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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
27.4 kcal/mol
Protein clashes
0
Internal clashes
18
Native overlap
contact recall 0.62, Jaccard 0.36
Reason: 18 internal clashes
18 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.441 kcal/mol/HA)
✓ Good fit quality (FQ -4.51)
✓ Good H-bonds (4 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (27.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-16.315
kcal/mol
LE
-0.441
kcal/mol/HA
Fit Quality
-4.51
FQ (Leeson)
HAC
37
heavy atoms
MW
501
Da
LogP
4.88
cLogP
Interaction summary
HB 4
HY 24
PI 2
CLASH 0
Interaction summary
HB 4
HY 24
PI 2
CLASH 0
| Final rank | 3.178 | Score | -16.315 |
|---|---|---|---|
| Inter norm | -0.573 | Intra norm | 0.132 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 4 |
| Artifact reason | geometry warning; 18 clashes; 1 protein clash; 1 cofactor-context clash; moderate strain Δ 27.4 | ||
| Residues |
CYS52
CYS57
FAD501
GLU18
GLY13
GLY49
GLY50
ILE339
LEU17
MET113
PRO336
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.36 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 268 | 2.630079909973411 | -0.658079 | -24.0081 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 213 | 3.0676599310111645 | -0.706539 | -23.7641 | 7 | 15 | 0 | 0.00 | - | - | no | Open |
| 266 | 3.1777508227757316 | -0.572857 | -16.3154 | 4 | 17 | 8 | 0.62 | - | - | no | Current |
| 262 | 3.3128101503028407 | -0.84944 | -24.9796 | 11 | 16 | 0 | 0.00 | - | - | no | Open |
| 244 | 3.630597105528765 | -1.02914 | -36.652 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 243 | 3.6890132466315455 | -0.792634 | -27.6005 | 12 | 20 | 0 | 0.00 | - | - | no | Open |
| 273 | 5.027501237967726 | -0.728973 | -21.3679 | 7 | 22 | 0 | 0.00 | - | - | no | Open |
| 232 | 5.4201557790674135 | -0.722783 | -24.5446 | 5 | 18 | 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
-16.315kcal/mol
Ligand efficiency (LE)
-0.4410kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.514
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
500.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.88
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
124.42kcal/mol
Minimised FF energy
96.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
797.6Ų
Total solvent-accessible surface area of free ligand
BSA total
495.6Ų
Buried surface area upon binding
BSA apolar
419.4Ų
Hydrophobic contacts buried
BSA polar
76.2Ų
Polar contacts buried
Fraction buried
62.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3238.3Ų
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
1491.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)