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
30.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.573 kcal/mol/HA)
✓ Good fit quality (FQ -5.53)
✓ Good H-bonds (5 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Very high strain energy (30.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-17.197
kcal/mol
LE
-0.573
kcal/mol/HA
Fit Quality
-5.53
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
0.73
cLogP
Interaction summary
HB 5
HY 15
PI 3
CLASH 2
Interaction summary
HB 5
HY 15
PI 3
CLASH 2
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 | 3.660 | Score | -17.197 |
|---|---|---|---|
| Inter norm | -0.743 | Intra norm | 0.170 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 5 |
| Artifact reason | geometry warning; 15 clashes; 2 protein clashes; high strain Δ 30.1 | ||
| Residues |
ASP116
GLU18
GLY112
ILE339
LEU17
LYS108
MET113
SER109
SER14
TRP21
TYR110
| ||
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 343 | 3.3806032224084737 | -1.02576 | -27.2232 | 8 | 17 | 0 | 0.00 | - | - | no | Open |
| 368 | 3.660113442346769 | -0.743051 | -17.1971 | 5 | 11 | 8 | 0.62 | - | - | no | Current |
| 344 | 3.680388032224625 | -1.41134 | -32.5815 | 8 | 17 | 0 | 0.00 | - | - | no | Open |
| 305 | 3.7841109715598766 | -0.942594 | -23.6684 | 9 | 18 | 0 | 0.00 | - | - | no | Open |
| 367 | 3.801123320082061 | -0.687097 | -19.2302 | 5 | 12 | 0 | 0.00 | - | - | no | Open |
| 331 | 4.968164464318635 | -1.07715 | -29.0268 | 11 | 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
-17.197kcal/mol
Ligand efficiency (LE)
-0.5732kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.530
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
427.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.73
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
187.00kcal/mol
Minimised FF energy
156.92kcal/mol
SASA & burial
✓ computed
SASA (unbound)
671.6Ų
Total solvent-accessible surface area of free ligand
BSA total
411.7Ų
Buried surface area upon binding
BSA apolar
330.0Ų
Hydrophobic contacts buried
BSA polar
81.7Ų
Polar contacts buried
Fraction buried
61.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3080.0Ų
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
1553.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)