FAIRMol

OHD_Leishmania_350

Pose ID 10859 Compound 399 Pose 16

DB fairmolDocking 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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand OHD_Leishmania_350
PDB5S9T↗

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
34.3 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.67, Jaccard 0.33, H-bond role recall 0.00
Burial
78%
Hydrophobic fit
100%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.867 kcal/mol/HA) ✓ Good fit quality (FQ -8.28) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (100%) ✗ Very high strain energy (34.3 kcal/mol) ✗ Geometry warnings
Score
-25.151
kcal/mol
LE
-0.867
kcal/mol/HA
Fit Quality
-8.28
FQ (Leeson)
HAC
29
heavy atoms
MW
411
Da
LogP
-4.55
cLogP
Strain ΔE
34.3 kcal/mol
SASA buried
78%
Lipo contact
100% BSA apolar/total
SASA unbound
772 Ų
Apolar buried
597 Ų

Interaction summary

HB 7 HY 20 PI 0 CLASH 6

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
Final rank3.488Score-25.151
Inter norm-0.867Intra norm0.000
Top1000noExcludedno
Contacts20H-bonds7
Artifact reasongeometry warning; 3 clashes; 2 protein clashes; high strain Δ 34.3
Residues
ALA284 ARG228 ARG287 FAD501 GLY195 GLY196 GLY197 GLY229 GLY286 ILE199 ILE285 LEU227 LEU332 LEU334 MET333 PHE198 PHE230 SER200 SER364 TYR221

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap8Native recall0.67
Jaccard0.33RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall1.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
22 0.026034593906726175 -0.910505 -26.4046 1 20 0 0.00 0.00 - no Open
31 1.893535960009002 -0.754031 -21.8669 5 12 0 0.00 0.00 - no Open
20 2.3400175302541997 -1.02046 -29.5932 7 21 0 0.00 0.00 - no Open
26 2.3479370783872295 -1.01555 -29.4509 7 21 0 0.00 0.00 - no Open
16 3.4877812498585308 -0.867403 -25.1507 7 20 8 0.67 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 -25.151kcal/mol
Ligand efficiency (LE) -0.8673kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.279
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 410.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) -4.55
Lipinski: ≤ 5
Rotatable bonds 0

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 490.55kcal/mol
Minimised FF energy 456.24kcal/mol

SASA & burial

✓ computed
SASA (unbound) 771.8Ų
Total solvent-accessible surface area of free ligand
BSA total 598.6Ų
Buried surface area upon binding
BSA apolar 597.4Ų
Hydrophobic contacts buried
BSA polar 1.3Ų
Polar contacts buried
Fraction buried 77.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 99.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6775.3Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2051.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)