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 (-0.951 kcal/mol/HA)
✓ Good fit quality (FQ -9.07)
✗ High strain energy (11.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.567
kcal/mol
LE
-0.951
kcal/mol/HA
Fit Quality
-9.07
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
4.59
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 11.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 4
Clashes 6
Severe clashes 0
| Final rank | 3.184967355927311 | Score | -27.5669 |
|---|---|---|---|
| Inter norm | -0.972893 | Intra norm | 0.022311 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 1 |
| Artifact reason | geometry warning; 7 clashes; 6 protein contact clashes; high strain Δ 20.1 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER95;A:TRP221;A:TYR174;A:TYR98 | ||
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.79 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 183 | 2.6524973836816628 | -0.93453 | -26.7901 | 0 | 15 | 15 | 0.79 | 0.00 | - | no | Open |
| 166 | 3.184967355927311 | -0.972893 | -27.5669 | 1 | 15 | 15 | 0.79 | 0.00 | - | no | Current |
| 182 | 4.6125044483965 | -1.12904 | -30.7227 | 4 | 17 | 13 | 0.68 | 0.20 | - | no | Open |
| 207 | 4.723685244314048 | -0.759738 | -18.573 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 98 | 4.928706460321411 | -0.771316 | -21.0817 | 1 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 167 | 5.865293042808408 | -0.980624 | -26.822 | 3 | 13 | 11 | 0.58 | 0.00 | - | yes | Open |
| 209 | 6.6762450716022075 | -0.722233 | -17.9379 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 97 | 6.758871973745717 | -1.00649 | -28.4867 | 1 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 99 | 6.9446623186933465 | -0.830883 | -23.779 | 1 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 181 | 7.556609259784765 | -1.16149 | -31.6116 | 3 | 18 | 14 | 0.74 | 0.20 | - | yes | Open |
| 208 | 10.990758953446976 | -0.742372 | -17.8666 | 0 | 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
-27.567kcal/mol
Ligand efficiency (LE)
-0.9506kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.074
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
434.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.59
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-8.70kcal/mol
Minimised FF energy
-20.37kcal/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.