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 strong
SASA done
Strain ΔE
15.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.92, Jaccard 0.69
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.967 kcal/mol/HA)
✓ Good fit quality (FQ -8.54)
✓ Good H-bonds (4 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Moderate strain (15.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-22.242
kcal/mol
LE
-0.967
kcal/mol/HA
Fit Quality
-8.54
FQ (Leeson)
HAC
23
heavy atoms
MW
434
Da
LogP
4.55
cLogP
Interaction summary
HB 4
HY 23
PI 1
CLASH 1
Interaction summary
HB 4
HY 23
PI 1
CLASH 1
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 1.635 | Score | -22.242 |
|---|---|---|---|
| Inter norm | -1.162 | Intra norm | 0.195 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ALA209
ALA77
ALA90
ARG74
GLY85
LEU73
LYS211
LYS89
MET70
PHE83
PRO212
PRO213
SER86
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 | 11 | Native recall | 0.92 |
| Jaccard | 0.69 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 674 | -0.35581719325196853 | -1.51692 | -33.6466 | 5 | 13 | 0 | 0.00 | - | - | no | Open |
| 667 | 0.7867127207647122 | -1.08247 | -22.6132 | 4 | 13 | 0 | 0.00 | - | - | no | Open |
| 659 | 1.0346738434927216 | -1.12263 | -25.5243 | 2 | 14 | 0 | 0.00 | - | - | no | Open |
| 660 | 1.4512381171061208 | -1.12084 | -24.9471 | 2 | 17 | 0 | 0.00 | - | - | no | Open |
| 658 | 1.635224726812735 | -1.16156 | -22.2419 | 4 | 15 | 11 | 0.92 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.242kcal/mol
Ligand efficiency (LE)
-0.9670kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.535
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
434.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.55
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.50kcal/mol
Minimised FF energy
51.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
565.0Ų
Total solvent-accessible surface area of free ligand
BSA total
434.8Ų
Buried surface area upon binding
BSA apolar
422.6Ų
Hydrophobic contacts buried
BSA polar
12.2Ų
Polar contacts buried
Fraction buried
76.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
97.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3133.9Ų
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
1492.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)