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 (-0.912 kcal/mol/HA)
✓ Good fit quality (FQ -8.61)
✗ High strain energy (16.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.544
kcal/mol
LE
-0.912
kcal/mol/HA
Fit Quality
-8.61
FQ (Leeson)
HAC
28
heavy atoms
MW
510
Da
LogP
4.70
cLogP
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 3
Clashes 3
Severe clashes 0
| Final rank | 2.922312572490235 | Score | -25.5437 |
|---|---|---|---|
| Inter norm | -0.942297 | Intra norm | 0.0300208 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 1 |
| Artifact reason | geometry warning; 12 clashes; 3 protein contact clashes; moderate strain Δ 15.6 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;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 | 14 | Native recall | 0.74 |
| Jaccard | 0.74 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 446 | 2.922312572490235 | -0.942297 | -25.5437 | 1 | 14 | 14 | 0.74 | 0.00 | - | no | Current |
| 680 | 4.3221175700632255 | -0.801109 | -20.573 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 445 | 4.43567618826608 | -1.04804 | -27.4325 | 1 | 16 | 13 | 0.68 | 0.00 | - | no | Open |
| 499 | 4.483953727115979 | -0.780884 | -20.2505 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 5.086367943684058 | -0.806287 | -19.0798 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 496 | 5.638224521413858 | -0.805574 | -18.9082 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 444 | 5.7269139376009885 | -1.02479 | -23.8764 | 1 | 17 | 14 | 0.74 | 0.00 | - | no | Open |
| 679 | 5.8092198217064155 | -0.713639 | -15.8124 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 498 | 6.817085452022836 | -0.824231 | -21.2058 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 443 | 7.126064482979538 | -1.0468 | -26.0129 | 3 | 17 | 13 | 0.68 | 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
-25.544kcal/mol
Ligand efficiency (LE)
-0.9123kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.612
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
509.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.70
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
45.00kcal/mol
Minimised FF energy
28.34kcal/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.