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
12.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.47, 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 (-0.651 kcal/mol/HA)
✓ Good fit quality (FQ -6.34)
✓ Good H-bonds (4 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (99%)
✗ Moderate strain (12.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-20.181
kcal/mol
LE
-0.651
kcal/mol/HA
Fit Quality
-6.34
FQ (Leeson)
HAC
31
heavy atoms
MW
538
Da
LogP
6.38
cLogP
Interaction summary
HB 4
HY 24
PI 2
CLASH 2
Interaction summary
HB 4
HY 24
PI 2
CLASH 2
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
| Final rank | 2.444 | Score | -20.181 |
|---|---|---|---|
| Inter norm | -0.744 | Intra norm | 0.093 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash | ||
| Residues |
ALA284
ALA365
ARG287
ARG331
GLY286
HIS359
ILE199
LEU332
LEU334
MET333
PHE198
PHE230
VAL366
| ||
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 | 0.47 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 667 | 0.21288028751871968 | -1.04117 | -31.6316 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 665 | 1.829106599470338 | -0.901066 | -22.6062 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 2.4436102006853537 | -0.743977 | -20.1815 | 4 | 13 | 8 | 0.67 | 0.00 | - | no | Current |
| 665 | 2.7469642685769946 | -0.904768 | -22.6527 | 2 | 20 | 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
-20.181kcal/mol
Ligand efficiency (LE)
-0.6510kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.342
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
538.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.38
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
58.86kcal/mol
Minimised FF energy
46.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
749.3Ų
Total solvent-accessible surface area of free ligand
BSA total
554.1Ų
Buried surface area upon binding
BSA apolar
548.0Ų
Hydrophobic contacts buried
BSA polar
6.2Ų
Polar contacts buried
Fraction buried
74.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
98.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6703.8Ų
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
2097.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)