FAIRMol

NMT-TY0563

Pose ID 9893 Compound 937 Pose 407

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 NMT-TY0563
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 strong SASA done
Strain ΔE
39.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.77, Jaccard 0.53
Burial
79%
Hydrophobic fit
62%
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 (-0.989 kcal/mol/HA) ✓ Good fit quality (FQ -8.72) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (79% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Very high strain energy (39.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-22.736
kcal/mol
LE
-0.989
kcal/mol/HA
Fit Quality
-8.72
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
1.19
cLogP
Final rank
2.5036
rank score
Inter norm
-1.194
normalised
Contacts
16
H-bonds 8
Strain ΔE
39.4 kcal/mol
SASA buried
79%
Lipo contact
62% BSA apolar/total
SASA unbound
568 Ų
Apolar buried
276 Ų

Interaction summary

HBD 3 HBA 3 HY 7 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

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

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.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap10Native recall0.77
Jaccard0.53RMSD-
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
287 2.281771617029549 -1.06786 -23.7408 5 18 0 0.00 - - no Open
343 2.4562087162844173 -1.10761 -25.4402 13 17 0 0.00 - - no Open
304 2.461814278287188 -0.94473 -20.9121 7 12 0 0.00 - - no Open
407 2.5036253322923585 -1.19433 -22.7362 8 16 10 0.77 - - no Current
266 2.5178884740350864 -1.23759 -27.3191 9 14 0 0.00 - - no Open
309 3.0017361607070128 -1.11231 -22.3337 10 15 0 0.00 - - no Open
328 3.3135670361627176 -0.980585 -18.4335 10 16 0 0.00 - - no Open
250 4.760381988626865 -1.22455 -27.6963 12 15 0 0.00 - - no Open
275 5.006226701203945 -1.35207 -29.9759 16 19 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 -22.736kcal/mol
Ligand efficiency (LE) -0.9885kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.725
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.19
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -84.20kcal/mol
Minimised FF energy -123.61kcal/mol

SASA & burial

✓ computed
SASA (unbound) 567.5Ų
Total solvent-accessible surface area of free ligand
BSA total 447.8Ų
Buried surface area upon binding
BSA apolar 276.4Ų
Hydrophobic contacts buried
BSA polar 171.4Ų
Polar contacts buried
Fraction buried 78.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 61.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2836.8Ų
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 1503.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)