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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.891 kcal/mol/HA)
✓ Good fit quality (FQ -8.84)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (38.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-29.397
kcal/mol
LE
-0.891
kcal/mol/HA
Fit Quality
-8.84
FQ (Leeson)
HAC
33
heavy atoms
MW
489
Da
LogP
1.87
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 38.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 2
Clashes 7
Severe clashes 0
| Final rank | 5.079619502877884 | Score | -29.3973 |
|---|---|---|---|
| Inter norm | -1.04599 | Intra norm | 0.155161 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 6 |
| Artifact reason | geometry warning; 13 clashes; 7 protein contact clashes; high strain Δ 31.7 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU209;A:LYS13;A:LYS178;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206;A:VAL211 | ||
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 | 0.68 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 526 | 5.079619502877884 | -1.04599 | -29.3973 | 6 | 18 | 15 | 0.79 | 0.60 | - | no | Current |
| 523 | 5.885075082260038 | -0.912642 | -26.0079 | 5 | 12 | 10 | 0.53 | 0.20 | - | no | Open |
| 615 | 6.348550663309508 | -0.77501 | -21.9316 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 525 | 8.692881932628051 | -0.812729 | -22.5381 | 4 | 10 | 7 | 0.37 | 0.20 | - | yes | Open |
| 524 | 11.034078440259401 | -1.13339 | -32.2301 | 8 | 17 | 14 | 0.74 | 0.40 | - | yes | Open |
| 614 | 11.667313535417904 | -0.659015 | -19.8074 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 522 | 57.05639209285751 | -1.06168 | -32.4347 | 9 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 613 | 61.002603882773435 | -0.662289 | -18.3289 | 4 | 16 | 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
-29.397kcal/mol
Ligand efficiency (LE)
-0.8908kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.839
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
489.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.87
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.99kcal/mol
Minimised FF energy
59.13kcal/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.