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 (-0.403 kcal/mol/HA)
✓ Good fit quality (FQ -3.92)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (29.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-12.485
kcal/mol
LE
-0.403
kcal/mol/HA
Fit Quality
-3.92
FQ (Leeson)
HAC
31
heavy atoms
MW
463
Da
LogP
5.31
cLogP
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 13
π–π 1
Clashes 4
Severe clashes 0
| Final rank | 5.058545229338493 | Score | -12.4848 |
|---|---|---|---|
| Inter norm | -0.495512 | Intra norm | 0.0927763 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 4 |
| Artifact reason | geometry warning; 12 clashes; 4 protein contact clashes; high strain Δ 39.5 | ||
| Residues | A:ASN402;A:GLU466;A:GLU467;A:HIS461;A:LEU399;A:PHE396;A:PRO398;A:SER464;A:THR397;A:THR463 | ||
Protein summary
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 2 |
| IFP residues | A:ASN402; A:GLU467; A:LEU399; A:PHE396; A:PRO398; A:SER394; A:SER470; A:THR397 | ||
| Current overlap | 6 | Native recall | 0.75 |
| Jaccard | 0.50 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.50 |
| H-bond same residue+role | 1 | Role recall | 1.00 |
| H-bond same residue | 1 | Residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 603 | 3.8044852916316727 | -0.64201 | -20.5404 | 5 | 16 | 7 | 0.88 | 1.00 | - | no | Open |
| 586 | 4.133639480999813 | -0.459657 | -14.3137 | 2 | 13 | 7 | 0.88 | 1.00 | - | no | Open |
| 606 | 4.35679852248012 | -0.482688 | -12.5267 | 3 | 10 | 6 | 0.75 | 1.00 | - | no | Open |
| 588 | 4.768513570953907 | -0.486377 | -11.4717 | 2 | 14 | 7 | 0.88 | 0.00 | - | no | Open |
| 604 | 4.897872850082145 | -0.647312 | -17.7174 | 3 | 13 | 5 | 0.62 | 1.00 | - | no | Open |
| 386 | 5.04889500330964 | -0.582249 | -15.3502 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 590 | 5.058545229338493 | -0.495512 | -12.4848 | 4 | 10 | 6 | 0.75 | 1.00 | - | no | Current |
| 388 | 6.699680434476487 | -0.876173 | -23.3192 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 392 | 7.357133203943192 | -0.60999 | -13.2463 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 595 | 53.63205230972664 | -0.576969 | -14.0648 | 4 | 11 | 8 | 1.00 | 1.00 | - | no | Open |
| 598 | 53.823562632082904 | -0.489728 | -15.4323 | 2 | 11 | 5 | 0.62 | 1.00 | - | no | Open |
| 593 | 53.951856578686 | -0.514805 | -12.1895 | 2 | 13 | 7 | 0.88 | 0.00 | - | no | Open |
| 592 | 54.34499684632277 | -0.508151 | -16.6176 | 2 | 13 | 7 | 0.88 | 1.00 | - | no | Open |
| 608 | 54.48600947378974 | -0.486729 | -12.6698 | 2 | 12 | 6 | 0.75 | 1.00 | - | no | Open |
| 591 | 54.6487906993372 | -0.458473 | -13.1069 | 4 | 9 | 5 | 0.62 | 0.00 | - | no | Open |
| 380 | 6.995481301245248 | -0.553748 | -11.4268 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 383 | 7.493309597392498 | -0.60514 | -14.0984 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 378 | 7.5527008820243635 | -0.642283 | -15.0328 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 594 | 54.636622114209594 | -0.539596 | -17.8162 | 4 | 11 | 5 | 0.62 | 1.00 | - | yes | Open |
| 597 | 54.994155520595946 | -0.541822 | -15.8613 | 2 | 10 | 6 | 0.75 | 0.00 | - | yes | Open |
| 605 | 55.00188070827766 | -0.533242 | -15.8009 | 3 | 12 | 7 | 0.88 | 1.00 | - | yes | Open |
| 607 | 55.18067594788496 | -0.538428 | -16.8563 | 2 | 14 | 7 | 0.88 | 1.00 | - | yes | Open |
| 587 | 55.373123738271175 | -0.51175 | -14.9857 | 4 | 9 | 7 | 0.88 | 1.00 | - | yes | Open |
| 395 | 55.53515338651712 | -0.606552 | -15.425 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 585 | 55.59791610234486 | -0.54959 | -14.884 | 3 | 10 | 8 | 1.00 | 1.00 | - | yes | Open |
| 596 | 55.86089068647122 | -0.538897 | -15.7883 | 2 | 12 | 8 | 1.00 | 0.00 | - | yes | Open |
| 601 | 56.07350512110974 | -0.564946 | -13.7397 | 2 | 12 | 8 | 1.00 | 1.00 | - | yes | Open |
| 589 | 56.121280930227165 | -0.56093 | -12.5425 | 2 | 12 | 7 | 0.88 | 0.00 | - | yes | Open |
| 600 | 56.23209528423411 | -0.541966 | -18.3447 | 3 | 10 | 7 | 0.88 | 0.00 | - | yes | Open |
| 393 | 56.23572476535945 | -0.683482 | -17.0219 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 602 | 56.32772230499301 | -0.49774 | -16.9141 | 5 | 9 | 4 | 0.50 | 1.00 | - | yes | Open |
| 379 | 56.6266773907136 | -0.547826 | -9.18538 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 385 | 56.70770719150399 | -0.731306 | -23.6734 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 381 | 56.88766429102111 | -0.810642 | -23.3319 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 387 | 56.91839106122524 | -0.714746 | -20.9139 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 391 | 57.01029957077979 | -0.717756 | -20.4792 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 389 | 57.14245644007512 | -0.769954 | -19.345 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 384 | 57.419456380965755 | -0.588605 | -14.6981 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 376 | 57.764354561242754 | -0.543591 | -15.164 | 2 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 382 | 57.79014964446977 | -0.736543 | -22.5192 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 390 | 57.809059650181844 | -0.771028 | -23.1672 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 397 | 57.90883832160699 | -0.617507 | -18.4212 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 398 | 57.984342221875046 | -0.83277 | -24.6131 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 377 | 58.19397974886769 | -0.658949 | -17.5313 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 394 | 58.19821300993624 | -0.766089 | -23.6755 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 599 | 58.35248215172916 | -0.515234 | -15.3395 | 3 | 8 | 6 | 0.75 | 0.00 | - | yes | Open |
| 396 | 60.01756934145726 | -0.677641 | -19.8411 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 399 | 61.76318792298458 | -0.634659 | -17.3185 | 4 | 11 | 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
-12.485kcal/mol
Ligand efficiency (LE)
-0.4027kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.924
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
463.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.31
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
100.22kcal/mol
Minimised FF energy
70.94kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. It will be calculated automatically
the next time this pose is loaded if a receptor PDB path is stored.