FAIRMol

NMT-TY0256

Pose ID 11161 Compound 3431 Pose 318

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-TY0256
PDB5S9T↗

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 mixed SASA done
Strain ΔE
29.4 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.42, Jaccard 0.24, H-bond role recall 0.00
Burial
82%
Hydrophobic fit
64%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.601 kcal/mol/HA) ✓ Good fit quality (FQ -11.45) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (82% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ High strain energy (29.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (5)
Score
-22.419
kcal/mol
LE
-1.601
kcal/mol/HA
Fit Quality
-11.45
FQ (Leeson)
HAC
14
heavy atoms
MW
214
Da
LogP
-0.77
cLogP
Strain ΔE
29.4 kcal/mol
SASA buried
82%
Lipo contact
64% BSA apolar/total
SASA unbound
393 Ų
Apolar buried
206 Ų

Interaction summary

HB 8 HY 5 PI 0 CLASH 4

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 rank2.537Score-22.419
Inter norm-1.651Intra norm0.050
Top1000noExcludedno
Contacts14H-bonds8
Artifact reasongeometry warning; 5 clashes; 2 protein clashes; moderate strain Δ 29.4
Residues
ARG361 ASP231 CYS375 GLY229 GLY376 HIS359 HIS428 ILE378 LEU332 PHE230 SER364 THR360 THR374 VAL362

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 overlap5Native recall0.42
Jaccard0.24RMSD-
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
297 1.419538648994274 -1.73008 -23.5894 11 16 0 0.00 0.00 - no Open
318 2.536806927860856 -1.6511 -22.4193 8 14 5 0.42 0.00 - no Current
224 2.799890130549648 -1.83486 -25.5537 15 11 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 -22.419kcal/mol
Ligand efficiency (LE) -1.6014kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.450
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 14HA

Physicochemical properties
Molecular weight 214.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.77
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -52.54kcal/mol
Minimised FF energy -81.93kcal/mol

SASA & burial

✓ computed
SASA (unbound) 393.1Ų
Total solvent-accessible surface area of free ligand
BSA total 323.9Ų
Buried surface area upon binding
BSA apolar 205.8Ų
Hydrophobic contacts buried
BSA polar 118.0Ų
Polar contacts buried
Fraction buried 82.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6244.9Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2084.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)