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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
37.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.83, Jaccard 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.645 kcal/mol/HA)
✓ Good fit quality (FQ -6.60)
✓ Good H-bonds (4 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Very high strain energy (37.7 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (6)
✗ Many internal clashes (14)
Score
-23.859
kcal/mol
LE
-0.645
kcal/mol/HA
Fit Quality
-6.60
FQ (Leeson)
HAC
37
heavy atoms
MW
526
Da
LogP
6.67
cLogP
Interaction summary
HB 4
HY 23
PI 0
CLASH 2
Interaction summary
HB 4
HY 23
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 | 1.889 | Score | -23.859 |
|---|---|---|---|
| Inter norm | -0.685 | Intra norm | 0.041 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | geometry warning; 14 clashes; 6 protein contact clashes; high strain Δ 36.8 | ||
| Residues |
ALA209
ALA90
ARG74
ASN208
ASN91
GLY85
LEU73
LYS211
LYS89
LYS93
MET70
PHE83
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 | 10 | Native recall | 0.83 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 546 | 1.762147411304352 | -0.688299 | -26.4287 | 0 | 18 | 0 | 0.00 | - | - | no | Open |
| 557 | 1.889460363131821 | -0.685334 | -23.8587 | 4 | 18 | 10 | 0.83 | - | - | no | Current |
| 535 | 2.469004843643862 | -0.756544 | -27.8503 | 3 | 17 | 1 | 0.08 | - | - | no | Open |
| 523 | 3.4046233442825438 | -0.544599 | -17.8162 | 5 | 11 | 0 | 0.00 | - | - | no | Open |
| 519 | 6.081198947712167 | -0.646973 | -22.4977 | 12 | 13 | 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
-23.859kcal/mol
Ligand efficiency (LE)
-0.6448kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.602
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
525.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.67
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
70.67kcal/mol
Minimised FF energy
32.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
828.3Ų
Total solvent-accessible surface area of free ligand
BSA total
600.2Ų
Buried surface area upon binding
BSA apolar
428.1Ų
Hydrophobic contacts buried
BSA polar
172.1Ų
Polar contacts buried
Fraction buried
72.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3223.1Ų
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
1481.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)