FAIRMol

NMT-TY0624

Pose ID 6352 Compound 616 Pose 256

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-TY0624

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
40.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.71, Jaccard 0.67, H-bond role recall 0.36
Burial
62%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
4 protein-contact clashes 4 intramolecular clashes 62% of hydrophobic surface is solvent-exposed (10/16 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 (-0.725 kcal/mol/HA) ✓ Good fit quality (FQ -6.68) ✓ Strong H-bond network (12 bonds) ✓ Good burial (62% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Extreme strain energy (40.6 kcal/mol) ✗ Geometry warnings ✗ Severe protein-contact clashes (14) ✗ Many internal clashes (11)
Score
-18.856
kcal/mol
LE
-0.725
kcal/mol/HA
Fit Quality
-6.68
FQ (Leeson)
HAC
26
heavy atoms
MW
396
Da
LogP
2.16
cLogP
Strain ΔE
40.6 kcal/mol
SASA buried
62%
Lipo contact
71% BSA apolar/total
SASA unbound
644 Ų
Apolar buried
286 Ų

Interaction summary

HB 12 HY 3 PI 1 CLASH 4 ⚠ Exposure 62%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
62% of hydrophobic surface is solvent-exposed (10/16 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 16 Buried (contacted) 6 Exposed 10 LogP 2.16 H-bonds 12
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)
Final rank2.495Score-18.856
Inter norm-0.975Intra norm0.230
Top1000noExcludedno
Contacts13H-bonds12
Artifact reasongeometry warning; 11 clashes; 14 protein contact clashes; high strain Δ 40.6
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 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 overlap12Native recall0.71
Jaccard0.67RMSD-
HB strict5Strict recall0.38
HB same residue+role4HB role recall0.36
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
323 0.604003958058523 -0.942657 -21.1902 4 15 0 0.00 0.00 - no Open
291 0.6323186320960439 -1.22038 -30.9952 10 13 0 0.00 0.00 - no Open
329 1.875810958250805 -0.873591 -23.2439 4 10 0 0.00 0.00 - no Open
290 2.002828557753335 -1.14993 -29.8501 9 14 0 0.00 0.00 - no Open
310 2.224044674964138 -0.998085 -25.5439 8 18 0 0.00 0.00 - no Open
274 2.2594370727836455 -1.19735 -30.4625 8 17 0 0.00 0.00 - no Open
363 2.3368706908166565 -1.24065 -32.9492 6 14 0 0.00 0.00 - no Open
296 2.3850699368176747 -1.30385 -33.7876 14 22 0 0.00 0.00 - no Open
256 2.4947555472898184 -0.974719 -18.8557 12 13 12 0.71 0.36 - no Current
354 2.712760058770864 -1.25519 -32.5296 10 15 0 0.00 0.00 - no Open
425 3.1536405973770054 -1.02037 -26.076 10 16 0 0.00 0.00 - no Open
270 3.5240590701875685 -1.13687 -30.0974 8 15 5 0.29 0.18 - no Open
349 3.8084335922387926 -0.992658 -26.3696 8 20 0 0.00 0.00 - no Open
380 3.892965236960112 -1.26373 -32.5926 8 16 0 0.00 0.00 - no Open
394 4.604769733373062 -0.872118 -21.6077 9 12 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 -18.856kcal/mol
Ligand efficiency (LE) -0.7252kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.682
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 26HA

Physicochemical properties
Molecular weight 395.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.16
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -36.94kcal/mol
Minimised FF energy -77.57kcal/mol

SASA & burial

✓ computed
SASA (unbound) 643.9Ų
Total solvent-accessible surface area of free ligand
BSA total 402.6Ų
Buried surface area upon binding
BSA apolar 286.4Ų
Hydrophobic contacts buried
BSA polar 116.2Ų
Polar contacts buried
Fraction buried 62.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2245.6Ų
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 649.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)