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
27.0 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 (-0.776 kcal/mol/HA)
✓ Good fit quality (FQ -7.15)
✓ Good H-bonds (4 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (27.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-20.169
kcal/mol
LE
-0.776
kcal/mol/HA
Fit Quality
-7.15
FQ (Leeson)
HAC
26
heavy atoms
MW
388
Da
LogP
2.69
cLogP
Interaction summary
HB 4
HY 24
PI 3
CLASH 3
Interaction summary
HB 4
HY 24
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 | 2.261 | Score | -20.169 |
|---|---|---|---|
| Inter norm | -0.793 | Intra norm | 0.017 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | geometry warning; 10 clashes; 1 protein clash; moderate strain Δ 27.0 | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
ILE339
LEU17
MET113
SER109
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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 352 | 0.6043615813653308 | -0.988227 | -26.017 | 1 | 13 | 0 | 0.00 | - | - | no | Open |
| 341 | 1.0424018304021976 | -0.916853 | -17.8895 | 2 | 16 | 0 | 0.00 | - | - | no | Open |
| 334 | 1.5455213211202086 | -0.958722 | -24.8957 | 3 | 17 | 0 | 0.00 | - | - | no | Open |
| 339 | 1.7701678738098026 | -1.08844 | -29.6256 | 9 | 14 | 0 | 0.00 | - | - | no | Open |
| 382 | 1.845972868808333 | -1.07526 | -28.3909 | 4 | 10 | 0 | 0.00 | - | - | no | Open |
| 316 | 1.851249825910153 | -1.28271 | -34.3935 | 9 | 13 | 0 | 0.00 | - | - | no | Open |
| 350 | 2.2605111440336363 | -0.792669 | -20.1687 | 4 | 13 | 8 | 0.62 | - | - | no | Current |
| 399 | 2.3523012290914926 | -1.09868 | -26.3499 | 5 | 14 | 0 | 0.00 | - | - | no | Open |
| 294 | 2.93020983059206 | -1.24579 | -31.2053 | 8 | 20 | 0 | 0.00 | - | - | no | Open |
| 454 | 3.1617246535209707 | -0.93915 | -24.9209 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 337 | 3.545405551412397 | -0.83845 | -21.4295 | 9 | 11 | 0 | 0.00 | - | - | no | Open |
| 417 | 3.73364200758271 | -0.890396 | -21.8774 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 382 | 4.085203326655005 | -0.971988 | -26.5371 | 7 | 17 | 0 | 0.00 | - | - | no | Open |
| 305 | 4.467618834823319 | -1.27421 | -28.5567 | 10 | 15 | 0 | 0.00 | - | - | no | Open |
| 332 | 5.279291077811236 | -1.29833 | -31.9328 | 9 | 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
-20.169kcal/mol
Ligand efficiency (LE)
-0.7757kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.147
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
388.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.69
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-76.20kcal/mol
Minimised FF energy
-103.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
605.9Ų
Total solvent-accessible surface area of free ligand
BSA total
459.4Ų
Buried surface area upon binding
BSA apolar
345.7Ų
Hydrophobic contacts buried
BSA polar
113.6Ų
Polar contacts buried
Fraction buried
75.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3061.7Ų
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
1461.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)