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
17.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.77, Jaccard 0.56
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 (-0.715 kcal/mol/HA)
✓ Good fit quality (FQ -6.82)
✓ Good H-bonds (3 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (17.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-20.723
kcal/mol
LE
-0.715
kcal/mol/HA
Fit Quality
-6.82
FQ (Leeson)
HAC
29
heavy atoms
MW
447
Da
LogP
5.33
cLogP
Final rank
2.6266
rank score
Inter norm
-0.739
normalised
Contacts
15
H-bonds 7
Interaction summary
HBD 2
HBA 1
PC 2
HY 9
PI 3
CLASH 4
Interaction summary
HBD 2
HBA 1
PC 2
HY 9
PI 3
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 10 | Native recall | 0.77 |
| Jaccard | 0.56 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 530 | 0.5250301583940824 | -1.13446 | -30.5126 | 5 | 18 | 0 | 0.00 | - | - | no | Open |
| 558 | 1.4699525519425631 | -0.921866 | -19.6322 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 536 | 1.9079564582586215 | -0.936292 | -22.7415 | 2 | 16 | 0 | 0.00 | - | - | no | Open |
| 563 | 2.0566042597876093 | -0.771845 | -14.9745 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 532 | 2.1972836050937206 | -0.843441 | -14.8348 | 1 | 17 | 0 | 0.00 | - | - | no | Open |
| 564 | 2.626611580182352 | -0.738634 | -20.7231 | 7 | 15 | 10 | 0.77 | - | - | no | Current |
| 560 | 2.7895108040750816 | -0.957168 | -24.9089 | 7 | 18 | 0 | 0.00 | - | - | no | Open |
| 548 | 4.529608506315844 | -1.15162 | -28.6945 | 10 | 21 | 0 | 0.00 | - | - | no | Open |
| 541 | 5.26808969809745 | -0.966454 | -25.0402 | 8 | 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
-20.723kcal/mol
Ligand efficiency (LE)
-0.7146kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.821
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
447.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.33
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-14.34kcal/mol
Minimised FF energy
-32.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
682.4Ų
Total solvent-accessible surface area of free ligand
BSA total
486.6Ų
Buried surface area upon binding
BSA apolar
365.1Ų
Hydrophobic contacts buried
BSA polar
121.5Ų
Polar contacts buried
Fraction buried
71.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3133.6Ų
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
1474.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)