FAIRMol

NMT-TY0671

Pose ID 11198 Compound 1300 Pose 355

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-TY0671
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
59.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.83, Jaccard 0.45, H-bond role recall 0.00
Burial
83%
Hydrophobic fit
62%
Reason: strain 59.1 kcal/mol
strain ΔE 59.1 kcal/mol 2 protein-contact clashes
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.802 kcal/mol/HA) ✓ Good fit quality (FQ -7.66) ✓ Good H-bonds (5 bonds) ✓ Deep burial (83% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Extreme strain energy (59.1 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-23.259
kcal/mol
LE
-0.802
kcal/mol/HA
Fit Quality
-7.66
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.49
cLogP
Final rank
4.5159
rank score
Inter norm
-0.794
normalised
Contacts
20
H-bonds 9
Strain ΔE
59.1 kcal/mol
SASA buried
83%
Lipo contact
62% BSA apolar/total
SASA unbound
638 Ų
Apolar buried
330 Ų

Interaction summary

HBD 3 HBA 2 HY 6 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.

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 overlap10Native recall0.83
Jaccard0.45RMSD-
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
327 1.113016812929585 -0.837606 -23.8962 1 14 0 0.00 0.00 - no Open
430 2.3252787033319144 -0.938777 -27.2792 10 16 0 0.00 0.00 - no Open
360 2.515614498002701 -1.00043 -29.7334 5 14 0 0.00 0.00 - no Open
401 3.832792503061684 -0.889515 -25.6391 11 18 0 0.00 0.00 - no Open
277 3.8876534768210544 -1.08809 -28.9894 10 19 0 0.00 0.00 - no Open
276 3.987457950263569 -0.9943 -24.6113 10 15 0 0.00 0.00 - no Open
301 3.991224331337767 -0.914304 -27.8504 10 14 0 0.00 0.00 - no Open
355 4.515890243073721 -0.794133 -23.2595 9 20 10 0.83 0.00 - no Current
278 5.236654933239286 -0.9719 -21.9883 11 22 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 -23.259kcal/mol
Ligand efficiency (LE) -0.8021kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.656
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.49
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 59.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -38.43kcal/mol
Minimised FF energy -97.53kcal/mol

SASA & burial

✓ computed
SASA (unbound) 638.5Ų
Total solvent-accessible surface area of free ligand
BSA total 527.8Ų
Buried surface area upon binding
BSA apolar 330.1Ų
Hydrophobic contacts buried
BSA polar 197.7Ų
Polar contacts buried
Fraction buried 82.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 62.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6410.2Ų
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 2057.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)