FAIRMol

TC409

Pose ID 13161 Compound 708 Pose 282

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 TC409
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
26.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 1.00
Burial
61%
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 (-0.801 kcal/mol/HA) ✓ Good fit quality (FQ -7.38) ✓ Strong H-bond network (8 bonds) ✓ Good burial (61% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ High strain energy (26.2 kcal/mol) ✗ Geometry warnings
Score
-20.839
kcal/mol
LE
-0.801
kcal/mol/HA
Fit Quality
-7.38
FQ (Leeson)
HAC
26
heavy atoms
MW
366
Da
LogP
2.92
cLogP
Strain ΔE
26.2 kcal/mol
SASA buried
61%
Lipo contact
74% BSA apolar/total
SASA unbound
649 Ų
Apolar buried
290 Ų

Interaction summary

HB 8 HY 11 PI 2 CLASH 2

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 rank2.731Score-20.839
Inter norm-0.824Intra norm0.023
Top1000noExcludedno
Contacts11H-bonds8
Artifact reasongeometry warning; 4 clashes; 2 protein clashes; moderate strain Δ 26.2
Residues
ASN402 GLU466 GLU467 LEU399 LYS410 PHE396 PRO398 PRO462 SER464 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 overlap6Native recall0.75
Jaccard0.46RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
253 0.19807840433788065 -0.837071 -18.4969 1 14 0 0.00 0.00 - no Open
231 0.5272779714366282 -0.937238 -23.9222 2 18 0 0.00 0.00 - no Open
237 0.6354838805780988 -1.25219 -31.6245 9 16 0 0.00 0.00 - no Open
284 0.7823962866555599 -1.09244 -27.8173 6 16 0 0.00 0.00 - no Open
202 0.8808999213169224 -1.09214 -28.6167 6 17 0 0.00 0.00 - no Open
241 1.4294098967066227 -1.27784 -31.7113 8 15 0 0.00 0.00 - no Open
278 1.5706253236876964 -1.06354 -25.3758 6 13 0 0.00 0.00 - no Open
169 2.374618991612418 -0.91184 -21.2224 16 18 0 0.00 0.00 - no Open
340 2.703325505043773 -0.877203 -22.0583 8 12 0 0.00 0.00 - no Open
282 2.7306916933281316 -0.8242 -20.8388 8 11 6 0.75 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 -20.839kcal/mol
Ligand efficiency (LE) -0.8015kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.384
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 366.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.92
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 26.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 40.01kcal/mol
Minimised FF energy 13.80kcal/mol

SASA & burial

✓ computed
SASA (unbound) 649.1Ų
Total solvent-accessible surface area of free ligand
BSA total 393.2Ų
Buried surface area upon binding
BSA apolar 290.3Ų
Hydrophobic contacts buried
BSA polar 102.9Ų
Polar contacts buried
Fraction buried 60.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3092.7Ų
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 1503.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)