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 (-1.095 kcal/mol/HA)
✓ Good fit quality (FQ -9.82)
✓ Good H-bonds (3 bonds)
✗ High strain energy (15.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-26.291
kcal/mol
LE
-1.095
kcal/mol/HA
Fit Quality
-9.82
FQ (Leeson)
HAC
24
heavy atoms
MW
401
Da
LogP
4.84
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 15.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 6
Clashes 5
Severe clashes 0
| Final rank | 2.92618531156925 | Score | -26.2906 |
|---|---|---|---|
| Inter norm | -1.16681 | Intra norm | 0.0713658 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | geometry warning; 10 clashes; 5 protein contact clashes; moderate strain Δ 15.1 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TRP221;A:TYR174;A:TYR98;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: permissive.
| 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 | 0.74 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
Hydrogen bonds
Mode: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2463 | 2.7987022811904225 | -1.08262 | -20.9198 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 969 | 2.808571801991689 | -1.22264 | -25.5784 | 3 | 14 | 14 | 0.74 | 0.20 | - | no | Open |
| 2464 | 2.866885825158193 | -1.03673 | -21.2526 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 970 | 2.92618531156925 | -1.16681 | -26.2906 | 3 | 14 | 14 | 0.74 | 0.20 | - | no | Current |
| 1220 | 3.473207146863788 | -1.28279 | -26.8387 | 1 | 14 | 14 | 0.74 | 0.00 | - | no | Open |
| 1221 | 3.5298908329704504 | -1.12772 | -25.0807 | 3 | 13 | 13 | 0.68 | 0.20 | - | no | Open |
| 2462 | 4.03491069258468 | -1.04639 | -22.0124 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2461 | 4.0643568591372174 | -1.03047 | -21.4763 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 956 | 4.838840042093441 | -0.999945 | -19.8731 | 0 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1064 | 5.0312206236412935 | -0.973313 | -20.1998 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1065 | 4.8478327579821805 | -1.0358 | -20.9894 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1063 | 5.307139313163413 | -0.855698 | -17.0141 | 0 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 957 | 5.687680835199031 | -0.685719 | -13.2604 | 1 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 954 | 7.13543081556128 | -1.20858 | -26.4233 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1062 | 7.9428998618738715 | -1.04639 | -23.5646 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 955 | 8.38934841134014 | -1.01248 | -23.4793 | 2 | 12 | 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
-26.291kcal/mol
Ligand efficiency (LE)
-1.0954kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.817
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
401.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.84
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
122.35kcal/mol
Minimised FF energy
107.23kcal/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.