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 (-1.271 kcal/mol/HA)
✓ Good fit quality (FQ -11.71)
✓ Good H-bonds (5 bonds)
✗ High strain energy (17.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-33.056
kcal/mol
LE
-1.271
kcal/mol/HA
Fit Quality
-11.71
FQ (Leeson)
HAC
26
heavy atoms
MW
349
Da
LogP
2.66
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 17.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 3
Clashes 3
Severe clashes 0
| Final rank | 3.0125821971341553 | Score | -33.0563 |
|---|---|---|---|
| Inter norm | -1.27335 | Intra norm | 0.00196006 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 14 clashes; 3 protein contact clashes; moderate strain Δ 17.8 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.75 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 124 | 2.6703811193531375 | -1.19335 | -31.6661 | 3 | 15 | 15 | 0.79 | 0.40 | - | no | Open |
| 125 | 3.0125821971341553 | -1.27335 | -33.0563 | 5 | 16 | 15 | 0.79 | 0.60 | - | no | Current |
| 344 | 3.076795751285623 | -1.22 | -33.0323 | 7 | 15 | 14 | 0.74 | 0.40 | - | no | Open |
| 346 | 3.166933847843848 | -1.22889 | -33.2731 | 7 | 16 | 15 | 0.79 | 0.40 | - | no | Open |
| 126 | 3.229832390803918 | -1.3032 | -33.8634 | 6 | 17 | 16 | 0.84 | 0.60 | - | no | Open |
| 407 | 3.5285402261316543 | -0.796002 | -22.686 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 345 | 3.6233898066763803 | -1.13311 | -29.5629 | 7 | 16 | 15 | 0.79 | 0.40 | - | no | Open |
| 70 | 3.773748892827031 | -0.835454 | -23.4446 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 71 | 4.24537012932554 | -0.753977 | -20.6512 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 347 | 4.402562706318352 | -1.17495 | -31.2717 | 9 | 17 | 16 | 0.84 | 0.60 | - | no | Open |
| 348 | 4.614801602740169 | -1.16741 | -30.0415 | 10 | 17 | 15 | 0.79 | 0.60 | - | no | Open |
| 409 | 5.670478116208788 | -0.86718 | -22.6639 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 406 | 5.561789232332192 | -0.673009 | -20.6308 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 343 | 6.09996248470212 | -1.22648 | -30.9466 | 4 | 16 | 15 | 0.79 | 0.40 | - | yes | Open |
| 408 | 7.3877144503744105 | -0.845241 | -23.1007 | 4 | 13 | 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
-33.056kcal/mol
Ligand efficiency (LE)
-1.2714kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.714
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
349.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-125.96kcal/mol
Minimised FF energy
-143.03kcal/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.