FAIRMol

NMT-TY0939

Pose ID 9931 Compound 912 Pose 445

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-TY0939
PDB9IFF↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
71.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.77, Jaccard 0.53
Burial
75%
Hydrophobic fit
55%
Reason: strain 71.4 kcal/mol
strain ΔE 71.4 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.854 kcal/mol/HA) ✓ Good fit quality (FQ -7.87) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (75% SASA buried) ✗ Extreme strain energy (71.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-22.210
kcal/mol
LE
-0.854
kcal/mol/HA
Fit Quality
-7.87
FQ (Leeson)
HAC
26
heavy atoms
MW
402
Da
LogP
0.54
cLogP
Final rank
3.5065
rank score
Inter norm
-0.904
normalised
Contacts
16
H-bonds 13
Strain ΔE
71.4 kcal/mol
SASA buried
75%
Lipo contact
55% BSA apolar/total
SASA unbound
615 Ų
Apolar buried
252 Ų

Interaction summary

HBD 4 HBA 4 HY 7 PI 0 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.

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 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
347 0.47311557931133086 -0.935109 -19.2367 4 13 0 0.00 - - no Open
322 1.415578661134894 -1.03243 -26.6288 12 15 0 0.00 - - no Open
374 1.7236615503669714 -1.05315 -30.1239 8 13 0 0.00 - - no Open
380 2.2523504511266683 -1.00941 -20.4416 7 16 0 0.00 - - no Open
298 3.331173736035127 -1.11268 -26.9067 10 14 0 0.00 - - no Open
327 3.4700047251715773 -0.87606 -20.3514 3 16 0 0.00 - - no Open
445 3.506483242040409 -0.904121 -22.2104 13 16 10 0.77 - - no Current
276 5.5461368627814105 -0.989799 -17.3373 15 17 0 0.00 - - no Open
339 6.810864659394439 -0.970214 -24.4372 16 15 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 -22.210kcal/mol
Ligand efficiency (LE) -0.8542kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.870
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 402.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.54
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 71.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -16.45kcal/mol
Minimised FF energy -87.86kcal/mol

SASA & burial

✓ computed
SASA (unbound) 614.9Ų
Total solvent-accessible surface area of free ligand
BSA total 461.0Ų
Buried surface area upon binding
BSA apolar 251.7Ų
Hydrophobic contacts buried
BSA polar 209.3Ų
Polar contacts buried
Fraction buried 75.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 54.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2812.9Ų
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 1510.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)