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 (-0.850 kcal/mol/HA) ✓ Good fit quality (FQ -8.20) ✓ Strong H-bond network (6 bonds) ✗ High strain energy (15.4 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-25.487

kcal/mol

-0.850

kcal/mol/HA

Fit Quality

-8.20

FQ (Leeson)

HAC

heavy atoms

428

LogP

3.96

cLogP

Strain ΔE

15.4 kcal/mol

SASA buried

computing…

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: mixed

Ligand efficiency: excellent

Geometry reliability: low

Reason: geometry warning, clashes, strain 15.4 kcal/mol

Interaction summary

Collapsible panels

H-bonds 6 Hydrophobic 24 π–π 1 Clashes 13 Severe clashes 1

Final rank	57.05814853463563	Score	-25.4869
Inter norm	-0.986427	Intra norm	0.136863
Top1000	no	Excluded	yes
Contacts	10	H-bonds	6
Artifact reason	excluded; geometry warning; 13 clashes; 1 protein clash; high strain Δ 21.3
Residues	A:ARG48;A:ASP52;A:ILE45;A:LYS57;A:MET53;A:PHE56;A:PRO50;A:THR54;A:TRP47;A:VAL49

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	6	Native recall	0.30
Jaccard	0.25	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
1989	3.4042682503112625	-0.827202	-24.5869	1	18	0	0.00	0.00	-	no	Open
1990	3.789293035523619	-0.908661	-23.0929	6	19	0	0.00	0.00	-	no	Open
1959	3.971001878631938	-0.894167	-21.6384	6	19	0	0.00	0.00	-	no	Open
1022	6.005623393135911	-0.880821	-21.3824	8	15	0	0.00	0.00	-	no	Open
2106	6.309156453229466	-0.931433	-24.3406	4	17	15	0.75	0.20	-	no	Open
1023	5.381743259486022	-0.77112	-19.0924	7	9	0	0.00	0.00	-	yes	Open
2107	57.05814853463563	-0.986427	-25.4869	6	10	6	0.30	0.00	-	yes	Current
1960	61.23608297525121	-0.888745	-22.3234	8	13	0	0.00	0.00	-	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 -25.487kcal/mol

Ligand efficiency (LE) -0.8496kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.195

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

Heavy atom count 30HA

Physicochemical properties

Molecular weight 427.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.96

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 15.41kcal/mol

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

Docked FF energy 82.40kcal/mol

Minimised FF energy 67.00kcal/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.

TC487