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 (-1.058 kcal/mol/HA)
✓ Good fit quality (FQ -10.10)
✓ Good H-bonds (3 bonds)
✗ High strain energy (18.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.681
kcal/mol
LE
-1.058
kcal/mol/HA
Fit Quality
-10.10
FQ (Leeson)
HAC
29
heavy atoms
MW
380
Da
LogP
3.75
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 18.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 4
Clashes 7
Severe clashes 0
| Final rank | 5.516591826421885 | Score | -30.6811 |
|---|---|---|---|
| Inter norm | -1.01555 | Intra norm | -0.0424189 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 18 clashes; 7 protein contact clashes; high strain Δ 21.6 | ||
| Residues | A:ARG14;A:CYS168;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;A:TYR174;D:HIS267 | ||
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.52 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1108 | 4.779037706975952 | -0.759313 | -18.371 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1215 | 5.321087890310703 | -0.90261 | -29.179 | 6 | 15 | 13 | 0.68 | 0.20 | - | no | Open |
| 1214 | 5.516591826421885 | -1.01555 | -30.6811 | 3 | 13 | 11 | 0.58 | 0.00 | - | no | Current |
| 1965 | 5.597076544968117 | -0.677289 | -25.4512 | 7 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 1459 | 5.8671810011782775 | -0.690177 | -21.1748 | 9 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1959 | 5.8766787579557445 | -0.755558 | -24.5417 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1110 | 6.172418380008201 | -0.671586 | -24.3307 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1217 | 6.537584727744445 | -0.854803 | -22.4686 | 2 | 13 | 13 | 0.68 | 0.20 | - | no | Open |
| 1550 | 6.839268589847438 | -1.12292 | -25.9684 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1461 | 7.247187454705978 | -0.597842 | -18.9552 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1212 | 7.534055496996133 | -1.1161 | -29.403 | 4 | 13 | 13 | 0.68 | 0.20 | - | no | Open |
| 1966 | 7.199445821387936 | -0.562465 | -14.091 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1106 | 7.262937806073767 | -0.664521 | -20.8962 | 0 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1111 | 7.401021571494323 | -0.704305 | -25.1026 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1963 | 7.48640559129271 | -0.649568 | -25.0317 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1107 | 7.4884342240689845 | -0.813121 | -29.4028 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1969 | 7.607540412497526 | -0.650669 | -21.374 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1960 | 7.615575583755688 | -0.747928 | -20.8971 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1109 | 7.729864991061228 | -0.702371 | -18.9817 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1962 | 7.8246433124644295 | -0.571021 | -20.9405 | 4 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1544 | 8.002763854435246 | -1.11746 | -33.8881 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1462 | 8.09737806071556 | -0.725144 | -22.9845 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1970 | 8.193471392181614 | -0.635494 | -21.101 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1460 | 8.316718448863208 | -0.781682 | -22.3166 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1220 | 8.414690347469241 | -0.969591 | -28.4594 | 4 | 14 | 13 | 0.68 | 0.20 | - | yes | Open |
| 1964 | 8.914021698113991 | -0.647234 | -21.2585 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1545 | 9.4738259901621 | -1.0294 | -31.7049 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1549 | 9.530957691105867 | -0.983664 | -29.9507 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1547 | 9.545204877588962 | -1.00858 | -27.9857 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1968 | 9.661530884736642 | -0.699214 | -23.0205 | 4 | 7 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1551 | 10.265090139669066 | -1.03061 | -31.7404 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1216 | 10.548811589948107 | -1.14197 | -32.3388 | 5 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1218 | 10.912142659448829 | -1.07146 | -30.4848 | 5 | 12 | 12 | 0.63 | 0.40 | - | yes | Open |
| 1548 | 11.04299461106699 | -0.882823 | -20.9744 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1961 | 11.674635982718529 | -0.676933 | -21.7893 | 6 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1967 | 11.941826009652797 | -0.63428 | -17.8458 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1211 | 12.830032228198476 | -1.01634 | -31.2455 | 4 | 22 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1219 | 13.085146946339075 | -0.869084 | -28.157 | 6 | 20 | 15 | 0.79 | 0.80 | - | yes | Open |
| 1546 | 14.286839365633618 | -0.954705 | -25.7123 | 14 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1213 | 15.722094605910264 | -0.700072 | -18.7872 | 5 | 18 | 12 | 0.63 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.681kcal/mol
Ligand efficiency (LE)
-1.0580kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.099
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
380.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.75
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.72kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
119.74kcal/mol
Minimised FF energy
101.02kcal/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.