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 (-1.262 kcal/mol/HA)
✓ Good fit quality (FQ -11.47)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (23.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-31.544
kcal/mol
LE
-1.262
kcal/mol/HA
Fit Quality
-11.47
FQ (Leeson)
HAC
25
heavy atoms
MW
357
Da
LogP
2.90
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 4
Clashes 8
Severe clashes 1
| Final rank | 5.055521957965125 | Score | -31.5443 |
|---|---|---|---|
| Inter norm | -1.2711 | Intra norm | 0.00933183 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 6 clashes; 1 protein clash; high strain Δ 30.6 | ||
| Residues | A:ARG14;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;A:TRP221;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 | 13 | Native recall | 0.68 |
| Jaccard | 0.68 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1466 | 2.8477131629182972 | -1.30953 | -25.835 | 10 | 18 | 14 | 0.74 | 0.60 | - | no | Open |
| 1463 | 3.0304964717786866 | -1.10855 | -27.5925 | 6 | 15 | 14 | 0.74 | 0.40 | - | no | Open |
| 1471 | 3.6087795664738165 | -1.09381 | -27.4192 | 9 | 15 | 14 | 0.74 | 0.40 | - | no | Open |
| 1462 | 3.8898375442236763 | -1.07512 | -19.8396 | 9 | 17 | 13 | 0.68 | 0.40 | - | no | Open |
| 1458 | 4.13664247473954 | -1.15707 | -27.1188 | 8 | 17 | 13 | 0.68 | 0.20 | - | no | Open |
| 1454 | 4.809549966072977 | -1.25985 | -18.678 | 9 | 17 | 13 | 0.68 | 0.40 | - | no | Open |
| 1457 | 4.950999044583919 | -0.963478 | -26.916 | 5 | 14 | 14 | 0.74 | 0.40 | - | no | Open |
| 1470 | 5.306059305256895 | -1.10271 | -16.4813 | 10 | 18 | 14 | 0.74 | 0.60 | - | no | Open |
| 1455 | 5.595314989092087 | -1.32299 | -30.6727 | 10 | 14 | 13 | 0.68 | 0.60 | - | no | Open |
| 1467 | 4.757758394915117 | -1.25127 | -26.5847 | 9 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1472 | 5.055521957965125 | -1.2711 | -31.5443 | 6 | 13 | 13 | 0.68 | 0.40 | - | yes | Current |
| 1464 | 5.582767786716264 | -1.01547 | -25.1179 | 6 | 14 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1459 | 5.736177440893634 | -1.053 | -22.7034 | 8 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1469 | 9.020591691372445 | -0.903973 | -21.2056 | 10 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1461 | 10.929929160468133 | -0.975303 | -23.9452 | 8 | 17 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1465 | 56.94610524761191 | -0.993543 | -25.3304 | 8 | 16 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1473 | 57.173722285686324 | -0.861845 | -14.3575 | 5 | 12 | 12 | 0.63 | 0.40 | - | yes | Open |
| 1456 | 57.86531934603744 | -1.37557 | -33.0446 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1460 | 60.74026888972618 | -1.1227 | -27.4724 | 9 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1468 | 62.61985228136424 | -1.29041 | -32.2414 | 12 | 16 | 16 | 0.84 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.544kcal/mol
Ligand efficiency (LE)
-1.2618kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.471
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
357.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.90
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
82.73kcal/mol
Minimised FF energy
59.09kcal/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.