FAIRMol

NMT-TY0959

Pose ID 6382 Compound 527 Pose 286

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-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
32.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.45
Burial
72%
Hydrophobic fit
74%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 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 ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.941 kcal/mol/HA) ✓ Good fit quality (FQ -8.78) ✓ Strong H-bond network (13 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (74%) ✗ Very high strain energy (32.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-25.394
kcal/mol
LE
-0.941
kcal/mol/HA
Fit Quality
-8.78
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
32.7 kcal/mol
SASA buried
72%
Lipo contact
74% BSA apolar/total
SASA unbound
646 Ų
Apolar buried
347 Ų

Interaction summary

HB 13 HY 1 PI 2 CLASH 3 ⚠ 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 13
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank4.081Score-25.394
Inter norm-0.908Intra norm-0.032
Top1000noExcludedno
Contacts15H-bonds13
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; high strain Δ 32.7
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 ASP13 ASP44 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
Jaccard0.60RMSD-
HB strict6Strict recall0.46
HB same residue+role5HB role recall0.45
HB same residue6HB residue recall0.55

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
350 0.3629211958252925 -0.926251 -24.8853 2 13 0 0.00 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 0 0.00 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 0 0.00 0.00 - no Open
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 12 0.71 0.45 - no Current
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 -25.394kcal/mol
Ligand efficiency (LE) -0.9405kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.775
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) 32.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -46.56kcal/mol
Minimised FF energy -79.25kcal/mol

SASA & burial

✓ computed
SASA (unbound) 645.6Ų
Total solvent-accessible surface area of free ligand
BSA total 467.5Ų
Buried surface area upon binding
BSA apolar 347.1Ų
Hydrophobic contacts buried
BSA polar 120.3Ų
Polar contacts buried
Fraction buried 72.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2231.7Ų
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 661.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)