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 (-0.775 kcal/mol/HA)
✓ Good fit quality (FQ -7.47)
✗ High strain energy (16.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.238
kcal/mol
LE
-0.775
kcal/mol/HA
Fit Quality
-7.47
FQ (Leeson)
HAC
30
heavy atoms
MW
423
Da
LogP
3.86
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 16.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 4
Clashes 6
Severe clashes 0
| Final rank | 4.580428798247684 | Score | -23.2376 |
|---|---|---|---|
| Inter norm | -0.766398 | Intra norm | -0.00818894 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 2 |
| Artifact reason | geometry warning; 14 clashes; 6 protein contact clashes; moderate strain Δ 17.7 | ||
| Residues | A:ALA170;A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO101;A:PRO210;A:PRO99;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 | 14 | Native recall | 0.74 |
| Jaccard | 0.64 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1581 | 4.247014679913494 | -0.96518 | -27.0539 | 3 | 15 | 11 | 0.58 | 0.00 | - | no | Open |
| 1576 | 4.580428798247684 | -0.766398 | -23.2376 | 2 | 17 | 14 | 0.74 | 0.00 | - | no | Current |
| 1711 | 5.196287967860225 | -1.09386 | -30.9983 | 7 | 16 | 13 | 0.68 | 0.40 | - | no | Open |
| 1578 | 5.332044520046493 | -0.825252 | -27.6203 | 4 | 16 | 14 | 0.74 | 0.00 | - | no | Open |
| 2255 | 6.066665559603152 | -0.604482 | -17.2138 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1580 | 6.31940022941304 | -0.879244 | -26.4837 | 3 | 14 | 12 | 0.63 | 0.20 | - | no | Open |
| 1579 | 7.058970651038209 | -1.01605 | -30.4842 | 5 | 17 | 12 | 0.63 | 0.40 | - | no | Open |
| 1715 | 6.471609843538507 | -1.09663 | -30.4758 | 6 | 17 | 14 | 0.74 | 0.20 | - | yes | Open |
| 2254 | 7.238175190149743 | -0.58138 | -12.9931 | 8 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2257 | 7.735197385341323 | -0.714979 | -22.6991 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1577 | 8.078359944911897 | -1.02208 | -26.2076 | 3 | 17 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1710 | 8.64640335131285 | -0.968881 | -26.5655 | 6 | 15 | 13 | 0.68 | 0.20 | - | yes | Open |
| 1714 | 8.712527030649726 | -0.907836 | -26.9783 | 7 | 15 | 12 | 0.63 | 0.20 | - | yes | Open |
| 1713 | 8.864757505691074 | -1.07522 | -39.1361 | 7 | 17 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1712 | 8.92456128425028 | -0.931748 | -32.6929 | 9 | 13 | 11 | 0.58 | 0.40 | - | yes | Open |
| 2256 | 10.121527670311838 | -0.528138 | -15.5278 | 5 | 10 | 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
-23.238kcal/mol
Ligand efficiency (LE)
-0.7746kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.472
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
422.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
50.59kcal/mol
Minimised FF energy
34.06kcal/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.