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 medium
Native mixed
SASA done
Strain ΔE
18.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.42, Jaccard 0.25
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.079 kcal/mol/HA)
✓ Good fit quality (FQ -9.20)
✓ Good H-bonds (5 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Moderate strain (18.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-22.655
kcal/mol
LE
-1.079
kcal/mol/HA
Fit Quality
-9.20
FQ (Leeson)
HAC
21
heavy atoms
MW
274
Da
LogP
3.24
cLogP
Interaction summary
HB 5
HY 22
PI 0
CLASH 4
Interaction summary
HB 5
HY 22
PI 0
CLASH 4
| Final rank | 3.441 | Score | -22.655 |
|---|---|---|---|
| Inter norm | -1.100 | Intra norm | 0.021 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ALA209
ALA90
ASN208
ASN91
GLY214
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
TRP92
TYR210
| ||
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
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 | 0.25 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 277 | -0.31095997506505085 | -1.49061 | -31.2086 | 7 | 12 | 0 | 0.00 | - | - | no | Open |
| 342 | 0.1477763323184262 | -1.21312 | -24.9144 | 3 | 15 | 0 | 0.00 | - | - | no | Open |
| 317 | 1.7283796893642227 | -1.07109 | -22.6445 | 4 | 12 | 0 | 0.00 | - | - | no | Open |
| 367 | 3.440919281474244 | -1.10017 | -22.6552 | 5 | 13 | 5 | 0.42 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.655kcal/mol
Ligand efficiency (LE)
-1.0788kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.202
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
274.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.24
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.00kcal/mol
Minimised FF energy
44.13kcal/mol
SASA & burial
✓ computed
SASA (unbound)
522.5Ų
Total solvent-accessible surface area of free ligand
BSA total
404.0Ų
Buried surface area upon binding
BSA apolar
391.6Ų
Hydrophobic contacts buried
BSA polar
12.5Ų
Polar contacts buried
Fraction buried
77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
96.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3091.4Ų
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
1492.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)