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 (-1.073 kcal/mol/HA) ✓ Good fit quality (FQ -8.80) ✓ Good H-bonds (4 bonds) ✗ Very high strain energy (21.8 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-20.390

kcal/mol

-1.073

kcal/mol/HA

Fit Quality

-8.80

FQ (Leeson)

HAC

heavy atoms

282

LogP

-0.14

cLogP

Strain ΔE

21.8 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 21.8 kcal/mol

Interaction summary

Collapsible panels

H-bonds 4 Hydrophobic 23 π–π 1 Clashes 4 Severe clashes 0

Final rank	3.369251717364752	Score	-20.3902
Inter norm	-1.12561	Intra norm	0.0524431
Top1000	no	Excluded	no
Contacts	18	H-bonds	4
Artifact reason	geometry warning; 8 clashes; 4 protein contact clashes; high strain Δ 34.3
Residues	A:ALA34;A:ASP54;A:GLY161;A:HIS182;A:ILE160;A:ILE47;A:LEU90;A:LEU97;A:MET55;A:MET82;A:NDP301;A:PHE58;A:PHE94;A:THR184;A:THR86;A:TYR57;A:VAL32;A:VAL33

Protein summary

223 residues

Protein target	T06	Atoms	3452
Residues	223	Chains	1
Residue summary	ARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

Native ligand reference

★ reference

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

Name	8RHT	Contacts	21
Pose	Open native pose	H-bonds	6
IFP residues	A:ALA34; A:ASP54; A:HIS182; A:ILE160; A:ILE47; A:LEU90; A:LEU97; A:MET55; A:NDP301; A:PHE233; A:PHE58; A:PHE94; A:PRO91; A:SER89; A:THR184; A:THR86; A:TRP49; A:TYR166; A:TYR57; A:VAL32; A:VAL33
Current overlap	16	Native recall	0.76
Jaccard	0.70	RMSD	-
H-bond strict	2	Strict recall	0.40
H-bond same residue+role	2	Role recall	0.50
H-bond same residue	2	Residue recall	0.50

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
720	2.2540039228974518	-1.10333	-19.281	4	17	16	0.76	0.50	-	no	Open
721	3.369251717364752	-1.12561	-20.3902	4	18	16	0.76	0.50	-	no	Current
587	4.317409554284386	-1.41075	-24.2398	4	12	0	0.00	0.00	-	no	Open
588	4.261723612344194	-1.20628	-20.6187	2	12	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 -20.390kcal/mol

Ligand efficiency (LE) -1.0732kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.796

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

Heavy atom count 19HA

Physicochemical properties

Molecular weight 282.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) -0.14

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 21.77kcal/mol

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

Docked FF energy -2.13kcal/mol

Minimised FF energy -23.90kcal/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.

NMT-TY0368