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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
23.6 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.20
Reason: 16 internal clashes
16 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.713 kcal/mol/HA)
✓ Good fit quality (FQ -7.19)
✓ Good H-bonds (3 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ High strain energy (23.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-24.941
kcal/mol
LE
-0.713
kcal/mol/HA
Fit Quality
-7.19
FQ (Leeson)
HAC
35
heavy atoms
MW
487
Da
LogP
5.51
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
Interaction summary
HB 3
HY 24
PI 2
CLASH 0
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
No clash · clashes detected for this pose.
| Final rank | 2.515 | Score | -24.941 |
|---|---|---|---|
| Inter norm | -0.736 | Intra norm | 0.023 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | geometry warning; 16 clashes; 1 protein clash; moderate strain Δ 23.6 | ||
| Residues |
ALA10
ASP22
GLU31
GLY117
ILE61
ILE8
LEU23
NAP201
PHE32
PHE35
PRO26
PRO27
PRO62
SER60
THR57
TRP25
TYR122
VAL116
VAL9
| ||
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 | 1 | Strict recall | 0.20 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 573 | 1.139126753197237 | -0.758922 | -27.678 | 1 | 19 | 17 | 0.81 | 0.20 | - | no | Open |
| 539 | 2.499590381428593 | -0.768703 | -21.9367 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 561 | 2.5151661921956268 | -0.735911 | -24.941 | 3 | 19 | 16 | 0.76 | 0.20 | - | no | Current |
| 555 | 3.10188278181573 | -0.807819 | -27.8714 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 567 | 3.219094182059697 | -0.593454 | -21.4676 | 3 | 16 | 0 | 0.00 | 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
-24.941kcal/mol
Ligand efficiency (LE)
-0.7126kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.188
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
486.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.51
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
2.57kcal/mol
Minimised FF energy
-21.01kcal/mol
SASA & burial
✓ computed
SASA (unbound)
768.4Ų
Total solvent-accessible surface area of free ligand
BSA total
644.7Ų
Buried surface area upon binding
BSA apolar
573.5Ų
Hydrophobic contacts buried
BSA polar
71.2Ų
Polar contacts buried
Fraction buried
83.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1749.9Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
622.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)