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 (-0.906 kcal/mol/HA)
✓ Good fit quality (FQ -8.64)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (21.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-26.264
kcal/mol
LE
-0.906
kcal/mol/HA
Fit Quality
-8.64
FQ (Leeson)
HAC
29
heavy atoms
MW
391
Da
LogP
3.16
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 21.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 6
Severe clashes 0
| Final rank | 4.911793331561885 | Score | -26.2637 |
|---|---|---|---|
| Inter norm | -0.969852 | Intra norm | 0.0642089 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | geometry warning; 15 clashes; 6 protein contact clashes; high strain Δ 28.3 | ||
| Residues | A:ALA212;A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:TYR174;A:VAL206;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 | 11 | Native recall | 0.58 |
| Jaccard | 0.50 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1175 | 4.895314637753896 | -0.953254 | -25.509 | 8 | 15 | 10 | 0.53 | 0.40 | - | no | Open |
| 1178 | 4.911793331561885 | -0.969852 | -26.2637 | 4 | 14 | 11 | 0.58 | 0.20 | - | no | Current |
| 875 | 5.8019469147812135 | -0.952034 | -22.6181 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 3141 | 6.206187989355319 | -0.683789 | -20.2 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1643 | 6.26192663058529 | -0.814323 | -15.248 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 871 | 7.295707917320146 | -1.05503 | -23.7801 | 9 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 1644 | 5.8219805951920165 | -0.777984 | -16.8789 | 12 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1173 | 5.982438471299099 | -1.1365 | -32.2539 | 5 | 15 | 11 | 0.58 | 0.20 | - | yes | Open |
| 1646 | 7.46543514631652 | -0.870114 | -18.0165 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1647 | 7.468199555098168 | -1.00384 | -22.8012 | 12 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3143 | 7.666307777407792 | -0.682081 | -19.5276 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3142 | 7.788713318867874 | -0.654736 | -12.1075 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1177 | 8.096386603343467 | -0.980929 | -22.2246 | 6 | 14 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1174 | 8.333397919111482 | -1.05112 | -21.8154 | 9 | 17 | 11 | 0.58 | 0.40 | - | yes | Open |
| 3138 | 8.419203456347173 | -0.805846 | -18.1081 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1642 | 8.846642392113733 | -0.893004 | -20.3623 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1176 | 9.19854934646507 | -1.01549 | -23.5272 | 9 | 16 | 11 | 0.58 | 0.40 | - | yes | Open |
| 876 | 9.291061629615944 | -0.992956 | -26.9292 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 872 | 9.6631280327509 | -1.11678 | -29.9725 | 9 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 874 | 9.824974884447565 | -0.842197 | -21.7597 | 5 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3140 | 10.370645383693853 | -0.683105 | -13.6563 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3139 | 10.714366377340529 | -0.726463 | -14.7476 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1645 | 11.893716106510757 | -0.927944 | -19.8428 | 12 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 873 | 15.955179947313706 | -0.919255 | -17.4661 | 9 | 18 | 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
-26.264kcal/mol
Ligand efficiency (LE)
-0.9056kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.645
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
391.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.16
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.75kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.86kcal/mol
Minimised FF energy
66.11kcal/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.