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 medium
Native mixed
SASA done
Strain ΔE
17.4 kcal/mol
Protein clashes
0
Internal clashes
5
Native overlap
contact recall 0.25, Jaccard 0.14, 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 (-1.459 kcal/mol/HA)
✓ Good fit quality (FQ -10.78)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ Moderate strain (17.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-21.891
kcal/mol
LE
-1.459
kcal/mol/HA
Fit Quality
-10.78
FQ (Leeson)
HAC
15
heavy atoms
MW
211
Da
LogP
0.44
cLogP
Interaction summary
HB 9
HY 4
PI 0
CLASH 0
Interaction summary
HB 9
HY 4
PI 0
CLASH 0
| Final rank | 3.181 | Score | -21.891 |
|---|---|---|---|
| Inter norm | -1.490 | Intra norm | 0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 9 |
| Artifact reason | geometry warning; 5 clashes; 3 protein clashes | ||
| Residues |
ALA363
ARG361
CYS375
GLY229
GLY376
HIS428
ILE378
LEU377
SER364
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 | 3 | Native recall | 0.25 |
| Jaccard | 0.14 | 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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 386 | 3.1537424582908806 | -1.59616 | -22.9103 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 3.181180781627081 | -1.48991 | -21.8913 | 9 | 12 | 3 | 0.25 | 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
-21.891kcal/mol
Ligand efficiency (LE)
-1.4594kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.784
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
15HA
Physicochemical properties
Molecular weight
211.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.44
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
96.61kcal/mol
Minimised FF energy
79.18kcal/mol
SASA & burial
✓ computed
SASA (unbound)
400.0Ų
Total solvent-accessible surface area of free ligand
BSA total
316.8Ų
Buried surface area upon binding
BSA apolar
212.2Ų
Hydrophobic contacts buried
BSA polar
104.6Ų
Polar contacts buried
Fraction buried
79.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6272.0Ų
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
2071.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)