FAIRMol

NMT-TY0623

Pose ID 11191 Compound 343 Pose 348

DB SELECTIONDocking 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-TY0623
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 high Native strong SASA done
Strain ΔE
27.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.28, H-bond role recall 0.00
Burial
76%
Hydrophobic fit
72%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.918 kcal/mol/HA) ✓ Good fit quality (FQ -8.76) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (76% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ High strain energy (27.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-26.616
kcal/mol
LE
-0.918
kcal/mol/HA
Fit Quality
-8.76
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
2.78
cLogP
Strain ΔE
27.4 kcal/mol
SASA buried
76%
Lipo contact
72% BSA apolar/total
SASA unbound
685 Ų
Apolar buried
373 Ų

Interaction summary

HB 8 HY 14 PI 1 CLASH 2
Final rank3.796Score-26.616
Inter norm-0.865Intra norm-0.053
Top1000noExcludedno
Contacts20H-bonds8
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 27.4
Residues
ALA363 ARG228 ARG361 CYS375 GLY196 GLY197 GLY229 GLY376 HIS359 ILE378 LEU227 LEU332 LEU377 PHE198 PHE230 SER364 THR360 THR374 VAL362 VAL381

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

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 overlap7Native recall0.58
Jaccard0.28RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
290 -0.07584312586851832 -1.13056 -32.0626 7 15 0 0.00 0.00 - no Open
322 0.30845358684249946 -0.891961 -22.9586 1 16 0 0.00 0.00 - no Open
277 0.7836269283764385 -0.966102 -28.607 8 17 0 0.00 0.00 - no Open
393 1.7697479735872257 -0.888141 -25.7806 6 15 0 0.00 0.00 - no Open
379 2.0583001140760584 -1.04849 -30.952 5 15 0 0.00 0.00 - no Open
424 2.557044498817305 -0.988533 -28.1895 8 17 0 0.00 0.00 - no Open
342 2.7977411127516505 -0.78462 -22.2614 10 10 0 0.00 0.00 - no Open
328 2.9974190872298045 -0.816997 -22.4353 4 15 0 0.00 0.00 - no Open
309 3.050671063739145 -0.980479 -28.998 6 18 0 0.00 0.00 - no Open
331 3.103020756997463 -0.788626 -21.3481 8 19 0 0.00 0.00 - no Open
353 3.2612201780631067 -1.05701 -30.407 7 17 0 0.00 0.00 - no Open
362 3.7208953487922924 -0.983933 -23.2803 7 17 0 0.00 0.00 - no Open
348 3.795992434048253 -0.864899 -26.6158 8 20 7 0.58 0.00 - no Current
289 3.87862843107247 -0.963867 -29.2468 8 19 0 0.00 0.00 - no Open
328 4.137080334224266 -0.976406 -27.277 12 18 0 0.00 0.00 - no Open
309 4.286815840501966 -0.801912 -23.8944 5 20 0 0.00 0.00 - no Open
269 4.88188196770325 -1.1395 -32.34 11 17 0 0.00 0.00 - no Open
255 5.815034729044303 -0.891682 -22.7371 13 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 -26.616kcal/mol
Ligand efficiency (LE) -0.9178kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.761
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.78
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -62.39kcal/mol
Minimised FF energy -89.75kcal/mol

SASA & burial

✓ computed
SASA (unbound) 684.6Ų
Total solvent-accessible surface area of free ligand
BSA total 520.7Ų
Buried surface area upon binding
BSA apolar 373.3Ų
Hydrophobic contacts buried
BSA polar 147.4Ų
Polar contacts buried
Fraction buried 76.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6496.4Ų
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 2082.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)