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
33.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.43, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.741 kcal/mol/HA)
✓ Good fit quality (FQ -7.15)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Very high strain energy (33.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-22.240
kcal/mol
LE
-0.741
kcal/mol/HA
Fit Quality
-7.15
FQ (Leeson)
HAC
30
heavy atoms
MW
407
Da
LogP
2.12
cLogP
Interaction summary
HB 7
HY 21
PI 2
CLASH 2
Interaction summary
HB 7
HY 21
PI 2
CLASH 2
| Final rank | 4.045 | Score | -22.240 |
|---|---|---|---|
| Inter norm | -0.843 | Intra norm | 0.101 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 7 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes; high strain Δ 33.5 | ||
| Residues |
ARG331
ARG361
CYS375
GLY197
GLY376
HIS359
HIS428
LEU227
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR360
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 | 9 | Native recall | 0.75 |
| Jaccard | 0.43 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 673 | 1.3531126534554743 | -0.845891 | -21.2625 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 1.8777160867948284 | -0.864778 | -21.3099 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 672 | 2.0326263552148536 | -1.14612 | -27.3148 | 14 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 676 | 4.045459939627847 | -0.842639 | -22.2401 | 7 | 18 | 9 | 0.75 | 0.00 | - | no | Current |
| 677 | 4.76347474340994 | -0.755331 | -17.0491 | 7 | 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
-22.240kcal/mol
Ligand efficiency (LE)
-0.7413kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.151
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
407.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.12
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.79kcal/mol
Minimised FF energy
33.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
710.4Ų
Total solvent-accessible surface area of free ligand
BSA total
566.5Ų
Buried surface area upon binding
BSA apolar
436.5Ų
Hydrophobic contacts buried
BSA polar
130.1Ų
Polar contacts buried
Fraction buried
79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6545.1Ų
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
2082.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)