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 (-1.009 kcal/mol/HA)
✓ Good fit quality (FQ -9.17)
✗ High strain energy (19.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.227
kcal/mol
LE
-1.009
kcal/mol/HA
Fit Quality
-9.17
FQ (Leeson)
HAC
25
heavy atoms
MW
354
Da
LogP
3.73
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 19.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 4
Clashes 8
Severe clashes 0
| Final rank | 4.173512865620554 | Score | -25.227 |
|---|---|---|---|
| Inter norm | -1.18648 | Intra norm | 0.177402 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 2 |
| Artifact reason | geometry warning; 11 clashes; 8 protein contact clashes; high strain Δ 20.2 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;A:TYR174 | ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.55 | 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: 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2704 | 3.9241151101944065 | -0.817639 | -14.774 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1966 | 4.173512865620554 | -1.18648 | -25.227 | 2 | 15 | 12 | 0.63 | 0.20 | - | no | Current |
| 2471 | 4.695288002351461 | -0.680181 | -14.4068 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2368 | 4.771586809092184 | -0.953281 | -16.6777 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2703 | 4.8979588920889485 | -0.849387 | -23.9657 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1965 | 5.711800839579892 | -1.15236 | -26.3818 | 3 | 16 | 14 | 0.74 | 0.20 | - | no | Open |
| 2367 | 7.004765791439771 | -0.75644 | -20.6734 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2366 | 5.1419543431780514 | -1.03947 | -21.6428 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2706 | 5.28083920891553 | -0.959996 | -20.1471 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2370 | 5.301103071930877 | -0.887228 | -19.6493 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2702 | 5.461822038255767 | -0.869612 | -19.2561 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2707 | 5.872577848401896 | -0.876064 | -23.2507 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2470 | 6.534338927527394 | -0.947887 | -19.8607 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2469 | 7.767455173050151 | -0.850102 | -16.5444 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2705 | 7.777974874753324 | -1.01307 | -21.9618 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2467 | 7.8995981474385335 | -0.886765 | -16.2724 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2371 | 7.995341391594921 | -0.739527 | -17.6193 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1969 | 8.135324973568435 | -1.10219 | -27.6752 | 6 | 16 | 11 | 0.58 | 0.40 | - | yes | Open |
| 2468 | 8.156427388204762 | -1.10317 | -24.9592 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1968 | 8.646081862941534 | -1.0862 | -24.2162 | 4 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 2472 | 9.090350553546367 | -0.824076 | -20.4991 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2369 | 9.243590923925963 | -0.833299 | -14.9795 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1967 | 9.409314113100834 | -1.04668 | -23.1903 | 7 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1964 | 10.016925584497834 | -1.21413 | -26.104 | 2 | 17 | 13 | 0.68 | 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
-25.227kcal/mol
Ligand efficiency (LE)
-1.0091kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.173
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
354.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.73
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
57.48kcal/mol
Minimised FF energy
37.57kcal/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.