Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
17.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.40, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.854 kcal/mol/HA)
✓ Good fit quality (FQ -7.87)
✓ Good H-bonds (5 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Moderate strain (17.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-22.204
kcal/mol
LE
-0.854
kcal/mol/HA
Fit Quality
-7.87
FQ (Leeson)
HAC
26
heavy atoms
MW
399
Da
LogP
4.85
cLogP
Interaction summary
HB 5
HY 24
PI 2
CLASH 2
Interaction summary
HB 5
HY 24
PI 2
CLASH 2
| Final rank | 1.842 | Score | -22.204 |
|---|---|---|---|
| Inter norm | -0.854 | Intra norm | 0.000 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash | ||
| Residues |
ARG287
ARG361
CYS375
FAD501
GLY229
GLY376
HIS359
LEU332
LEU334
MET333
PHE198
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 | 8 | Native recall | 0.67 |
| Jaccard | 0.40 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 415 | 0.7067403089329425 | -1.2582 | -30.6077 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 1.0913425355892699 | -0.855067 | -20.4389 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 414 | 1.1639069284048813 | -1.1191 | -26.8464 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 462 | 1.841593328223823 | -0.854383 | -22.2042 | 5 | 16 | 8 | 0.67 | 0.00 | - | no | Current |
| 401 | 1.97218672047719 | -1.08105 | -22.5838 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 2.322335104540528 | -0.789116 | -18.7871 | 5 | 12 | 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
-22.204kcal/mol
Ligand efficiency (LE)
-0.8540kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.868
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
398.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
43.94kcal/mol
Minimised FF energy
26.77kcal/mol
SASA & burial
✓ computed
SASA (unbound)
645.4Ų
Total solvent-accessible surface area of free ligand
BSA total
514.1Ų
Buried surface area upon binding
BSA apolar
355.8Ų
Hydrophobic contacts buried
BSA polar
158.2Ų
Polar contacts buried
Fraction buried
79.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6467.2Ų
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
2053.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)