FAIRMol

NMT-TY0927

Pose ID 9925 Compound 401 Pose 439

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-TY0927
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
30.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.69, Jaccard 0.56
Burial
73%
Hydrophobic fit
64%
Reason: no major geometry red flags detected
2 protein-contact clashes 45% of hydrophobic surface appears solvent-exposed (5/11 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.256 kcal/mol/HA) ✓ Good fit quality (FQ -10.72) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Very high strain energy (30.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-26.382
kcal/mol
LE
-1.256
kcal/mol/HA
Fit Quality
-10.72
FQ (Leeson)
HAC
21
heavy atoms
MW
327
Da
LogP
0.87
cLogP
Final rank
4.3452
rank score
Inter norm
-1.195
normalised
Contacts
12
H-bonds 10
Strain ΔE
30.9 kcal/mol
SASA buried
73%
Lipo contact
64% BSA apolar/total
SASA unbound
516 Ų
Apolar buried
241 Ų

Interaction summary

HBD 4 HBA 2 HY 4 PI 0 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: strict.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap9Native recall0.69
Jaccard0.56RMSD-
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
291 1.0967612246539307 -1.34511 -30.2038 9 11 0 0.00 - - no Open
322 1.293053659419753 -1.2063 -25.6189 8 19 0 0.00 - - no Open
270 1.7191106795656168 -1.17853 -22.541 16 12 0 0.00 - - no Open
390 2.3538397766138504 -1.22354 -25.7047 7 15 0 0.00 - - no Open
373 2.4588288780248044 -1.25312 -26.3897 6 14 0 0.00 - - no Open
336 2.886003700201454 -1.17246 -25.6474 10 17 0 0.00 - - no Open
317 2.9899836999992475 -1.31975 -28.8678 11 16 0 0.00 - - no Open
408 4.174722979043151 -1.08565 -21.6821 10 10 0 0.00 - - no Open
439 4.345171388067734 -1.19467 -26.3824 10 12 9 0.69 - - 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 -26.382kcal/mol
Ligand efficiency (LE) -1.2563kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.716
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 21HA

Physicochemical properties
Molecular weight 327.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.87
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -35.59kcal/mol
Minimised FF energy -66.44kcal/mol

SASA & burial

✓ computed
SASA (unbound) 516.1Ų
Total solvent-accessible surface area of free ligand
BSA total 379.1Ų
Buried surface area upon binding
BSA apolar 241.1Ų
Hydrophobic contacts buried
BSA polar 138.0Ų
Polar contacts buried
Fraction buried 73.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2832.1Ų
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 1522.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)