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
27.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.44
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.951 kcal/mol/HA)
✓ Good fit quality (FQ -8.39)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ High strain energy (27.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-21.866
kcal/mol
LE
-0.951
kcal/mol/HA
Fit Quality
-8.39
FQ (Leeson)
HAC
23
heavy atoms
MW
355
Da
LogP
1.24
cLogP
Interaction summary
HB 6
HY 20
PI 3
CLASH 3
Interaction summary
HB 6
HY 20
PI 3
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 | 3.409 | Score | -21.866 |
|---|---|---|---|
| Inter norm | -0.917 | Intra norm | -0.033 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; moderate strain Δ 27.1 | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
ILE106
ILE339
LEU17
MET113
SER109
SER14
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.44 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 331 | 1.3228782768357632 | -0.988725 | -21.382 | 6 | 21 | 0 | 0.00 | - | - | no | Open |
| 448 | 2.0202156311418653 | -1.04987 | -23.3278 | 11 | 16 | 0 | 0.00 | - | - | no | Open |
| 384 | 2.1854242149608547 | -1.27322 | -27.2564 | 7 | 14 | 0 | 0.00 | - | - | no | Open |
| 299 | 2.2389127358641843 | -1.24419 | -29.3361 | 6 | 13 | 0 | 0.00 | - | - | no | Open |
| 287 | 2.3154637769101583 | -1.38961 | -30.3716 | 8 | 18 | 0 | 0.00 | - | - | no | Open |
| 399 | 2.65237204898312 | -1.17856 | -26.8652 | 7 | 15 | 0 | 0.00 | - | - | no | Open |
| 356 | 2.8549181624908866 | -0.876878 | -18.7703 | 8 | 10 | 0 | 0.00 | - | - | no | Open |
| 373 | 2.922208161032249 | -1.07201 | -27.243 | 10 | 18 | 0 | 0.00 | - | - | no | Open |
| 327 | 3.247305073357421 | -1.26001 | -30.536 | 11 | 14 | 0 | 0.00 | - | - | no | Open |
| 345 | 3.4094655135949186 | -0.917319 | -21.8665 | 6 | 13 | 8 | 0.62 | - | - | no | Current |
| 327 | 3.8869349881270736 | -1.02919 | -23.7369 | 7 | 14 | 0 | 0.00 | - | - | no | Open |
| 278 | 4.034060494388567 | -1.09949 | -24.4644 | 11 | 15 | 0 | 0.00 | - | - | no | Open |
| 294 | 4.318729724082746 | -1.18135 | -26.7685 | 11 | 12 | 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
-21.866kcal/mol
Ligand efficiency (LE)
-0.9507kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.391
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
355.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.24
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-32.65kcal/mol
Minimised FF energy
-59.72kcal/mol
SASA & burial
✓ computed
SASA (unbound)
559.9Ų
Total solvent-accessible surface area of free ligand
BSA total
423.1Ų
Buried surface area upon binding
BSA apolar
279.6Ų
Hydrophobic contacts buried
BSA polar
143.4Ų
Polar contacts buried
Fraction buried
75.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3005.5Ų
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
1457.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)