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
13.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.54, Jaccard 0.35
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.744 kcal/mol/HA)
✓ Good fit quality (FQ -6.67)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (65% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (13.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-17.857
kcal/mol
LE
-0.744
kcal/mol/HA
Fit Quality
-6.67
FQ (Leeson)
HAC
24
heavy atoms
MW
388
Da
LogP
3.01
cLogP
Interaction summary
HB 6
HY 19
PI 2
CLASH 3
Interaction summary
HB 6
HY 19
PI 2
CLASH 3
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 | 2.110 | Score | -17.857 |
|---|---|---|---|
| Inter norm | -0.869 | Intra norm | 0.124 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash | ||
| Residues |
CYS52
FAD501
GLU18
GLY13
GLY49
GLY50
ILE339
LEU17
MET113
SER14
THR335
TRP21
TYR110
VAL53
| ||
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 | 0.35 | 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 | 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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 520 | 1.2270308809147576 | -1.07904 | -22.3479 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 466 | 1.3960566685464946 | -0.978615 | -19.8378 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 529 | 1.8964983291467667 | -1.2551 | -26.806 | 5 | 18 | 0 | 0.00 | - | - | no | Open |
| 509 | 2.109812166352889 | -0.868531 | -17.8569 | 6 | 14 | 7 | 0.54 | - | - | no | Current |
| 483 | 3.176394285752612 | -1.50262 | -35.0845 | 13 | 22 | 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
-17.857kcal/mol
Ligand efficiency (LE)
-0.7440kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.668
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
388.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.01
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-119.47kcal/mol
Minimised FF energy
-133.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
626.1Ų
Total solvent-accessible surface area of free ligand
BSA total
407.6Ų
Buried surface area upon binding
BSA apolar
291.9Ų
Hydrophobic contacts buried
BSA polar
115.7Ų
Polar contacts buried
Fraction buried
65.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3001.9Ų
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
1564.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)