FAIRMol

OHD_Babesia_14

Pose ID 12918 Compound 5241 Pose 39

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_Babesia_14
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 strong SASA done
Strain ΔE
60.4 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.88, Jaccard 0.54, H-bond role recall 0.00
Burial
57%
Hydrophobic fit
90%
Reason: 15 internal clashes, strain 60.4 kcal/mol
strain ΔE 60.4 kcal/mol 15 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Good LE (-0.301 kcal/mol/HA) ✓ Good fit quality (FQ -3.01) ✓ Good H-bonds (5 bonds) ✓ Good burial (57% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Extreme strain energy (60.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-10.234
kcal/mol
LE
-0.301
kcal/mol/HA
Fit Quality
-3.01
FQ (Leeson)
HAC
34
heavy atoms
MW
461
Da
LogP
5.15
cLogP
Strain ΔE
60.4 kcal/mol
SASA buried
57%
Lipo contact
90% BSA apolar/total
SASA unbound
772 Ų
Apolar buried
395 Ų

Interaction summary

HB 5 HY 24 PI 1 CLASH 0
Final rank2.882Score-10.234
Inter norm-0.586Intra norm0.285
Top1000noExcludedno
Contacts12H-bonds5
Artifact reasongeometry warning; 15 clashes; 1 protein clash; high strain Δ 60.4
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 MET400 PHE396 PRO398 PRO462 SER394 THR397 THR463

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 overlap7Native recall0.88
Jaccard0.54RMSD-
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
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.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
39 2.8822610853296444 -0.586279 -10.2343 5 12 7 0.88 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 -10.234kcal/mol
Ligand efficiency (LE) -0.3010kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -3.012
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 460.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.15
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 60.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 85.33kcal/mol
Minimised FF energy 24.89kcal/mol

SASA & burial

✓ computed
SASA (unbound) 771.6Ų
Total solvent-accessible surface area of free ligand
BSA total 437.9Ų
Buried surface area upon binding
BSA apolar 394.6Ų
Hydrophobic contacts buried
BSA polar 43.2Ų
Polar contacts buried
Fraction buried 56.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3261.3Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1501.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)