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
23.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.67, Jaccard 0.36, H-bond role recall 0.00
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 (-0.821 kcal/mol/HA)
✓ Good fit quality (FQ -8.00)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (23.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-25.457
kcal/mol
LE
-0.821
kcal/mol/HA
Fit Quality
-8.00
FQ (Leeson)
HAC
31
heavy atoms
MW
451
Da
LogP
4.63
cLogP
Interaction summary
HB 6
HY 23
PI 2
CLASH 4
Interaction summary
HB 6
HY 23
PI 2
CLASH 4
| Final rank | 4.175 | Score | -25.457 |
|---|---|---|---|
| Inter norm | -0.802 | Intra norm | -0.021 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 6 |
| Artifact reason | geometry warning; 15 clashes; 2 protein clashes; moderate strain Δ 23.5 | ||
| Residues |
ALA284
ARG228
ARG287
FAD501
GLY197
GLY229
GLY286
ILE199
ILE285
LEU227
LEU332
MET333
PHE198
PHE230
SER200
SER364
THR374
TYR221
| ||
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 | 8 | Native recall | 0.67 |
| Jaccard | 0.36 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 42 | 1.0426031739314607 | -0.836239 | -27.5481 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 1.9318321877769988 | -1.03087 | -29.6858 | 7 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 2.3469721121039115 | -0.816895 | -23.6732 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 36 | 3.074788073515166 | -0.631542 | -21.1495 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 3.138153233369263 | -0.890921 | -26.4119 | 9 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 13 | 3.1677712491206673 | -0.987749 | -24.3059 | 14 | 25 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 3.4007343352884067 | -0.989543 | -31.2451 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 20 | 3.844040829625686 | -0.799136 | -21.7562 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 4.174650705505495 | -0.802112 | -25.4569 | 6 | 18 | 8 | 0.67 | 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
-25.457kcal/mol
Ligand efficiency (LE)
-0.8212kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.000
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
450.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.63
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
16.18kcal/mol
Minimised FF energy
-7.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
718.8Ų
Total solvent-accessible surface area of free ligand
BSA total
600.5Ų
Buried surface area upon binding
BSA apolar
482.6Ų
Hydrophobic contacts buried
BSA polar
117.9Ų
Polar contacts buried
Fraction buried
83.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6535.3Ų
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
2114.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)