FAIRMol

NMT-TY0527

Pose ID 11167 Compound 3415 Pose 324

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-TY0527
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
16.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.44, H-bond role recall 0.00
Burial
81%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.109 kcal/mol/HA) ✓ Good fit quality (FQ -9.09) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Moderate strain (16.6 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-21.073
kcal/mol
LE
-1.109
kcal/mol/HA
Fit Quality
-9.09
FQ (Leeson)
HAC
19
heavy atoms
MW
276
Da
LogP
2.33
cLogP
Strain ΔE
16.6 kcal/mol
SASA buried
81%
Lipo contact
76% BSA apolar/total
SASA unbound
512 Ų
Apolar buried
318 Ų

Interaction summary

HB 8 HY 19 PI 3 CLASH 2

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.725Score-21.073
Inter norm-1.231Intra norm0.122
Top1000noExcludedno
Contacts14H-bonds8
Artifact reasongeometry warning; 7 clashes; 2 protein clashes
Residues
ALA365 ARG228 GLY196 GLY197 ILE226 LEU225 LEU227 LEU332 LEU334 PHE198 PHE230 SER364 TYR221 VAL366

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
Jaccard0.44RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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
236 2.5491699034847026 -1.40877 -24.392 9 16 0 0.00 0.00 - no Open
324 2.724837397517155 -1.23132 -21.0728 8 14 8 0.67 0.00 - 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 -21.073kcal/mol
Ligand efficiency (LE) -1.1091kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.091
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 276.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.33
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 16.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -35.74kcal/mol
Minimised FF energy -52.30kcal/mol

SASA & burial

✓ computed
SASA (unbound) 511.9Ų
Total solvent-accessible surface area of free ligand
BSA total 416.6Ų
Buried surface area upon binding
BSA apolar 317.6Ų
Hydrophobic contacts buried
BSA polar 99.0Ų
Polar contacts buried
Fraction buried 81.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6391.7Ų
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 2053.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)