Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T10

L. infantum R5P L. infantum

Ligand NMT-TY0955

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

62.3 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.76, Jaccard 0.68, H-bond role recall 0.27

Burial

68%

Hydrophobic fit

60%

Reason: strain 62.3 kcal/mol

strain ΔE 62.3 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 57% of hydrophobic surface appears solvent-exposed (8/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

EcoTox / ADMET In-silico prediction only

Fish LC₅₀

Not classified (>100 mg/L)

Daphnia EC₅₀

Not classified (>100 mg/L)

Algae IC₅₀

Not classified (>100 mg/L)

Bioaccum.

Not B (BCF≤2000)

Persistent

ADMET alerts (in-silico)

hERG Low Ames Clear DILI Low

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.843 kcal/mol/HA) ✓ Good fit quality (FQ -7.77) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (68% SASA buried) ✗ Extreme strain energy (62.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)

Score

-21.920

kcal/mol

-0.843

kcal/mol/HA

Fit Quality

-7.77

FQ (Leeson)

HAC

heavy atoms

400

LogP

1.84

cLogP

Final rank

3.8009

rank score

Inter norm

-0.946

normalised

Contacts

H-bonds 14

Strain ΔE

62.3 kcal/mol

SASA buried

68%

Lipo contact

60% BSA apolar/total

SASA unbound

636 Å²

Apolar buried

259 Å²

Interaction summary

HBD 1 HBA 6 PC 1 HY 1 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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: 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	13	Native recall	0.76
Jaccard	0.68	RMSD	-
HB strict	4	Strict recall	0.31
HB same residue+role	3	HB role recall	0.27
HB same residue	4	HB residue recall	0.36

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
283	3.8009441902059766	-0.946259	-21.9204	14	15	13	0.76	0.27	-	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 -21.920kcal/mol

Ligand efficiency (LE) -0.8431kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.768

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 400.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.84

Lipinski: ≤ 5

Rotatable bonds 9

Conformational strain (MMFF94s)

Strain energy (ΔE) 62.26kcal/mol

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

Docked FF energy -65.15kcal/mol

Minimised FF energy -127.41kcal/mol

SASA & burial

✓ computed

SASA (unbound) 636.0Å²

Total solvent-accessible surface area of free ligand

BSA total 433.7Å²

Buried surface area upon binding

BSA apolar 258.5Å²

Hydrophobic contacts buried

BSA polar 175.2Å²

Polar contacts buried

Fraction buried 68.2%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 59.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -2184.9Å²

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 648.6Å²

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