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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
34.2 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.77, Jaccard 0.56
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.612 kcal/mol/HA)
✓ Good fit quality (FQ -6.02)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Very high strain energy (34.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-19.585
kcal/mol
LE
-0.612
kcal/mol/HA
Fit Quality
-6.02
FQ (Leeson)
HAC
32
heavy atoms
MW
474
Da
LogP
2.84
cLogP
Interaction summary
HB 8
HY 24
PI 2
CLASH 6
Interaction summary
HB 8
HY 24
PI 2
CLASH 6
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
| Final rank | 2.895 | Score | -19.585 |
|---|---|---|---|
| Inter norm | -0.671 | Intra norm | 0.059 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 8 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; high strain Δ 34.0 | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
ILE106
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
VAL58
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 10 | Native recall | 0.77 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Receptor context
1 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 1
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 341 | 1.1339898602829128 | -0.748485 | -23.9309 | 5 | 20 | 0 | 0.00 | - | - | no | Open |
| 303 | 1.3372398954075264 | -0.804404 | -24.1855 | 3 | 21 | 0 | 0.00 | - | - | no | Open |
| 283 | 2.139474337523808 | -0.817859 | -25.2468 | 5 | 15 | 0 | 0.00 | - | - | no | Open |
| 371 | 2.559480306330345 | -0.816062 | -23.2325 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 354 | 2.6386474714478307 | -0.812846 | -23.9788 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 301 | 2.8439180620978584 | -0.787716 | -20.8602 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 321 | 2.895404379539044 | -0.670765 | -19.5853 | 8 | 15 | 10 | 0.77 | - | - | no | Current |
| 275 | 3.0839455449061752 | -0.895097 | -27.2356 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 263 | 3.997061431046954 | -0.87282 | -25.9359 | 11 | 18 | 0 | 0.00 | - | - | no | Open |
| 323 | 5.661054598843183 | -0.800961 | -21.9554 | 9 | 18 | 0 | 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
-19.585kcal/mol
Ligand efficiency (LE)
-0.6120kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.019
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
473.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.84
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-99.20kcal/mol
Minimised FF energy
-133.39kcal/mol
SASA & burial
✓ computed
SASA (unbound)
706.5Ų
Total solvent-accessible surface area of free ligand
BSA total
477.6Ų
Buried surface area upon binding
BSA apolar
326.1Ų
Hydrophobic contacts buried
BSA polar
151.6Ų
Polar contacts buried
Fraction buried
67.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3096.1Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1482.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)