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 (-1.106 kcal/mol/HA)
✓ Good fit quality (FQ -10.55)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (23.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-32.063
kcal/mol
LE
-1.106
kcal/mol/HA
Fit Quality
-10.55
FQ (Leeson)
HAC
29
heavy atoms
MW
430
Da
LogP
2.95
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 4
Clashes 6
Severe clashes 1
| Final rank | 5.33342663415995 | Score | -32.0626 |
|---|---|---|---|
| Inter norm | -1.13056 | Intra norm | 0.0249485 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 9 clashes; 1 protein clash; high strain Δ 32.4 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:LYS13;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;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 | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 697 | 4.111869370838596 | -0.783239 | -21.0506 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2162 | 4.160367745988031 | -0.900131 | -25.1198 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 888 | 4.217108361780335 | -0.946723 | -27.6766 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2237 | 4.865431678161478 | -0.89763 | -26.216 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1126 | 4.8686146851245455 | -0.838861 | -23.2646 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 905 | 5.175923461383732 | -1.04284 | -29.8066 | 8 | 15 | 13 | 0.68 | 0.40 | - | no | Open |
| 1456 | 5.223536796494479 | -0.735896 | -20.1767 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2892 | 5.22909899959636 | -0.662423 | -17.0424 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2890 | 5.455210245567124 | -0.988533 | -28.1895 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 694 | 5.786245041902012 | -0.880811 | -22.0131 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1452 | 6.013139980281577 | -0.634418 | -19.2177 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 3016 | 6.251017197186693 | -0.768463 | -22.7 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1659 | 6.2751756362903715 | -0.541586 | -13.9837 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 3018 | 6.7448423629921095 | -0.707602 | -20.9845 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1120 | 7.425725553546979 | -0.766774 | -17.9539 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 904 | 5.33342663415995 | -1.13056 | -32.0626 | 7 | 15 | 13 | 0.68 | 0.40 | - | yes | Current |
| 1451 | 5.372642978855648 | -0.816997 | -22.4353 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 696 | 5.631307573983764 | -0.891961 | -22.9586 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2240 | 5.769141070471637 | -0.964791 | -27.7965 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 691 | 5.874523547019165 | -0.848711 | -22.8084 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2891 | 6.0803235992972775 | -0.867501 | -24.3801 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 693 | 6.381858579800904 | -0.797707 | -19.6108 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 890 | 6.6310907873120595 | -1.0321 | -30.4483 | 11 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2889 | 6.632517283437798 | -0.909325 | -26.346 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1660 | 6.654720537576164 | -0.679352 | -19.0459 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1124 | 6.680622041373457 | -0.980479 | -28.998 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 886 | 6.990004823159294 | -0.931537 | -27.7624 | 10 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2893 | 7.028890759874217 | -0.89602 | -24.5623 | 3 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3017 | 7.282527151918403 | -0.694543 | -18.6488 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1455 | 7.28857938202843 | -0.705212 | -21.3947 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1661 | 7.393584592531386 | -0.536629 | -17.7769 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1122 | 7.415192842704657 | -0.953078 | -26.9353 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1121 | 7.433688193272738 | -0.851974 | -25.3205 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 692 | 7.663184594704354 | -0.790924 | -23.3276 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2894 | 7.770109274167497 | -0.836537 | -23.1271 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 887 | 7.791360287068626 | -0.881316 | -23.8612 | 9 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1123 | 7.834059104489801 | -0.756434 | -17.2618 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1657 | 7.871755774865798 | -0.78462 | -22.2614 | 10 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2238 | 8.214714916097323 | -1.05701 | -30.407 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 906 | 8.296488181721106 | -1.03268 | -27.9931 | 7 | 16 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1658 | 8.391396300191012 | -0.623777 | -18.4307 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 695 | 8.435239028514085 | -0.78252 | -23.2915 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1457 | 8.749866929549075 | -0.809909 | -22.2852 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2895 | 8.953466088372053 | -0.772983 | -17.3909 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1125 | 9.166248154570393 | -0.710372 | -19.9427 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2239 | 9.76977400798912 | -0.885729 | -23.2838 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3015 | 9.97558583116345 | -0.888141 | -25.7806 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 891 | 10.356900298932489 | -0.916863 | -24.7112 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 889 | 10.75346303605972 | -0.87622 | -22.4413 | 11 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1454 | 10.828262197522555 | -0.812525 | -22.2931 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 892 | 10.944842238652809 | -1.03923 | -24.512 | 13 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1453 | 12.656895850984805 | -0.79869 | -24.3006 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2163 | 13.045205356730103 | -0.983933 | -23.2803 | 7 | 17 | 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
-32.063kcal/mol
Ligand efficiency (LE)
-1.1056kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.554
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.95
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-12.73kcal/mol
Minimised FF energy
-36.04kcal/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.