FAIRMol

Z19351911

Pose ID 13547 Compound 1327 Pose 668

DB fairmolDocking 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 Z19351911
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
31.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.58, H-bond role recall 0.00
Burial
53%
Hydrophobic fit
77%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.663 kcal/mol/HA) ✓ Good fit quality (FQ -6.26) ✓ Strong H-bond network (7 bonds) ✓ Good burial (53% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Very high strain energy (31.8 kcal/mol) ✗ Geometry warnings
Score
-18.562
kcal/mol
LE
-0.663
kcal/mol/HA
Fit Quality
-6.26
FQ (Leeson)
HAC
28
heavy atoms
MW
402
Da
LogP
1.69
cLogP
Strain ΔE
31.8 kcal/mol
SASA buried
53%
Lipo contact
77% BSA apolar/total
SASA unbound
696 Ų
Apolar buried
285 Ų

Interaction summary

HB 7 HY 7 PI 1 CLASH 1

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 rank3.595Score-18.562
Inter norm-0.759Intra norm0.096
Top1000noExcludedno
Contacts11H-bonds7
Artifact reasongeometry warning; 4 clashes; 3 protein clashes; high strain Δ 31.8
Residues
ASN402 GLU466 GLU467 LEU399 LYS410 PHE396 PRO398 SER394 SER395 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 overlap7Native recall0.88
Jaccard0.58RMSD-
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
662 2.716970984984871 -0.977747 -26.6192 4 15 0 0.00 0.00 - no Open
668 3.594572209745617 -0.758989 -18.5622 7 11 7 0.88 0.00 - no Current
662 4.155870107544533 -1.03776 -28.5784 15 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 -18.562kcal/mol
Ligand efficiency (LE) -0.6629kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.258
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 402.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.69
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -15.54kcal/mol
Minimised FF energy -47.33kcal/mol

SASA & burial

✓ computed
SASA (unbound) 696.2Ų
Total solvent-accessible surface area of free ligand
BSA total 370.2Ų
Buried surface area upon binding
BSA apolar 284.9Ų
Hydrophobic contacts buried
BSA polar 85.3Ų
Polar contacts buried
Fraction buried 53.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3059.8Ų
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 1508.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)