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 mixed
SASA done
Strain ΔE
13.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.54, Jaccard 0.35
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.571 kcal/mol/HA)
✓ Good fit quality (FQ -5.45)
✓ Good H-bonds (5 bonds)
✓ Good burial (65% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (13.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-16.549
kcal/mol
LE
-0.571
kcal/mol/HA
Fit Quality
-5.45
FQ (Leeson)
HAC
29
heavy atoms
MW
386
Da
LogP
5.42
cLogP
Interaction summary
HB 5
HY 21
PI 2
CLASH 3
Interaction summary
HB 5
HY 21
PI 2
CLASH 3
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 | 3.148 | Score | -16.549 |
|---|---|---|---|
| Inter norm | -0.711 | Intra norm | 0.141 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash | ||
| Residues |
ASP116
CYS52
GLU18
GLY13
GLY15
GLY49
GLY50
ILE339
LEU17
MET113
SER14
TRP21
TYR110
VAL53
| ||
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 | 7 | Native recall | 0.54 |
| Jaccard | 0.35 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 323 | 1.9880960137870662 | -1.21642 | -31.5302 | 6 | 15 | 0 | 0.00 | - | - | no | Open |
| 420 | 2.548705262181661 | -0.798165 | -21.0698 | 6 | 13 | 0 | 0.00 | - | - | no | Open |
| 357 | 3.147742695757834 | -0.711274 | -16.5493 | 5 | 14 | 7 | 0.54 | - | - | no | Current |
| 340 | 3.304872371779209 | -0.822248 | -9.70627 | 7 | 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
-16.549kcal/mol
Ligand efficiency (LE)
-0.5707kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.447
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
386.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.42
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
89.22kcal/mol
Minimised FF energy
75.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
692.8Ų
Total solvent-accessible surface area of free ligand
BSA total
449.2Ų
Buried surface area upon binding
BSA apolar
334.7Ų
Hydrophobic contacts buried
BSA polar
114.6Ų
Polar contacts buried
Fraction buried
64.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3139.8Ų
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
1505.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)