Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
26.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.43, H-bond role recall 1.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.578 kcal/mol/HA)
✓ Good fit quality (FQ -5.63)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (26.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-17.915
kcal/mol
LE
-0.578
kcal/mol/HA
Fit Quality
-5.63
FQ (Leeson)
HAC
31
heavy atoms
MW
498
Da
LogP
4.09
cLogP
Interaction summary
HB 7
HY 24
PI 2
CLASH 3
Interaction summary
HB 7
HY 24
PI 2
CLASH 3
| Final rank | 2.346 | Score | -17.915 |
|---|---|---|---|
| Inter norm | -0.744 | Intra norm | 0.166 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 7 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; moderate strain Δ 26.8 | ||
| Residues |
ARG287
ARG331
ARG361
ASP330
CYS375
GLY229
GLY376
HIS359
HIS428
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR360
THR374
VAL362
| ||
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
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 | 9 | Native recall | 0.75 |
| Jaccard | 0.43 | RMSD | - |
| HB strict | 1 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 651 | 1.2636502207322342 | -0.848526 | -22.0344 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 656 | 1.3945405974040013 | -1.03109 | -23.2357 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 663 | 2.3456112024268174 | -0.744151 | -17.9154 | 7 | 18 | 9 | 0.75 | 1.00 | - | no | Current |
| 665 | 3.6065487690211078 | -0.845392 | -21.6251 | 7 | 15 | 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
-17.915kcal/mol
Ligand efficiency (LE)
-0.5779kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.630
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
498.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.09
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
20.32kcal/mol
Minimised FF energy
-6.53kcal/mol
SASA & burial
✓ computed
SASA (unbound)
753.1Ų
Total solvent-accessible surface area of free ligand
BSA total
603.9Ų
Buried surface area upon binding
BSA apolar
414.0Ų
Hydrophobic contacts buried
BSA polar
189.8Ų
Polar contacts buried
Fraction buried
80.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6521.4Ų
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
2100.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)