FAIRMol

NMT-TY0945

Pose ID 13235 Compound 457 Pose 356

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand NMT-TY0945
PDB9IFH↗

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 strong SASA done
Strain ΔE
30.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.64, H-bond role recall 1.00
Burial
52%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.816 kcal/mol/HA) ✓ Good fit quality (FQ -7.20) ✓ Strong H-bond network (8 bonds) ✓ Good burial (52% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ Very high strain energy (30.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-18.770
kcal/mol
LE
-0.816
kcal/mol/HA
Fit Quality
-7.20
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
1.65
cLogP
Strain ΔE
30.8 kcal/mol
SASA buried
52%
Lipo contact
79% BSA apolar/total
SASA unbound
574 Ų
Apolar buried
238 Ų

Interaction summary

HB 8 HY 9 PI 1 CLASH 1

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 rank2.855Score-18.770
Inter norm-0.877Intra norm0.061
Top1000noExcludedno
Contacts10H-bonds8
Artifact reasongeometry warning; 6 clashes; 2 protein clashes; high strain Δ 30.8
Residues
GLU467 LEU399 MET393 MET471 PHE396 PRO398 SER394 SER395 SER470 THR397

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap7Native recall0.88
Jaccard0.64RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221

Receptor context

1 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 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
331 1.3228782768357632 -0.988725 -21.382 6 21 0 0.00 0.00 - no Open
448 2.0202156311418653 -1.04987 -23.3278 11 16 0 0.00 0.00 - no Open
384 2.1854242149608547 -1.27322 -27.2564 7 14 0 0.00 0.00 - no Open
299 2.2389127358641843 -1.24419 -29.3361 6 13 0 0.00 0.00 - no Open
287 2.3154637769101583 -1.38961 -30.3716 8 18 0 0.00 0.00 - no Open
399 2.65237204898312 -1.17856 -26.8652 7 15 0 0.00 0.00 - no Open
356 2.8549181624908866 -0.876878 -18.7703 8 10 7 0.88 1.00 - no Current
373 2.922208161032249 -1.07201 -27.243 10 18 0 0.00 0.00 - no Open
327 3.247305073357421 -1.26001 -30.536 11 14 0 0.00 0.00 - no Open
345 3.4094655135949186 -0.917319 -21.8665 6 13 0 0.00 0.00 - no Open
327 3.8869349881270736 -1.02919 -23.7369 7 14 0 0.00 0.00 - no Open
278 4.034060494388567 -1.09949 -24.4644 11 15 0 0.00 0.00 - no Open
294 4.318729724082746 -1.18135 -26.7685 11 12 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 -18.770kcal/mol
Ligand efficiency (LE) -0.8161kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.203
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.65
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -60.41kcal/mol
Minimised FF energy -91.19kcal/mol

SASA & burial

✓ computed
SASA (unbound) 574.4Ų
Total solvent-accessible surface area of free ligand
BSA total 301.2Ų
Buried surface area upon binding
BSA apolar 237.7Ų
Hydrophobic contacts buried
BSA polar 63.5Ų
Polar contacts buried
Fraction buried 52.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2985.8Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1483.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)