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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
19.2 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.75, Jaccard 0.36, H-bond role recall 1.00
Reason: 16 internal clashes
16 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.688 kcal/mol/HA)
✓ Good fit quality (FQ -7.04)
✓ Good H-bonds (4 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ Moderate strain (19.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-25.459
kcal/mol
LE
-0.688
kcal/mol/HA
Fit Quality
-7.04
FQ (Leeson)
HAC
37
heavy atoms
MW
495
Da
LogP
3.17
cLogP
Interaction summary
HB 4
HY 15
PI 2
CLASH 0
Interaction summary
HB 4
HY 15
PI 2
CLASH 0
| Final rank | 3.402 | Score | -25.459 |
|---|---|---|---|
| Inter norm | -0.705 | Intra norm | 0.017 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 4 |
| Artifact reason | geometry warning; 16 clashes; 2 protein clashes | ||
| Residues |
ALA284
ARG228
ARG287
ARG331
ARG361
CYS375
GLY196
GLY197
GLY229
GLY286
GLY376
ILE199
ILE285
LEU227
LEU332
MET333
PHE198
PHE230
SER364
THR374
TYR221
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 | 9 | Native recall | 0.75 |
| Jaccard | 0.36 | 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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 588 | 1.5543546702625013 | -0.713314 | -20.9945 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 608 | 2.0766764902935386 | -0.5118 | -19.6174 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 2.6078520185526837 | -0.64407 | -22.2884 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 3.4018392328834 | -0.705475 | -25.459 | 4 | 22 | 9 | 0.75 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.459kcal/mol
Ligand efficiency (LE)
-0.6881kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.045
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
494.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.17
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
76.25kcal/mol
Minimised FF energy
57.04kcal/mol
SASA & burial
✓ computed
SASA (unbound)
844.1Ų
Total solvent-accessible surface area of free ligand
BSA total
690.8Ų
Buried surface area upon binding
BSA apolar
623.6Ų
Hydrophobic contacts buried
BSA polar
67.2Ų
Polar contacts buried
Fraction buried
81.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6742.8Ų
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
2091.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)