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 (-1.096 kcal/mol/HA)
✓ Good fit quality (FQ -10.35)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (34.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-30.695
kcal/mol
LE
-1.096
kcal/mol/HA
Fit Quality
-10.35
FQ (Leeson)
HAC
28
heavy atoms
MW
407
Da
LogP
2.17
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 34.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 24
π–π 4
Clashes 15
Severe clashes 1
| Final rank | 8.48815336331865 | Score | -30.6948 |
|---|---|---|---|
| Inter norm | -1.07128 | Intra norm | -0.0249606 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 10 |
| Artifact reason | excluded; geometry warning; 7 clashes; 1 protein clash; high strain Δ 48.3 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU209;A:LYS178;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 | 0.67 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 989 | 3.7026146676839202 | -0.847015 | -20.9707 | 8 | 13 | 11 | 0.58 | 0.40 | - | no | Open |
| 2471 | 5.356300865916946 | -0.946596 | -19.4906 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2477 | 5.424535775169938 | -0.75486 | -20.3871 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2470 | 5.480628229756417 | -0.796142 | -19.2132 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 966 | 5.741868723057045 | -0.671456 | -22.2646 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 992 | 8.250680108043879 | -0.724373 | -22.4328 | 4 | 15 | 13 | 0.68 | 0.20 | - | no | Open |
| 2474 | 4.765970443518974 | -0.719083 | -23.5779 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 964 | 6.208741223113114 | -0.829208 | -24.5552 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2475 | 6.8501345162847675 | -0.796954 | -19.8135 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 965 | 7.808679323785041 | -0.324046 | -16.9009 | 0 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 987 | 7.9337257545555 | -1.16732 | -26.0463 | 8 | 16 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2476 | 8.042282007680157 | -0.692223 | -20.38 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 999 | 8.48815336331865 | -1.07128 | -30.6948 | 10 | 16 | 14 | 0.74 | 0.60 | - | yes | Current |
| 997 | 9.283113985438447 | -1.08037 | -32.6614 | 8 | 16 | 16 | 0.84 | 0.60 | - | yes | Open |
| 2472 | 9.365195563766376 | -0.645254 | -17.7185 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2473 | 9.502470234778503 | -0.702144 | -17.6104 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 962 | 9.786986742731663 | -0.7954 | -22.5432 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 961 | 9.813830918028195 | -0.52745 | -17.8168 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 963 | 10.841676721380608 | -0.545951 | -18.8723 | 9 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 991 | 12.355933974482328 | -0.932378 | -27.2209 | 8 | 15 | 12 | 0.63 | 0.40 | - | yes | Open |
| 993 | 12.981250816214166 | -1.25157 | -37.0671 | 11 | 18 | 15 | 0.79 | 0.60 | - | yes | Open |
| 988 | 14.819619846229365 | -1.15094 | -27.0703 | 6 | 20 | 14 | 0.74 | 0.20 | - | yes | Open |
| 995 | 15.210244163474998 | -1.18316 | -32.2939 | 12 | 15 | 12 | 0.63 | 0.60 | - | yes | Open |
| 990 | 16.438541935752454 | -0.797478 | -18.0912 | 9 | 20 | 15 | 0.79 | 0.20 | - | yes | Open |
| 994 | 17.216575200845806 | -1.09531 | -21.7016 | 9 | 19 | 15 | 0.79 | 0.20 | - | yes | Open |
| 998 | 17.94707806486477 | -0.937324 | -25.5489 | 9 | 19 | 14 | 0.74 | 0.40 | - | yes | Open |
| 986 | 18.348764863018 | -1.00494 | -25.4863 | 8 | 21 | 15 | 0.79 | 0.00 | - | yes | Open |
| 996 | 19.499999369602268 | -0.984137 | -24.8242 | 9 | 21 | 15 | 0.79 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.695kcal/mol
Ligand efficiency (LE)
-1.0962kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.349
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
407.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.17
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.98kcal/mol
Minimised FF energy
1.33kcal/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.