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 (-0.564 kcal/mol/HA) ✓ Good fit quality (FQ -5.73) ✓ Good H-bonds (3 bonds) ✗ High strain energy (12.4 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-20.290

kcal/mol

-0.564

kcal/mol/HA

Fit Quality

-5.73

FQ (Leeson)

HAC

heavy atoms

487

LogP

4.95

cLogP

Strain ΔE

12.4 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 12.4 kcal/mol

Interaction summary

Collapsible panels

H-bonds 3 Hydrophobic 24 π–π 2 Clashes 4 Severe clashes 0

Final rank	4.172182705475963	Score	-20.29
Inter norm	-0.687195	Intra norm	0.123585
Top1000	no	Excluded	no
Contacts	17	H-bonds	3
Artifact reason	geometry warning; 16 clashes; 4 protein contact clashes; moderate strain Δ 17.8
Residues	A:ARG29;A:ASN65;A:ASP22;A:GLY21;A:ILE61;A:ILE8;A:LEU23;A:LEU28;A:LEU68;A:NAP201;A:PHE32;A:PHE35;A:PRO27;A:PRO62;A:SER60;A:THR57;A:VAL116

Protein summary

200 residues

Protein target	T02	Atoms	3128
Residues	200	Chains	2
Residue summary	LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

Native ligand reference

★ reference

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

Name	5SD8	Contacts	21
Pose	Open native pose	H-bonds	5
IFP residues	A:ALA10; A:ASN65; A:ASP22; A:GLN36; A:GLU31; A:GLY117; A:GLY21; A:ILE61; A:ILE8; A:LEU23; A:LEU68; A:NAP201; A:PHE32; A:PHE35; A:PRO62; A:SER60; A:THR137; A:THR57; A:TYR122; A:VAL116; A:VAL9
Current overlap	14	Native recall	0.67
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

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
1954	4.172182705475963	-0.687195	-20.29	3	17	14	0.67	0.00	-	no	Current
1953	5.989464138450463	-0.705968	-21.027	3	18	16	0.76	0.40	-	no	Open
990	6.442977655601891	-0.721187	-22.5888	7	13	0	0.00	0.00	-	no	Open
631	6.444321292213236	-0.84285	-27.2267	5	14	0	0.00	0.00	-	no	Open
630	6.527573863183832	-0.935701	-28.41	9	13	0	0.00	0.00	-	yes	Open
989	7.925280221930736	-0.676757	-20.4246	7	18	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 -20.290kcal/mol

Ligand efficiency (LE) -0.5636kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.728

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

Heavy atom count 36HA

Physicochemical properties

Molecular weight 486.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.95

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 12.41kcal/mol

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

Docked FF energy 106.46kcal/mol

Minimised FF energy 94.05kcal/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.

TC343