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
11.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.77, Jaccard 0.53
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.773 kcal/mol/HA)
✓ Good fit quality (FQ -7.53)
✓ Good H-bonds (4 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Moderate strain (11.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-23.966
kcal/mol
LE
-0.773
kcal/mol/HA
Fit Quality
-7.53
FQ (Leeson)
HAC
31
heavy atoms
MW
406
Da
LogP
4.85
cLogP
Interaction summary
HB 4
HY 17
PI 4
CLASH 2
Interaction summary
HB 4
HY 17
PI 4
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 2.681 | Score | -23.966 |
|---|---|---|---|
| Inter norm | -0.849 | Intra norm | 0.076 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
GLY50
ILE106
ILE339
LEU17
MET113
SER109
SER14
THR335
TRP21
TYR110
VAL53
VAL58
| ||
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 | 10 | Native recall | 0.77 |
| Jaccard | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 429 | 0.3763685020700806 | -1.11733 | -30.2356 | 4 | 13 | 0 | 0.00 | - | - | no | Open |
| 456 | 0.8291394658452832 | -1.13404 | -36.6273 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 460 | 1.4845961023568308 | -0.936064 | -28.1676 | 4 | 18 | 0 | 0.00 | - | - | no | Open |
| 479 | 2.2465523555658673 | -1.07372 | -31.8463 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 478 | 2.6811516906246866 | -0.848983 | -23.9664 | 4 | 16 | 10 | 0.77 | - | - | no | Current |
| 431 | 2.7950112958399265 | -0.797896 | -16.0129 | 3 | 18 | 0 | 0.00 | - | - | no | Open |
| 531 | 2.9396166091762534 | -0.774253 | -20.0016 | 6 | 13 | 0 | 0.00 | - | - | no | Open |
| 440 | 5.900848019733364 | -0.907256 | -20.21 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 457 | 7.7386159492059985 | -1.02476 | -29.1943 | 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
-23.966kcal/mol
Ligand efficiency (LE)
-0.7731kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.532
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
406.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
170.21kcal/mol
Minimised FF energy
159.25kcal/mol
SASA & burial
✓ computed
SASA (unbound)
649.2Ų
Total solvent-accessible surface area of free ligand
BSA total
454.1Ų
Buried surface area upon binding
BSA apolar
366.0Ų
Hydrophobic contacts buried
BSA polar
88.1Ų
Polar contacts buried
Fraction buried
70.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3111.1Ų
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
1493.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)