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 (-1.356 kcal/mol/HA)
✓ Good fit quality (FQ -12.95)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (22.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-39.327
kcal/mol
LE
-1.356
kcal/mol/HA
Fit Quality
-12.95
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.46
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 22.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 24
π–π 3
Clashes 8
Severe clashes 0
| Final rank | 5.099464498447895 | Score | -39.3269 |
|---|---|---|---|
| Inter norm | -1.16396 | Intra norm | -0.192143 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 9 |
| Artifact reason | geometry warning; 12 clashes; 8 protein contact clashes; high strain Δ 31.2 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:TYR98 | ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.68 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 947 | 3.685796895602662 | -1.15115 | -30.8536 | 10 | 13 | 13 | 0.68 | 0.40 | - | no | Open |
| 945 | 4.01589966986883 | -1.16385 | -39.1929 | 11 | 14 | 13 | 0.68 | 0.40 | - | no | Open |
| 1508 | 4.545654326349949 | -0.601787 | -23.7857 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3053 | 4.6469712824838325 | -0.615403 | -18.6524 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2938 | 4.893433566307431 | -0.914081 | -26.2321 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 946 | 5.099464498447895 | -1.16396 | -39.3269 | 9 | 13 | 13 | 0.68 | 0.60 | - | no | Current |
| 2283 | 5.587246581638521 | -0.868032 | -23.4287 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1215 | 5.597812162690021 | -0.893438 | -24.523 | 5 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 2939 | 5.91595891871275 | -0.7364 | -22.3903 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1166 | 5.9714898924218405 | -0.782661 | -21.9471 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1167 | 6.328841122786455 | -0.820539 | -23.1705 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1212 | 6.399801172572356 | -0.867267 | -31.1176 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2281 | 6.505309085875486 | -0.806459 | -25.853 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1056 | 6.757643329791728 | -0.913873 | -22.4923 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2278 | 7.089451804269929 | -0.922707 | -32.0998 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 1510 | 6.278580802045207 | -0.668175 | -16.8338 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1054 | 6.892013669930548 | -0.954315 | -23.4905 | 12 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1509 | 7.008371354667256 | -0.695582 | -17.2833 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1507 | 7.438275695918752 | -0.644618 | -24.9097 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3052 | 7.663031767295704 | -0.84589 | -24.7448 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1053 | 7.723839908221002 | -0.918774 | -23.8187 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2282 | 7.75755817382527 | -0.990903 | -25.5451 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1165 | 7.878558658148589 | -0.777158 | -21.8061 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1213 | 8.36934802716161 | -0.865914 | -22.5926 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2279 | 8.382404387946393 | -0.933107 | -27.3468 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1214 | 8.394175177881948 | -0.988746 | -29.6316 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1052 | 8.422637548759578 | -0.93638 | -33.6314 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2937 | 8.757853424058045 | -0.880444 | -26.2327 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1055 | 9.119079605330361 | -0.970755 | -26.4205 | 11 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1164 | 9.615793555772534 | -0.764226 | -27.7249 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1051 | 10.248109841291988 | -0.758542 | -28.9482 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2284 | 10.751445528226279 | -0.967121 | -26.3674 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 948 | 11.261270625310344 | -1.08614 | -27.3435 | 7 | 20 | 15 | 0.79 | 0.40 | - | yes | Open |
| 2280 | 12.509670080167565 | -0.881243 | -31.503 | 7 | 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
-39.327kcal/mol
Ligand efficiency (LE)
-1.3561kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.945
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.46
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-12.92kcal/mol
Minimised FF energy
-34.97kcal/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.