FAIRMol

NMT-TY0949

Pose ID 9935 Compound 470 Pose 449

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-TY0949
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
38.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.69, Jaccard 0.53
Burial
70%
Hydrophobic fit
78%
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 (-0.851 kcal/mol/HA) ✓ Good fit quality (FQ -7.84) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Very high strain energy (38.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-22.124
kcal/mol
LE
-0.851
kcal/mol/HA
Fit Quality
-7.84
FQ (Leeson)
HAC
26
heavy atoms
MW
398
Da
LogP
2.41
cLogP
Strain ΔE
38.5 kcal/mol
SASA buried
70%
Lipo contact
78% BSA apolar/total
SASA unbound
687 Ų
Apolar buried
378 Ų

Interaction summary

HB 7 HY 15 PI 0 CLASH 1

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
Final rank3.039Score-22.124
Inter norm-0.936Intra norm0.084
Top1000noExcludedno
Contacts13H-bonds7
Artifact reasongeometry warning; 7 clashes; 2 protein clashes; high strain Δ 38.5
Residues
ALA209 ALA90 ARG74 ASN208 LEU73 LYS211 LYS89 MET70 PRO187 PRO212 PRO213 TYR210 VAL88

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
Jaccard0.53RMSD-
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
308 1.187393889152574 -1.24825 -32.0593 12 16 0 0.00 - - no Open
332 1.4475060831931013 -0.908297 -19.3579 6 20 0 0.00 - - no Open
330 1.6375996430401702 -1.02694 -24.5463 9 15 0 0.00 - - no Open
386 2.393790139348862 -1.04478 -27.2992 5 16 0 0.00 - - no Open
400 2.7019247705431835 -1.02254 -26.6795 7 14 0 0.00 - - no Open
449 3.0390383540467387 -0.935536 -22.1242 7 13 9 0.69 - - no Current
328 3.0575053314665115 -0.939746 -23.408 9 14 0 0.00 - - no Open
296 3.653354242498257 -1.03529 -23.94 10 14 0 0.00 - - no Open
374 3.6668719210657295 -0.875287 -20.8265 12 18 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 -22.124kcal/mol
Ligand efficiency (LE) -0.8509kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.840
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 397.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.41
Lipinski: ≤ 5
Rotatable bonds 11

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -86.55kcal/mol
Minimised FF energy -125.09kcal/mol

SASA & burial

✓ computed
SASA (unbound) 686.9Ų
Total solvent-accessible surface area of free ligand
BSA total 482.8Ų
Buried surface area upon binding
BSA apolar 377.8Ų
Hydrophobic contacts buried
BSA polar 105.0Ų
Polar contacts buried
Fraction buried 70.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3006.2Ų
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 1514.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)