Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T15

T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site

Ligand OHD_Babesia_18

PDB9IFF↗

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

51.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.92, Jaccard 0.55

Burial

64%

Hydrophobic fit

89%

Reason: strain 51.2 kcal/mol

strain ΔE 51.2 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 77% of hydrophobic surface is solvent-exposed (37/48 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Daphnia EC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Algae IC₅₀

Cat. 1 — Very toxic (≤1 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

Yes

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Acceptable LE (-0.249 kcal/mol/HA) ✓ Good fit quality (FQ -2.85) ✓ Good H-bonds (3 bonds) ✓ Good burial (64% SASA buried) ✓ Lipophilic contacts well-matched (89%) ✗ Extreme strain energy (51.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)

Score

-15.451

kcal/mol

-0.249

kcal/mol/HA

Fit Quality

-2.85

FQ (Leeson)

HAC

heavy atoms

875

LogP

5.60

cLogP

Final rank

3.0475

rank score

Inter norm

-0.387

normalised

Contacts

H-bonds 6

Strain ΔE

51.2 kcal/mol

SASA buried

64%

Lipo contact

89% BSA apolar/total

SASA unbound

1211 Å²

Apolar buried

686 Å²

Interaction summary

HBD 1 HBA 2 HY 7 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)

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

PI · π–π interactions

No pi · π–π interactions detected for this pose.

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	9IFF	Contacts	13
Pose	Open native pose	HB	0
IFP residues	ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap	12	Native recall	0.92
Jaccard	0.55	RMSD	-
HB strict	0	Strict recall	-
HB same residue+role	0	HB role recall	-
HB same residue	0	HB residue recall	-

Protein summary

489 residues

Protein target	T15	Atoms	7420
Residues	489	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:204

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
26	3.0474853481225366	-0.386833	-15.4511	6	21	12	0.92	-	-	no	Current

Molecular metrics

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

✓ Metrics available

Scoring & efficiency

Docking score -15.451kcal/mol

Ligand efficiency (LE) -0.2492kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -2.854

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

Heavy atom count 62HA

Physicochemical properties

Molecular weight 875.1Da

Lipinski: ≤ 500 Da

LogP (cLogP) 5.60

Lipinski: ≤ 5

Rotatable bonds 11

Conformational strain (MMFF94s)

Strain energy (ΔE) 51.24kcal/mol

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

Docked FF energy 150.18kcal/mol

Minimised FF energy 98.94kcal/mol

SASA & burial

✓ computed

SASA (unbound) 1210.6Å²

Total solvent-accessible surface area of free ligand

BSA total 768.2Å²

Buried surface area upon binding

BSA apolar 685.9Å²

Hydrophobic contacts buried

BSA polar 82.3Å²

Polar contacts buried

Fraction buried 63.5%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 89.3%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -3581.4Å²

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 4005.2Å²

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

Complex non-polar SASA 1513.2Å²

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