Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
13.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.54, Jaccard 0.39
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.983 kcal/mol/HA)
✓ Good fit quality (FQ -8.53)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (61%)
✗ Moderate strain (13.4 kcal/mol)
✗ Geometry warnings
Score
-21.620
kcal/mol
LE
-0.983
kcal/mol/HA
Fit Quality
-8.53
FQ (Leeson)
HAC
22
heavy atoms
MW
333
Da
LogP
2.74
cLogP
Interaction summary
HB 6
HY 18
PI 2
CLASH 2
Interaction summary
HB 6
HY 18
PI 2
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 | 1.547 | Score | -21.620 |
|---|---|---|---|
| Inter norm | -0.994 | Intra norm | 0.011 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 6 |
| Artifact reason | geometry warning; 1 clash; 1 protein clash | ||
| Residues |
CYS52
GLU18
GLY13
GLY49
ILE339
LEU17
MET113
SER14
THR335
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 | 0.39 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 377 | 1.203407316066101 | -1.44123 | -29.4257 | 7 | 16 | 0 | 0.00 | - | - | no | Open |
| 364 | 1.4803074616739718 | -1.45342 | -33.2394 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 429 | 1.546574384664465 | -0.993888 | -21.6201 | 6 | 12 | 7 | 0.54 | - | - | no | Current |
| 409 | 2.0041694598625175 | -1.07628 | -20.4611 | 8 | 11 | 0 | 0.00 | - | - | no | Open |
| 389 | 2.5970311124973797 | -1.1137 | -24.5546 | 5 | 15 | 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
-21.620kcal/mol
Ligand efficiency (LE)
-0.9827kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.532
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
333.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.74
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
18.65kcal/mol
Minimised FF energy
5.29kcal/mol
SASA & burial
✓ computed
SASA (unbound)
556.4Ų
Total solvent-accessible surface area of free ligand
BSA total
389.1Ų
Buried surface area upon binding
BSA apolar
236.8Ų
Hydrophobic contacts buried
BSA polar
152.3Ų
Polar contacts buried
Fraction buried
69.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2991.9Ų
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
1450.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)