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 high
Native mixed
SASA done
Strain ΔE
15.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.42, Jaccard 0.21, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.242 kcal/mol/HA)
✓ Good fit quality (FQ -10.40)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (85% SASA buried)
✗ Moderate strain (15.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-24.849
kcal/mol
LE
-1.242
kcal/mol/HA
Fit Quality
-10.40
FQ (Leeson)
HAC
20
heavy atoms
MW
313
Da
LogP
0.64
cLogP
Interaction summary
HB 8
HY 6
PI 0
CLASH 1
Interaction summary
HB 8
HY 6
PI 0
CLASH 1
| Final rank | 3.459 | Score | -24.849 |
|---|---|---|---|
| Inter norm | -1.221 | Intra norm | -0.021 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 8 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ALA363
ARG361
ASP231
CYS375
GLY229
GLY376
HIS359
HIS428
ILE378
LEU332
LEU377
PHE230
SER364
THR360
THR374
VAL362
VAL381
| ||
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 | 5 | Native recall | 0.42 |
| Jaccard | 0.21 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 256 | 0.15772456433515986 | -1.39322 | -27.5062 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 326 | 1.7660606604934106 | -1.01819 | -19.6306 | 9 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 277 | 1.8546395330541607 | -1.1627 | -22.7243 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 335 | 1.9539662524601658 | -1.4959 | -28.3343 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 298 | 2.257908716162415 | -1.0958 | -22.0596 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 400 | 2.419978712999776 | -1.28962 | -25.9234 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 274 | 2.725557170482087 | -1.20833 | -23.6186 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 2.95166993836523 | -1.43344 | -26.7737 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 256 | 3.0930541913905487 | -1.30737 | -26.3803 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 336 | 3.114127828859795 | -1.30283 | -25.5336 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 348 | 3.3534428929750644 | -1.35737 | -25.171 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 320 | 3.4590025533125908 | -1.2212 | -24.8485 | 8 | 17 | 5 | 0.42 | 0.00 | - | no | Current |
| 230 | 3.7784047479922487 | -1.38875 | -26.8164 | 11 | 13 | 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
-24.849kcal/mol
Ligand efficiency (LE)
-1.2424kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.397
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
313.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.64
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-80.30kcal/mol
Minimised FF energy
-96.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
467.0Ų
Total solvent-accessible surface area of free ligand
BSA total
395.5Ų
Buried surface area upon binding
BSA apolar
187.6Ų
Hydrophobic contacts buried
BSA polar
208.0Ų
Polar contacts buried
Fraction buried
84.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
47.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6238.2Ų
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
2074.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)