Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T10

L. infantum R5P L. infantum

Ligand Z57045660

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

23.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.94, Jaccard 0.76, H-bond role recall 0.45

Burial

78%

Hydrophobic fit

84%

Reason: 13 protein-contact clashes, 13 internal clashes

13 protein-contact clashes 13 intramolecular clashes

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Daphnia EC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Algae IC₅₀

Cat. 2 — Toxic (1–10 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

Yes

ADMET alerts (in-silico)

hERG High Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.730 kcal/mol/HA) ✓ Good fit quality (FQ -7.30) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ High strain energy (23.3 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (20) ✗ Many internal clashes (14)

Score

-24.815

kcal/mol

-0.730

kcal/mol/HA

Fit Quality

-7.30

FQ (Leeson)

HAC

heavy atoms

498

LogP

3.87

cLogP

Final rank

3.9396

rank score

Inter norm

-0.702

normalised

Contacts

H-bonds 12

Strain ΔE

23.3 kcal/mol

SASA buried

78%

Lipo contact

84% BSA apolar/total

SASA unbound

764 Å²

Apolar buried

500 Å²

Interaction summary

HBA 10 HY 5 PI 2 CLASH 13

HBD/HBA · H-bonds (geometric)

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

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	0.76	RMSD	-
HB strict	7	Strict recall	0.54
HB same residue+role	5	HB role recall	0.45
HB same residue	5	HB residue recall	0.45

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
463	3.9395826377503713	-0.702486	-24.8149	12	20	16	0.94	0.45	-	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 -24.815kcal/mol

Ligand efficiency (LE) -0.7298kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.303

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

Heavy atom count 34HA

Physicochemical properties

Molecular weight 498.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.87

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 23.31kcal/mol

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

Docked FF energy 76.67kcal/mol

Minimised FF energy 53.35kcal/mol

SASA & burial

✓ computed

SASA (unbound) 764.3Å²

Total solvent-accessible surface area of free ligand

BSA total 592.9Å²

Buried surface area upon binding

BSA apolar 500.2Å²

Hydrophobic contacts buried

BSA polar 92.8Å²

Polar contacts buried

Fraction buried 77.6%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 84.4%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2370.7Å²

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 694.2Å²

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