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 (-1.038 kcal/mol/HA)
✓ Good fit quality (FQ -9.56)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (19.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-26.990
kcal/mol
LE
-1.038
kcal/mol/HA
Fit Quality
-9.56
FQ (Leeson)
HAC
26
heavy atoms
MW
367
Da
LogP
3.69
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 19.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 21
π–π 3
Clashes 9
Severe clashes 0
| Final rank | 4.301836178432678 | Score | -26.9896 |
|---|---|---|---|
| Inter norm | -1.24956 | Intra norm | 0.211504 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 9 protein contact clashes; high strain Δ 23.6 | ||
| Residues | A:ARG14;A:ASP161;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:SER207;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 | 0.62 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 514 | 3.9662958483665713 | -1.01732 | -26.0095 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 520 | 4.301836178432678 | -1.24956 | -26.9896 | 8 | 15 | 13 | 0.68 | 0.80 | - | no | Current |
| 353 | 4.596450420236221 | -1.07887 | -32.1101 | 6 | 16 | 14 | 0.74 | 0.40 | - | no | Open |
| 672 | 4.753100092565043 | -0.786201 | -16.7503 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 5.048193273144377 | -1.04441 | -18.5458 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 387 | 5.840056262686303 | -0.859948 | -22.1403 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 385 | 5.8674133039578855 | -0.855196 | -21.9631 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 670 | 5.890359289671385 | -0.61506 | -16.5311 | 6 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 389 | 6.54930298271091 | -0.861186 | -17.6196 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 6.575484509827401 | -0.861514 | -17.4613 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 386 | 7.031484444432119 | -0.869502 | -18.8868 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 8.444381253918266 | -0.945702 | -19.3234 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 515 | 5.002267750236572 | -0.786048 | -21.7552 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 671 | 5.675461707062585 | -0.7826 | -16.3145 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 521 | 6.259841322912159 | -1.26883 | -25.9434 | 11 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 669 | 6.297290514047962 | -0.767859 | -17.5137 | 4 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 616 | 7.085290123456148 | -0.865828 | -17.4641 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 355 | 8.935425138100962 | -1.16958 | -24.324 | 9 | 17 | 16 | 0.84 | 0.80 | - | yes | Open |
| 354 | 11.033255109762516 | -0.996602 | -26.325 | 8 | 14 | 14 | 0.74 | 0.80 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.990kcal/mol
Ligand efficiency (LE)
-1.0381kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.564
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
366.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.69
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
53.66kcal/mol
Minimised FF energy
34.03kcal/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.