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 mixed
SASA done
Strain ΔE
32.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.42, Jaccard 0.24
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.824 kcal/mol/HA)
✓ Good fit quality (FQ -7.69)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (32.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-22.250
kcal/mol
LE
-0.824
kcal/mol/HA
Fit Quality
-7.69
FQ (Leeson)
HAC
27
heavy atoms
MW
412
Da
LogP
2.00
cLogP
Interaction summary
HB 8
HY 21
PI 0
CLASH 2
Interaction summary
HB 8
HY 21
PI 0
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 3.731 | Score | -22.250 |
|---|---|---|---|
| Inter norm | -0.843 | Intra norm | 0.019 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; high strain Δ 32.1 | ||
| Residues |
ALA209
ALA90
ASN208
ASN245
ASN91
GLY246
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
TRP92
TYR210
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 5 | Native recall | 0.42 |
| Jaccard | 0.24 | 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 | T16 | Atoms | 7551 |
|---|---|---|---|
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 299 | 1.8876907766116682 | -0.899978 | -24.074 | 4 | 19 | 0 | 0.00 | - | - | no | Open |
| 365 | 1.9584529086935094 | -0.970498 | -25.3035 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 384 | 3.731144168472944 | -0.843044 | -22.2495 | 8 | 14 | 5 | 0.42 | - | - | no | Current |
| 315 | 4.166541027799073 | -0.793203 | -20.8181 | 9 | 16 | 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
-22.250kcal/mol
Ligand efficiency (LE)
-0.8241kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.688
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
411.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.00
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-72.64kcal/mol
Minimised FF energy
-104.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
658.6Ų
Total solvent-accessible surface area of free ligand
BSA total
447.0Ų
Buried surface area upon binding
BSA apolar
350.0Ų
Hydrophobic contacts buried
BSA polar
97.0Ų
Polar contacts buried
Fraction buried
67.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.3%
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
1440.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)