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 (-0.774 kcal/mol/HA)
✓ Good fit quality (FQ -7.61)
✗ Very high strain energy (29.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.766
kcal/mol
LE
-0.774
kcal/mol/HA
Fit Quality
-7.61
FQ (Leeson)
HAC
32
heavy atoms
MW
423
Da
LogP
3.87
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 29.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 4
Clashes 12
Severe clashes 0
| Final rank | 7.781050852582138 | Score | -24.7664 |
|---|---|---|---|
| Inter norm | -1.01052 | Intra norm | 0.23657 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 20 clashes; 12 protein contact clashes; high strain Δ 29.8 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;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 | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 882 | 3.68015874069592 | -0.758599 | -23.1905 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 618 | 4.753718222757358 | -0.879782 | -27.9333 | 0 | 11 | 8 | 0.42 | 0.00 | - | no | Open |
| 880 | 4.760586587214268 | -0.789752 | -25.2392 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 876 | 4.865720514621524 | -0.80982 | -25.2682 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 5.2705305231790405 | -0.881861 | -28.2029 | 0 | 11 | 8 | 0.42 | 0.00 | - | no | Open |
| 806 | 5.387341035556807 | -0.80016 | -25.685 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 878 | 5.717936949193543 | -0.823674 | -25.1139 | 0 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 610 | 5.896851545489233 | -0.88753 | -28.019 | 1 | 13 | 9 | 0.47 | 0.00 | - | no | Open |
| 609 | 5.912714715887796 | -1.02151 | -29.0331 | 1 | 18 | 16 | 0.84 | 0.00 | - | no | Open |
| 883 | 7.483230480035522 | -0.74954 | -21.634 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 7.781050852582138 | -1.01052 | -24.7664 | 1 | 16 | 15 | 0.79 | 0.20 | - | no | Current |
| 613 | 8.164514631771638 | -0.879609 | -27.0241 | 0 | 17 | 15 | 0.79 | 0.00 | - | no | Open |
| 615 | 5.871673633146488 | -1.02301 | -27.44 | 0 | 15 | 14 | 0.74 | 0.00 | - | yes | Open |
| 801 | 6.1364179169700765 | -0.774794 | -24.3976 | 0 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 881 | 6.176569636524991 | -0.838986 | -26.0928 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 873 | 6.2987060644719 | -0.84473 | -26.2076 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 877 | 6.460596193474383 | -0.823996 | -25.8147 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 803 | 6.696921226225941 | -0.778381 | -24.3934 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 802 | 6.737152572584959 | -0.80934 | -24.9207 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 800 | 6.828955810971412 | -0.797342 | -23.8658 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 620 | 6.890565349006715 | -0.992624 | -28.6432 | 0 | 15 | 13 | 0.68 | 0.00 | - | yes | Open |
| 807 | 6.924363385512182 | -0.789267 | -24.8433 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 798 | 7.197254895005341 | -0.83178 | -25.6924 | 0 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 617 | 7.25695253679321 | -0.943383 | -24.9559 | 0 | 17 | 16 | 0.84 | 0.00 | - | yes | Open |
| 874 | 7.455804747405748 | -0.790897 | -20.6835 | 0 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 797 | 7.481414084461965 | -0.82142 | -26.2502 | 0 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 805 | 7.9142323766242315 | -0.819836 | -26.4257 | 0 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 884 | 55.83634397036696 | -0.843594 | -26.1424 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 616 | 56.02875660341615 | -1.00343 | -28.9633 | 0 | 15 | 13 | 0.68 | 0.00 | - | yes | Open |
| 619 | 56.83784189917394 | -1.00164 | -26.3548 | 0 | 15 | 14 | 0.74 | 0.00 | - | yes | Open |
| 804 | 57.194339723439576 | -0.77967 | -23.1691 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 612 | 57.4222504101707 | -1.08289 | -32.3895 | 1 | 17 | 15 | 0.79 | 0.00 | - | yes | Open |
| 799 | 57.975958599277476 | -0.773564 | -19.6304 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 875 | 58.73167053078245 | -0.687968 | -20.6455 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 808 | 58.975628311942216 | -0.757633 | -22.2892 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 879 | 59.98350652153543 | -0.688332 | -19.289 | 0 | 19 | 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
-24.766kcal/mol
Ligand efficiency (LE)
-0.7740kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.611
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
422.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.87
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
167.30kcal/mol
Minimised FF energy
138.09kcal/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.