Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
33.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.45, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
71% of hydrophobic surface is solvent-exposed (24/34 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.501 kcal/mol/HA)
✓ Good fit quality (FQ -5.32)
✓ Good H-bonds (3 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (96%)
✗ Very high strain energy (33.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (23)
Score
-21.543
kcal/mol
LE
-0.501
kcal/mol/HA
Fit Quality
-5.32
FQ (Leeson)
HAC
43
heavy atoms
MW
654
Da
LogP
7.33
cLogP
Final rank
3.9691
rank score
Inter norm
-0.522
normalised
Contacts
17
H-bonds 3
Interaction summary
HBD 2
HBA 1
HY 5
PI 1
CLASH 3
Interaction summary
HBD 2
HBA 1
HY 5
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
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.
| Name | 5S9T | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA365
ARG228
ARG331
GLY229
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL366
| ||
| Current overlap | 9 | Native recall | 0.75 |
| Jaccard | 0.45 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
1033 residues
| Protein target | T17 | Atoms | 15160 |
|---|---|---|---|
| Residues | 1033 | Chains | 2 |
| Residue summary | VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408 | ||
Receptor context
2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
B:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 26 | 2.1688970873774895 | -0.58667 | -27.5364 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 9 | 2.3190570076294623 | -0.603254 | -21.9181 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 21 | 2.872325018187148 | -0.635792 | -24.439 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 3.3402080092915787 | -0.686468 | -26.5185 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 13 | 3.9691236791986175 | -0.521697 | -21.5427 | 3 | 17 | 9 | 0.75 | 0.00 | - | no | Current |
| 9 | 4.4414998865683915 | -0.646675 | -23.9393 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.543kcal/mol
Ligand efficiency (LE)
-0.5010kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.324
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
43HA
Physicochemical properties
Molecular weight
654.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.33
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
285.60kcal/mol
Minimised FF energy
252.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
835.1Ų
Total solvent-accessible surface area of free ligand
BSA total
595.2Ų
Buried surface area upon binding
BSA apolar
574.5Ų
Hydrophobic contacts buried
BSA polar
20.7Ų
Polar contacts buried
Fraction buried
71.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
96.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6713.4Ų
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
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2140.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)