FAIRMol

NMT-TY0607

Pose ID 14526 Compound 617 Pose 288

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-TY0607

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
35.8 kcal/mol
Protein clashes
10
Internal clashes
10
Native overlap
contact recall 0.52, Jaccard 0.35, H-bond role recall 0.45
Burial
94%
Hydrophobic fit
66%
Reason: 10 protein-contact clashes, 10 internal clashes
10 protein-contact clashes 10 intramolecular clashes 92% of hydrophobic surface is solvent-exposed (12/13 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 (-1.299 kcal/mol/HA) ✓ Good fit quality (FQ -11.47) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Very high strain energy (35.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-29.885
kcal/mol
LE
-1.299
kcal/mol/HA
Fit Quality
-11.47
FQ (Leeson)
HAC
23
heavy atoms
MW
353
Da
LogP
1.01
cLogP
Final rank
5.3708
rank score
Inter norm
-1.314
normalised
Contacts
21
H-bonds 16
Strain ΔE
35.8 kcal/mol
SASA buried
94%
Lipo contact
66% BSA apolar/total
SASA unbound
562 Ų
Apolar buried
353 Ų

Interaction summary

HBD 2 HBA 8 HY 2 PI 0 CLASH 10

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

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 overlap11Native recall0.52
Jaccard0.35RMSD-
HB strict6Strict recall0.40
HB same residue+role5HB role recall0.45
HB same residue5HB residue recall0.45

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
316 1.9160126527138646 -0.936024 -21.449 5 12 0 0.00 0.00 - no Open
278 1.9632061033636858 -1.23187 -29.5802 9 14 0 0.00 0.00 - no Open
335 2.279560783148469 -0.836864 -20.633 9 11 0 0.00 0.00 - no Open
298 2.4959341423803725 -1.18433 -27.7045 6 17 1 0.05 0.00 - no Open
350 2.8871935436214495 -1.13026 -23.8892 7 15 0 0.00 0.00 - no Open
328 3.34922510797409 -0.990588 -23.4443 11 12 0 0.00 0.00 - no Open
385 3.5748823696267844 -1.1536 -27.6164 8 16 0 0.00 0.00 - no Open
347 3.741128851709964 -1.38593 -32.0766 10 15 0 0.00 0.00 - no Open
366 3.895818972211368 -1.29627 -28.5384 8 15 0 0.00 0.00 - no Open
339 4.420406439957224 -0.972962 -25.0114 8 18 0 0.00 0.00 - no Open
248 4.628592872571314 -1.0994 -24.8798 15 14 0 0.00 0.00 - no Open
288 5.3707651519523365 -1.31364 -29.8849 16 21 11 0.52 0.45 - 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 -29.885kcal/mol
Ligand efficiency (LE) -1.2993kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.468
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 23HA

Physicochemical properties
Molecular weight 353.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.01
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -83.01kcal/mol
Minimised FF energy -118.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 562.3Ų
Total solvent-accessible surface area of free ligand
BSA total 530.4Ų
Buried surface area upon binding
BSA apolar 352.6Ų
Hydrophobic contacts buried
BSA polar 177.8Ų
Polar contacts buried
Fraction buried 94.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1245.3Ų
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 500.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)