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
32.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.58, Jaccard 0.33, H-bond role recall 0.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.002 kcal/mol/HA)
✓ Good fit quality (FQ -8.85)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Very high strain energy (32.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-23.054
kcal/mol
LE
-1.002
kcal/mol/HA
Fit Quality
-8.85
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
1.48
cLogP
Interaction summary
HB 9
HY 12
PI 1
CLASH 4
Interaction summary
HB 9
HY 12
PI 1
CLASH 4
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
| Final rank | 4.582 | Score | -23.054 |
|---|---|---|---|
| Inter norm | -0.986 | Intra norm | -0.016 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 9 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes; high strain Δ 32.8 | ||
| Residues |
ALA363
ARG361
CYS375
GLY229
GLY376
HIS428
ILE378
LEU332
LEU334
LEU377
PHE198
PHE230
SER364
THR360
THR374
VAL362
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 7 | Native recall | 0.58 |
| Jaccard | 0.33 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 288 | 0.20192228123766293 | -1.21712 | -29.6937 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 370 | 0.6348683777601668 | -1.142 | -24.918 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 314 | 2.0007556183948436 | -1.31447 | -28.3882 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 314 | 4.248882186101904 | -1.31492 | -26.8174 | 9 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 267 | 4.381996393690403 | -1.05285 | -23.0598 | 14 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 362 | 4.581830996133959 | -0.986025 | -23.0541 | 9 | 16 | 7 | 0.58 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.054kcal/mol
Ligand efficiency (LE)
-1.0024kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.847
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.48
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-42.32kcal/mol
Minimised FF energy
-75.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
566.6Ų
Total solvent-accessible surface area of free ligand
BSA total
469.4Ų
Buried surface area upon binding
BSA apolar
334.4Ų
Hydrophobic contacts buried
BSA polar
135.0Ų
Polar contacts buried
Fraction buried
82.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6423.7Ų
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
2036.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)