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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
19.4 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.67, Jaccard 0.42, H-bond role recall 0.00
Reason: no major geometry red flags detected
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.063 kcal/mol/HA)
✓ Good fit quality (FQ -9.53)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (19.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-25.508
kcal/mol
LE
-1.063
kcal/mol/HA
Fit Quality
-9.53
FQ (Leeson)
HAC
24
heavy atoms
MW
369
Da
LogP
0.38
cLogP
Interaction summary
HB 9
HY 22
PI 1
CLASH 0
Interaction summary
HB 9
HY 22
PI 1
CLASH 0
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
No clash · clashes detected for this pose.
| Final rank | 3.459 | Score | -25.508 |
|---|---|---|---|
| Inter norm | -1.031 | Intra norm | -0.032 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 9 |
| Artifact reason | geometry warning; 5 clashes; 3 protein clashes | ||
| Residues |
ALA363
ARG361
CYS375
GLY229
GLY376
HIS359
LEU332
LEU334
MET333
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 | 8 | Native recall | 0.67 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 374 | 2.0865146822246143 | -1.38198 | -34.324 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 413 | 2.6943961769928566 | -0.984124 | -21.2873 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 410 | 2.7399256456858576 | -1.07947 | -26.8497 | 10 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 459 | 3.458566031907076 | -1.03078 | -25.5076 | 9 | 15 | 8 | 0.67 | 0.00 | - | no | Current |
| 392 | 3.7441207624658626 | -1.27643 | -28.7503 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 387 | 4.41582415185168 | -1.27937 | -27.7085 | 14 | 16 | 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
-25.508kcal/mol
Ligand efficiency (LE)
-1.0628kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.525
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
369.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.38
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-22.66kcal/mol
Minimised FF energy
-42.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
588.9Ų
Total solvent-accessible surface area of free ligand
BSA total
473.6Ų
Buried surface area upon binding
BSA apolar
334.9Ų
Hydrophobic contacts buried
BSA polar
138.7Ų
Polar contacts buried
Fraction buried
80.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6421.9Ų
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
2043.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)