FAIRMol

NMT-TY0950

Pose ID 11218 Compound 472 Pose 375

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-TY0950
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
73.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.39, H-bond role recall 0.00
Burial
83%
Hydrophobic fit
64%
Reason: strain 73.5 kcal/mol
strain ΔE 73.5 kcal/mol 1 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.899 kcal/mol/HA) ✓ Good fit quality (FQ -8.67) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (64%) ✗ Extreme strain energy (73.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-26.972
kcal/mol
LE
-0.899
kcal/mol/HA
Fit Quality
-8.67
FQ (Leeson)
HAC
30
heavy atoms
MW
449
Da
LogP
2.29
cLogP
Final rank
5.0377
rank score
Inter norm
-0.792
normalised
Contacts
20
H-bonds 11
Strain ΔE
73.5 kcal/mol
SASA buried
83%
Lipo contact
64% BSA apolar/total
SASA unbound
660 Ų
Apolar buried
348 Ų

Interaction summary

HBD 1 HBA 5 HY 7 PI 2 CLASH 1

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.

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: permissive.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap9Native recall0.75
Jaccard0.39RMSD-
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
309 0.5895690721633616 -1.13622 -30.3874 8 14 0 0.00 0.00 - no Open
333 1.8528949720612344 -0.871094 -20.4231 9 21 0 0.00 0.00 - no Open
346 2.5049995109775236 -0.695293 -19.385 7 15 0 0.00 0.00 - no Open
329 2.6038043516621086 -0.791328 -24.4665 8 18 0 0.00 0.00 - no Open
401 2.709367825056947 -0.898773 -29.2983 11 18 0 0.00 0.00 - no Open
387 3.039354788128348 -0.955566 -25.9011 5 16 0 0.00 0.00 - no Open
377 3.518911435161691 -0.919501 -27.1237 4 18 0 0.00 0.00 - no Open
413 4.842529649555529 -0.778884 -24.2965 7 14 0 0.00 0.00 - no Open
375 5.037684319007355 -0.791884 -26.972 11 20 9 0.75 0.00 - no Current
281 5.05415737661994 -0.818782 -20.1411 11 15 0 0.00 0.00 - no Open
297 5.381934307588437 -1.09518 -27.9587 10 19 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 -26.972kcal/mol
Ligand efficiency (LE) -0.8991kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.673
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 448.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.29
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 73.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -38.92kcal/mol
Minimised FF energy -112.38kcal/mol

SASA & burial

✓ computed
SASA (unbound) 660.3Ų
Total solvent-accessible surface area of free ligand
BSA total 546.3Ų
Buried surface area upon binding
BSA apolar 347.8Ų
Hydrophobic contacts buried
BSA polar 198.5Ų
Polar contacts buried
Fraction buried 82.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 63.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6454.7Ų
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 2050.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)