcal/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.

Z26548007