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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
29.8 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.69, Jaccard 0.56
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.858 kcal/mol/HA)
✓ Good fit quality (FQ -8.01)
✓ Good H-bonds (4 bonds)
✓ Deep burial (70% SASA buried)
✗ High strain energy (29.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-23.166
kcal/mol
LE
-0.858
kcal/mol/HA
Fit Quality
-8.01
FQ (Leeson)
HAC
27
heavy atoms
MW
413
Da
LogP
0.29
cLogP
Final rank
4.5734
rank score
Inter norm
-0.835
normalised
Contacts
12
H-bonds 8
Interaction summary
HBD 3
HBA 1
HY 5
PI 2
CLASH 6
Interaction summary
HBD 3
HBA 1
HY 5
PI 2
CLASH 6
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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 | 9 | Native recall | 0.69 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 295 | 0.5423581016361587 | -0.908946 | -23.8937 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 280 | 1.2557418732819279 | -1.2295 | -32.8994 | 12 | 13 | 0 | 0.00 | - | - | no | Open |
| 317 | 2.0959718116207378 | -0.939852 | -26.3471 | 7 | 14 | 0 | 0.00 | - | - | no | Open |
| 272 | 4.2796583723172725 | -1.00885 | -29.0965 | 11 | 14 | 0 | 0.00 | - | - | no | Open |
| 317 | 4.5002092837441765 | -1.00198 | -28.4384 | 16 | 16 | 0 | 0.00 | - | - | no | Open |
| 312 | 4.573359825393999 | -0.835257 | -23.1655 | 8 | 12 | 9 | 0.69 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.166kcal/mol
Ligand efficiency (LE)
-0.8580kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.005
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
413.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.29
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-76.86kcal/mol
Minimised FF energy
-106.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
629.5Ų
Total solvent-accessible surface area of free ligand
BSA total
443.3Ų
Buried surface area upon binding
BSA apolar
260.5Ų
Hydrophobic contacts buried
BSA polar
182.8Ų
Polar contacts buried
Fraction buried
70.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
58.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2981.0Ų
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
1463.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)