FAIRMol

NMT-TY0959

Pose ID 7106 Compound 527 Pose 332

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-TY0959

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
39.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.52, H-bond role recall 0.20
Burial
87%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.035 kcal/mol/HA) ✓ Good fit quality (FQ -9.66) ✓ Good H-bonds (3 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ Very high strain energy (39.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-27.949
kcal/mol
LE
-1.035
kcal/mol/HA
Fit Quality
-9.66
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Final rank
3.3588
rank score
Inter norm
-1.081
normalised
Contacts
17
H-bonds 7
Strain ΔE
39.7 kcal/mol
SASA buried
87%
Lipo contact
70% BSA apolar/total
SASA unbound
642 Ų
Apolar buried
390 Ų

Interaction summary

HBD 3 HY 8 PI 3 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
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 overlap12Native recall0.67
Jaccard0.52RMSD-
HB strict1Strict recall0.20
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.25

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
350 0.3629211958252925 -0.926251 -24.8853 2 13 1 0.06 0.00 - no Open
308 0.8712687604222177 -1.14475 -30.9484 7 15 0 0.00 0.00 - no Open
313 1.3142726160638258 -1.30957 -33.6603 12 15 0 0.00 0.00 - no Open
337 1.7652358533706136 -0.983958 -24.6706 6 21 0 0.00 0.00 - no Open
326 1.9773175739360493 -1.1336 -31.1195 10 21 0 0.00 0.00 - no Open
291 2.165473959343045 -1.26034 -34.3636 9 22 0 0.00 0.00 - no Open
301 2.480529293523874 -1.03512 -28.7525 9 12 1 0.06 0.00 - no Open
391 2.9008417563283935 -1.06217 -28.0759 7 15 0 0.00 0.00 - no Open
405 2.9806369013586718 -1.18262 -29.8648 6 15 0 0.00 0.00 - no Open
381 3.0321874169205607 -1.08611 -28.6887 6 16 0 0.00 0.00 - no Open
379 3.2808649478445537 -0.969429 -25.6956 10 17 0 0.00 0.00 - no Open
332 3.3588118370115048 -1.08116 -27.9486 7 17 12 0.67 0.20 - no Current
416 3.387046221950613 -0.924839 -25.7132 8 13 0 0.00 0.00 - no Open
334 3.429500560915679 -1.04914 -24.4852 8 15 0 0.00 0.00 - no Open
349 3.654496302035269 -0.850128 -21.98 8 14 0 0.00 0.00 - no Open
302 3.8731875216797746 -1.1408 -30.4082 8 22 0 0.00 0.00 - no Open
286 4.0813402406540185 -0.908062 -25.3939 13 15 0 0.00 0.00 - no Open
358 4.09740218547716 -0.710564 -18.8071 6 10 0 0.00 0.00 - no Open
336 4.132326379777683 -0.942975 -24.3804 7 17 0 0.00 0.00 - no Open
453 4.769829786717276 -1.02855 -27.026 8 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 -27.949kcal/mol
Ligand efficiency (LE) -1.0351kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.657
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -11.04kcal/mol
Minimised FF energy -50.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 642.3Ų
Total solvent-accessible surface area of free ligand
BSA total 557.6Ų
Buried surface area upon binding
BSA apolar 390.2Ų
Hydrophobic contacts buried
BSA polar 167.4Ų
Polar contacts buried
Fraction buried 86.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.0%
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 938.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)