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 high
Native strong
SASA done
Strain ΔE
18.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.47
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.742 kcal/mol/HA)
✓ Good fit quality (FQ -7.23)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Moderate strain (18.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-23.002
kcal/mol
LE
-0.742
kcal/mol/HA
Fit Quality
-7.23
FQ (Leeson)
HAC
31
heavy atoms
MW
438
Da
LogP
4.68
cLogP
Final rank
2.5427
rank score
Inter norm
-0.773
normalised
Contacts
16
H-bonds 3
Interaction summary
HBD 1
HY 10
PI 1
CLASH 2
Interaction summary
HBD 1
HY 10
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
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: 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 | 9 | Native recall | 0.75 |
| Jaccard | 0.47 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 374 | 0.9142285008841533 | -0.946247 | -15.1976 | 8 | 17 | 0 | 0.00 | - | - | no | Open |
| 390 | 1.1579939788406024 | -0.849606 | -17.5793 | 8 | 22 | 0 | 0.00 | - | - | no | Open |
| 379 | 1.5717938515166427 | -1.12965 | -20.7033 | 7 | 16 | 0 | 0.00 | - | - | no | Open |
| 486 | 2.542688235109596 | -0.772745 | -23.0022 | 3 | 16 | 9 | 0.75 | - | - | no | Current |
| 505 | 3.754932846913862 | -0.867518 | -15.1812 | 3 | 15 | 0 | 0.00 | - | - | no | Open |
| 395 | 4.039848054099025 | -0.765663 | -20.3618 | 4 | 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
-23.002kcal/mol
Ligand efficiency (LE)
-0.7420kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.229
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
437.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.68
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-14.16kcal/mol
Minimised FF energy
-32.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
724.5Ų
Total solvent-accessible surface area of free ligand
BSA total
550.6Ų
Buried surface area upon binding
BSA apolar
474.7Ų
Hydrophobic contacts buried
BSA polar
76.0Ų
Polar contacts buried
Fraction buried
76.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3228.6Ų
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
1464.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)