FAIRMol

NMT-TY0622

Pose ID 13220 Compound 524 Pose 341

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 NMT-TY0622
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
30.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.67, H-bond role recall 1.00
Burial
53%
Hydrophobic fit
81%
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 (-0.888 kcal/mol/HA) ✓ Good fit quality (FQ -8.07) ✓ Strong H-bond network (9 bonds) ✓ Good burial (53% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Very high strain energy (30.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-22.198
kcal/mol
LE
-0.888
kcal/mol/HA
Fit Quality
-8.07
FQ (Leeson)
HAC
25
heavy atoms
MW
381
Da
LogP
2.18
cLogP
Strain ΔE
30.5 kcal/mol
SASA buried
53%
Lipo contact
81% BSA apolar/total
SASA unbound
614 Ų
Apolar buried
262 Ų

Interaction summary

HB 9 HY 9 PI 1 CLASH 1
Final rank1.928Score-22.198
Inter norm-0.859Intra norm-0.029
Top1000noExcludedno
Contacts12H-bonds9
Artifact reasongeometry warning; 6 clashes; 1 protein clash; high strain Δ 30.5
Residues
ARG472 ASN402 GLU467 LEU399 MET393 MET471 PHE396 PRO398 SER394 SER395 SER470 THR397

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 overlap8Native recall1.00
Jaccard0.67RMSD-
HB strict1Strict recall0.50
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
308 0.3842150656616825 -0.951549 -25.0395 4 17 0 0.00 0.00 - no Open
276 1.2600618081157402 -1.12204 -28.7499 9 15 0 0.00 0.00 - no Open
288 1.7018393222780244 -1.13668 -28.6792 9 14 0 0.00 0.00 - no Open
352 1.9271195694416656 -1.10716 -29.8519 6 13 0 0.00 0.00 - no Open
341 1.927730112535267 -0.859185 -22.1976 9 12 8 1.00 1.00 - no Current
273 1.9961552376915304 -1.35584 -31.5197 14 17 0 0.00 0.00 - no Open
327 2.0961391154894002 -0.86609 -19.9983 5 13 0 0.00 0.00 - no Open
392 2.3248094781583672 -0.940735 -21.0428 11 16 0 0.00 0.00 - no Open
308 2.8353655663354234 -1.13363 -28.9578 5 19 0 0.00 0.00 - no Open
378 2.966730885309019 -1.23963 -28.1056 8 15 0 0.00 0.00 - no Open
423 3.5162080347453757 -1.16596 -29.4186 9 16 0 0.00 0.00 - no Open
361 3.58426702200673 -1.22019 -28.4754 6 15 0 0.00 0.00 - no Open
268 3.6431928517433407 -1.15199 -28.179 10 14 0 0.00 0.00 - no Open
327 3.7246234846293826 -1.02174 -24.8257 12 17 0 0.00 0.00 - no Open
347 3.9186485478235458 -1.05383 -26.5042 6 19 0 0.00 0.00 - no Open
269 4.208957465627367 -1.25064 -26.887 9 18 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 -22.198kcal/mol
Ligand efficiency (LE) -0.8879kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.072
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 381.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.18
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -47.75kcal/mol
Minimised FF energy -78.26kcal/mol

SASA & burial

✓ computed
SASA (unbound) 613.6Ų
Total solvent-accessible surface area of free ligand
BSA total 323.7Ų
Buried surface area upon binding
BSA apolar 261.8Ų
Hydrophobic contacts buried
BSA polar 61.9Ų
Polar contacts buried
Fraction buried 52.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3029.8Ų
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 1490.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)