Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T11

L. infantum SIR2 L. infantum

Ligand NMT-TY0430

3D complex viewer

Strict H-bonds Permissive H-bonds

Viewer legend

Protein receptor

Pocket residues

Cofactor context

Docked ligand

Overall assessment

Weak SASA cached

Weak or marginal quality

Binding strong Geometry medium Native strong SASA done

Strain ΔE

32.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.67, Jaccard 0.67, H-bond role recall 0.40

Burial

74%

Hydrophobic fit

69%

Reason: no major geometry red flags detected

1 protein-contact clashes

EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model

ECOscore

0.846

aquatic tox · BCF · biodeg.

GDS₃ (3-block)

0.609

ADMET + ECO + DL

ADMETscore (GDS)

0.611

absorption · distr. · metab.

DLscore

0.464

drug-likeness

P(SAFE)

0.22

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 (-1.287 kcal/mol/HA) ✓ Good fit quality (FQ -11.18) ✓ Good H-bonds (4 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (69%) ✗ Very high strain energy (32.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)

Score

-28.321

kcal/mol

-1.287

kcal/mol/HA

Fit Quality

-11.18

FQ (Leeson)

HAC

heavy atoms

318

LogP

2.34

cLogP

Final rank

3.2797

rank score

Inter norm

-1.126

normalised

Contacts

H-bonds 6

Strain ΔE

32.7 kcal/mol

SASA buried

74%

Lipo contact

69% BSA apolar/total

SASA unbound

546 Å²

Apolar buried

279 Å²

Interaction summary

HBD 1 HBA 3 PC 1 HY 5 PI 4 CLASH 1

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PC · Polar contacts (possible, no H geometry)

HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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	5OL0	Contacts	18
Pose	Open native pose	HB	0
IFP residues	ASN193 GLN220 GLU192 GLY191 HIS144 HIS222 ILE126 LEU194 LEU226 PHE189 PHE190 PHE199 PHE74 PRO223 THR71 VAL187 VAL188 VAL221
Current overlap	12	Native recall	0.67
Jaccard	0.67	RMSD	-
HB strict	2	Strict recall	0.40
HB same residue+role	2	HB role recall	0.40
HB same residue	3	HB residue recall	0.75

Protein summary

287 residues

Protein target	T11	Atoms	4391
Residues	287	Chains	1
Residue summary	LEU:627; ARG:432; VAL:384; GLU:316; PHE:300; ILE:285; ALA:260; PRO:238; HIS:187; ASP:157; LYS:154; SER:154; THR:154; GLY:147; ASN:140; TYR:126

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
275	3.2797458089608083	-1.12625	-28.3212	6	12	12	0.67	0.40	-	no	Current
232	3.7207708318686143	-1.08194	-26.135	9	18	0	0.00	0.00	-	no	Open

Molecular metrics

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

✓ Metrics available

Scoring & efficiency

Docking score -28.321kcal/mol

Ligand efficiency (LE) -1.2873kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.176

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

Heavy atom count 22HA

Physicochemical properties

Molecular weight 318.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.34

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 32.66kcal/mol

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

Docked FF energy 7.53kcal/mol

Minimised FF energy -25.14kcal/mol

SASA & burial

✓ computed

SASA (unbound) 546.2Å²

Total solvent-accessible surface area of free ligand

BSA total 403.7Å²

Buried surface area upon binding

BSA apolar 279.3Å²

Hydrophobic contacts buried

BSA polar 124.4Å²

Polar contacts buried

Fraction buried 73.9%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 69.2%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1829.4Å²

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 2380.0Å²

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

Complex non-polar SASA 963.0Å²

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