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 (-0.836 kcal/mol/HA)
✓ Good fit quality (FQ -8.29)
✓ Good H-bonds (4 bonds)
✗ High strain energy (16.2 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-27.587
kcal/mol
LE
-0.836
kcal/mol/HA
Fit Quality
-8.29
FQ (Leeson)
HAC
33
heavy atoms
MW
470
Da
LogP
1.01
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 16.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 4
Severe clashes 2
| Final rank | 6.481198542807896 | Score | -27.5867 |
|---|---|---|---|
| Inter norm | -0.934559 | Intra norm | 0.098598 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 13 clashes; 2 protein clashes; high strain Δ 26.0 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:GLY205;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;A:TYR174;A:VAL206;D:HIS267 | ||
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.64 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 302 | 3.9860687920387985 | -0.9575 | -30.1747 | 3 | 17 | 13 | 0.68 | 0.20 | - | no | Open |
| 300 | 4.3272878461670805 | -0.965463 | -30.8185 | 4 | 18 | 14 | 0.74 | 0.20 | - | no | Open |
| 285 | 5.231504149698444 | -0.659157 | -19.475 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 346 | 5.60254511896347 | -0.782613 | -23.6958 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 290 | 5.938552167628018 | -0.672761 | -18.3358 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 304 | 6.572872071357608 | -0.973068 | -29.7928 | 4 | 14 | 13 | 0.68 | 0.20 | - | no | Open |
| 291 | 7.155712493188818 | -0.66175 | -18.1239 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 445 | 7.973284889658977 | -0.699925 | -20.8199 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 309 | 4.82681093965365 | -0.997243 | -32.7976 | 4 | 16 | 14 | 0.74 | 0.20 | - | yes | Open |
| 306 | 5.164003713644711 | -0.941996 | -32.0971 | 5 | 17 | 13 | 0.68 | 0.20 | - | yes | Open |
| 452 | 5.8812256287031905 | -0.512021 | -14.9391 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 444 | 6.3830777535264716 | -0.76774 | -23.9323 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 347 | 6.409530599725645 | -0.816114 | -23.4194 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 345 | 6.470663545371229 | -0.750934 | -19.3598 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 301 | 6.481198542807896 | -0.934559 | -27.5867 | 4 | 17 | 14 | 0.74 | 0.20 | - | yes | Current |
| 307 | 6.487057634962475 | -0.942111 | -28.535 | 5 | 17 | 13 | 0.68 | 0.20 | - | yes | Open |
| 308 | 6.8456395263648355 | -0.956853 | -31.5022 | 4 | 15 | 13 | 0.68 | 0.20 | - | yes | Open |
| 351 | 6.877815637033599 | -0.745062 | -22.8815 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 443 | 7.370560713826118 | -0.655696 | -20.7904 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 287 | 7.5483458309976355 | -0.708024 | -21.7881 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 288 | 7.571889232026937 | -0.637708 | -16.5609 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 292 | 7.774632387200143 | -0.675826 | -21.5744 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 303 | 8.13297909655951 | -0.900104 | -27.9134 | 3 | 17 | 13 | 0.68 | 0.00 | - | yes | Open |
| 449 | 8.595557378637675 | -0.667343 | -20.9737 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 448 | 8.847743222449747 | -0.776292 | -23.4709 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 447 | 9.113446898681987 | -0.682169 | -19.47 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 446 | 9.301048973873257 | -0.726233 | -20.3934 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 344 | 9.445882725342084 | -0.835467 | -22.0253 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 286 | 10.740138196408115 | -0.590263 | -18.7671 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 348 | 11.196932345418627 | -0.707432 | -18.787 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 349 | 11.443707668920624 | -0.836386 | -22.2364 | 11 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 451 | 12.167405230381888 | -0.764605 | -23.7193 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 305 | 56.05670399758412 | -1.00617 | -31.9861 | 3 | 16 | 14 | 0.74 | 0.00 | - | yes | Open |
| 450 | 57.81625667748613 | -0.740291 | -23.9227 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 289 | 58.012726517662 | -0.662831 | -14.5682 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 350 | 62.6597058222105 | -0.796536 | -21.4081 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.587kcal/mol
Ligand efficiency (LE)
-0.8360kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.294
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
469.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.01
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
172.50kcal/mol
Minimised FF energy
156.32kcal/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.