FAIRMol

NMT-TY0977

Pose ID 14571 Compound 3188 Pose 333

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
T22
L. donovani rab5a L. donovani
Ligand NMT-TY0977

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 strong SASA done
Strain ΔE
35.3 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.62, Jaccard 0.48, H-bond role recall 0.36
Burial
87%
Hydrophobic fit
72%
Reason: 8 internal clashes
8 protein-contact clashes 8 intramolecular clashes 77% of hydrophobic surface is solvent-exposed (10/13 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 (-1.341 kcal/mol/HA) ✓ Good fit quality (FQ -11.64) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (87% SASA buried) ✓ Lipophilic contacts well-matched (72%) ✗ Very high strain energy (35.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-29.508
kcal/mol
LE
-1.341
kcal/mol/HA
Fit Quality
-11.64
FQ (Leeson)
HAC
22
heavy atoms
MW
340
Da
LogP
1.66
cLogP
Strain ΔE
35.3 kcal/mol
SASA buried
87%
Lipo contact
72% BSA apolar/total
SASA unbound
570 Ų
Apolar buried
354 Ų

Interaction summary

HB 8 HY 4 PI 0 CLASH 8 ⚠ Exposure 76%

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
77% of hydrophobic surface is solvent-exposed (10/13 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 13 Buried (contacted) 3 Exposed 10 LogP 1.66 H-bonds 8
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)
Final rank4.569Score-29.508
Inter norm-1.400Intra norm0.059
Top1000noExcludedno
Contacts19H-bonds8
Artifact reasongeometry warning; 7 clashes; 3 protein clashes; high strain Δ 35.3
Residues
ALA158 ALA24 ALA70 ASN126 ASP68 GLU73 GLY23 GLY25 GLY71 ILE29 LYS127 LYS159 LYS26 PHE38 SER22 SER27 SER28 THR44 THR69

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
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 overlap13Native recall0.62
Jaccard0.48RMSD-
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
340 1.0139970207698543 -1.27417 -26.6955 9 14 0 0.00 0.00 - no Open
288 4.170702248235619 -1.10047 -25.0737 12 11 0 0.00 0.00 - no Open
333 4.569152508881392 -1.40034 -29.5081 8 19 13 0.62 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 -29.508kcal/mol
Ligand efficiency (LE) -1.3413kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.645
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 340.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.66
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -60.74kcal/mol
Minimised FF energy -96.07kcal/mol

SASA & burial

✓ computed
SASA (unbound) 569.6Ų
Total solvent-accessible surface area of free ligand
BSA total 495.5Ų
Buried surface area upon binding
BSA apolar 354.2Ų
Hydrophobic contacts buried
BSA polar 141.3Ų
Polar contacts buried
Fraction buried 87.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 71.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1265.5Ų
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 504.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)