FAIRMol

Z49596617

Pose ID 13323 Compound 5302 Pose 444

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 Z49596617
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
12.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.45, H-bond role recall 0.00
Burial
49%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.705 kcal/mol/HA) ✓ Good fit quality (FQ -6.87) ✓ Strong H-bond network (6 bonds) ✓ Good burial (49% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Moderate strain (12.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-21.859
kcal/mol
LE
-0.705
kcal/mol/HA
Fit Quality
-6.87
FQ (Leeson)
HAC
31
heavy atoms
MW
438
Da
LogP
3.01
cLogP
Strain ΔE
12.5 kcal/mol
SASA buried
49%
Lipo contact
77% BSA apolar/total
SASA unbound
705 Ų
Apolar buried
268 Ų

Interaction summary

HB 6 HY 20 PI 1 CLASH 3

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
Final rank4.395Score-21.859
Inter norm-0.637Intra norm-0.068
Top1000noExcludedno
Contacts8H-bonds6
Artifact reasongeometry warning; 17 clashes; 2 protein clashes
Residues
ASN402 LEU399 PHE396 PRO398 PRO462 SER464 THR397 THR463

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 overlap5Native recall0.62
Jaccard0.45RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
444 4.394795441422891 -0.636947 -21.859 6 8 5 0.62 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 -21.859kcal/mol
Ligand efficiency (LE) -0.7051kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.870
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 437.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.01
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 83.53kcal/mol
Minimised FF energy 71.06kcal/mol

SASA & burial

✓ computed
SASA (unbound) 705.0Ų
Total solvent-accessible surface area of free ligand
BSA total 347.6Ų
Buried surface area upon binding
BSA apolar 267.9Ų
Hydrophobic contacts buried
BSA polar 79.6Ų
Polar contacts buried
Fraction buried 49.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3153.1Ų
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 1500.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)