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
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.191 kcal/mol/HA)
✓ Good fit quality (FQ -10.68)
✓ Good H-bonds (4 bonds)
✗ Moderate strain (9.9 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.588
kcal/mol
LE
-1.191
kcal/mol/HA
Fit Quality
-10.68
FQ (Leeson)
HAC
24
heavy atoms
MW
319
Da
LogP
2.43
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 20
π–π 2
Clashes 4
Severe clashes 1
| Final rank | 3.504500720696464 | Score | -28.5885 |
|---|---|---|---|
| Inter norm | -1.19584 | Intra norm | 0.00465409 |
| Top1000 | no | Excluded | yes |
| Contacts | 9 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 9 clashes; 1 protein clash | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:CYS168;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TYR174 | ||
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 | 0.40 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 126 | 1.8435112218976308 | -0.690515 | -14.2963 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 184 | 2.317576996818913 | -1.01479 | -23.7757 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 125 | 2.9008582012742403 | -0.723463 | -17.1359 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 180 | 3.030401403393202 | -0.887044 | -19.2768 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 185 | 3.2981704070445255 | -1.02469 | -22.2575 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 141 | 3.51589567129302 | -1.29654 | -30.1623 | 4 | 17 | 12 | 0.63 | 0.20 | - | no | Open |
| 138 | 4.402206773601835 | -1.36817 | -32.1481 | 4 | 18 | 14 | 0.74 | 0.40 | - | no | Open |
| 140 | 3.504500720696464 | -1.19584 | -28.5885 | 4 | 9 | 8 | 0.42 | 0.40 | - | yes | Current |
| 186 | 3.851229187743746 | -0.936971 | -21.1673 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 183 | 4.801963500332432 | -1.03119 | -21.904 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 127 | 5.619031412901554 | -0.995798 | -20.4897 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 178 | 6.6742764884020795 | -0.986924 | -21.9731 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 187 | 6.921103547064138 | -1.08084 | -26.0882 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 179 | 7.274016823255133 | -0.903788 | -18.9904 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 139 | 54.913698566729934 | -1.09349 | -26.5244 | 4 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 182 | 55.1737873814679 | -1.04352 | -21.1082 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 124 | 55.950361766477734 | -0.878313 | -19.9266 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 177 | 58.9496774163436 | -0.831588 | -18.8583 | 4 | 19 | 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
-28.588kcal/mol
Ligand efficiency (LE)
-1.1912kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.675
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
319.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.43
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
44.57kcal/mol
Minimised FF energy
34.70kcal/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.