FAIRMol

Z223826364

Pose ID 13371 Compound 4300 Pose 492

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 Z223826364
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
27.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Burial
44%
Hydrophobic fit
68%
Reason: 1 severe internal clashes
1 severe internal clashes 1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.724 kcal/mol/HA) ✓ Good fit quality (FQ -6.58) ✓ Good H-bonds (5 bonds) ✓ Good burial (44% SASA buried) ✓ Lipophilic contacts well-matched (68%) ✗ High strain energy (27.4 kcal/mol) ✗ Geometry warnings
Score
-18.110
kcal/mol
LE
-0.724
kcal/mol/HA
Fit Quality
-6.58
FQ (Leeson)
HAC
25
heavy atoms
MW
365
Da
LogP
2.84
cLogP
Strain ΔE
27.4 kcal/mol
SASA buried
44%
Lipo contact
68% BSA apolar/total
SASA unbound
578 Ų
Apolar buried
176 Ų

Interaction summary

HB 5 HY 14 PI 1 CLASH 1 Severe 1
Final rank1.601Score-18.110
Inter norm-0.747Intra norm0.022
Top1000noExcludedno
Contacts7H-bonds5
Artifact reasongeometry warning; 3 clashes; 1 protein clash; moderate strain Δ 27.4
Residues
ASN402 LEU399 LYS410 PHE396 PRO398 SER395 THR397

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 overlap5Native recall0.62
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
492 1.6014055927374748 -0.746844 -18.1096 5 7 5 0.62 0.00 - no Current
551 1.6059920393199745 -0.971222 -23.3622 6 9 0 0.00 0.00 - no Open
488 4.206459564715441 -1.22556 -31.1307 12 17 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 -18.110kcal/mol
Ligand efficiency (LE) -0.7244kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.585
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 365.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.84
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -26.52kcal/mol
Minimised FF energy -53.88kcal/mol

SASA & burial

✓ computed
SASA (unbound) 577.8Ų
Total solvent-accessible surface area of free ligand
BSA total 256.9Ų
Buried surface area upon binding
BSA apolar 175.9Ų
Hydrophobic contacts buried
BSA polar 81.0Ų
Polar contacts buried
Fraction buried 44.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 68.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3000.3Ų
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 1496.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)