FAIRMol

NMT-TY0607

Pose ID 13214 Compound 617 Pose 335

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 NMT-TY0607
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
29.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.88, Jaccard 0.58, H-bond role recall 1.00
Burial
56%
Hydrophobic fit
80%
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 (-0.897 kcal/mol/HA) ✓ Good fit quality (FQ -7.92) ✓ Strong H-bond network (6 bonds) ✓ Good burial (56% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ High strain energy (29.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-20.633
kcal/mol
LE
-0.897
kcal/mol/HA
Fit Quality
-7.92
FQ (Leeson)
HAC
23
heavy atoms
MW
353
Da
LogP
1.01
cLogP
Final rank
2.2796
rank score
Inter norm
-0.837
normalised
Contacts
11
H-bonds 9
Strain ΔE
29.2 kcal/mol
SASA buried
56%
Lipo contact
80% BSA apolar/total
SASA unbound
578 Ų
Apolar buried
258 Ų

Interaction summary

HBD 4 HBA 2 HY 5 PI 1 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

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 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
316 1.9160126527138646 -0.936024 -21.449 5 12 0 0.00 0.00 - no Open
278 1.9632061033636858 -1.23187 -29.5802 9 14 0 0.00 0.00 - no Open
335 2.279560783148469 -0.836864 -20.633 9 11 7 0.88 1.00 - no Current
298 2.4959341423803725 -1.18433 -27.7045 6 17 0 0.00 0.00 - no Open
350 2.8871935436214495 -1.13026 -23.8892 7 15 0 0.00 0.00 - no Open
328 3.34922510797409 -0.990588 -23.4443 11 12 0 0.00 0.00 - no Open
385 3.5748823696267844 -1.1536 -27.6164 8 16 0 0.00 0.00 - no Open
347 3.741128851709964 -1.38593 -32.0766 10 15 0 0.00 0.00 - no Open
366 3.895818972211368 -1.29627 -28.5384 8 15 0 0.00 0.00 - no Open
339 4.420406439957224 -0.972962 -25.0114 8 18 0 0.00 0.00 - no Open
248 4.628592872571314 -1.0994 -24.8798 15 14 0 0.00 0.00 - no Open
288 5.3707651519523365 -1.31364 -29.8849 16 21 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 -20.633kcal/mol
Ligand efficiency (LE) -0.8971kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.917
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.01
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -91.99kcal/mol
Minimised FF energy -121.18kcal/mol

SASA & burial

✓ computed
SASA (unbound) 578.4Ų
Total solvent-accessible surface area of free ligand
BSA total 321.3Ų
Buried surface area upon binding
BSA apolar 258.1Ų
Hydrophobic contacts buried
BSA polar 63.2Ų
Polar contacts buried
Fraction buried 55.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 80.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2975.7Ų
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 1492.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)