FAIRMol

OHD_Leishmania_350

Pose ID 12900 Compound 5216 Pose 21

DB SELECTIONDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand OHD_Leishmania_350
PDB9IFH↗

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 mixed SASA done
Strain ΔE
52.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.50, Jaccard 0.29, H-bond role recall 0.00
Burial
53%
Hydrophobic fit
99%
Reason: strain 52.9 kcal/mol
strain ΔE 52.9 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.729 kcal/mol/HA) ✓ Good fit quality (FQ -6.96) ✓ Good H-bonds (4 bonds) ✓ Good burial (53% SASA buried) ✓ Lipophilic contacts well-matched (99%) ✗ Extreme strain energy (52.9 kcal/mol) ✗ Geometry warnings
Score
-21.137
kcal/mol
LE
-0.729
kcal/mol/HA
Fit Quality
-6.96
FQ (Leeson)
HAC
29
heavy atoms
MW
410
Da
LogP
-3.52
cLogP
Strain ΔE
52.9 kcal/mol
SASA buried
53%
Lipo contact
99% BSA apolar/total
SASA unbound
719 Ų
Apolar buried
377 Ų

Interaction summary

HB 4 HY 7 PI 0 CLASH 1
Final rank2.438Score-21.137
Inter norm-0.729Intra norm0.000
Top1000noExcludedno
Contacts10H-bonds4
Artifact reasongeometry warning; 3 clashes; 2 protein clashes; high strain Δ 52.8
Residues
ARG472 GLU467 MET393 MET471 PHE396 SER394 SER395 SER470 THR473 TYR455

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221

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:FAD501

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap4Native recall0.50
Jaccard0.29RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
21 2.4381456875285537 -0.728893 -21.1371 4 10 4 0.50 0.00 - 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 -21.137kcal/mol
Ligand efficiency (LE) -0.7289kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.958
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 409.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) -3.52
Lipinski: ≤ 5
Rotatable bonds 0

Conformational strain (MMFF94s)
Strain energy (ΔE) 52.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 337.33kcal/mol
Minimised FF energy 284.39kcal/mol

SASA & burial

✓ computed
SASA (unbound) 719.5Ų
Total solvent-accessible surface area of free ligand
BSA total 379.8Ų
Buried surface area upon binding
BSA apolar 377.0Ų
Hydrophobic contacts buried
BSA polar 2.8Ų
Polar contacts buried
Fraction buried 52.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 99.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3316.7Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1469.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)