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 (-1.270 kcal/mol/HA)
✓ Good fit quality (FQ -11.03)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (61.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.939
kcal/mol
LE
-1.270
kcal/mol/HA
Fit Quality
-11.03
FQ (Leeson)
HAC
22
heavy atoms
MW
313
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 61.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 11
π–π 2
Clashes 4
Severe clashes 0
| Final rank | 4.363881452084701 | Score | -27.9395 |
|---|---|---|---|
| Inter norm | -1.45296 | Intra norm | 0.182983 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 4 clashes; 4 protein contact clashes; high strain Δ 66.8 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;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 | 0.74 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 725 | 3.881764876434319 | -1.33785 | -34.4254 | 10 | 15 | 13 | 0.68 | 0.40 | - | no | Open |
| 717 | 4.363881452084701 | -1.45296 | -27.9395 | 7 | 14 | 14 | 0.74 | 0.60 | - | no | Current |
| 721 | 4.744809893168181 | -1.28409 | -31.1737 | 4 | 13 | 13 | 0.68 | 0.40 | - | no | Open |
| 713 | 52.25597153574474 | -1.32351 | -30.8251 | 6 | 12 | 11 | 0.58 | 0.60 | - | no | Open |
| 727 | 52.82554429742053 | -1.37162 | -30.9653 | 5 | 16 | 15 | 0.79 | 0.20 | - | no | Open |
| 722 | 52.901475344989514 | -1.15628 | -30.0541 | 10 | 15 | 14 | 0.74 | 0.40 | - | no | Open |
| 715 | 52.681550447846675 | -1.40997 | -33.9149 | 6 | 12 | 11 | 0.58 | 0.60 | - | yes | Open |
| 724 | 52.96105829878437 | -1.30612 | -32.8938 | 7 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 714 | 53.05253336422005 | -1.24508 | -31.8992 | 6 | 14 | 14 | 0.74 | 0.20 | - | yes | Open |
| 726 | 53.2539328674189 | -1.33035 | -29.904 | 7 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 719 | 54.00588526028555 | -1.36162 | -30.065 | 8 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 718 | 54.33639916166939 | -1.2155 | -30.6199 | 10 | 15 | 15 | 0.79 | 0.40 | - | yes | Open |
| 723 | 54.48952671147026 | -1.37213 | -32.3628 | 9 | 14 | 14 | 0.74 | 0.20 | - | yes | Open |
| 728 | 54.50548997474227 | -1.26343 | -31.9045 | 8 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 716 | 54.90253392845565 | -1.31928 | -32.7137 | 7 | 15 | 14 | 0.74 | 0.20 | - | yes | Open |
| 720 | 55.17790347223977 | -1.36133 | -31.8488 | 9 | 14 | 14 | 0.74 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.939kcal/mol
Ligand efficiency (LE)
-1.2700kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.026
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
313.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.87
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
61.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
88.14kcal/mol
Minimised FF energy
26.21kcal/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.