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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.440 kcal/mol/HA)
✓ Good fit quality (FQ -12.29)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (28.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.251
kcal/mol
LE
-1.440
kcal/mol/HA
Fit Quality
-12.29
FQ (Leeson)
HAC
21
heavy atoms
MW
296
Da
LogP
3.95
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 28.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 5
Clashes 1
Severe clashes 0
| Final rank | 1.8094926016800954 | Score | -30.251 |
|---|---|---|---|
| Inter norm | -1.51369 | Intra norm | 0.0731664 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 4 |
| Artifact reason | geometry warning; 10 clashes; 1 protein contact clash; high strain Δ 28.5 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;A:TYR174 | ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.63 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2298 | 1.8094926016800954 | -1.51369 | -30.251 | 4 | 12 | 12 | 0.63 | 0.40 | - | no | Current |
| 2296 | 1.9512416501298655 | -1.47574 | -29.1699 | 4 | 13 | 13 | 0.68 | 0.40 | - | no | Open |
| 2302 | 2.707906926486136 | -1.2664 | -26.1533 | 4 | 13 | 13 | 0.68 | 0.40 | - | no | Open |
| 2300 | 4.803600744771669 | -1.22572 | -25.6935 | 1 | 13 | 13 | 0.68 | 0.00 | - | yes | Open |
| 2304 | 4.887450691370397 | -1.51538 | -29.8632 | 4 | 12 | 12 | 0.63 | 0.40 | - | yes | Open |
| 2301 | 6.890026058531293 | -1.31227 | -28.4451 | 2 | 14 | 10 | 0.53 | 0.00 | - | yes | Open |
| 2299 | 7.100478870042108 | -1.44839 | -28.9218 | 4 | 14 | 10 | 0.53 | 0.40 | - | yes | Open |
| 2297 | 7.452351767091396 | -1.49031 | -28.8047 | 6 | 16 | 12 | 0.63 | 0.60 | - | yes | Open |
| 2295 | 7.802695787467352 | -1.76656 | -34.9296 | 6 | 16 | 12 | 0.63 | 0.80 | - | yes | Open |
| 2303 | 11.453274606467794 | -1.31098 | -23.5287 | 4 | 15 | 12 | 0.63 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.251kcal/mol
Ligand efficiency (LE)
-1.4405kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.287
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
296.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.95
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.25kcal/mol
Minimised FF energy
71.30kcal/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.