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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
24.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.40, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.666 kcal/mol/HA)
✓ Good fit quality (FQ -6.43)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (24.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-19.990
kcal/mol
LE
-0.666
kcal/mol/HA
Fit Quality
-6.43
FQ (Leeson)
HAC
30
heavy atoms
MW
396
Da
LogP
4.43
cLogP
Interaction summary
HB 9
HY 10
PI 1
CLASH 2
Interaction summary
HB 9
HY 10
PI 1
CLASH 2
| Final rank | 4.755 | Score | -19.990 |
|---|---|---|---|
| Inter norm | -0.756 | Intra norm | 0.090 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 9 |
| Artifact reason | geometry warning; 14 clashes; 3 protein clashes; moderate strain Δ 24.6 | ||
| Residues |
ARG228
ARG331
ARG361
CYS375
GLY229
GLY376
HIS359
ILE378
LEU332
LEU377
MET333
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 | 8 | Native recall | 0.67 |
| Jaccard | 0.40 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 479 | 0.6279445494347249 | -0.84408 | -21.9705 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 406 | 0.915129823933346 | -0.83686 | -13.244 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 449 | 1.908233052533173 | -0.74441 | -18.4215 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 431 | 4.433335430960952 | -0.660659 | -19.3115 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 4.754749031571437 | -0.756172 | -19.9896 | 9 | 16 | 8 | 0.67 | 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
-19.990kcal/mol
Ligand efficiency (LE)
-0.6663kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.428
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
396.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.43
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
166.20kcal/mol
Minimised FF energy
141.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
676.7Ų
Total solvent-accessible surface area of free ligand
BSA total
489.6Ų
Buried surface area upon binding
BSA apolar
381.4Ų
Hydrophobic contacts buried
BSA polar
108.2Ų
Polar contacts buried
Fraction buried
72.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6483.9Ų
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
2147.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)