FAIRMol

NMT-TY0404

Pose ID 13204 Compound 2338 Pose 325

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-TY0404
PDB9IFH↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native strong SASA done
Strain ΔE
18.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.42, H-bond role recall 1.00
Burial
60%
Hydrophobic fit
57%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.975 kcal/mol/HA) ✓ Good fit quality (FQ -7.99) ✓ Good H-bonds (4 bonds) ✓ Good burial (60% SASA buried) ✗ Moderate strain (18.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-18.528
kcal/mol
LE
-0.975
kcal/mol/HA
Fit Quality
-7.99
FQ (Leeson)
HAC
19
heavy atoms
MW
298
Da
LogP
1.23
cLogP
Final rank
2.7895
rank score
Inter norm
-1.048
normalised
Contacts
9
H-bonds 5
Strain ΔE
18.3 kcal/mol
SASA buried
60%
Lipo contact
57% BSA apolar/total
SASA unbound
471 Ų
Apolar buried
160 Ų

Interaction summary

HBD 3 HBA 1 HY 3 PI 2 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

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.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap5Native recall0.62
Jaccard0.42RMSD-
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
274 0.004259456452601552 -1.19998 -22.0537 7 16 0 0.00 0.00 - no Open
297 1.499994412154343 -1.10284 -19.4731 9 11 0 0.00 0.00 - no Open
397 2.0693543880229 -1.44348 -27.3657 9 14 0 0.00 0.00 - no Open
325 2.7894550963165585 -1.04816 -18.5277 5 9 5 0.62 1.00 - no Current
370 2.970470011926121 -1.44374 -27.3571 8 14 0 0.00 0.00 - no Open
227 3.892181034674322 -1.33338 -23.5436 14 11 0 0.00 0.00 - no Open
259 5.237778050113307 -1.63455 -29.0298 12 17 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 -18.528kcal/mol
Ligand efficiency (LE) -0.9751kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.993
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 298.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.23
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 18.29kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -70.01kcal/mol
Minimised FF energy -88.29kcal/mol

SASA & burial

✓ computed
SASA (unbound) 470.9Ų
Total solvent-accessible surface area of free ligand
BSA total 281.1Ų
Buried surface area upon binding
BSA apolar 160.3Ų
Hydrophobic contacts buried
BSA polar 120.7Ų
Polar contacts buried
Fraction buried 59.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 57.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2852.3Ų
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 1488.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)