Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
py3Dmol interaction viewer
Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.913 kcal/mol/HA)
✓ Good fit quality (FQ -9.21)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (20.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-31.956
kcal/mol
LE
-0.913
kcal/mol/HA
Fit Quality
-9.21
FQ (Leeson)
HAC
35
heavy atoms
MW
481
Da
LogP
-0.59
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 20.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 14
π–π 1
Clashes 7
Severe clashes 3
⚠ Hydrophobic exposure 56%
Partial hydrophobic solvent exposure
57% of hydrophobic surface appears solvent-exposed (13/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23
Buried (contacted) 10
Exposed 13
LogP -0.59
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 9.767739220053992 | Score | -31.9556 |
|---|---|---|---|
| Inter norm | -0.812027 | Intra norm | -0.100991 |
| Top1000 | no | Excluded | yes |
| Contacts | 22 | H-bonds | 8 |
| Artifact reason | excluded; geometry warning; 13 clashes; 3 protein clashes; high strain Δ 46.5 | ||
| Residues | A:ALA10;A:ASP22;A:GLU31;A:ILE61;A:ILE8;A:LEU23;A:LEU68;A:NAP201;A:PHE135;A:PHE32;A:PHE35;A:PRO26;A:PRO27;A:PRO62;A:SER60;A:THR137;A:THR57;A:TRP25;A:TYR122;A:TYR34;A:VAL116;A:VAL9 | ||
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 | ||
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 | H-bonds | 5 |
| IFP residues | A:ALA10; A:ASN65; A:ASP22; A:GLN36; A:GLU31; A:GLY117; A:GLY21; A:ILE61; A:ILE8; A:LEU23; A:LEU68; A:NAP201; A:PHE32; A:PHE35; A:PRO62; A:SER60; A:THR137; A:THR57; A:TYR122; A:VAL116; A:VAL9 | ||
| Current overlap | 17 | Native recall | 0.81 |
| Jaccard | 0.65 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.60 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
Hydrogen bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
Hydrophobic contacts
Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | Contacts | Native overlap | Native recall | HB role recall | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 66 | 6.938548188579787 | -0.808005 | -24.1866 | 5 | 18 | 14 | 0.67 | 0.40 | - | no | Open |
| 69 | 9.188319575486904 | -0.759759 | -20.925 | 13 | 22 | 17 | 0.81 | 0.80 | - | yes | Open |
| 68 | 9.674745267475345 | -0.790283 | -19.9878 | 8 | 18 | 14 | 0.67 | 0.60 | - | yes | Open |
| 70 | 9.767739220053992 | -0.812027 | -31.9556 | 8 | 22 | 17 | 0.81 | 0.60 | - | yes | Current |
| 67 | 10.947027023285257 | -0.740443 | -21.4498 | 8 | 22 | 19 | 0.90 | 0.20 | - | yes | Open |
| 71 | 11.267955533191873 | -0.766528 | -24.5835 | 5 | 18 | 13 | 0.62 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.956kcal/mol
Ligand efficiency (LE)
-0.9130kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.209
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
480.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.59
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
129.68kcal/mol
Minimised FF energy
109.11kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.