Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
33.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.69, Jaccard 0.47
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Good LE (-0.365 kcal/mol/HA)
✓ Good fit quality (FQ -3.62)
✓ Strong H-bond network (7 bonds)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (33.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-12.037
kcal/mol
LE
-0.365
kcal/mol/HA
Fit Quality
-3.62
FQ (Leeson)
HAC
33
heavy atoms
MW
444
Da
LogP
2.81
cLogP
Interaction summary
HB 7
HY 21
PI 4
CLASH 5
Interaction summary
HB 7
HY 21
PI 4
CLASH 5
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 | 3.795 | Score | -12.037 |
|---|---|---|---|
| Inter norm | -0.635 | Intra norm | 0.270 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; high strain Δ 33.7 | ||
| Residues |
CYS52
CYS57
GLU18
GLY13
GLY49
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
VAL58
| ||
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 | 0.47 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 107 | 3.0600943336589412 | -0.709938 | -15.6066 | 6 | 18 | 0 | 0.00 | - | - | no | Open |
| 120 | 3.709365957737637 | -0.857733 | -23.7658 | 6 | 18 | 0 | 0.00 | - | - | no | Open |
| 111 | 3.744987385031119 | -0.801755 | -22.2493 | 7 | 20 | 0 | 0.00 | - | - | no | Open |
| 94 | 3.794876174926199 | -0.635092 | -12.0369 | 7 | 15 | 9 | 0.69 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-12.037kcal/mol
Ligand efficiency (LE)
-0.3648kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.619
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
443.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.81
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
30.98kcal/mol
Minimised FF energy
-2.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
764.6Ų
Total solvent-accessible surface area of free ligand
BSA total
490.2Ų
Buried surface area upon binding
BSA apolar
385.0Ų
Hydrophobic contacts buried
BSA polar
105.2Ų
Polar contacts buried
Fraction buried
64.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3230.6Ų
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
1471.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)