FAIRMol

OHD_TbNat_70

Pose ID 12958 Compound 5193 Pose 79

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand OHD_TbNat_70
PDB9IFH↗

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
36.1 kcal/mol
Protein clashes
4
Internal clashes
7
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 1.00
Burial
50%
Hydrophobic fit
84%
Reason: 7 internal clashes
4 protein-contact clashes 7 intramolecular clashes 60% of hydrophobic surface is solvent-exposed (18/30 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.575 kcal/mol/HA) ✓ Good fit quality (FQ -5.80) ✓ Good H-bonds (4 bonds) ✓ Good burial (50% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (36.1 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Internal clashes (7)
Score
-20.132
kcal/mol
LE
-0.575
kcal/mol/HA
Fit Quality
-5.80
FQ (Leeson)
HAC
35
heavy atoms
MW
489
Da
LogP
5.18
cLogP
Final rank
1.0022
rank score
Inter norm
-0.564
normalised
Contacts
11
H-bonds 6
Strain ΔE
36.1 kcal/mol
SASA buried
50%
Lipo contact
84% BSA apolar/total
SASA unbound
680 Ų
Apolar buried
283 Ų

Interaction summary

HBD 3 HBA 1 HY 4 PI 0 CLASH 0

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

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

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: permissive.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.46RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
90 0.9024379389445512 -0.571056 -19.8093 6 11 6 0.75 1.00 - no Open
79 1.0021972144081828 -0.564156 -20.1316 6 11 6 0.75 1.00 - 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 -20.132kcal/mol
Ligand efficiency (LE) -0.5752kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.802
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 35HA

Physicochemical properties
Molecular weight 488.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.18
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 36.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 142.74kcal/mol
Minimised FF energy 106.68kcal/mol

SASA & burial

✓ computed
SASA (unbound) 680.0Ų
Total solvent-accessible surface area of free ligand
BSA total 337.4Ų
Buried surface area upon binding
BSA apolar 283.3Ų
Hydrophobic contacts buried
BSA polar 54.0Ų
Polar contacts buried
Fraction buried 49.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3188.5Ų
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 1465.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)