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 mixed
SASA done
Strain ΔE
29.8 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.48, Jaccard 0.38, H-bond role recall 0.20
Reason: 8 internal clashes
8 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.403 kcal/mol/HA)
✓ Good fit quality (FQ -12.76)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (29.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-35.079
kcal/mol
LE
-1.403
kcal/mol/HA
Fit Quality
-12.76
FQ (Leeson)
HAC
25
heavy atoms
MW
384
Da
LogP
1.87
cLogP
Interaction summary
HB 7
HY 22
PI 2
CLASH 0
Interaction summary
HB 7
HY 22
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 | 1.694 | Score | -35.079 |
|---|---|---|---|
| Inter norm | -1.110 | Intra norm | -0.293 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; moderate strain Δ 29.8 | ||
| Residues |
ALA10
ARG29
GLU31
ILE8
LEU23
LEU28
NAP201
PHE32
PHE35
PRO27
THR137
TRP25
TYR122
TYR34
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 | 10 | Native recall | 0.48 |
| Jaccard | 0.38 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 287 | 0.2889363470792667 | -1.17363 | -34.4435 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 301 | 0.33636184693753507 | -1.28042 | -37.0847 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 1.6944481255547275 | -1.10989 | -35.0793 | 7 | 15 | 10 | 0.48 | 0.20 | - | no | Current |
| 348 | 2.340534198261076 | -0.750315 | -27.2784 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 365 | 2.384677313196986 | -1.122 | -26.8033 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 2.490147275515508 | -0.958879 | -23.2168 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 387 | 2.663891229748762 | -1.07597 | -35.3267 | 7 | 18 | 13 | 0.62 | 0.20 | - | no | Open |
| 312 | 3.254369887786896 | -1.09907 | -28.4908 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 312 | 4.011697433010601 | -1.24919 | -32.1298 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 360 | 4.4832135088166 | -0.913499 | -22.0946 | 10 | 17 | 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
-35.079kcal/mol
Ligand efficiency (LE)
-1.4032kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.756
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
383.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.87
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-39.48kcal/mol
Minimised FF energy
-69.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
628.7Ų
Total solvent-accessible surface area of free ligand
BSA total
499.6Ų
Buried surface area upon binding
BSA apolar
378.6Ų
Hydrophobic contacts buried
BSA polar
121.0Ų
Polar contacts buried
Fraction buried
79.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1547.8Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
602.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)