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
23.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.35, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.574 kcal/mol/HA)
✓ Good fit quality (FQ -5.69)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (23.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-18.935
kcal/mol
LE
-0.574
kcal/mol/HA
Fit Quality
-5.69
FQ (Leeson)
HAC
33
heavy atoms
MW
452
Da
LogP
4.67
cLogP
Interaction summary
HB 6
HY 14
PI 1
CLASH 2
Interaction summary
HB 6
HY 14
PI 1
CLASH 2
| Final rank | 3.667 | Score | -18.935 |
|---|---|---|---|
| Inter norm | -0.698 | Intra norm | 0.124 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 6 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; moderate strain Δ 22.6 | ||
| Residues |
ALA284
ARG228
ARG287
ARG331
GLY197
GLY229
GLY286
GLY376
HIS428
ILE199
ILE378
LEU332
LEU377
MET333
PHE198
PHE230
SER200
THR374
VAL381
| ||
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 | 0.35 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 268 | 0.974102900606285 | -0.753355 | -22.1827 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 275 | 2.048310136114584 | -0.934394 | -26.071 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 315 | 3.3238944949654337 | -0.72587 | -20.4346 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 291 | 3.5287369862351285 | -0.96868 | -26.5329 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 314 | 3.6667135220935343 | -0.697525 | -18.9353 | 6 | 19 | 8 | 0.67 | 1.00 | - | no | Current |
| 211 | 4.016080999071254 | -0.860195 | -23.0569 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 218 | 4.624022710023361 | -0.952362 | -25.0393 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 322 | 4.667651235211368 | -0.611785 | -19.6032 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 341 | 4.781422519779941 | -0.793315 | -20.1332 | 4 | 20 | 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
-18.935kcal/mol
Ligand efficiency (LE)
-0.5738kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.693
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
451.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.67
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.25kcal/mol
Minimised FF energy
25.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
759.2Ų
Total solvent-accessible surface area of free ligand
BSA total
584.8Ų
Buried surface area upon binding
BSA apolar
454.4Ų
Hydrophobic contacts buried
BSA polar
130.3Ų
Polar contacts buried
Fraction buried
77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6610.0Ų
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
2079.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)