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 medium
Native strong
SASA done
Strain ΔE
16.0 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.041 kcal/mol/HA)
✓ Good fit quality (FQ -9.46)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (16.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-26.026
kcal/mol
LE
-1.041
kcal/mol/HA
Fit Quality
-9.46
FQ (Leeson)
HAC
25
heavy atoms
MW
338
Da
LogP
3.69
cLogP
Final rank
1.7289
rank score
Inter norm
-1.028
normalised
Contacts
19
H-bonds 1
Interaction summary
HBA 1
HY 12
PI 2
CLASH 3
Interaction summary
HBA 1
HY 12
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
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 | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
VAL116
VAL9
| ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
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:NAP201
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 178 | 1.7288641901609214 | -1.0276 | -26.0264 | 1 | 19 | 16 | 0.76 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.026kcal/mol
Ligand efficiency (LE)
-1.0411kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.464
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
338.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.69
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
37.75kcal/mol
Minimised FF energy
21.78kcal/mol
SASA & burial
✓ computed
SASA (unbound)
604.6Ų
Total solvent-accessible surface area of free ligand
BSA total
570.9Ų
Buried surface area upon binding
BSA apolar
469.2Ų
Hydrophobic contacts buried
BSA polar
101.7Ų
Polar contacts buried
Fraction buried
94.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1567.1Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
610.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)