FAIRMol

NMT-TY0920

Pose ID 7093 Compound 544 Pose 319

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
T11
L. infantum SIR2 L. infantum
Ligand NMT-TY0920

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
39.3 kcal/mol
Protein clashes
4
Internal clashes
11
Native overlap
contact recall 0.72, Jaccard 0.72, H-bond role recall 0.60
Burial
72%
Hydrophobic fit
80%
Reason: 11 internal clashes
4 protein-contact clashes 11 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.904 kcal/mol/HA) ✓ Good fit quality (FQ -8.53) ✓ Good H-bonds (5 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (80%) ✗ Very high strain energy (39.3 kcal/mol) ✗ Geometry warnings ✗ Minor protein-contact clashes (4) ✗ Many internal clashes (11)
Score
-25.301
kcal/mol
LE
-0.904
kcal/mol/HA
Fit Quality
-8.53
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.07
cLogP
Strain ΔE
39.3 kcal/mol
SASA buried
72%
Lipo contact
80% BSA apolar/total
SASA unbound
644 Ų
Apolar buried
371 Ų

Interaction summary

HB 5 HY 24 PI 3 CLASH 0

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
No clash · clashes detected for this pose.
Final rank0.994Score-25.301
Inter norm-0.944Intra norm0.040
Top1000noExcludedno
Contacts13H-bonds5
Artifact reasongeometry warning; 11 clashes; 4 protein contact clashes; high strain Δ 39.3
Residues
GLN220 GLU192 GLY191 HIS144 HIS222 LEU194 PHE189 PHE190 PHE74 PRO223 THR71 VAL188 VAL221

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5OL0Contacts18
PoseOpen native poseHB0
IFP residues
ASN193 GLN220 GLU192 GLY191 HIS144 HIS222 ILE126 LEU194 LEU226 PHE189 PHE190 PHE199 PHE74 PRO223 THR71 VAL187 VAL188 VAL221
Current overlap13Native recall0.72
Jaccard0.72RMSD-
HB strict3Strict recall0.60
HB same residue+role3HB role recall0.60
HB same residue2HB residue recall0.50

Protein summary

287 residues
Protein targetT11Atoms4391
Residues287Chains1
Residue summaryLEU:627; ARG:432; VAL:384; GLU:316; PHE:300; ILE:285; ALA:260; PRO:238; HIS:187; ASP:157; LYS:154; SER:154; THR:154; GLY:147; ASN:140; TYR:126

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
302 0.5239567590025211 -1.18433 -30.604 9 13 0 0.00 0.00 - no Open
319 0.9940520654587742 -0.944043 -25.3008 5 13 13 0.72 0.60 - no Current
320 1.0669444827431311 -0.878088 -31.4505 3 16 0 0.00 0.00 - no Open
345 1.1134646347622539 -0.877657 -23.1229 3 15 1 0.06 0.00 - no Open
369 1.570299553280359 -0.935163 -25.1037 6 14 0 0.00 0.00 - no Open
285 1.846962516011115 -1.10054 -35.0271 11 16 0 0.00 0.00 - no Open
333 2.430240854014312 -0.961348 -34.1213 11 17 0 0.00 0.00 - no Open
313 2.7355217655896267 -0.945999 -28.0195 7 18 0 0.00 0.00 - no Open
388 3.1357764599548372 -1.01979 -35.0482 6 16 0 0.00 0.00 - no Open
366 3.33349022232488 -1.04252 -32.8619 6 15 0 0.00 0.00 - no Open
313 3.427850034969361 -1.24397 -30.3675 11 26 0 0.00 0.00 - no Open
342 3.492057571577017 -0.785111 -22.7794 9 15 0 0.00 0.00 - no Open
295 3.616137840018539 -0.981468 -32.0097 7 17 0 0.00 0.00 - no Open
437 3.855523120955258 -0.937716 -27.4849 10 13 0 0.00 0.00 - no Open
349 4.8296015227220686 -0.681525 -25.7042 8 9 0 0.00 0.00 - no Open
361 5.231781681702861 -0.899682 -33.3801 11 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 -25.301kcal/mol
Ligand efficiency (LE) -0.9036kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.530
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.07
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -10.19kcal/mol
Minimised FF energy -49.45kcal/mol

SASA & burial

✓ computed
SASA (unbound) 644.1Ų
Total solvent-accessible surface area of free ligand
BSA total 465.4Ų
Buried surface area upon binding
BSA apolar 371.3Ų
Hydrophobic contacts buried
BSA polar 94.1Ų
Polar contacts buried
Fraction buried 72.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1905.0Ų
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 2380.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 958.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)