FAIRMol

NMT-TY0655

Pose ID 6355 Compound 642 Pose 259

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
T10
L. infantum R5P L. infantum
Ligand NMT-TY0655

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
34.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.27
Burial
69%
Hydrophobic fit
76%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 68% of hydrophobic surface is solvent-exposed (13/19 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 (-0.910 kcal/mol/HA) ✓ Good fit quality (FQ -8.68) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (69% SASA buried) ✓ Lipophilic contacts well-matched (76%) ✗ Very high strain energy (34.4 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-26.380
kcal/mol
LE
-0.910
kcal/mol/HA
Fit Quality
-8.68
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.70
cLogP
Strain ΔE
34.4 kcal/mol
SASA buried
69%
Lipo contact
76% BSA apolar/total
SASA unbound
682 Ų
Apolar buried
357 Ų

Interaction summary

HB 12 HY 2 PI 1 CLASH 3 ⚠ Exposure 68%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
68% of hydrophobic surface is solvent-exposed (13/19 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 19 Buried (contacted) 6 Exposed 13 LogP 2.7 H-bonds 12
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.781Score-26.380
Inter norm-0.939Intra norm0.029
Top1000noExcludedno
Contacts15H-bonds12
Artifact reasongeometry warning; 10 clashes; 2 protein clashes; high strain Δ 34.4
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 ASP44 CYS72 GLY73 HIS105 HIS14 HIS141 SER46 THR45 TYR49

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
Jaccard0.60RMSD-
HB strict4Strict recall0.31
HB same residue+role3HB role recall0.27
HB same residue4HB residue recall0.36

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
326 0.39386311158270365 -0.8634 -22.2003 2 17 0 0.00 0.00 - no Open
293 1.2975525399078252 -1.10036 -23.287 13 17 0 0.00 0.00 - no Open
332 1.3509669263374375 -0.818891 -24.2435 5 11 0 0.00 0.00 - no Open
398 1.4248474191431448 -0.818797 -26.084 9 16 0 0.00 0.00 - no Open
357 3.063569507923383 -0.975157 -27.1958 7 17 0 0.00 0.00 - no Open
313 3.4863292709253897 -0.889455 -25.7264 6 20 0 0.00 0.00 - no Open
259 3.781044729591084 -0.939023 -26.3803 12 15 12 0.71 0.27 - no Current
295 3.793518326281322 -1.06178 -33.4595 9 16 0 0.00 0.00 - no Open
353 3.8794253242713035 -0.880948 -26.168 8 19 0 0.00 0.00 - no Open
274 3.9330832604554944 -1.0997 -26.5256 10 16 5 0.29 0.18 - no Open
429 4.328176057542405 -0.891399 -26.3856 9 19 0 0.00 0.00 - no Open
311 4.455028773878592 -0.79909 -20.9919 7 19 0 0.00 0.00 - no Open
383 4.505896017581984 -0.958315 -29.9041 7 16 0 0.00 0.00 - no Open
366 4.645579286679848 -1.01887 -29.87 8 20 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 -26.380kcal/mol
Ligand efficiency (LE) -0.9097kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.683
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 29HA

Physicochemical properties
Molecular weight 431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.70
Lipinski: ≤ 5
Rotatable bonds 9

Conformational strain (MMFF94s)
Strain energy (ΔE) 34.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -52.72kcal/mol
Minimised FF energy -87.12kcal/mol

SASA & burial

✓ computed
SASA (unbound) 682.4Ų
Total solvent-accessible surface area of free ligand
BSA total 468.0Ų
Buried surface area upon binding
BSA apolar 356.9Ų
Hydrophobic contacts buried
BSA polar 111.1Ų
Polar contacts buried
Fraction buried 68.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2259.7Ų
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 665.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)