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
16.0 kcal/mol
Protein clashes
0
Internal clashes
4
Native overlap
contact recall 0.54, Jaccard 0.37
Reason: no major geometry red flags detected
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.138 kcal/mol/HA)
✓ Good fit quality (FQ -9.12)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (76% SASA buried)
✗ Moderate strain (16.0 kcal/mol)
✗ Geometry warnings
Score
-20.477
kcal/mol
LE
-1.138
kcal/mol/HA
Fit Quality
-9.12
FQ (Leeson)
HAC
18
heavy atoms
MW
294
Da
LogP
3.38
cLogP
Interaction summary
HB 6
HY 22
PI 3
CLASH 0
Interaction summary
HB 6
HY 22
PI 3
CLASH 0
| Final rank | 0.566 | Score | -20.477 |
|---|---|---|---|
| Inter norm | -1.256 | Intra norm | 0.118 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 4 clashes; 1 protein clash | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
GLY50
ILE339
LEU17
MET113
SER14
THR335
TRP21
TYR110
VAL53
| ||
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| 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 | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 7 | Native recall | 0.54 |
| Jaccard | 0.37 | 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
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 416 | -0.02197705513071642 | -1.35055 | -24.9974 | 7 | 14 | 0 | 0.00 | - | - | no | Open |
| 398 | 0.4756929644349943 | -1.47357 | -25.319 | 3 | 11 | 0 | 0.00 | - | - | no | Open |
| 424 | 0.5658076263964957 | -1.25601 | -20.4768 | 6 | 13 | 7 | 0.54 | - | - | no | Current |
| 368 | 0.9142477678312333 | -1.41951 | -23.8348 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 383 | 1.962238201095857 | -1.51574 | -25.6489 | 10 | 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
-20.477kcal/mol
Ligand efficiency (LE)
-1.1376kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.117
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
294.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.38
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
23.76kcal/mol
Minimised FF energy
7.74kcal/mol
SASA & burial
✓ computed
SASA (unbound)
501.2Ų
Total solvent-accessible surface area of free ligand
BSA total
381.5Ų
Buried surface area upon binding
BSA apolar
201.0Ų
Hydrophobic contacts buried
BSA polar
180.5Ų
Polar contacts buried
Fraction buried
76.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
52.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2927.4Ų
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
1465.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)