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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.959 kcal/mol/HA)
✓ Good fit quality (FQ -8.59)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (33.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-23.010
kcal/mol
LE
-0.959
kcal/mol/HA
Fit Quality
-8.59
FQ (Leeson)
HAC
24
heavy atoms
MW
364
Da
LogP
3.09
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 33.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 2
Clashes 16
Severe clashes 1
| Final rank | 57.87811255701455 | Score | -23.01 |
|---|---|---|---|
| Inter norm | -1.10471 | Intra norm | 0.145962 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | excluded; hard geometry fail; 1 severe clash; 1 protein clash; high strain Δ 33.6 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.65 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 514 | 3.1225749605738837 | -1.2316 | -30.3948 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 513 | 4.199704213015665 | -1.31498 | -30.1723 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 147 | 4.707055286748198 | -0.713226 | -16.9731 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 342 | 4.764137351182391 | -1.17025 | -30.8053 | 8 | 14 | 14 | 0.74 | 0.40 | - | no | Open |
| 340 | 4.860760566575231 | -1.16884 | -25.2625 | 7 | 12 | 12 | 0.63 | 0.40 | - | no | Open |
| 575 | 4.867226381151449 | -0.716238 | -16.5363 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 511 | 4.893061446364197 | -1.31444 | -30.0878 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 146 | 5.396235171926832 | -0.772602 | -16.9951 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 145 | 5.555211082660297 | -0.776961 | -15.6789 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 574 | 7.1184215629651675 | -0.871672 | -21.7874 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 144 | 55.21398991276847 | -0.773692 | -17.5705 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 512 | 55.26043892889386 | -1.14784 | -21.3159 | 9 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 341 | 57.87811255701455 | -1.10471 | -23.01 | 6 | 14 | 13 | 0.68 | 0.40 | - | yes | Current |
| 339 | 59.77774067304024 | -1.1023 | -23.0579 | 5 | 14 | 13 | 0.68 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.010kcal/mol
Ligand efficiency (LE)
-0.9588kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.592
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
364.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.09
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-117.18kcal/mol
Minimised FF energy
-150.14kcal/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.