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 (-1.286 kcal/mol/HA)
✓ Good fit quality (FQ -11.17)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (19.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.294
kcal/mol
LE
-1.286
kcal/mol/HA
Fit Quality
-11.17
FQ (Leeson)
HAC
22
heavy atoms
MW
338
Da
LogP
4.01
cLogP
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 21
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 2.862657882285701 | Score | -28.2945 |
|---|---|---|---|
| Inter norm | -1.46501 | Intra norm | 0.178893 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 8 |
| Artifact reason | geometry warning; 3 clashes; 8 protein contact clashes; high strain Δ 27.3 | ||
| 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
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 | 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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 709 | 2.428301583564728 | -1.28615 | -25.8079 | 8 | 17 | 16 | 0.84 | 0.60 | - | no | Open |
| 809 | 2.862657882285701 | -1.46501 | -28.2945 | 8 | 13 | 13 | 0.68 | 0.20 | - | no | Current |
| 1047 | 2.8875597911216913 | -0.92973 | -17.5668 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 984 | 3.209858072408278 | -1.09517 | -21.6566 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 810 | 3.223976694411096 | -1.3611 | -23.4229 | 10 | 13 | 13 | 0.68 | 0.20 | - | no | Open |
| 808 | 4.091499979284675 | -1.48592 | -26.126 | 8 | 13 | 13 | 0.68 | 0.20 | - | no | Open |
| 712 | 2.9662881653437343 | -1.35137 | -27.1477 | 6 | 14 | 14 | 0.74 | 0.40 | - | yes | Open |
| 711 | 3.4722246272024035 | -1.15195 | -20.6805 | 7 | 12 | 12 | 0.63 | 0.40 | - | yes | Open |
| 1045 | 4.248139559050531 | -1.21411 | -23.6042 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 985 | 5.054451581641908 | -0.997149 | -19.777 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1048 | 5.217677319409357 | -1.0922 | -21.3075 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 710 | 5.349640619638379 | -1.28432 | -21.1214 | 8 | 12 | 12 | 0.63 | 0.40 | - | yes | Open |
| 982 | 6.247471639250551 | -1.05281 | -18.9823 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 983 | 6.3984681808428725 | -1.00281 | -18.1211 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 807 | 7.197939495020938 | -1.28687 | -26.03 | 5 | 16 | 15 | 0.79 | 0.40 | - | yes | Open |
| 1046 | 7.862624388908564 | -1.22425 | -24.6194 | 6 | 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
-28.294kcal/mol
Ligand efficiency (LE)
-1.2861kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.166
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
338.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.01
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
41.33kcal/mol
Minimised FF energy
21.95kcal/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.