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
26.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.33, Jaccard 0.20, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.959 kcal/mol/HA)
✓ Good fit quality (FQ -8.03)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ High strain energy (26.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-19.181
kcal/mol
LE
-0.959
kcal/mol/HA
Fit Quality
-8.03
FQ (Leeson)
HAC
20
heavy atoms
MW
301
Da
LogP
0.51
cLogP
Interaction summary
HB 9
HY 16
PI 0
CLASH 1
Interaction summary
HB 9
HY 16
PI 0
CLASH 1
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
| Final rank | 3.935 | Score | -19.181 |
|---|---|---|---|
| Inter norm | -1.181 | Intra norm | 0.214 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 9 |
| Artifact reason | geometry warning; 5 clashes; 4 protein clashes; moderate strain Δ 26.6 | ||
| Residues |
ALA284
ARG287
ARG331
ASP330
FAD501
GLY197
GLY286
ILE199
LEU332
MET333
PHE198
SER200
| ||
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 | 4 | Native recall | 0.33 |
| Jaccard | 0.20 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 51 | 1.7406734057768396 | -1.55099 | -25.3992 | 14 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 63 | 2.0699265523486603 | -1.3784 | -25.6176 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 3.037310309051502 | -1.6924 | -29.4294 | 12 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 60 | 3.9346894583368592 | -1.18087 | -19.1811 | 9 | 12 | 4 | 0.33 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.181kcal/mol
Ligand efficiency (LE)
-0.9591kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.026
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
301.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.51
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
60.34kcal/mol
Minimised FF energy
33.72kcal/mol
SASA & burial
✓ computed
SASA (unbound)
507.1Ų
Total solvent-accessible surface area of free ligand
BSA total
429.7Ų
Buried surface area upon binding
BSA apolar
293.2Ų
Hydrophobic contacts buried
BSA polar
136.4Ų
Polar contacts buried
Fraction buried
84.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6326.1Ų
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
2078.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)