FAIRMol

NMT-TY0625

Pose ID 7085 Compound 587 Pose 311

DB SELECTIONDocking 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-TY0625

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
31.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.78, Jaccard 0.78, H-bond role recall 0.60
Burial
78%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.043 kcal/mol/HA) ✓ Good fit quality (FQ -9.73) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (78% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Very high strain energy (31.2 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-28.171
kcal/mol
LE
-1.043
kcal/mol/HA
Fit Quality
-9.73
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.27
cLogP
Strain ΔE
31.2 kcal/mol
SASA buried
78%
Lipo contact
76% BSA apolar/total
SASA unbound
652 Ų
Apolar buried
387 Ų

Interaction summary

HB 9 HY 24 PI 5 CLASH 5 ⚠ Exposure 35%
⚠️Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 11 Exposed 6 LogP 2.27 H-bonds 9
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank3.295Score-28.171
Inter norm-0.982Intra norm-0.061
Top1000noExcludedno
Contacts14H-bonds9
Artifact reasongeometry warning; 9 clashes; 2 protein clashes; high strain Δ 31.2
Residues
ASN193 GLU192 GLY191 HIS144 HIS222 ILE126 LEU194 PHE189 PHE190 PHE74 PRO223 VAL187 VAL188 VAL221

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

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 overlap14Native recall0.78
Jaccard0.78RMSD-
HB strict3Strict recall0.60
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.75

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
324 0.20723889343453514 -0.951386 -23.6661 1 14 1 0.06 0.00 - no Open
275 0.9061196009967781 -1.22993 -32.9032 9 20 0 0.00 0.00 - no Open
292 1.1768621845493887 -1.20358 -35.0455 10 11 0 0.00 0.00 - no Open
291 1.218230612835466 -1.06543 -26.4823 10 13 0 0.00 0.00 - no Open
310 1.511827099897129 -0.901999 -22.8948 4 17 0 0.00 0.00 - no Open
330 1.9924960648131407 -0.979613 -23.342 4 14 0 0.00 0.00 - no Open
343 2.359267355874073 -0.89635 -23.6694 9 12 0 0.00 0.00 - no Open
426 2.4909161669113518 -0.907217 -24.1632 10 17 0 0.00 0.00 - no Open
278 2.509428388171617 -1.0319 -28.1397 6 13 1 0.06 0.00 - no Open
297 2.63967730557778 -1.25147 -33.606 12 23 0 0.00 0.00 - no Open
355 3.229453768262364 -1.09247 -22.9997 10 19 0 0.00 0.00 - no Open
311 3.2950567359488305 -0.981974 -28.1708 9 14 14 0.78 0.60 - no Current
395 3.4109746243775096 -0.855223 -23.6426 8 13 0 0.00 0.00 - no Open
350 3.483682559989441 -0.96476 -27.5634 8 19 0 0.00 0.00 - no Open
381 3.5214059746730104 -1.11325 -28.0276 6 14 0 0.00 0.00 - no Open
364 4.0288364719309 -1.09005 -30.4446 8 17 0 0.00 0.00 - no Open
272 4.1996467964885476 -1.16921 -29.9755 9 17 0 0.00 0.00 - no Open
332 4.352390042161908 -0.822496 -24.9609 10 15 0 0.00 0.00 - no Open
271 4.392965189680496 -1.27398 -34.4428 11 15 0 0.00 0.00 - no Open
330 5.564206722433145 -0.904232 -20.3369 11 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 -28.171kcal/mol
Ligand efficiency (LE) -1.0434kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.734
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.27
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -58.17kcal/mol
Minimised FF energy -89.40kcal/mol

SASA & burial

✓ computed
SASA (unbound) 652.3Ų
Total solvent-accessible surface area of free ligand
BSA total 507.4Ų
Buried surface area upon binding
BSA apolar 386.9Ų
Hydrophobic contacts buried
BSA polar 120.5Ų
Polar contacts buried
Fraction buried 77.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1893.2Ų
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 2380.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 969.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)