Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T10

L. infantum R5P L. infantum

Ligand OHD_Leishmania_263

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

59.5 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.94, Jaccard 0.89, H-bond role recall 0.55

Burial

69%

Hydrophobic fit

67%

Reason: 6 internal clashes, strain 59.5 kcal/mol

strain ΔE 59.5 kcal/mol 6 protein-contact clashes 6 intramolecular clashes 76% of hydrophobic surface is solvent-exposed (13/17 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. 3 — Harmful (10–100 mg/L)

Daphnia EC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Algae IC₅₀

Cat. 3 — Harmful (10–100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.687 kcal/mol/HA) ✓ Good fit quality (FQ -6.24) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Extreme strain energy (59.5 kcal/mol) ✗ Geometry warnings

Score

-17.169

kcal/mol

-0.687

kcal/mol/HA

Fit Quality

-6.24

FQ (Leeson)

HAC

heavy atoms

339

LogP

2.92

cLogP

Final rank

5.0442

rank score

Inter norm

-0.948

normalised

Contacts

H-bonds 16

Strain ΔE

59.5 kcal/mol

SASA buried

69%

Lipo contact

67% BSA apolar/total

SASA unbound

637 Å²

Apolar buried

296 Å²

Interaction summary

HBA 9 HY 2 PI 1 CLASH 6

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

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: permissive.

Name	6FXW	Contacts	17
Pose	Open native pose	HB	0
IFP residues	ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap	16	Native recall	0.94
Jaccard	0.89	RMSD	-
HB strict	7	Strict recall	0.54
HB same residue+role	6	HB role recall	0.55
HB same residue	6	HB residue recall	0.55

Protein summary

155 residues

Protein target	T10	Atoms	4590
Residues	155	Chains	1
Residue summary	ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
10	5.044170754055897	-0.947634	-17.1689	16	17	16	0.94	0.55	-	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 -17.169kcal/mol

Ligand efficiency (LE) -0.6868kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.243

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

Heavy atom count 25HA

Physicochemical properties

Molecular weight 339.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.92

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 59.52kcal/mol

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

Docked FF energy 143.54kcal/mol

Minimised FF energy 84.03kcal/mol

SASA & burial

✓ computed

SASA (unbound) 637.1Å²

Total solvent-accessible surface area of free ligand

BSA total 441.8Å²

Buried surface area upon binding

BSA apolar 296.4Å²

Hydrophobic contacts buried

BSA polar 145.4Å²

Polar contacts buried

Fraction buried 69.3%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 67.1%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2213.8Å²

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 2417.4Å²

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

Complex non-polar SASA 692.1Å²

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