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 (-0.840 kcal/mol/HA)
✓ Good fit quality (FQ -8.33)
✓ Good H-bonds (4 bonds)
✗ High strain energy (11.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.718
kcal/mol
LE
-0.840
kcal/mol/HA
Fit Quality
-8.33
FQ (Leeson)
HAC
33
heavy atoms
MW
437
Da
LogP
4.18
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 11.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 4
Clashes 8
Severe clashes 0
| Final rank | 5.090336285448495 | Score | -27.7183 |
|---|---|---|---|
| Inter norm | -0.926719 | Intra norm | 0.0867696 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 4 |
| Artifact reason | geometry warning; 15 clashes; 8 protein contact clashes; high strain Δ 20.5 | ||
| Residues | A:ALA170;A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174 | ||
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 | 0.57 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1255 | 4.616307073007681 | -0.938877 | -28.027 | 1 | 15 | 13 | 0.68 | 0.00 | - | no | Open |
| 1257 | 4.682139965464474 | -0.88116 | -32.7 | 2 | 16 | 13 | 0.68 | 0.00 | - | no | Open |
| 1926 | 4.951772887353425 | -0.649184 | -22.7413 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1256 | 5.0743968174095855 | -0.901447 | -31.5128 | 1 | 14 | 14 | 0.74 | 0.00 | - | no | Open |
| 1253 | 5.090336285448495 | -0.926719 | -27.7183 | 4 | 17 | 13 | 0.68 | 0.20 | - | no | Current |
| 3255 | 5.31013454222435 | -0.620321 | -17.3649 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1260 | 5.420804168989676 | -0.98698 | -34.2142 | 4 | 15 | 14 | 0.74 | 0.20 | - | no | Open |
| 1964 | 5.490476525537056 | -0.759998 | -27.8344 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1960 | 5.435046185174143 | -0.763952 | -23.7542 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1966 | 6.417110151763541 | -0.642166 | -20.1168 | 10 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1924 | 6.767612968604404 | -0.666951 | -19.8887 | 1 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1967 | 6.812356160161252 | -0.673096 | -23.7788 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3259 | 6.850509176532082 | -0.626504 | -18.2783 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1962 | 6.856423989655616 | -0.583819 | -17.4884 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1963 | 6.971153502993543 | -0.725789 | -25.7936 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1254 | 7.064757346429985 | -1.11002 | -33.6375 | 6 | 17 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1928 | 7.078981044259291 | -0.618178 | -20.6319 | 1 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3256 | 7.573888650897698 | -0.730218 | -21.2852 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3254 | 7.977932257095286 | -0.737357 | -22.0076 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1925 | 8.089251287205565 | -0.680606 | -23.5838 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1929 | 8.293796566937688 | -0.608097 | -21.7724 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1927 | 8.318030158190856 | -0.635109 | -21.678 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1965 | 8.707722913780852 | -0.744743 | -30.7702 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1259 | 8.920998109815828 | -0.920118 | -23.0834 | 4 | 14 | 11 | 0.58 | 0.20 | - | yes | Open |
| 3253 | 9.16384234888578 | -0.704223 | -18.3288 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1258 | 9.320446146195936 | -0.950144 | -36.1064 | 7 | 15 | 12 | 0.63 | 0.20 | - | yes | Open |
| 3260 | 9.806877715855332 | -0.623094 | -18.7645 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3258 | 10.07595844227343 | -0.675727 | -25.9047 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3257 | 10.989443476396431 | -0.731324 | -24.5876 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1961 | 11.702313307601445 | -0.697842 | -23.2471 | 8 | 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
-27.718kcal/mol
Ligand efficiency (LE)
-0.8399kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.334
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
437.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.18
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.84kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
100.68kcal/mol
Minimised FF energy
88.84kcal/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.