FAIRMol

NMT-TY0615

Pose ID 6347 Compound 624 Pose 251

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
T10
L. infantum R5P L. infantum
Ligand NMT-TY0615

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
27.5 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.71, Jaccard 0.63, H-bond role recall 0.27
Burial
70%
Hydrophobic fit
75%
Reason: 6 internal clashes
6 protein-contact clashes 6 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (12/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.767 kcal/mol/HA) ✓ Good fit quality (FQ -7.24) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ High strain energy (27.5 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-21.464
kcal/mol
LE
-0.767
kcal/mol/HA
Fit Quality
-7.24
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Strain ΔE
27.5 kcal/mol
SASA buried
70%
Lipo contact
75% BSA apolar/total
SASA unbound
635 Ų
Apolar buried
337 Ų

Interaction summary

HB 11 HY 1 PI 1 CLASH 6 ⚠ Exposure 66%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (12/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 18 Buried (contacted) 6 Exposed 12 LogP 2.31 H-bonds 11
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank5.021Score-21.464
Inter norm-0.870Intra norm0.103
Top1000noExcludedno
Contacts14H-bonds11
Artifact reasongeometry warning; 9 clashes; 2 protein clashes; moderate strain Δ 27.5
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 HIS105 HIS14 HIS141 SER46 THR45 TYR49

Protein summary

155 residues
Protein targetT10Atoms4590
Residues155Chains1
Residue summaryILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXWContacts17
PoseOpen native poseHB0
IFP residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 LEU101 THR74 TYR49
Current overlap12Native recall0.71
Jaccard0.63RMSD-
HB strict4Strict recall0.31
HB same residue+role3HB role recall0.27
HB same residue4HB residue recall0.36

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
286 0.1465605854321825 -1.19394 -32.9525 8 16 0 0.00 0.00 - no Open
319 0.36642347467445924 -0.879437 -22.3358 1 16 0 0.00 0.00 - no Open
419 0.8391962853228202 -0.877673 -24.4346 5 16 0 0.00 0.00 - no Open
304 1.173755634996843 -0.883006 -24.7401 4 20 0 0.00 0.00 - no Open
302 2.436367550694648 -0.950939 -25.3338 9 16 0 0.00 0.00 - no Open
355 2.444543107656295 -1.08753 -30.4423 6 15 0 0.00 0.00 - no Open
322 2.4446601818421776 -0.791024 -19.9765 6 14 0 0.00 0.00 - no Open
336 2.463593334913157 -0.803657 -21.4576 9 10 0 0.00 0.00 - no Open
330 2.5563520520351584 -0.78044 -19.9576 8 16 0 0.00 0.00 - no Open
263 3.041922657056329 -1.11762 -30.5736 10 16 5 0.29 0.36 - no Open
389 3.368666501110512 -0.85198 -23.3125 6 13 0 0.00 0.00 - no Open
349 3.9250362007127744 -1.05025 -29.8637 9 11 0 0.00 0.00 - no Open
372 4.026339219876199 -1.18223 -30.309 8 16 0 0.00 0.00 - no Open
291 4.327872741509822 -1.07289 -25.4854 16 24 0 0.00 0.00 - no Open
342 4.655876379256122 -0.889836 -26.7374 6 17 0 0.00 0.00 - no Open
251 5.021275157969677 -0.869737 -21.4644 11 14 12 0.71 0.27 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -21.464kcal/mol
Ligand efficiency (LE) -0.7666kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -7.237
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.31
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -55.69kcal/mol
Minimised FF energy -83.17kcal/mol

SASA & burial

✓ computed
SASA (unbound) 634.7Ų
Total solvent-accessible surface area of free ligand
BSA total 446.5Ų
Buried surface area upon binding
BSA apolar 336.7Ų
Hydrophobic contacts buried
BSA polar 109.8Ų
Polar contacts buried
Fraction buried 70.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 75.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2210.8Ų
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 2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 666.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)