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 mixed
SASA done
Strain ΔE
20.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.42, Jaccard 0.25
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.043 kcal/mol/HA)
✓ Good fit quality (FQ -9.21)
✓ Good H-bonds (4 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (20.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-23.991
kcal/mol
LE
-1.043
kcal/mol/HA
Fit Quality
-9.21
FQ (Leeson)
HAC
23
heavy atoms
MW
375
Da
LogP
1.81
cLogP
Final rank
3.5612
rank score
Inter norm
-1.072
normalised
Contacts
13
H-bonds 6
Interaction summary
HBD 1
HBA 3
HY 5
PI 0
CLASH 1
Interaction summary
HBD 1
HBA 3
HY 5
PI 0
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 5 | Native recall | 0.42 |
| Jaccard | 0.25 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 361 | 2.928981575060389 | -1.18606 | -26.5253 | 4 | 17 | 0 | 0.00 | - | - | no | Open |
| 462 | 3.5611515835005716 | -1.07153 | -23.9906 | 6 | 13 | 5 | 0.42 | - | - | no | Current |
| 338 | 3.9315534075534533 | -1.1776 | -25.6128 | 13 | 15 | 0 | 0.00 | - | - | no | Open |
| 361 | 3.9368268407414826 | -1.63301 | -34.2943 | 11 | 21 | 0 | 0.00 | - | - | no | Open |
| 386 | 4.140880293503326 | -1.19197 | -25.8274 | 11 | 17 | 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
-23.991kcal/mol
Ligand efficiency (LE)
-1.0431kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.206
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
374.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.81
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-136.71kcal/mol
Minimised FF energy
-157.04kcal/mol
SASA & burial
✓ computed
SASA (unbound)
584.3Ų
Total solvent-accessible surface area of free ligand
BSA total
442.6Ų
Buried surface area upon binding
BSA apolar
339.0Ų
Hydrophobic contacts buried
BSA polar
103.5Ų
Polar contacts buried
Fraction buried
75.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3005.8Ų
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
1491.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)