Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
29.4 kcal/mol
Protein clashes
0
Internal clashes
18
Native overlap
contact recall 0.92, Jaccard 0.50, H-bond role recall 0.00
Reason: 18 internal clashes
18 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (14/40 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.404 kcal/mol/HA)
✓ Good fit quality (FQ -4.32)
✓ Good H-bonds (3 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (98%)
✗ High strain energy (29.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-17.776
kcal/mol
LE
-0.404
kcal/mol/HA
Fit Quality
-4.32
FQ (Leeson)
HAC
44
heavy atoms
MW
584
Da
LogP
8.34
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
⚠ Exposure 35%
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
⚠ Exposure 35%
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
No clash · clashes detected for this pose.
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (14/40 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 40
Buried (contacted) 26
Exposed 14
LogP 8.34
H-bonds 3
Exposed fragments:
phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 2.569 | Score | -17.776 |
|---|---|---|---|
| Inter norm | -0.518 | Intra norm | 0.114 |
| Top1000 | no | Excluded | no |
| Contacts | 21 | H-bonds | 3 |
| Artifact reason | geometry warning; 18 clashes; 1 protein clash; moderate strain Δ 27.9 | ||
| Residues |
ALA284
ALA365
ARG287
ARG331
GLY197
GLY229
GLY286
GLY376
HIS428
ILE199
ILE378
LEU332
LEU334
LEU377
MET333
PHE198
PHE230
SER200
SER364
THR374
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 | 11 | Native recall | 0.92 |
| Jaccard | 0.50 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 257 | 2.569055394195097 | -0.518156 | -17.7761 | 3 | 21 | 11 | 0.92 | 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
-17.776kcal/mol
Ligand efficiency (LE)
-0.4040kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.317
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
44HA
Physicochemical properties
Molecular weight
583.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
8.34
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
144.42kcal/mol
Minimised FF energy
115.03kcal/mol
SASA & burial
✓ computed
SASA (unbound)
922.2Ų
Total solvent-accessible surface area of free ligand
BSA total
707.8Ų
Buried surface area upon binding
BSA apolar
693.2Ų
Hydrophobic contacts buried
BSA polar
14.6Ų
Polar contacts buried
Fraction buried
76.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6900.8Ų
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
2068.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)