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 (-1.162 kcal/mol/HA)
✓ Good fit quality (FQ -10.26)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (31.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-26.735
kcal/mol
LE
-1.162
kcal/mol/HA
Fit Quality
-10.26
FQ (Leeson)
HAC
23
heavy atoms
MW
418
Da
LogP
3.99
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 31.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 3
Clashes 5
Severe clashes 0
| Final rank | 4.052191143806661 | Score | -26.7345 |
|---|---|---|---|
| Inter norm | -1.35382 | Intra norm | 0.191452 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 5 protein contact clashes; high strain Δ 35.9 | ||
| Residues | A:ARG14;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2123 | 3.147137998015864 | -1.27045 | -28.8464 | 4 | 15 | 12 | 0.63 | 0.40 | - | no | Open |
| 2121 | 4.052191143806661 | -1.35382 | -26.7345 | 5 | 15 | 13 | 0.68 | 0.40 | - | no | Current |
| 2402 | 5.510543545637167 | -1.05302 | -22.7281 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2403 | 6.273461535201744 | -1.10268 | -21.9465 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2399 | 6.9187620841731965 | -0.953668 | -19.0291 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2120 | 7.022757653614741 | -1.17918 | -26.9923 | 6 | 15 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2122 | 7.031065021123041 | -1.17244 | -25.2926 | 2 | 15 | 12 | 0.63 | 0.00 | - | yes | Open |
| 2125 | 7.300044920974371 | -1.11838 | -21.7629 | 6 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2398 | 7.513610526364036 | -1.14089 | -22.4652 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2401 | 8.118166628989945 | -1.18314 | -26.8681 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2400 | 8.36649552164866 | -1.11783 | -22.0205 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2404 | 8.859630447944713 | -0.940517 | -14.4467 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2124 | 10.942952911685403 | -1.08324 | -17.5287 | 3 | 16 | 12 | 0.63 | 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
-26.735kcal/mol
Ligand efficiency (LE)
-1.1624kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.259
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
418.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.99
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
118.04kcal/mol
Minimised FF energy
86.98kcal/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.