FAIRMol

Z1431006656

Pose ID 13304 Compound 4684 Pose 425

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 Z1431006656
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
40.5 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 1.00, Jaccard 0.73, H-bond role recall 0.00
Burial
56%
Hydrophobic fit
77%
Reason: 10 internal clashes
10 intramolecular clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.666 kcal/mol/HA) ✓ Good fit quality (FQ -6.36) ✓ Strong H-bond network (6 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ Extreme strain energy (40.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-19.322
kcal/mol
LE
-0.666
kcal/mol/HA
Fit Quality
-6.36
FQ (Leeson)
HAC
29
heavy atoms
MW
389
Da
LogP
3.03
cLogP
Strain ΔE
40.5 kcal/mol
SASA buried
56%
Lipo contact
77% BSA apolar/total
SASA unbound
696 Ų
Apolar buried
297 Ų

Interaction summary

HB 6 HY 13 PI 1 CLASH 0

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
No clash · clashes detected for this pose.
Final rank3.532Score-19.322
Inter norm-0.662Intra norm-0.005
Top1000noExcludedno
Contacts11H-bonds6
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; high strain Δ 40.5
Residues
ASN402 GLU467 LEU399 MET400 PHE396 PRO398 SER394 SER464 SER470 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 overlap8Native recall1.00
Jaccard0.73RMSD-
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
425 3.532343833663366 -0.661511 -19.3223 6 11 8 1.00 0.00 - no Current
495 4.455305081196523 -0.869352 -25.3756 5 14 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 -19.322kcal/mol
Ligand efficiency (LE) -0.6663kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.360
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 389.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.03
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 59.41kcal/mol
Minimised FF energy 18.87kcal/mol

SASA & burial

✓ computed
SASA (unbound) 696.0Ų
Total solvent-accessible surface area of free ligand
BSA total 387.6Ų
Buried surface area upon binding
BSA apolar 297.5Ų
Hydrophobic contacts buried
BSA polar 90.1Ų
Polar contacts buried
Fraction buried 55.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3145.5Ų
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 1510.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)