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
29.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.42, Jaccard 0.26
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.630 kcal/mol/HA)
✓ Good fit quality (FQ -6.35)
✓ Strong H-bond network (8 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (29.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-22.040
kcal/mol
LE
-0.630
kcal/mol/HA
Fit Quality
-6.35
FQ (Leeson)
HAC
35
heavy atoms
MW
491
Da
LogP
3.03
cLogP
Interaction summary
HB 8
HY 14
PI 0
CLASH 2
Interaction summary
HB 8
HY 14
PI 0
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 4.463 | Score | -22.040 |
|---|---|---|---|
| Inter norm | -0.652 | Intra norm | 0.022 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 8 |
| Artifact reason | geometry warning; 11 clashes; 3 protein clashes; moderate strain Δ 26.9 | ||
| Residues |
ALA244
ALA90
ASN208
ASN245
ASN91
GLY214
GLY215
LYS211
LYS89
MET70
PRO212
PRO213
| ||
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 | 0.26 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 103 | 0.7335967964123885 | -0.812994 | -29.3628 | 7 | 22 | 0 | 0.00 | - | - | no | Open |
| 70 | 2.654905691267158 | -0.765524 | -26.5273 | 5 | 19 | 0 | 0.00 | - | - | no | Open |
| 94 | 2.9316764632768817 | -0.547099 | -18.289 | 5 | 11 | 0 | 0.00 | - | - | no | Open |
| 83 | 3.3231984253375964 | -0.688759 | -23.5171 | 7 | 16 | 0 | 0.00 | - | - | no | Open |
| 60 | 4.401661597940852 | -0.891311 | -30.7842 | 11 | 19 | 0 | 0.00 | - | - | no | Open |
| 60 | 4.462694745665272 | -0.652079 | -22.0403 | 8 | 12 | 5 | 0.42 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.040kcal/mol
Ligand efficiency (LE)
-0.6297kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.352
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
490.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.03
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.45kcal/mol
Minimised FF energy
26.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
815.5Ų
Total solvent-accessible surface area of free ligand
BSA total
497.7Ų
Buried surface area upon binding
BSA apolar
374.4Ų
Hydrophobic contacts buried
BSA polar
123.3Ų
Polar contacts buried
Fraction buried
61.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3233.9Ų
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
1497.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)