FAIRMol

NMT-TY0929

Pose ID 6368 Compound 484 Pose 272

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-TY0929

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
46.3 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.65, Jaccard 0.61, H-bond role recall 0.45
Burial
67%
Hydrophobic fit
71%
Reason: strain 46.3 kcal/mol
strain ΔE 46.3 kcal/mol 5 protein-contact clashes 5 intramolecular clashes 65% of hydrophobic surface is solvent-exposed (11/17 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 ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.728 kcal/mol/HA) ✓ Good fit quality (FQ -6.79) ✓ Strong H-bond network (16 bonds) ✓ Deep burial (67% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Extreme strain energy (46.3 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-19.664
kcal/mol
LE
-0.728
kcal/mol/HA
Fit Quality
-6.79
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
46.3 kcal/mol
SASA buried
67%
Lipo contact
71% BSA apolar/total
SASA unbound
612 Ų
Apolar buried
291 Ų

Interaction summary

HB 16 HY 3 PI 1 CLASH 5 ⚠ Exposure 64%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (11/17 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 17 Buried (contacted) 6 Exposed 11 LogP 2.03 H-bonds 16
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank5.409Score-19.664
Inter norm-0.937Intra norm0.209
Top1000noExcludedno
Contacts12H-bonds16
Artifact reasongeometry warning; 12 clashes; 3 protein clashes; high strain Δ 46.3
Residues
ALA15 ARG116 ARG140 ARG144 ASP13 CYS72 GLY73 HIS105 HIS14 HIS141 SER46 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 overlap11Native recall0.65
Jaccard0.61RMSD-
HB strict6Strict recall0.46
HB same residue+role5HB role recall0.45
HB same residue5HB residue recall0.45

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
346 0.35538722495997677 -0.978913 -25.6036 2 13 0 0.00 0.00 - no Open
293 1.274900942951345 -1.03583 -28.5719 7 12 0 0.00 0.00 - no Open
323 1.3627403067812827 -0.906394 -18.7308 3 16 0 0.00 0.00 - no Open
375 2.0500114754417558 -1.04631 -29.6312 5 15 0 0.00 0.00 - no Open
318 2.0823117440239103 -1.13317 -28.9361 12 15 0 0.00 0.00 - no Open
322 2.294639162656896 -0.986167 -29.4161 5 20 0 0.00 0.00 - no Open
441 2.5220455662358785 -0.89302 -25.8372 8 15 0 0.00 0.00 - no Open
338 2.659289984590069 -0.997905 -24.9728 12 15 0 0.00 0.00 - no Open
392 2.7685730244744846 -1.12247 -31.1016 6 15 0 0.00 0.00 - no Open
333 3.6903577688505305 -0.859379 -21.1312 9 16 0 0.00 0.00 - no Open
343 3.8983164634663794 -0.849572 -21.6991 9 14 0 0.00 0.00 - no Open
372 3.9624227153920875 -1.10356 -28.0126 4 18 0 0.00 0.00 - no Open
282 4.021294943242523 -1.239 -35.8435 9 17 0 0.00 0.00 - no Open
316 4.705477255827921 -1.17836 -28.5533 9 21 0 0.00 0.00 - no Open
287 4.830955251729373 -1.16188 -25.6924 10 15 5 0.29 0.27 - no Open
353 5.092204702816937 -0.795238 -22.7627 7 12 0 0.00 0.00 - no Open
272 5.40909853377186 -0.937498 -19.6641 16 12 11 0.65 0.45 - no Current
409 5.703467463727863 -0.909529 -26.8524 10 16 0 0.00 0.00 - no Open
296 6.199766084150915 -1.0563 -30.5291 13 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 -19.664kcal/mol
Ligand efficiency (LE) -0.7283kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.795
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) 46.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -12.06kcal/mol
Minimised FF energy -58.37kcal/mol

SASA & burial

✓ computed
SASA (unbound) 611.8Ų
Total solvent-accessible surface area of free ligand
BSA total 408.0Ų
Buried surface area upon binding
BSA apolar 291.3Ų
Hydrophobic contacts buried
BSA polar 116.7Ų
Polar contacts buried
Fraction buried 66.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2202.1Ų
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 670.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)