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 -9.44)
✓ Good H-bonds (4 bonds)
✗ High strain energy (18.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.948
kcal/mol
LE
-1.038
kcal/mol/HA
Fit Quality
-9.44
FQ (Leeson)
HAC
25
heavy atoms
MW
360
Da
LogP
3.08
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 18.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 3
Clashes 14
Severe clashes 2
| Final rank | 8.94217550270557 | Score | -25.9475 |
|---|---|---|---|
| Inter norm | -1.2401 | Intra norm | 0.2022 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 14 clashes; 2 protein clashes; high strain Δ 23.0 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLN166;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:LYS224;A:MET163;A:NAP301;A:PHE97;A:PRO167;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206;D:ALA268;D:HIS267 | ||
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 | 0.50 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 154 | 3.2647270944415454 | -1.43855 | -37.0939 | 7 | 15 | 14 | 0.74 | 0.60 | - | no | Open |
| 163 | 3.923634335542542 | -1.41004 | -36.7713 | 7 | 15 | 14 | 0.74 | 0.60 | - | no | Open |
| 152 | 4.032774323432423 | -1.41401 | -35.9656 | 8 | 13 | 13 | 0.68 | 0.60 | - | no | Open |
| 153 | 4.05295365258212 | -1.40115 | -31.8632 | 5 | 15 | 15 | 0.79 | 0.60 | - | no | Open |
| 159 | 4.460793495034131 | -0.987262 | -24.4949 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 165 | 4.943555891383486 | -1.45605 | -36.1942 | 6 | 19 | 16 | 0.84 | 0.60 | - | no | Open |
| 214 | 5.026717940305855 | -1.15696 | -29.4478 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 215 | 6.226668573901347 | -1.09769 | -22.099 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 216 | 5.705849276982087 | -1.05077 | -24.8626 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 164 | 8.94217550270557 | -1.2401 | -25.9475 | 4 | 20 | 13 | 0.68 | 0.00 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.948kcal/mol
Ligand efficiency (LE)
-1.0379kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.435
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
359.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
36.41kcal/mol
Minimised FF energy
18.34kcal/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.