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 (-1.204 kcal/mol/HA)
✓ Good fit quality (FQ -11.09)
✓ Good H-bonds (5 bonds)
✗ High strain energy (17.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-31.302
kcal/mol
LE
-1.204
kcal/mol/HA
Fit Quality
-11.09
FQ (Leeson)
HAC
26
heavy atoms
MW
349
Da
LogP
2.66
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 17.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 4
Clashes 2
Severe clashes 0
| Final rank | 2.6063318911184816 | Score | -31.3019 |
|---|---|---|---|
| Inter norm | -1.15151 | Intra norm | -0.0524063 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 13 clashes; 2 protein contact clashes; moderate strain Δ 18.3 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:GLY205;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.75 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 486 | 2.569525141618116 | -1.31932 | -35.1131 | 6 | 16 | 16 | 0.84 | 0.60 | - | no | Open |
| 487 | 2.5706233481366123 | -1.21244 | -32.7468 | 6 | 16 | 15 | 0.79 | 0.40 | - | no | Open |
| 485 | 2.6063318911184816 | -1.15151 | -31.3019 | 5 | 16 | 15 | 0.79 | 0.40 | - | no | Current |
| 482 | 2.746560948394498 | -1.24922 | -33.3657 | 4 | 16 | 15 | 0.79 | 0.60 | - | no | Open |
| 483 | 3.0881037770074276 | -1.16846 | -31.7187 | 4 | 16 | 15 | 0.79 | 0.40 | - | no | Open |
| 515 | 3.1059336830861044 | -1.03863 | -26.8521 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 520 | 3.3538301153175993 | -1.08354 | -31.3099 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 3.356499595837022 | -1.01808 | -26.9593 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 484 | 3.4584880697646083 | -1.20344 | -32.1171 | 4 | 16 | 15 | 0.79 | 0.60 | - | no | Open |
| 471 | 3.831713010045734 | -0.79224 | -20.5914 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 658 | 3.9501692319057424 | -0.985528 | -25.2336 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 4.064825162545956 | -1.07948 | -31.1184 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 519 | 4.251722486273004 | -1.105 | -31.8661 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 518 | 4.4601038974391924 | -0.999455 | -26.722 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 4.636093622647474 | -0.769462 | -22.2181 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 625 | 4.803546563768789 | -0.803217 | -21.7247 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 472 | 5.396863692971612 | -0.903161 | -25.3504 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 5.419036919500527 | -0.806911 | -21.6887 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 5.678253723502912 | -0.820976 | -21.4741 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 5.111686360577248 | -0.945538 | -24.3472 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 470 | 5.9141819054849005 | -0.771259 | -22.3003 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 467 | 5.94005831272731 | -0.751539 | -21.2439 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 579 | 6.556874896407342 | -0.8562 | -22.5503 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 624 | 7.0886128301442595 | -0.70565 | -21.0809 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 623 | 7.34512433450863 | -0.72924 | -20.2579 | 4 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 469 | 8.234825837583921 | -0.726875 | -18.3807 | 2 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 576 | 8.723183317896952 | -0.739238 | -19.674 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 577 | 9.658071359179605 | -0.757797 | -20.8286 | 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
-31.302kcal/mol
Ligand efficiency (LE)
-1.2039kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.092
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
349.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-125.49kcal/mol
Minimised FF energy
-143.05kcal/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.