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 (-0.673 kcal/mol/HA)
✓ Good fit quality (FQ -6.49)
✗ High strain energy (13.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.190
kcal/mol
LE
-0.673
kcal/mol/HA
Fit Quality
-6.49
FQ (Leeson)
HAC
30
heavy atoms
MW
399
Da
LogP
3.42
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 13.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 3
Clashes 5
Severe clashes 0
| Final rank | 3.645310442279257 | Score | -20.1903 |
|---|---|---|---|
| Inter norm | -0.620809 | Intra norm | -0.0522008 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 2 |
| Artifact reason | geometry warning; 11 clashes; 5 protein contact clashes; moderate strain Δ 14.4 | ||
| Residues | A:ARG14;A:LEU208;A:LEU209;A:LYS114;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TYR98 | ||
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 | 0.50 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 662 | 3.645310442279257 | -0.620809 | -20.1903 | 2 | 11 | 10 | 0.53 | 0.20 | - | no | Current |
| 658 | 5.946912658772893 | -0.964374 | -28.5484 | 1 | 17 | 12 | 0.63 | 0.00 | - | no | Open |
| 656 | 5.3022857083799275 | -1.02366 | -29.3388 | 1 | 18 | 14 | 0.74 | 0.00 | - | yes | Open |
| 661 | 6.918944324914556 | -0.784578 | -22.4662 | 2 | 11 | 8 | 0.42 | 0.20 | - | yes | Open |
| 651 | 7.106490681562764 | -0.625911 | -18.0071 | 1 | 11 | 9 | 0.47 | 0.20 | - | yes | Open |
| 650 | 7.775682514053509 | -0.925604 | -16.2869 | 2 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 654 | 7.915336387760832 | -0.890753 | -20.5344 | 2 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 652 | 8.585268445025196 | -0.945524 | -24.3242 | 1 | 18 | 13 | 0.68 | 0.00 | - | yes | Open |
| 655 | 9.2475841540719 | -0.651262 | -17.5338 | 1 | 11 | 9 | 0.47 | 0.20 | - | yes | Open |
| 663 | 56.74400776727596 | -1.03735 | -29.4712 | 1 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 657 | 56.95628912620001 | -0.968237 | -20.6844 | 2 | 21 | 15 | 0.79 | 0.20 | - | yes | Open |
| 659 | 57.212325907207735 | -0.962844 | -25.4027 | 3 | 19 | 14 | 0.74 | 0.20 | - | yes | Open |
| 660 | 57.45071296749822 | -0.878981 | -18.4367 | 1 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 664 | 58.16650395574976 | -0.900094 | -23.646 | 1 | 18 | 13 | 0.68 | 0.00 | - | yes | Open |
| 649 | 58.27317098965996 | -1.07291 | -26.1517 | 2 | 19 | 15 | 0.79 | 0.00 | - | yes | Open |
| 653 | 61.02652196241503 | -0.982144 | -22.1956 | 3 | 19 | 15 | 0.79 | 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
-20.190kcal/mol
Ligand efficiency (LE)
-0.6730kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.492
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
398.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.42
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.88kcal/mol
Minimised FF energy
73.21kcal/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.