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 (-0.895 kcal/mol/HA)
✓ Good fit quality (FQ -9.17)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (21.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-33.126
kcal/mol
LE
-0.895
kcal/mol/HA
Fit Quality
-9.17
FQ (Leeson)
HAC
37
heavy atoms
MW
494
Da
LogP
4.59
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 21.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 7
Clashes 10
Severe clashes 1
| Final rank | 7.351286921462457 | Score | -33.1264 |
|---|---|---|---|
| Inter norm | -1.00732 | Intra norm | 0.112008 |
| Top1000 | no | Excluded | yes |
| Contacts | 21 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 17 clashes; 1 protein clash; high strain Δ 20.0 | ||
| Residues | A:ALA170;A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;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 | 16 | Native recall | 0.84 |
| Jaccard | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 304 | 4.618637155274895 | -0.803058 | -28.5727 | 10 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 227 | 4.823152433370709 | -1.14683 | -33.4245 | 7 | 20 | 16 | 0.84 | 0.80 | - | no | Open |
| 197 | 4.832421871029605 | -0.633104 | -20.201 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 197 | 5.121721553289744 | -0.649791 | -18.9976 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 207 | 5.142565175193588 | -0.544743 | -15.1314 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 204 | 5.158661328225735 | -1.11363 | -36.2955 | 9 | 21 | 15 | 0.79 | 0.80 | - | no | Open |
| 228 | 5.235002079928121 | -0.934212 | -30.9377 | 5 | 18 | 16 | 0.84 | 0.80 | - | no | Open |
| 178 | 6.391970965155197 | -0.611124 | -18.0149 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 7.1983409405374275 | -0.537335 | -16.6239 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 196 | 7.475422160355843 | -0.717527 | -22.2933 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 302 | 7.904069850528994 | -0.906033 | -25.6212 | 7 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 226 | 7.351286921462457 | -1.00732 | -33.1264 | 4 | 21 | 16 | 0.84 | 0.60 | - | yes | Current |
| 201 | 7.373429719771494 | -1.03536 | -33.075 | 7 | 20 | 18 | 0.95 | 0.80 | - | yes | Open |
| 202 | 7.880459488386842 | -1.14596 | -33.7036 | 7 | 21 | 17 | 0.89 | 0.80 | - | yes | Open |
| 252 | 7.895986744012289 | -0.711971 | -23.6267 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 203 | 8.070886547796118 | -1.0222 | -30.5113 | 5 | 19 | 15 | 0.79 | 0.60 | - | yes | Open |
| 229 | 8.291873648095919 | -1.0842 | -35.0367 | 11 | 20 | 18 | 0.95 | 0.80 | - | yes | Open |
| 303 | 8.45361427934496 | -0.798578 | -23.1576 | 8 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 205 | 8.645287298237387 | -0.511082 | -14.8838 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 176 | 9.267056293692587 | -0.607051 | -16.0283 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 305 | 10.742603935914689 | -0.965604 | -29.7543 | 10 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 177 | 10.93161836458181 | -0.600757 | -17.5629 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 206 | 11.386361520289974 | -0.546086 | -14.5867 | 6 | 14 | 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
-33.126kcal/mol
Ligand efficiency (LE)
-0.8953kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.166
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
493.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.59
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
123.79kcal/mol
Minimised FF energy
102.34kcal/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.