Docking pose detail

Molecular metrics status: done

RDKit SASA-based burial metrics are cached.

SASA cached

T04

L. major PTR1 L. major

Ligand OHD_Leishmania_91

PDB7PXX↗

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

45.7 kcal/mol

Protein clashes

Internal clashes

Native overlap

contact recall 0.68, Jaccard 0.57, H-bond role recall 0.20

Burial

68%

Hydrophobic fit

83%

Reason: 12 internal clashes, strain 45.7 kcal/mol

strain ΔE 45.7 kcal/mol 12 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

ADMET alerts (in-silico)

hERG High Ames Clear DILI Risk

Molecular report

Full metrics ↗

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

✓ Excellent LE (-0.603 kcal/mol/HA) ✓ Good fit quality (FQ -6.09) ✓ Deep burial (68% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ Extreme strain energy (45.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)

Score

-21.120

kcal/mol

-0.603

kcal/mol/HA

Fit Quality

-6.09

FQ (Leeson)

HAC

heavy atoms

487

LogP

4.57

cLogP

Final rank

0.8744

rank score

Inter norm

-0.701

normalised

Contacts

H-bonds 1

Strain ΔE

45.7 kcal/mol

SASA buried

68%

Lipo contact

83% BSA apolar/total

SASA unbound

860 Å²

Apolar buried

486 Å²

Interaction summary

HBA 1 HY 9 PI 3 CLASH 0

HBD/HBA · H-bonds (geometric)

HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

PI · π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

No clash · clashes detected for this pose.

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	7PXX	Contacts	19
Pose	Open native pose	HB	0
IFP residues	ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap	13	Native recall	0.68
Jaccard	0.57	RMSD	-
HB strict	1	Strict recall	0.17
HB same residue+role	1	HB role recall	0.20
HB same residue	1	HB residue recall	0.20

Protein summary

308 residues

Protein target	T04	Atoms	4210
Residues	308	Chains	3
Residue summary	LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

Receptor context

1 kept / 0 excluded

Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.

Kept context 1 Excluded HETATM 0

Kept cofactors / ions

A:NDP302

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	CT	CT overlap	CT recall	HB role rec.	RMSD	Excluded
2	0.8744355439854383	-0.701254	-21.1197	1	17	13	0.68	0.20	-	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 -21.120kcal/mol

Ligand efficiency (LE) -0.6034kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.086

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

Heavy atom count 35HA

Physicochemical properties

Molecular weight 486.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.57

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 45.66kcal/mol

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

Docked FF energy 61.46kcal/mol

Minimised FF energy 15.80kcal/mol

SASA & burial

✓ computed

SASA (unbound) 859.5Å²

Total solvent-accessible surface area of free ligand

BSA total 587.9Å²

Buried surface area upon binding

BSA apolar 485.9Å²

Hydrophobic contacts buried

BSA polar 102.0Å²

Polar contacts buried

Fraction buried 68.4%

> 60 % indicates good pocket engagement

Lipophilic contact ratio 82.6%

BSA apolar / BSA total — high = hydrophobic driver

Δ Non-polar SASA -1848.5Å²

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 2179.4Å²

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

Complex non-polar SASA 1083.1Å²

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