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 (-1.123 kcal/mol/HA)
✓ Good fit quality (FQ -10.48)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (12.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.324
kcal/mol
LE
-1.123
kcal/mol/HA
Fit Quality
-10.48
FQ (Leeson)
HAC
27
heavy atoms
MW
375
Da
LogP
4.61
cLogP
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 3
Clashes 8
Severe clashes 0
| Final rank | 3.837743384940019 | Score | -30.3243 |
|---|---|---|---|
| Inter norm | -1.27797 | Intra norm | 0.154849 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 8 |
| Artifact reason | geometry warning; 11 clashes; 8 protein contact clashes; moderate strain Δ 13.9 | ||
| Residues | A:ARG14;A:ASP161;A:GLY205;A:LEU209;A:NAP301;A:PHE97;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL206;A:VAL211 | ||
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | 12 | Native recall | 0.63 |
| Jaccard | 0.60 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2007 | 3.837743384940019 | -1.27797 | -30.3243 | 8 | 13 | 12 | 0.63 | 0.40 | - | no | Current |
| 2008 | 4.319663192694337 | -1.2732 | -32.9427 | 8 | 14 | 13 | 0.68 | 0.40 | - | no | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.324kcal/mol
Ligand efficiency (LE)
-1.1231kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.478
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
375.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.61
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.70kcal/mol
Minimised FF energy
36.26kcal/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.