Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T20

T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)

Ligand ulfkktlib_876

PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Reject SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

55.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.88, Jaccard 0.44, H-bond role recall 0.00

Burial

49%

Hydrophobic fit

85%

Reason: strain 55.7 kcal/mol

strain ΔE 55.7 kcal/mol 1 protein-contact clashes 67% of hydrophobic surface is solvent-exposed (33/49 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.482 kcal/mol/HA) ✓ Good fit quality (FQ -5.51) ✓ Good H-bonds (3 bonds) ✓ Good burial (49% SASA buried) ✓ Lipophilic contacts well-matched (85%) ✗ Extreme strain energy (55.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)

Score

-29.859

kcal/mol

-0.482

kcal/mol/HA

Fit Quality

-5.51

FQ (Leeson)

HAC

heavy atoms

852

LogP

9.35

cLogP

Final rank

3.3201

rank score

Inter norm

-0.339

normalised

Contacts

H-bonds 4

Strain ΔE

55.7 kcal/mol

SASA buried

49%

Lipo contact

85% BSA apolar/total

SASA unbound

1205 Å²

Apolar buried

500 Å²

Interaction summary

HBD 1 HBA 2 HY 5 PI 1 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference

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

Name	9IFH	Contacts	8
Pose	Open native pose	HB	0
IFP residues	ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap	7	Native recall	0.88
Jaccard	0.44	RMSD	-
HB strict	0	Strict recall	0.00
HB same residue+role	0	HB role recall	0.00
HB same residue	0	HB residue recall	0.00

Protein summary

492 residues

Protein target	T20	Atoms	7539
Residues	492	Chains	1
Residue summary	VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:FAD501

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
218	3.3200539928894	-0.339102	-29.8591	4	15	7	0.88	0.00	-	no	Current
180	3.726631731152153	-0.385691	-34.6355	8	12	0	0.00	0.00	-	no	Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -29.859kcal/mol

Ligand efficiency (LE) -0.4816kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.515

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

Heavy atom count 62HA

Physicochemical properties

Molecular weight 852.1Da

Lipinski: ≤ 500 Da

LogP (cLogP) 9.35

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 55.69kcal/mol

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

Docked FF energy 232.23kcal/mol

Minimised FF energy 176.54kcal/mol

SASA & burial

✓ computed

SASA (unbound) 1204.9Å²

Total solvent-accessible surface area of free ligand

BSA total 586.4Å²

Buried surface area upon binding

BSA apolar 500.1Å²

Hydrophobic contacts buried

BSA polar 86.4Å²

Polar contacts buried

Fraction buried 48.7%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 85.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3642.2Å²

SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.

Receptor non-polar SASA 4069.8Å²

Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)

Complex non-polar SASA 1505.0Å²

Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)