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 (-0.889 kcal/mol/HA)
✓ Good fit quality (FQ -9.10)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (27.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-32.886
kcal/mol
LE
-0.889
kcal/mol/HA
Fit Quality
-9.10
FQ (Leeson)
HAC
37
heavy atoms
MW
497
Da
LogP
3.61
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 27.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 12
Severe clashes 3
| Final rank | 11.045688259864761 | Score | -32.8858 |
|---|---|---|---|
| Inter norm | -0.902903 | Intra norm | 0.0140973 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 18 clashes; 3 protein clashes; high strain Δ 28.4 | ||
| Residues | A:ALA212;A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:SER207;A:TRP221;A:TYR174;A:VAL164;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 | 14 | Native recall | 0.74 |
| Jaccard | 0.56 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 506 | 8.220436372584897 | -0.739655 | -25.8434 | 4 | 15 | 10 | 0.53 | 0.40 | - | no | Open |
| 509 | 8.757704974260532 | -0.739408 | -27.6116 | 7 | 18 | 13 | 0.68 | 0.40 | - | no | Open |
| 507 | 7.372566748999489 | -0.868269 | -31.1607 | 7 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 514 | 8.797213922191535 | -0.805164 | -25.2666 | 5 | 20 | 13 | 0.68 | 0.40 | - | yes | Open |
| 511 | 9.490887063646172 | -0.886526 | -28.2295 | 2 | 19 | 13 | 0.68 | 0.20 | - | yes | Open |
| 512 | 10.562437505559807 | -0.793721 | -24.8292 | 6 | 16 | 13 | 0.68 | 0.60 | - | yes | Open |
| 510 | 10.671787548210144 | -0.766329 | -27.7565 | 5 | 19 | 13 | 0.68 | 0.40 | - | yes | Open |
| 505 | 11.045688259864761 | -0.902903 | -32.8858 | 4 | 20 | 14 | 0.74 | 0.20 | - | yes | Current |
| 508 | 58.025992348601946 | -0.881517 | -31.4214 | 6 | 15 | 12 | 0.63 | 0.40 | - | yes | Open |
| 513 | 61.414431719673274 | -0.810375 | -30.6728 | 3 | 19 | 14 | 0.74 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-32.886kcal/mol
Ligand efficiency (LE)
-0.8888kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.100
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
496.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.61
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
36.99kcal/mol
Minimised FF energy
9.55kcal/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.