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
19.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.69, Jaccard 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.111 kcal/mol/HA)
✓ Good fit quality (FQ -10.37)
✓ Good H-bonds (5 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (19.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-30.004
kcal/mol
LE
-1.111
kcal/mol/HA
Fit Quality
-10.37
FQ (Leeson)
HAC
27
heavy atoms
MW
420
Da
LogP
4.91
cLogP
Interaction summary
HB 5
HY 24
PI 3
CLASH 1
Interaction summary
HB 5
HY 24
PI 3
CLASH 1
| Final rank | 1.656 | Score | -30.004 |
|---|---|---|---|
| Inter norm | -0.828 | Intra norm | -0.283 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
VAL58
| ||
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 | 9 | Native recall | 0.69 |
| Jaccard | 0.50 | 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 353 | 1.1309772480652507 | -0.909194 | -24.5341 | 1 | 16 | 0 | 0.00 | - | - | no | Open |
| 396 | 1.6564984240851197 | -0.828175 | -30.0044 | 5 | 14 | 9 | 0.69 | - | - | no | Current |
| 320 | 3.128678427280238 | -1.21241 | -29.8201 | 9 | 18 | 0 | 0.00 | - | - | no | Open |
| 352 | 3.4666152745243677 | -1.18227 | -29.7471 | 10 | 15 | 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
-30.004kcal/mol
Ligand efficiency (LE)
-1.1113kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.368
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
419.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.91
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
69.85kcal/mol
Minimised FF energy
50.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
661.9Ų
Total solvent-accessible surface area of free ligand
BSA total
470.4Ų
Buried surface area upon binding
BSA apolar
332.4Ų
Hydrophobic contacts buried
BSA polar
138.0Ų
Polar contacts buried
Fraction buried
71.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.7%
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
1483.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)