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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
9.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.44, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.951 kcal/mol/HA)
✓ Good fit quality (FQ -8.11)
✓ Good H-bonds (4 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (9.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-19.966
kcal/mol
LE
-0.951
kcal/mol/HA
Fit Quality
-8.11
FQ (Leeson)
HAC
21
heavy atoms
MW
294
Da
LogP
3.30
cLogP
Interaction summary
HB 4
HY 20
PI 3
CLASH 1
Interaction summary
HB 4
HY 20
PI 3
CLASH 1
| Final rank | 1.486 | Score | -19.966 |
|---|---|---|---|
| Inter norm | -1.059 | Intra norm | 0.108 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ALA284
ARG287
ARG331
GLY197
GLY286
ILE199
LEU332
LEU334
MET333
PHE198
PHE230
SER200
SER364
VAL366
| ||
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 | 8 | Native recall | 0.67 |
| Jaccard | 0.44 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 402 | 1.2167690104404725 | -1.34895 | -25.6842 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 485 | 1.4860261846578509 | -1.05884 | -19.9656 | 4 | 14 | 8 | 0.67 | 1.00 | - | no | Current |
| 425 | 2.519301932614363 | -1.38873 | -28.5459 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 418 | 3.3781155952566757 | -1.17369 | -21.3034 | 12 | 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
-19.966kcal/mol
Ligand efficiency (LE)
-0.9507kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.110
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
294.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.30
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
18.49kcal/mol
Minimised FF energy
9.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
504.6Ų
Total solvent-accessible surface area of free ligand
BSA total
437.7Ų
Buried surface area upon binding
BSA apolar
287.6Ų
Hydrophobic contacts buried
BSA polar
150.1Ų
Polar contacts buried
Fraction buried
86.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6316.2Ų
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
2071.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)