FAIRMol

Z49638306

Pose ID 9995 Compound 3538 Pose 509

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand Z49638306
PDB9IFF↗

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 mixed SASA done
Strain ΔE
18.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.38, Jaccard 0.26
Burial
61%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.781 kcal/mol/HA) ✓ Good fit quality (FQ -7.54) ✓ Strong H-bond network (7 bonds) ✓ Good burial (61% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Moderate strain (18.2 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (17)
Score
-23.445
kcal/mol
LE
-0.781
kcal/mol/HA
Fit Quality
-7.54
FQ (Leeson)
HAC
30
heavy atoms
MW
398
Da
LogP
3.86
cLogP
Strain ΔE
18.2 kcal/mol
SASA buried
61%
Lipo contact
74% BSA apolar/total
SASA unbound
671 Ų
Apolar buried
300 Ų

Interaction summary

HB 7 HY 20 PI 0 CLASH 3

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank3.249Score-23.445
Inter norm-0.794Intra norm0.012
Top1000noExcludedno
Contacts11H-bonds7
Artifact reasongeometry warning; 17 clashes; 1 protein clash
Residues
ALA90 GLY214 GLY215 GLY246 ILE247 LYS211 LYS216 LYS89 PRO212 PRO213 TYR210

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap5Native recall0.38
Jaccard0.26RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
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:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
383 1.2287636357355942 -1.0501 -37.6676 7 20 0 0.00 - - no Open
420 1.5304501302166158 -0.780324 -26.3523 4 13 0 0.00 - - no Open
436 2.785856035332341 -0.980801 -34.63 7 16 0 0.00 - - no Open
497 2.955093255524448 -0.865923 -27.6702 5 14 0 0.00 - - no Open
509 3.2491331708059237 -0.794232 -23.4452 7 11 5 0.38 - - no Current
465 4.004368900998721 -0.799974 -24.3755 4 18 0 0.00 - - no Open
391 4.4407993593659 -1.07037 -31.267 12 18 0 0.00 - - no Open
426 4.8004481778310115 -0.756591 -25.3759 10 12 0 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 -23.445kcal/mol
Ligand efficiency (LE) -0.7815kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.539
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.86
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 115.34kcal/mol
Minimised FF energy 97.14kcal/mol

SASA & burial

✓ computed
SASA (unbound) 670.9Ų
Total solvent-accessible surface area of free ligand
BSA total 407.3Ų
Buried surface area upon binding
BSA apolar 299.8Ų
Hydrophobic contacts buried
BSA polar 107.4Ų
Polar contacts buried
Fraction buried 60.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2970.8Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1578.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)