FAIRMol

NMT-TY0541

Pose ID 11169 Compound 519 Pose 326

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-TY0541
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
37.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.42, H-bond role recall 1.00
Burial
84%
Hydrophobic fit
67%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.905 kcal/mol/HA) ✓ Good fit quality (FQ -7.99) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (84% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ Very high strain energy (37.7 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (7) ✗ Internal clashes (7)
Score
-20.813
kcal/mol
LE
-0.905
kcal/mol/HA
Fit Quality
-7.99
FQ (Leeson)
HAC
23
heavy atoms
MW
338
Da
LogP
-0.31
cLogP
Final rank
1.1131
rank score
Inter norm
-0.995
normalised
Contacts
15
H-bonds 11
Strain ΔE
37.7 kcal/mol
SASA buried
84%
Lipo contact
67% BSA apolar/total
SASA unbound
555 Ų
Apolar buried
313 Ų

Interaction summary

HBD 3 HBA 3 HY 6 PI 1 CLASH 1

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

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: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap8Native recall0.67
Jaccard0.42RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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
272 1.0565588024106063 -1.4079 -31.3306 13 10 0 0.00 0.00 - no Open
283 1.0848647482644131 -1.1194 -19.7839 10 17 0 0.00 0.00 - no Open
326 1.1131363785864183 -0.995394 -20.8134 11 15 8 0.67 1.00 - no Current
306 1.3109441700977569 -1.30513 -28.49 8 13 0 0.00 0.00 - no Open
338 2.507643872441264 -1.2541 -29.5019 11 11 0 0.00 0.00 - no Open
260 2.5369634862341512 -1.09721 -19.3469 9 17 0 0.00 0.00 - no Open
351 2.9440503822357695 -1.14284 -20.5628 11 18 0 0.00 0.00 - no Open
271 4.247260498455184 -1.47831 -27.6122 16 23 0 0.00 0.00 - no Open
282 4.363777071020779 -1.0561 -24.2018 7 16 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 -20.813kcal/mol
Ligand efficiency (LE) -0.9049kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.987
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 338.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.31
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 37.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -138.81kcal/mol
Minimised FF energy -176.54kcal/mol

SASA & burial

✓ computed
SASA (unbound) 554.9Ų
Total solvent-accessible surface area of free ligand
BSA total 465.7Ų
Buried surface area upon binding
BSA apolar 313.1Ų
Hydrophobic contacts buried
BSA polar 152.6Ų
Polar contacts buried
Fraction buried 83.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 67.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6384.2Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2054.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)