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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.059 kcal/mol/HA)
✓ Good fit quality (FQ -10.21)
✓ Strong H-bond network (11 bonds)
✗ High strain energy (14.2 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-31.768
kcal/mol
LE
-1.059
kcal/mol/HA
Fit Quality
-10.21
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
3.80
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 14.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 11
Hydrophobic 16
π–π 1
Clashes 14
Severe clashes 3
| Final rank | 59.506899099693776 | Score | -31.7677 |
|---|---|---|---|
| Inter norm | -1.16463 | Intra norm | 0.105702 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 11 |
| Artifact reason | excluded; geometry warning; 12 clashes; 3 protein clashes; high strain Δ 21.6 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:LEU208;A:LEU209;A:LYS13;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TYR174;A:TYR98;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 | 10 | Native recall | 0.53 |
| Jaccard | 0.45 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2068 | 1.662464669832739 | -0.787792 | -21.0846 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1076 | 3.3713557393494122 | -0.939642 | -26.2628 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2069 | 3.429425798449819 | -0.859805 | -26.3343 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 832 | 3.6913987876806305 | -1.09336 | -28.971 | 4 | 17 | 14 | 0.74 | 0.20 | - | no | Open |
| 2098 | 4.124685217253968 | -0.870106 | -23.9953 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1180 | 6.129882628094019 | -0.763914 | -17.6165 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1077 | 5.414514005732158 | -0.93437 | -24.8321 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2099 | 55.51799674244559 | -0.814425 | -25.8415 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1181 | 56.44278604343296 | -0.776336 | -19.1475 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 833 | 59.506899099693776 | -1.16463 | -31.7677 | 11 | 13 | 10 | 0.53 | 0.60 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.768kcal/mol
Ligand efficiency (LE)
-1.0589kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.215
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.80
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.71kcal/mol
Minimised FF energy
40.49kcal/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.