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 strong
SASA done
Strain ΔE
28.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.83, Jaccard 0.56, H-bond role recall 1.00
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.702 kcal/mol/HA)
✓ Good fit quality (FQ -6.84)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (28.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-21.762
kcal/mol
LE
-0.702
kcal/mol/HA
Fit Quality
-6.84
FQ (Leeson)
HAC
31
heavy atoms
MW
469
Da
LogP
6.28
cLogP
Interaction summary
HB 2
HY 24
PI 2
CLASH 4
Interaction summary
HB 2
HY 24
PI 2
CLASH 4
| Final rank | 3.772 | Score | -21.762 |
|---|---|---|---|
| Inter norm | -0.721 | Intra norm | 0.019 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 2 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 28.9 | ||
| Residues |
ALA284
ARG228
ARG287
ARG331
ASP330
GLY197
GLY229
ILE199
ILE288
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
| ||
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 | 10 | Native recall | 0.83 |
| Jaccard | 0.56 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 594 | 1.3410706819170013 | -1.07491 | -32.7142 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 592 | 2.522743900294449 | -0.986254 | -30.4983 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 610 | 3.1552936204718893 | -0.718939 | -21.2695 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 592 | 3.563539399678035 | -0.923231 | -29.0561 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 605 | 3.7722593377195173 | -0.721287 | -21.7618 | 2 | 16 | 10 | 0.83 | 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
-21.762kcal/mol
Ligand efficiency (LE)
-0.7020kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.839
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
469.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.28
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.03kcal/mol
Minimised FF energy
70.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
727.2Ų
Total solvent-accessible surface area of free ligand
BSA total
585.9Ų
Buried surface area upon binding
BSA apolar
483.1Ų
Hydrophobic contacts buried
BSA polar
102.8Ų
Polar contacts buried
Fraction buried
80.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6544.7Ų
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
2138.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)