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 (-0.905 kcal/mol/HA)
✓ Good fit quality (FQ -9.27)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (40.8 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-33.494
kcal/mol
LE
-0.905
kcal/mol/HA
Fit Quality
-9.27
FQ (Leeson)
HAC
37
heavy atoms
MW
496
Da
LogP
3.01
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 40.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 1
| Final rank | 7.889939574465711 | Score | -33.4936 |
|---|---|---|---|
| Inter norm | -1.00259 | Intra norm | 0.0973607 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash; high strain Δ 42.5 | ||
| Residues | A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS13;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;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 | 0.43 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 426 | 7.280582007698453 | -0.604065 | -25.9193 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 550 | 8.56395987988495 | -0.635297 | -23.9027 | 0 | 12 | 8 | 0.42 | 0.00 | - | no | Open |
| 553 | 7.889939574465711 | -1.00259 | -33.4936 | 4 | 14 | 10 | 0.53 | 0.20 | - | yes | Current |
| 424 | 8.728427355444964 | -0.701393 | -28.636 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 549 | 9.006466742494736 | -0.769515 | -20.4526 | 2 | 15 | 14 | 0.74 | 0.00 | - | yes | Open |
| 425 | 9.156266917873012 | -0.55833 | -21.7907 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 557 | 9.854946626590817 | -0.781511 | -21.2806 | 4 | 15 | 11 | 0.58 | 0.40 | - | yes | Open |
| 551 | 9.88309817824124 | -0.679673 | -23.9178 | 1 | 16 | 15 | 0.79 | 0.00 | - | yes | Open |
| 554 | 9.968772683681642 | -0.826235 | -29.6922 | 4 | 17 | 12 | 0.63 | 0.40 | - | yes | Open |
| 547 | 10.153810319343709 | -0.877129 | -21.9546 | 5 | 17 | 12 | 0.63 | 0.40 | - | yes | Open |
| 428 | 10.22669710836076 | -0.647191 | -25.6146 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 430 | 10.976010584329913 | -0.581287 | -23.3065 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 546 | 11.608747690282017 | -0.962991 | -33.0296 | 2 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 429 | 11.740703788396587 | -0.759156 | -29.7609 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 556 | 12.290202122810731 | -0.876275 | -24.7175 | 2 | 17 | 14 | 0.74 | 0.40 | - | yes | Open |
| 552 | 12.558817461599707 | -0.732265 | -21.4954 | 3 | 17 | 15 | 0.79 | 0.40 | - | yes | Open |
| 431 | 57.65269250162953 | -0.609649 | -25.2329 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 427 | 57.664160181325165 | -0.688281 | -20.3089 | 5 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 548 | 58.789443003616896 | -0.83156 | -22.6323 | 5 | 18 | 15 | 0.79 | 0.40 | - | yes | Open |
| 555 | 63.84542835529065 | -0.824293 | -28.9176 | 5 | 15 | 11 | 0.58 | 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
-33.494kcal/mol
Ligand efficiency (LE)
-0.9052kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.268
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
495.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.01
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
125.99kcal/mol
Minimised FF energy
85.17kcal/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.