FAIRMol

NMT-TY0549

Pose ID 6335 Compound 411 Pose 239

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-TY0549

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
40.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.83, H-bond role recall 0.55
Burial
62%
Hydrophobic fit
59%
Reason: no major geometry red flags detected
2 protein-contact clashes 71% of hydrophobic surface is solvent-exposed (10/14 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 (-1.079 kcal/mol/HA) ✓ Good fit quality (FQ -10.07) ✓ Strong H-bond network (16 bonds) ✓ Good burial (62% SASA buried) ✗ Extreme strain energy (40.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-29.141
kcal/mol
LE
-1.079
kcal/mol/HA
Fit Quality
-10.07
FQ (Leeson)
HAC
27
heavy atoms
MW
395
Da
LogP
-1.19
cLogP
Strain ΔE
40.1 kcal/mol
SASA buried
62%
Lipo contact
59% BSA apolar/total
SASA unbound
653 Ų
Apolar buried
239 Ų

Interaction summary

HB 16 HY 3 PI 1 CLASH 2 ⚠ Exposure 71%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (10/14 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 14 Buried (contacted) 4 Exposed 10 LogP -1.19 H-bonds 16
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank4.314Score-29.141
Inter norm-1.005Intra norm-0.074
Top1000noExcludedno
Contacts16H-bonds16
Artifact reasongeometry warning; 8 clashes; 3 protein clashes; high strain Δ 40.1
Residues
ALA15 ARG116 ARG140 ARG144 ASN106 CYS72 GLY73 GLY75 GLY77 HIS105 HIS14 HIS141 ILE76 MET78 THR74 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 overlap15Native recall0.88
Jaccard0.83RMSD-
HB strict7Strict recall0.54
HB same residue+role6HB role recall0.55
HB same residue7HB residue recall0.64

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
263 1.9619591920682486 -1.07778 -26.3261 11 17 0 0.00 0.00 - no Open
307 1.973236208634677 -0.911074 -24.9818 7 15 0 0.00 0.00 - no Open
270 2.217204642698369 -1.21946 -32.7493 11 15 0 0.00 0.00 - no Open
352 2.4054056429997805 -0.963314 -22.8123 12 19 0 0.00 0.00 - no Open
276 2.4644015191207718 -1.23884 -34.4996 16 21 0 0.00 0.00 - no Open
287 2.4692123455684767 -0.887788 -22.8583 6 18 0 0.00 0.00 - no Open
293 2.5523531210354715 -1.25212 -32.8271 13 20 0 0.00 0.00 - no Open
264 3.2494165124044274 -1.31147 -36.2843 14 18 0 0.00 0.00 - no Open
377 3.300748553183803 -0.898096 -26.0956 7 13 0 0.00 0.00 - no Open
324 3.301523972802756 -0.915736 -26.3877 13 13 0 0.00 0.00 - no Open
239 4.313905727494139 -1.00534 -29.1414 16 16 15 0.88 0.55 - no Current
273 4.418567444093437 -1.2144 -31.3287 15 26 0 0.00 0.00 - no Open
284 4.844348523444292 -1.06372 -30.1625 10 15 0 0.00 0.00 - no Open
250 4.926468000366607 -1.2862 -36.0618 15 17 5 0.29 0.27 - 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 -29.141kcal/mol
Ligand efficiency (LE) -1.0793kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.070
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 395.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.19
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 40.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -153.39kcal/mol
Minimised FF energy -193.45kcal/mol

SASA & burial

✓ computed
SASA (unbound) 653.3Ų
Total solvent-accessible surface area of free ligand
BSA total 402.4Ų
Buried surface area upon binding
BSA apolar 239.0Ų
Hydrophobic contacts buried
BSA polar 163.4Ų
Polar contacts buried
Fraction buried 61.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 59.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2143.0Ų
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 697.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)