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
31.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.77, Jaccard 0.56
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.499 kcal/mol/HA)
✓ Good fit quality (FQ -5.14)
✓ Strong H-bond network (6 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Very high strain energy (31.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (26)
Score
-18.953
kcal/mol
LE
-0.499
kcal/mol/HA
Fit Quality
-5.14
FQ (Leeson)
HAC
38
heavy atoms
MW
514
Da
LogP
3.69
cLogP
Interaction summary
HB 6
HY 24
PI 3
CLASH 1
Interaction summary
HB 6
HY 24
PI 3
CLASH 1
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 | 2.679 | Score | -18.953 |
|---|---|---|---|
| Inter norm | -0.553 | Intra norm | 0.055 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 26 clashes; 2 protein contact clashes; high strain Δ 31.4 | ||
| Residues |
ASP116
CYS52
GLU18
GLY112
GLY13
GLY49
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
| ||
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 462 | 2.6793416393777094 | -0.5533 | -18.953 | 6 | 15 | 10 | 0.77 | - | - | no | Current |
| 432 | 3.4976585301058143 | -0.667301 | -26.6508 | 1 | 14 | 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
-18.953kcal/mol
Ligand efficiency (LE)
-0.4988kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.142
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
513.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.69
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
149.98kcal/mol
Minimised FF energy
118.62kcal/mol
SASA & burial
✓ computed
SASA (unbound)
823.2Ų
Total solvent-accessible surface area of free ligand
BSA total
526.7Ų
Buried surface area upon binding
BSA apolar
420.5Ų
Hydrophobic contacts buried
BSA polar
106.2Ų
Polar contacts buried
Fraction buried
64.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3255.7Ų
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
1507.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)