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 (-1.114 kcal/mol/HA)
✓ Good fit quality (FQ -10.13)
✓ Good H-bonds (4 bonds)
✗ High strain energy (14.5 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-27.853
kcal/mol
LE
-1.114
kcal/mol/HA
Fit Quality
-10.13
FQ (Leeson)
HAC
25
heavy atoms
MW
344
Da
LogP
2.08
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 14.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 23
π–π 1
Clashes 11
Severe clashes 0
| Final rank | 4.278491982231375 | Score | -27.8534 |
|---|---|---|---|
| Inter norm | -1.14936 | Intra norm | 0.0352218 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | geometry warning; 8 clashes; 11 protein contact clashes; moderate strain Δ 16.3 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:SER207;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 | 14 | Native recall | 0.74 |
| Jaccard | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 280 | 2.895921407661222 | -1.09894 | -24.1623 | 6 | 15 | 13 | 0.68 | 0.40 | - | no | Open |
| 177 | 3.7118923633706116 | -1.08724 | -23.8881 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 281 | 3.8069432923038637 | -1.06962 | -26.6251 | 4 | 16 | 14 | 0.74 | 0.40 | - | no | Open |
| 203 | 3.8143501460276124 | -0.925128 | -21.7189 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 273 | 4.078245683244583 | -1.18612 | -28.706 | 4 | 16 | 14 | 0.74 | 0.40 | - | no | Open |
| 277 | 4.278491982231375 | -1.14936 | -27.8534 | 4 | 16 | 14 | 0.74 | 0.40 | - | no | Current |
| 272 | 3.4217775945225872 | -1.20735 | -26.6499 | 6 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 276 | 4.349365273738883 | -1.19624 | -25.786 | 7 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 211 | 4.351155508037664 | -0.870862 | -21.1258 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 271 | 5.000250206115846 | -1.36988 | -33.4963 | 9 | 15 | 14 | 0.74 | 0.60 | - | yes | Open |
| 279 | 5.126145103812303 | -1.23305 | -30.1377 | 9 | 14 | 13 | 0.68 | 0.60 | - | yes | Open |
| 274 | 5.2462377996531915 | -1.23536 | -30.2361 | 5 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 173 | 5.587412437695855 | -1.03109 | -22.4337 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 206 | 5.623397304387711 | -0.783104 | -19.1367 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 169 | 6.1781616990200305 | -1.13806 | -26.4485 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 174 | 6.9299868687335096 | -1.27341 | -29.8656 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 207 | 7.111225182702581 | -0.831112 | -17.0935 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 170 | 7.227080540346497 | -1.27856 | -29.2521 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 178 | 7.443509634901709 | -1.27189 | -30.5071 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 167 | 7.4470704028265216 | -1.13514 | -26.0969 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 171 | 8.108093599831854 | -1.11327 | -26.7014 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 210 | 8.116809004005383 | -0.816898 | -18.6843 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 208 | 8.175251752610752 | -0.862282 | -21.5723 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 202 | 8.289028205894592 | -1.10025 | -25.1435 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 175 | 9.20553497461885 | -1.10759 | -26.8075 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 209 | 10.327422349886822 | -1.00996 | -24.8844 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 201 | 10.806611945031236 | -1.12259 | -25.857 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 278 | 54.884919210224076 | -1.15437 | -28.6973 | 5 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 270 | 55.09338546050683 | -1.28815 | -31.1159 | 5 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 275 | 56.44579575100415 | -1.32319 | -31.9299 | 10 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 205 | 59.65584187736786 | -0.894925 | -20.2023 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 168 | 60.222972011750436 | -0.967539 | -22.0034 | 7 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 176 | 60.29103948963416 | -0.946031 | -21.329 | 5 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 172 | 61.028793135629755 | -0.88877 | -19.8038 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 204 | 61.06060687838571 | -1.04929 | -25.2941 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 212 | 61.373957862957624 | -1.07174 | -25.3942 | 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
-27.853kcal/mol
Ligand efficiency (LE)
-1.1141kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.129
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
344.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.08
Lipinski: ≤ 5
Rotatable bonds
1
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.28kcal/mol
Minimised FF energy
39.82kcal/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.