FAIRMol

TC391

Pose ID 13158 Compound 3114 Pose 279

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 TC391
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
18.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.50, H-bond role recall 0.00
Burial
61%
Hydrophobic fit
82%
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 (-0.565 kcal/mol/HA) ✓ Good fit quality (FQ -5.45) ✓ Strong H-bond network (6 bonds) ✓ Good burial (61% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (18.5 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Many internal clashes (15)
Score
-16.962
kcal/mol
LE
-0.565
kcal/mol/HA
Fit Quality
-5.45
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
4.90
cLogP
Strain ΔE
18.5 kcal/mol
SASA buried
61%
Lipo contact
82% BSA apolar/total
SASA unbound
698 Ų
Apolar buried
353 Ų

Interaction summary

HB 6 HY 15 PI 2 CLASH 3
Final rank2.064Score-16.962
Inter norm-0.669Intra norm0.104
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 15 clashes; 7 protein contact clashes
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 MET393 PHE396 PRO398 PRO462 SER394 SER395 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
Jaccard0.50RMSD-
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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
249 1.089440178396187 -0.844931 -21.6098 3 15 0 0.00 0.00 - no Open
237 1.9932837433636637 -1.14932 -32.894 13 13 0 0.00 0.00 - no Open
279 2.0643017699037225 -0.669226 -16.9623 6 13 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 -16.962kcal/mol
Ligand efficiency (LE) -0.5654kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.454
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.90
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 78.53kcal/mol
Minimised FF energy 60.02kcal/mol

SASA & burial

✓ computed
SASA (unbound) 697.7Ų
Total solvent-accessible surface area of free ligand
BSA total 428.7Ų
Buried surface area upon binding
BSA apolar 353.1Ų
Hydrophobic contacts buried
BSA polar 75.6Ų
Polar contacts buried
Fraction buried 61.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3148.4Ų
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 1488.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)