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
28.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.58, Jaccard 0.37
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.542 kcal/mol/HA)
✓ Good fit quality (FQ -5.55)
✓ Good H-bonds (3 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (92%)
✗ High strain energy (28.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-20.062
kcal/mol
LE
-0.542
kcal/mol/HA
Fit Quality
-5.55
FQ (Leeson)
HAC
37
heavy atoms
MW
504
Da
LogP
3.54
cLogP
Interaction summary
HB 3
HY 24
PI 0
CLASH 2
Interaction summary
HB 3
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 | 4.343 | Score | -20.062 |
|---|---|---|---|
| Inter norm | -0.633 | Intra norm | 0.091 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | geometry warning; 18 clashes; 2 protein clashes; moderate strain Δ 28.2 | ||
| Residues |
ALA90
ASN91
GLY214
GLY215
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
SER86
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 | 0.37 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 207 | 1.6021140156532505 | -0.742388 | -22.559 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 184 | 4.342542748412277 | -0.632834 | -20.0625 | 3 | 14 | 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
-20.062kcal/mol
Ligand efficiency (LE)
-0.5422kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.551
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
503.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.54
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
76.28kcal/mol
Minimised FF energy
48.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
795.3Ų
Total solvent-accessible surface area of free ligand
BSA total
540.2Ų
Buried surface area upon binding
BSA apolar
499.3Ų
Hydrophobic contacts buried
BSA polar
40.9Ų
Polar contacts buried
Fraction buried
67.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3366.8Ų
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
1453.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)