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 (-0.646 kcal/mol/HA)
✓ Good fit quality (FQ -6.61)
✗ Very high strain energy (43.9 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.903
kcal/mol
LE
-0.646
kcal/mol/HA
Fit Quality
-6.61
FQ (Leeson)
HAC
37
heavy atoms
MW
497
Da
LogP
1.59
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 43.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 0
Hydrophobic 24
π–π 1
Clashes 9
Severe clashes 0
| Final rank | 8.56395987988495 | Score | -23.9027 |
|---|---|---|---|
| Inter norm | -0.635297 | Intra norm | -0.010721 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 0 |
| Artifact reason | geometry warning; 20 clashes; 9 protein contact clashes; high strain Δ 51.0 | ||
| Residues | A:ALA212;A:ARG14;A:GLU217;A:GLY214;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:TYR174;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 | 8 | Native recall | 0.42 |
| Jaccard | 0.35 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
Hydrogen bonds
No hydrogen bonds detected for this pose.
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 | Current |
| 553 | 7.889939574465711 | -1.00259 | -33.4936 | 4 | 14 | 10 | 0.53 | 0.20 | - | yes | Open |
| 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
-23.903kcal/mol
Ligand efficiency (LE)
-0.6460kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.614
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
496.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.59
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
43.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
130.98kcal/mol
Minimised FF energy
87.08kcal/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.