FAIRMol

NMT-TY0254

Pose ID 14491 Compound 5504 Pose 253

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
T22
L. donovani rab5a L. donovani
Ligand NMT-TY0254

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 mixed SASA done
Strain ΔE
27.4 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.43, Jaccard 0.31, H-bond role recall 0.36
Burial
94%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 100% of hydrophobic surface is solvent-exposed (7/7 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 (-2.263 kcal/mol/HA) ✓ Good fit quality (FQ -16.18) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (27.4 kcal/mol) ✗ Geometry warnings
Score
-31.675
kcal/mol
LE
-2.263
kcal/mol/HA
Fit Quality
-16.18
FQ (Leeson)
HAC
14
heavy atoms
MW
278
Da
LogP
0.41
cLogP
Final rank
3.0953
rank score
Inter norm
-2.286
normalised
Contacts
17
H-bonds 15
Strain ΔE
27.4 kcal/mol
SASA buried
94%
Lipo contact
71% BSA apolar/total
SASA unbound
402 Ų
Apolar buried
268 Ų

Interaction summary

HBD 3 HBA 5 HY 0 PI 0 CLASH 5

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap9Native recall0.43
Jaccard0.31RMSD-
HB strict6Strict recall0.40
HB same residue+role4HB role recall0.36
HB same residue4HB residue recall0.36

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
253 3.0952549134871976 -2.28584 -31.6752 15 17 9 0.43 0.36 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -31.675kcal/mol
Ligand efficiency (LE) -2.2625kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -16.177
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 14HA

Physicochemical properties
Molecular weight 278.1Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.41
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 27.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -65.77kcal/mol
Minimised FF energy -93.17kcal/mol

SASA & burial

✓ computed
SASA (unbound) 402.0Ų
Total solvent-accessible surface area of free ligand
BSA total 376.9Ų
Buried surface area upon binding
BSA apolar 267.9Ų
Hydrophobic contacts buried
BSA polar 109.0Ų
Polar contacts buried
Fraction buried 93.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1153.0Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 506.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)