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 high
Native strong
SASA done
Strain ΔE
26.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.39
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.912 kcal/mol/HA)
✓ Good fit quality (FQ -8.29)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ High strain energy (26.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-22.794
kcal/mol
LE
-0.912
kcal/mol/HA
Fit Quality
-8.29
FQ (Leeson)
HAC
25
heavy atoms
MW
333
Da
LogP
3.25
cLogP
Interaction summary
HB 9
HY 24
PI 0
CLASH 2
Interaction summary
HB 9
HY 24
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 | 5.382 | Score | -22.794 |
|---|---|---|---|
| Inter norm | -0.907 | Intra norm | -0.005 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 9 |
| Artifact reason | geometry warning; 11 clashes; 4 protein clashes; moderate strain Δ 26.5 | ||
| Residues |
ALA209
ALA90
ASN208
LEU73
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
TRP92
TYR210
VAL88
| ||
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 | 7 | Native recall | 0.58 |
| Jaccard | 0.39 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 629 | 3.214217008528215 | -1.43831 | -35.4726 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 619 | 5.3820672255276865 | -0.907117 | -22.7936 | 9 | 13 | 7 | 0.58 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.794kcal/mol
Ligand efficiency (LE)
-0.9117kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.289
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
333.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.25
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
53.62kcal/mol
Minimised FF energy
27.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
580.5Ų
Total solvent-accessible surface area of free ligand
BSA total
420.8Ų
Buried surface area upon binding
BSA apolar
350.1Ų
Hydrophobic contacts buried
BSA polar
70.7Ų
Polar contacts buried
Fraction buried
72.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3131.8Ų
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
1448.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)