Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T10

L. infantum R5P L. infantum

Ligand Z56791301

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Promising but geometrically suspicious

Binding strong Geometry low Native strong SASA done

Strain ΔE

30.6 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.88, Jaccard 0.88, H-bond role recall 0.73

Burial

68%

Hydrophobic fit

70%

Reason: 7 internal clashes

7 protein-contact clashes 7 intramolecular clashes 65% of hydrophobic surface is solvent-exposed (13/20 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 GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.451

ADMET + ECO + DL

ADMETscore (GDS)

0.520

absorption · distr. · metab.

DLscore

0.431

drug-likeness

P(SAFE)

0.18

GDS classification

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Risk

Molecular report

Full metrics ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-1.069 kcal/mol/HA) ✓ Good fit quality (FQ -10.20) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (30.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-30.994

kcal/mol

-1.069

kcal/mol/HA

Fit Quality

-10.20

FQ (Leeson)

HAC

heavy atoms

428

LogP

4.44

cLogP

Final rank

5.0407

rank score

Inter norm

-0.823

normalised

Contacts

H-bonds 15

Strain ΔE

30.6 kcal/mol

SASA buried

68%

Lipo contact

70% BSA apolar/total

SASA unbound

683 Å²

Apolar buried

325 Å²

Interaction summary

HBA 8 HY 2 PI 2 CLASH 7

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.

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	15	Native recall	0.88
Jaccard	0.88	RMSD	-
HB strict	10	Strict recall	0.77
HB same residue+role	8	HB role recall	0.73
HB same residue	8	HB residue recall	0.73

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
513	5.040696656455916	-0.823001	-30.9938	15	15	15	0.88	0.73	-	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 -30.994kcal/mol

Ligand efficiency (LE) -1.0688kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.202

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

Heavy atom count 29HA

Physicochemical properties

Molecular weight 427.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.44

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 30.58kcal/mol

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

Docked FF energy -8.88kcal/mol

Minimised FF energy -39.46kcal/mol

SASA & burial

✓ computed

SASA (unbound) 683.0Å²

Total solvent-accessible surface area of free ligand

BSA total 465.4Å²

Buried surface area upon binding

BSA apolar 324.8Å²

Hydrophobic contacts buried

BSA polar 140.6Å²

Polar contacts buried

Fraction buried 68.1%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 69.8%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2224.8Å²

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 706.5Å²

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