FAIRMol

Z28978240

Pose ID 13369 Compound 3657 Pose 490

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 Z28978240
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 high Native strong SASA done
Strain ΔE
21.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.50, H-bond role recall 1.00
Burial
60%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.652 kcal/mol/HA) ✓ Good fit quality (FQ -6.29) ✓ Good H-bonds (5 bonds) ✓ Good burial (60% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (21.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-19.559
kcal/mol
LE
-0.652
kcal/mol/HA
Fit Quality
-6.29
FQ (Leeson)
HAC
30
heavy atoms
MW
444
Da
LogP
2.50
cLogP
Strain ΔE
21.1 kcal/mol
SASA buried
60%
Lipo contact
74% BSA apolar/total
SASA unbound
669 Ų
Apolar buried
293 Ų

Interaction summary

HB 5 HY 21 PI 2 CLASH 2
Final rank2.611Score-19.559
Inter norm-0.662Intra norm0.010
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 5 clashes; 2 protein clashes; moderate strain Δ 21.1
Residues
ASN402 GLU466 GLU467 LEU399 MET400 PHE396 PRO398 PRO462 SER394 SER395 SER464 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 strict2Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
511 0.39436596976904614 -0.715154 -21.5162 4 16 0 0.00 0.00 - no Open
483 1.7620362114443309 -0.816397 -22.9647 4 16 0 0.00 0.00 - no Open
490 2.610889302737764 -0.661563 -19.5593 5 13 7 0.88 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 -19.559kcal/mol
Ligand efficiency (LE) -0.6520kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.289
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 443.9Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.50
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 21.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -27.41kcal/mol
Minimised FF energy -48.51kcal/mol

SASA & burial

✓ computed
SASA (unbound) 668.7Ų
Total solvent-accessible surface area of free ligand
BSA total 397.8Ų
Buried surface area upon binding
BSA apolar 293.2Ų
Hydrophobic contacts buried
BSA polar 104.6Ų
Polar contacts buried
Fraction buried 59.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3073.0Ų
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 1511.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)