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
24.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.92, Jaccard 0.55, H-bond role recall 1.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.669 kcal/mol/HA)
✓ Good fit quality (FQ -6.58)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (24.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-21.407
kcal/mol
LE
-0.669
kcal/mol/HA
Fit Quality
-6.58
FQ (Leeson)
HAC
32
heavy atoms
MW
489
Da
LogP
5.72
cLogP
Interaction summary
HB 6
HY 22
PI 1
CLASH 3
Interaction summary
HB 6
HY 22
PI 1
CLASH 3
| Final rank | 3.044 | Score | -21.407 |
|---|---|---|---|
| Inter norm | -0.743 | Intra norm | 0.074 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 6 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; moderate strain Δ 24.9 | ||
| Residues |
ALA363
ALA365
ARG287
ARG331
CYS375
GLY229
GLY286
GLY376
ILE378
LEU332
LEU334
LEU377
MET333
PHE198
PHE230
SER364
THR374
VAL362
VAL366
| ||
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 | 11 | Native recall | 0.92 |
| Jaccard | 0.55 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 510 | 0.44269170806396874 | -1.00413 | -30.7602 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 544 | 1.5733765538674693 | -0.675582 | -18.7344 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 503 | 2.309850622994656 | -0.7127 | -11.5838 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 541 | 3.0441164591847025 | -0.743402 | -21.4074 | 6 | 19 | 11 | 0.92 | 1.00 | - | no | Current |
| 512 | 3.446651160020602 | -0.610102 | -13.3601 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 511 | 4.060375456898433 | -0.923649 | -20.4653 | 9 | 21 | 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
-21.407kcal/mol
Ligand efficiency (LE)
-0.6690kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.579
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
489.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.72
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-16.06kcal/mol
Minimised FF energy
-40.91kcal/mol
SASA & burial
✓ computed
SASA (unbound)
741.6Ų
Total solvent-accessible surface area of free ligand
BSA total
601.1Ų
Buried surface area upon binding
BSA apolar
469.9Ų
Hydrophobic contacts buried
BSA polar
131.2Ų
Polar contacts buried
Fraction buried
81.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6582.0Ų
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
2081.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)