Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T10

L. infantum R5P L. infantum

Ligand Z30000918

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

32.2 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.82, Jaccard 0.78, H-bond role recall 0.55

Burial

75%

Hydrophobic fit

75%

Reason: 6 internal clashes

6 protein-contact clashes 6 intramolecular clashes 44% of hydrophobic surface appears solvent-exposed (8/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.282

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.406

ADMET + ECO + DL

ADMETscore (GDS)

0.410

absorption · distr. · metab.

DLscore

0.472

drug-likeness

P(SAFE)

0.37

GDS classification

ADMET alerts (in-silico)

hERG Medium Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.726 kcal/mol/HA) ✓ Good fit quality (FQ -6.69) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Very high strain energy (32.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)

Score

-18.870

kcal/mol

-0.726

kcal/mol/HA

Fit Quality

-6.69

FQ (Leeson)

HAC

heavy atoms

439

LogP

2.65

cLogP

Final rank

3.4040

rank score

Inter norm

-0.930

normalised

Contacts

H-bonds 12

Strain ΔE

32.2 kcal/mol

SASA buried

75%

Lipo contact

75% BSA apolar/total

SASA unbound

652 Å²

Apolar buried

366 Å²

Interaction summary

HBA 7 HY 3 PI 2 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	14	Native recall	0.82
Jaccard	0.78	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
427	0.8008082662207936	-1.04017	-27.8349	2	18	0	0.00	0.00	-	no	Open
358	3.4040258727933566	-0.930282	-18.8703	12	15	14	0.82	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 -18.870kcal/mol

Ligand efficiency (LE) -0.7258kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.687

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 439.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.65

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 32.22kcal/mol

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

Docked FF energy 39.20kcal/mol

Minimised FF energy 6.98kcal/mol

SASA & burial

✓ computed

SASA (unbound) 651.6Å²

Total solvent-accessible surface area of free ligand

BSA total 489.7Å²

Buried surface area upon binding

BSA apolar 365.7Å²

Hydrophobic contacts buried

BSA polar 124.0Å²

Polar contacts buried

Fraction buried 75.2%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 74.7%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2215.2Å²

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 2417.4Å²

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

Complex non-polar SASA 729.7Å²

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