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
22.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.42, Jaccard 0.23
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.939 kcal/mol/HA)
✓ Good fit quality (FQ -8.29)
✓ Good H-bonds (5 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ High strain energy (22.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-21.602
kcal/mol
LE
-0.939
kcal/mol/HA
Fit Quality
-8.29
FQ (Leeson)
HAC
23
heavy atoms
MW
300
Da
LogP
3.75
cLogP
Interaction summary
HB 5
HY 18
PI 0
CLASH 3
Interaction summary
HB 5
HY 18
PI 0
CLASH 3
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 | 3.358 | Score | -21.602 |
|---|---|---|---|
| Inter norm | -0.985 | Intra norm | 0.045 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; moderate strain Δ 22.9 | ||
| Residues |
ALA209
ALA90
ASN208
ASN91
GLU186
GLY214
LYS211
LYS89
LYS93
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 | 0.23 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 276 | -0.13976627593331645 | -1.47676 | -33.8684 | 7 | 13 | 0 | 0.00 | - | - | no | Open |
| 266 | -0.1272805151622386 | -1.43749 | -33.0386 | 7 | 13 | 0 | 0.00 | - | - | no | Open |
| 291 | 0.5901992826957818 | -0.955457 | -20.9268 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 270 | 0.7471206776409113 | -1.09931 | -23.5478 | 2 | 19 | 0 | 0.00 | - | - | no | Open |
| 316 | 1.8816462000984255 | -1.05627 | -24.1642 | 4 | 14 | 0 | 0.00 | - | - | no | Open |
| 212 | 2.886404467202735 | -1.21041 | -25.7311 | 5 | 21 | 0 | 0.00 | - | - | no | Open |
| 366 | 3.3581943353758192 | -0.985005 | -21.6018 | 5 | 15 | 5 | 0.42 | - | - | no | Current |
| 264 | 5.09030891194505 | -1.02523 | -22.5298 | 4 | 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
-21.602kcal/mol
Ligand efficiency (LE)
-0.9392kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.289
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
300.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.75
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
72.67kcal/mol
Minimised FF energy
49.77kcal/mol
SASA & burial
✓ computed
SASA (unbound)
574.5Ų
Total solvent-accessible surface area of free ligand
BSA total
450.2Ų
Buried surface area upon binding
BSA apolar
437.1Ų
Hydrophobic contacts buried
BSA polar
13.0Ų
Polar contacts buried
Fraction buried
78.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3139.1Ų
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
1496.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)