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 (-1.007 kcal/mol/HA)
✓ Good fit quality (FQ -9.62)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (53.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-29.215
kcal/mol
LE
-1.007
kcal/mol/HA
Fit Quality
-9.62
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.24
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 53.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 16
π–π 2
Clashes 3
Severe clashes 0
| Final rank | 5.194744469520547 | Score | -29.2147 |
|---|---|---|---|
| Inter norm | -1.05637 | Intra norm | 0.0489695 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 10 |
| Artifact reason | geometry warning; 12 clashes; 3 protein contact clashes; high strain Δ 56.5 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:LYS13;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:SER95;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 | 0.59 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 916 | 5.194744469520547 | -1.05637 | -29.2147 | 10 | 16 | 13 | 0.68 | 0.40 | - | no | Current |
| 724 | 6.580882417339167 | -0.810972 | -23.4402 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 721 | 6.599036618838861 | -0.837495 | -23.1884 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1491 | 7.223604446069228 | -0.680884 | -18.4245 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 720 | 7.391454624519243 | -0.806419 | -21.5031 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 723 | 7.953276889660888 | -0.837606 | -23.8962 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1492 | 8.490206507067263 | -0.656455 | -17.3738 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 722 | 8.341946070184282 | -0.831049 | -24.0079 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1490 | 10.463263440781503 | -0.69889 | -16.9651 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 725 | 10.736459109308974 | -0.764619 | -22.1244 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1489 | 10.8937577549664 | -0.639637 | -17.0216 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 917 | 11.150441952654768 | -0.935377 | -22.5489 | 11 | 17 | 13 | 0.68 | 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
-29.215kcal/mol
Ligand efficiency (LE)
-1.0074kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.616
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.24
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
53.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
27.74kcal/mol
Minimised FF energy
-25.91kcal/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.