Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
18.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.42, Jaccard 0.28
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.787 kcal/mol/HA)
✓ Good fit quality (FQ -7.05)
✓ Good H-bonds (3 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (18.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-18.890
kcal/mol
LE
-0.787
kcal/mol/HA
Fit Quality
-7.05
FQ (Leeson)
HAC
24
heavy atoms
MW
343
Da
LogP
2.11
cLogP
Interaction summary
HB 3
HY 18
PI 0
CLASH 1
Interaction summary
HB 3
HY 18
PI 0
CLASH 1
| Final rank | 1.815 | Score | -18.890 |
|---|---|---|---|
| Inter norm | -0.964 | Intra norm | 0.177 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 3 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ALA209
ALA90
GLY214
GLY215
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
TYR210
| ||
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
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 | 0.28 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 130 | 0.6710015680972891 | -0.942234 | -15.332 | 1 | 18 | 0 | 0.00 | - | - | no | Open |
| 108 | 1.8147398157015295 | -0.96444 | -18.8902 | 3 | 11 | 5 | 0.42 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-18.890kcal/mol
Ligand efficiency (LE)
-0.7871kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.054
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
343.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.11
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
2.57kcal/mol
Minimised FF energy
-15.51kcal/mol
SASA & burial
✓ computed
SASA (unbound)
627.7Ų
Total solvent-accessible surface area of free ligand
BSA total
399.2Ų
Buried surface area upon binding
BSA apolar
312.9Ų
Hydrophobic contacts buried
BSA polar
86.3Ų
Polar contacts buried
Fraction buried
63.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3142.5Ų
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
1465.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)