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 (-0.520 kcal/mol/HA)
✓ Good fit quality (FQ -4.79)
✓ Good H-bonds (4 bonds)
✗ High strain energy (13.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-13.513
kcal/mol
LE
-0.520
kcal/mol/HA
Fit Quality
-4.79
FQ (Leeson)
HAC
26
heavy atoms
MW
354
Da
LogP
2.25
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 13.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 1
Clashes 5
Severe clashes 0
| Final rank | 3.7270423491341726 | Score | -13.5132 |
|---|---|---|---|
| Inter norm | -0.623379 | Intra norm | 0.103641 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 3 |
| Artifact reason | geometry warning; 7 clashes; 5 protein contact clashes; high strain Δ 29.0 | ||
| Residues | A:ALA212;A:CYS168;A:GLU217;A:GLY205;A:GLY214;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:TRP221;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 | 9 | Native recall | 0.47 |
| Jaccard | 0.38 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2501 | 2.8622111621057558 | -0.851112 | -17.9625 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2284 | 3.4507059134889064 | -1.11963 | -25.3441 | 8 | 14 | 14 | 0.74 | 0.60 | - | no | Open |
| 2498 | 3.5715989039646927 | -0.904855 | -22.0004 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2287 | 3.7270423491341726 | -0.623379 | -13.5132 | 3 | 14 | 9 | 0.47 | 0.00 | - | no | Current |
| 2502 | 3.73228396028984 | -0.866444 | -26.6767 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2283 | 4.336540293128799 | -0.615568 | -14.2345 | 4 | 15 | 11 | 0.58 | 0.00 | - | no | Open |
| 2708 | 4.601556820783774 | -0.819026 | -16.5296 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2797 | 4.685771653969921 | -0.799809 | -20.1413 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2795 | 4.779944335954869 | -0.779991 | -16.2375 | 6 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 2288 | 4.917407070158971 | -1.03042 | -23.9314 | 6 | 13 | 11 | 0.58 | 0.60 | - | no | Open |
| 2791 | 5.072270948828102 | -0.794023 | -18.3397 | 7 | 7 | 0 | 0.00 | 0.00 | - | no | Open |
| 2709 | 5.432656891982814 | -0.820339 | -16.0947 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2290 | 7.244905893717198 | -1.11596 | -21.5905 | 9 | 15 | 13 | 0.68 | 0.60 | - | no | Open |
| 2792 | 4.367507784873852 | -0.732902 | -15.5868 | 11 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2790 | 4.8548898772728 | -0.659226 | -13.048 | 11 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2496 | 4.922466146660042 | -0.758547 | -19.2495 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2289 | 5.255419596376982 | -0.556845 | -13.1004 | 4 | 12 | 9 | 0.47 | 0.00 | - | yes | Open |
| 2286 | 5.416724772948112 | -1.16843 | -27.0158 | 8 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 2714 | 5.477711359461774 | -1.02254 | -22.6688 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2494 | 5.527479954546358 | -0.89329 | -21.2736 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2794 | 5.543309178842383 | -0.692884 | -14.5964 | 11 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2799 | 6.06163571208625 | -0.840897 | -14.1398 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2798 | 6.14863387587142 | -0.746412 | -14.0623 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2793 | 6.356495655852853 | -0.788763 | -15.6922 | 6 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2706 | 6.533011658068624 | -0.852693 | -19.4532 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2499 | 6.661025197830658 | -0.929633 | -21.3574 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2500 | 6.807716131034391 | -0.705046 | -18.1617 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2713 | 6.839326902184313 | -0.910574 | -18.7469 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2503 | 6.928217279209356 | -1.02422 | -25.5677 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2705 | 6.995416596579722 | -0.71602 | -14.7951 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2285 | 7.077253716729309 | -0.544189 | -14.5153 | 3 | 14 | 11 | 0.58 | 0.20 | - | yes | Open |
| 2711 | 7.138735949731882 | -0.835863 | -23.8275 | 7 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2710 | 7.36282430530167 | -0.802353 | -20.9209 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2704 | 7.393630303432996 | -0.975173 | -18.3243 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2703 | 7.647620943229677 | -1.01658 | -22.7801 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2789 | 7.6739943905844665 | -0.924801 | -16.978 | 8 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2788 | 8.078867642488934 | -0.727627 | -14.8512 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2495 | 8.099118139034449 | -0.90221 | -21.1838 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2796 | 8.271898093931657 | -0.720498 | -18.3921 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2712 | 8.40071450794128 | -0.93114 | -28.0893 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2497 | 9.40251142619558 | -0.807509 | -18.0839 | 8 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2707 | 9.48837237442649 | -0.914761 | -17.7651 | 8 | 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
-13.513kcal/mol
Ligand efficiency (LE)
-0.5197kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.789
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
354.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.25
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
73.75kcal/mol
Minimised FF energy
60.10kcal/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.