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 (-1.365 kcal/mol/HA)
✓ Good fit quality (FQ -12.04)
✗ High strain energy (19.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-31.389
kcal/mol
LE
-1.365
kcal/mol/HA
Fit Quality
-12.04
FQ (Leeson)
HAC
23
heavy atoms
MW
343
Da
LogP
4.67
cLogP
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 7
Severe clashes 0
| Final rank | 3.6021220444997133 | Score | -31.3889 |
|---|---|---|---|
| Inter norm | -1.28928 | Intra norm | -0.0754483 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 1 |
| Artifact reason | geometry warning; 9 clashes; 7 protein contact clashes; high strain Δ 22.9 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:TRP221;A:TYR174;A:VAL206 | ||
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| Residue summary | LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 6 |
| IFP residues | A:ARG14; A:ASP161; A:CYS168; A:GLY205; A:LEU208; A:LEU209; A:LYS178; A:MET213; A:NAP301; A:PHE171; A:PHE97; A:PRO210; A:PRO99; A:SER207; A:SER95; A:TRP221; A:TYR174; A:TYR98; A:VAL206 | ||
| Current overlap | 13 | Native recall | 0.68 |
| Jaccard | 0.68 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2362 | 2.9650887442105436 | -1.13891 | -30.3459 | 1 | 12 | 12 | 0.63 | 0.00 | - | no | Open |
| 2360 | 3.0206159107306734 | -1.13801 | -25.1298 | 1 | 12 | 12 | 0.63 | 0.00 | - | no | Open |
| 2363 | 3.6021220444997133 | -1.28928 | -31.3889 | 1 | 13 | 13 | 0.68 | 0.20 | - | no | Current |
| 2361 | 3.6221867520846573 | -1.13393 | -25.0201 | 1 | 13 | 13 | 0.68 | 0.20 | - | no | Open |
| 3019 | 4.565328450590989 | -0.947343 | -24.4468 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 3018 | 6.265726631676909 | -1.08382 | -25.5871 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3017 | 6.527330848851234 | -0.840207 | -19.3993 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3020 | 8.411018072258297 | -0.86015 | -22.7911 | 5 | 14 | 0 | 0.00 | 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
-31.389kcal/mol
Ligand efficiency (LE)
-1.3647kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.045
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
342.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.67
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
50.80kcal/mol
Minimised FF energy
31.69kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. It will be calculated automatically
the next time this pose is loaded if a receptor PDB path is stored.