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
20.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.69, Jaccard 0.53
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.652 kcal/mol/HA)
✓ Good fit quality (FQ -6.01)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (67%)
✗ High strain energy (20.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-16.965
kcal/mol
LE
-0.652
kcal/mol/HA
Fit Quality
-6.01
FQ (Leeson)
HAC
26
heavy atoms
MW
367
Da
LogP
2.95
cLogP
Interaction summary
HB 6
HY 24
PI 3
CLASH 4
Interaction summary
HB 6
HY 24
PI 3
CLASH 4
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 | 3.807 | Score | -16.965 |
|---|---|---|---|
| Inter norm | -0.815 | Intra norm | 0.163 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 20.2 | ||
| Residues |
CYS52
GLU18
GLY13
ILE106
ILE339
LEU17
MET113
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 | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 313 | 0.8712913457919358 | -1.07999 | -25.8552 | 3 | 16 | 0 | 0.00 | - | - | no | Open |
| 259 | 1.0887783330232708 | -1.16095 | -30.3355 | 8 | 18 | 0 | 0.00 | - | - | no | Open |
| 310 | 1.5345591015763724 | -0.726221 | -16.5713 | 4 | 10 | 0 | 0.00 | - | - | no | Open |
| 229 | 2.0704697110349266 | -0.998736 | -19.793 | 2 | 14 | 0 | 0.00 | - | - | no | Open |
| 256 | 2.3416472278121194 | -1.03745 | -25.3269 | 2 | 11 | 0 | 0.00 | - | - | no | Open |
| 245 | 2.6468222692756207 | -1.26083 | -33.0935 | 10 | 12 | 0 | 0.00 | - | - | no | Open |
| 191 | 3.0336689687352054 | -1.09429 | -28.6535 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 277 | 3.806776809599375 | -0.815034 | -16.965 | 6 | 13 | 9 | 0.69 | - | - | no | Current |
| 214 | 3.8581501940359018 | -1.22756 | -28.0706 | 10 | 18 | 0 | 0.00 | - | - | no | Open |
| 297 | 3.8864053339831193 | -0.911524 | -23.3962 | 3 | 13 | 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
-16.965kcal/mol
Ligand efficiency (LE)
-0.6525kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.012
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
367.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.95
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-64.06kcal/mol
Minimised FF energy
-84.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
586.4Ų
Total solvent-accessible surface area of free ligand
BSA total
416.1Ų
Buried surface area upon binding
BSA apolar
280.3Ų
Hydrophobic contacts buried
BSA polar
135.7Ų
Polar contacts buried
Fraction buried
71.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3020.6Ų
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
1478.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)