FAIRMol

NMT-TY0563

Pose ID 11171 Compound 937 Pose 328

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand NMT-TY0563
PDB5S9T↗

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
30.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.50, Jaccard 0.27, H-bond role recall 0.00
Burial
74%
Hydrophobic fit
57%
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 -7.07) ✓ Good H-bonds (5 bonds) ✓ Deep burial (74% SASA buried) ✗ Very high strain energy (30.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-18.433
kcal/mol
LE
-0.801
kcal/mol/HA
Fit Quality
-7.07
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
0.77
cLogP
Final rank
3.3136
rank score
Inter norm
-0.981
normalised
Contacts
16
H-bonds 10
Strain ΔE
30.8 kcal/mol
SASA buried
74%
Lipo contact
57% BSA apolar/total
SASA unbound
554 Ų
Apolar buried
236 Ų

Interaction summary

HBD 3 HBA 2 HY 5 PI 1 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap6Native recall0.50
Jaccard0.27RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
287 2.281771617029549 -1.06786 -23.7408 5 18 0 0.00 0.00 - no Open
343 2.4562087162844173 -1.10761 -25.4402 13 17 0 0.00 0.00 - no Open
304 2.461814278287188 -0.94473 -20.9121 7 12 0 0.00 0.00 - no Open
407 2.5036253322923585 -1.19433 -22.7362 8 16 0 0.00 0.00 - no Open
266 2.5178884740350864 -1.23759 -27.3191 9 14 0 0.00 0.00 - no Open
309 3.0017361607070128 -1.11231 -22.3337 10 15 0 0.00 0.00 - no Open
328 3.3135670361627176 -0.980585 -18.4335 10 16 6 0.50 0.00 - no Current
250 4.760381988626865 -1.22455 -27.6963 12 15 0 0.00 0.00 - no Open
275 5.006226701203945 -1.35207 -29.9759 16 19 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 -18.433kcal/mol
Ligand efficiency (LE) -0.8015kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.073
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.77
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -63.55kcal/mol
Minimised FF energy -94.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 554.4Ų
Total solvent-accessible surface area of free ligand
BSA total 413.2Ų
Buried surface area upon binding
BSA apolar 235.9Ų
Hydrophobic contacts buried
BSA polar 177.3Ų
Polar contacts buried
Fraction buried 74.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 57.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6292.8Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2095.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)