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 (-0.928 kcal/mol/HA)
✓ Good fit quality (FQ -9.04)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (43.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.767
kcal/mol
LE
-0.928
kcal/mol/HA
Fit Quality
-9.04
FQ (Leeson)
HAC
31
heavy atoms
MW
460
Da
LogP
2.45
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 43.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 4
Clashes 11
Severe clashes 0
| Final rank | 6.747806517070467 | Score | -28.7665 |
|---|---|---|---|
| Inter norm | -0.894113 | Intra norm | -0.0338382 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | geometry warning; 12 clashes; 11 protein contact clashes; high strain Δ 39.4 | ||
| Residues | A:ARG14;A:CYS168;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.79 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1409 | 4.720540780765134 | -0.678049 | -22.7701 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1085 | 5.188723468653403 | -0.683854 | -19.6141 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2867 | 5.441569620280367 | -0.656291 | -23.1726 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 674 | 5.7275250426142 | -0.63082 | -19.1454 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2868 | 5.728742557846616 | -0.739757 | -21.8215 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 6.027688328238083 | -0.698125 | -19.3749 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1412 | 6.095507294223708 | -0.670061 | -18.7458 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 680 | 6.264615674994543 | -0.817403 | -24.3544 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 840 | 6.740687317007522 | -0.866533 | -25.8891 | 10 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 838 | 6.747806517070467 | -0.894113 | -28.7665 | 4 | 15 | 15 | 0.79 | 0.20 | - | no | Current |
| 2988 | 6.996450237398408 | -0.512611 | -13.327 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 857 | 7.204994151610824 | -0.807855 | -20.869 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 856 | 7.530706653270757 | -0.75223 | -18.246 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1411 | 5.8182078932657095 | -0.63516 | -21.0519 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1081 | 7.008257426895746 | -0.749433 | -22.5359 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1410 | 7.726804555812281 | -0.688838 | -21.2454 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 843 | 7.940138167415152 | -0.822646 | -25.6602 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1083 | 8.049240373378417 | -0.758159 | -19.3829 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1413 | 8.052365729883867 | -0.746215 | -21.9956 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 841 | 8.410622241239839 | -0.830398 | -25.3341 | 10 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2993 | 8.459568651342243 | -0.671843 | -19.9691 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 839 | 8.52686326203941 | -0.832925 | -26.1255 | 10 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2869 | 8.929338495530981 | -0.797244 | -23.8892 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2990 | 8.940301499150374 | -0.749265 | -22.332 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2991 | 8.964538214880902 | -0.636965 | -19.7808 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1408 | 8.975374303126808 | -0.622431 | -20.2624 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 837 | 9.286327825423637 | -0.947531 | -30.2708 | 4 | 16 | 16 | 0.84 | 0.20 | - | yes | Open |
| 842 | 9.411094609568961 | -0.952432 | -27.504 | 10 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 860 | 9.432059988153865 | -0.670719 | -18.4525 | 5 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2992 | 9.55378513987933 | -0.725083 | -21.9304 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1082 | 9.836902883338551 | -0.75468 | -21.4837 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 855 | 10.525798797897501 | -0.672042 | -20.8726 | 3 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2989 | 10.632691284579789 | -0.699499 | -18.8696 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 854 | 11.901254393258906 | -0.733074 | -22.8368 | 1 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 858 | 12.177521063753984 | -0.673896 | -20.1728 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1084 | 12.329028591880858 | -0.599773 | -16.7908 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2870 | 12.355384800228938 | -0.630499 | -21.335 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 681 | 12.914722145160836 | -1.01004 | -29.7967 | 8 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1080 | 13.002566846985312 | -0.761146 | -20.91 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 859 | 13.755043533300725 | -0.687116 | -19.9577 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1086 | 14.324157210907305 | -0.73349 | -20.4831 | 6 | 15 | 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
-28.767kcal/mol
Ligand efficiency (LE)
-0.9280kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.040
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
459.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.45
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
42.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
22.80kcal/mol
Minimised FF energy
-20.16kcal/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.