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
32.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.67, Jaccard 0.44
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
52% of hydrophobic surface appears solvent-exposed (13/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.636 kcal/mol/HA)
✓ Good fit quality (FQ -6.31)
✓ Good H-bonds (4 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (32.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-20.977
kcal/mol
LE
-0.636
kcal/mol/HA
Fit Quality
-6.31
FQ (Leeson)
HAC
33
heavy atoms
MW
475
Da
LogP
4.89
cLogP
Final rank
4.5782
rank score
Inter norm
-0.731
normalised
Contacts
14
H-bonds 4
Interaction summary
HBD 1
HBA 3
HY 4
PI 0
CLASH 3
Interaction summary
HBD 1
HBA 3
HY 4
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA90
ARG74
GLY85
LEU73
LYS89
MET70
PHE83
PRO212
PRO213
SER86
SER87
VAL88
| ||
| Current overlap | 8 | Native recall | 0.67 |
| 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 | T16 | Atoms | 7551 |
|---|---|---|---|
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 495 | 0.7636299668614087 | -0.944298 | -31.6224 | 5 | 18 | 0 | 0.00 | - | - | no | Open |
| 547 | 1.3092080501017846 | -0.748973 | -24.4712 | 3 | 18 | 0 | 0.00 | - | - | no | Open |
| 568 | 2.1136660153511535 | -0.774735 | -23.372 | 2 | 20 | 0 | 0.00 | - | - | no | Open |
| 508 | 2.363635055852463 | -0.896611 | -27.6232 | 10 | 17 | 0 | 0.00 | - | - | no | Open |
| 506 | 2.512933131032401 | -0.972941 | -29.8517 | 9 | 26 | 0 | 0.00 | - | - | no | Open |
| 547 | 2.7275152541986074 | -0.63594 | -20.531 | 2 | 15 | 0 | 0.00 | - | - | no | Open |
| 530 | 3.647484580817899 | -0.738297 | -22.9327 | 4 | 17 | 0 | 0.00 | - | - | no | Open |
| 517 | 3.7491718068183464 | -0.73996 | -23.338 | 12 | 20 | 0 | 0.00 | - | - | no | Open |
| 555 | 4.578227095484919 | -0.730577 | -20.9774 | 4 | 14 | 8 | 0.67 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.977kcal/mol
Ligand efficiency (LE)
-0.6357kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.307
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
474.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.89
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
102.83kcal/mol
Minimised FF energy
70.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
732.1Ų
Total solvent-accessible surface area of free ligand
BSA total
480.1Ų
Buried surface area upon binding
BSA apolar
344.0Ų
Hydrophobic contacts buried
BSA polar
136.0Ų
Polar contacts buried
Fraction buried
65.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3159.2Ų
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
1468.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)