FAIRMol

Z27873696

Pose ID 13356 Compound 1398 Pose 477

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 Z27873696
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
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
30.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 0.00
Burial
56%
Hydrophobic fit
84%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.613 kcal/mol/HA) ✓ Good fit quality (FQ -5.97) ✓ Strong H-bond network (6 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ Very high strain energy (30.3 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (14)
Score
-19.000
kcal/mol
LE
-0.613
kcal/mol/HA
Fit Quality
-5.97
FQ (Leeson)
HAC
31
heavy atoms
MW
472
Da
LogP
2.16
cLogP
Strain ΔE
30.3 kcal/mol
SASA buried
56%
Lipo contact
84% BSA apolar/total
SASA unbound
714 Ų
Apolar buried
333 Ų

Interaction summary

HB 6 HY 9 PI 1 CLASH 2
Final rank2.000Score-19.000
Inter norm-0.629Intra norm0.016
Top1000noExcludedno
Contacts11H-bonds6
Artifact reasongeometry warning; 14 clashes; 6 protein contact clashes; high strain Δ 30.3
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 LYS407 MET400 PHE396 PRO398 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 overlap6Native recall0.75
Jaccard0.46RMSD-
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
449 0.9543235955270444 -0.805705 -26.6154 4 20 0 0.00 0.00 - no Open
477 1.999555085717567 -0.6289 -18.9999 6 11 6 0.75 0.00 - no Current
491 3.364629749418482 -0.902193 -30.345 4 13 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -19.000kcal/mol
Ligand efficiency (LE) -0.6129kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.971
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 471.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.16
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 98.84kcal/mol
Minimised FF energy 68.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 713.7Ų
Total solvent-accessible surface area of free ligand
BSA total 399.3Ų
Buried surface area upon binding
BSA apolar 333.4Ų
Hydrophobic contacts buried
BSA polar 65.9Ų
Polar contacts buried
Fraction buried 56.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3111.2Ų
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 1522.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)