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 medium
Native mixed
SASA done
Strain ΔE
38.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.42, Jaccard 0.24, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (6/12 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 (-1.098 kcal/mol/HA)
✓ Good fit quality (FQ -9.53)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (79% SASA buried)
✗ Very high strain energy (38.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-24.155
kcal/mol
LE
-1.098
kcal/mol/HA
Fit Quality
-9.53
FQ (Leeson)
HAC
22
heavy atoms
MW
341
Da
LogP
1.09
cLogP
Interaction summary
HB 12
HY 4
PI 0
CLASH 2
⚠ Exposure 50%
Interaction summary
HB 12
HY 4
PI 0
CLASH 2
⚠ Exposure 50%
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 12
Buried (contacted) 6
Exposed 6
LogP 1.09
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 4.759 | Score | -24.155 |
|---|---|---|---|
| Inter norm | -1.028 | Intra norm | -0.072 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 12 |
| Artifact reason | geometry warning; 11 clashes; 3 protein clashes; high strain Δ 38.9 | ||
| Residues |
ALA363
ARG361
CYS375
GLY229
GLY376
HIS359
HIS428
LEU332
LEU377
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 | 5 | Native recall | 0.42 |
| Jaccard | 0.24 | 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 290 | 1.2400918844836533 | -1.32566 | -31.3991 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 280 | 1.9479445650642564 | -1.4541 | -34.0963 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 316 | 2.5592650100209733 | -1.17281 | -27.0734 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 351 | 3.2313434384288184 | -0.875523 | -24.1215 | 7 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 4.637274696060762 | -1.28123 | -30.212 | 11 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 364 | 4.759061949290954 | -1.02841 | -24.1546 | 12 | 14 | 5 | 0.42 | 0.00 | - | no | Current |
| 268 | 4.912505546384761 | -1.13782 | -27.2844 | 16 | 17 | 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
-24.155kcal/mol
Ligand efficiency (LE)
-1.0979kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.532
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.09
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-32.53kcal/mol
Minimised FF energy
-71.45kcal/mol
SASA & burial
✓ computed
SASA (unbound)
501.1Ų
Total solvent-accessible surface area of free ligand
BSA total
394.2Ų
Buried surface area upon binding
BSA apolar
230.6Ų
Hydrophobic contacts buried
BSA polar
163.7Ų
Polar contacts buried
Fraction buried
78.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
58.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6325.3Ų
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
2073.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)