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
33.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.85, Jaccard 0.65
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.560 kcal/mol/HA)
✓ Good fit quality (FQ -5.40)
✓ Good H-bonds (4 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (33.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-16.800
kcal/mol
LE
-0.560
kcal/mol/HA
Fit Quality
-5.40
FQ (Leeson)
HAC
30
heavy atoms
MW
403
Da
LogP
3.03
cLogP
Final rank
2.8715
rank score
Inter norm
-0.687
normalised
Contacts
15
H-bonds 8
Interaction summary
HBD 2
HBA 2
HY 7
PI 2
CLASH 1
Interaction summary
HBD 2
HBA 2
HY 7
PI 2
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
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 | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 11 | Native recall | 0.85 |
| Jaccard | 0.65 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 326 | 1.255230868429765 | -1.0168 | -17.678 | 10 | 14 | 0 | 0.00 | - | - | no | Open |
| 363 | 2.4201993079394484 | -0.837563 | -15.4698 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 309 | 2.4530033927416857 | -1.04657 | -19.3533 | 10 | 22 | 0 | 0.00 | - | - | no | Open |
| 408 | 2.543924748760653 | -0.765399 | -20.1583 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 373 | 2.871454078971141 | -0.687431 | -16.7999 | 8 | 15 | 11 | 0.85 | - | - | no | Current |
| 351 | 3.435621331133259 | -1.1298 | -31.8256 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 396 | 3.8141055144953935 | -0.961525 | -24.1747 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 310 | 4.211492505753235 | -0.858106 | -20.1831 | 13 | 18 | 0 | 0.00 | - | - | no | Open |
| 441 | 4.434742941113284 | -0.898265 | -24.4959 | 8 | 15 | 0 | 0.00 | - | - | no | Open |
| 335 | 4.486660047343685 | -1.08146 | -25.0099 | 10 | 18 | 0 | 0.00 | - | - | no | Open |
| 364 | 4.617676895036009 | -0.887025 | -22.2533 | 14 | 16 | 0 | 0.00 | - | - | no | Open |
| 369 | 4.998871688363223 | -0.936316 | -24.6894 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 470 | 5.42133093270557 | -0.784075 | -18.4526 | 11 | 12 | 0 | 0.00 | - | - | no | Open |
| 333 | 5.7276750524644395 | -1.05567 | -30.4394 | 16 | 22 | 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
-16.800kcal/mol
Ligand efficiency (LE)
-0.5600kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.402
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
403.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.03
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
115.72kcal/mol
Minimised FF energy
82.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
685.3Ų
Total solvent-accessible surface area of free ligand
BSA total
493.8Ų
Buried surface area upon binding
BSA apolar
387.3Ų
Hydrophobic contacts buried
BSA polar
106.5Ų
Polar contacts buried
Fraction buried
72.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3136.1Ų
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
1476.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)