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 mixed
SASA done
Strain ΔE
14.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.50, Jaccard 0.26, 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 (-0.926 kcal/mol/HA)
✓ Good fit quality (FQ -8.63)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (14.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-24.990
kcal/mol
LE
-0.926
kcal/mol/HA
Fit Quality
-8.63
FQ (Leeson)
HAC
27
heavy atoms
MW
401
Da
LogP
3.74
cLogP
Interaction summary
HB 8
HY 23
PI 1
CLASH 2
Interaction summary
HB 8
HY 23
PI 1
CLASH 2
| Final rank | 3.831 | Score | -24.990 |
|---|---|---|---|
| Inter norm | -0.915 | Intra norm | -0.011 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 8 |
| Artifact reason | geometry warning; 7 clashes; 3 protein clashes | ||
| Residues |
ALA284
ARG228
ARG287
ARG331
FAD501
GLY196
GLY197
GLY286
ILE199
ILE226
ILE285
LEU227
LEU332
LEU334
MET333
PHE198
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 | 6 | Native recall | 0.50 |
| Jaccard | 0.26 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 569 | 0.36532912233574083 | -1.30221 | -32.7212 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 569 | 2.3737859879803827 | -0.913048 | -17.8893 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 589 | 2.791741137083932 | -1.08787 | -23.2147 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 599 | 3.8312358695408832 | -0.914807 | -24.99 | 8 | 17 | 6 | 0.50 | 0.00 | - | no | Current |
| 562 | 3.9390179097197437 | -1.12619 | -30.2577 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 4.131557866139451 | -0.953971 | -23.907 | 11 | 15 | 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
-24.990kcal/mol
Ligand efficiency (LE)
-0.9256kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.635
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
400.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.74
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-53.94kcal/mol
Minimised FF energy
-67.97kcal/mol
SASA & burial
✓ computed
SASA (unbound)
606.7Ų
Total solvent-accessible surface area of free ligand
BSA total
493.4Ų
Buried surface area upon binding
BSA apolar
368.6Ų
Hydrophobic contacts buried
BSA polar
124.8Ų
Polar contacts buried
Fraction buried
81.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6408.1Ų
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
2111.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)