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 (-1.331 kcal/mol/HA)
✓ Good fit quality (FQ -11.14)
✓ Strong H-bond network (13 bonds)
✗ Very high strain energy (20.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-26.616
kcal/mol
LE
-1.331
kcal/mol/HA
Fit Quality
-11.14
FQ (Leeson)
HAC
20
heavy atoms
MW
296
Da
LogP
-0.27
cLogP
Interaction summary
Collapsible panels
H-bonds 13
Hydrophobic 3
π–π 2
Clashes 11
Severe clashes 4
| Final rank | 9.542291570199374 | Score | -26.616 |
|---|---|---|---|
| Inter norm | -1.33149 | Intra norm | 0.000696117 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 13 |
| Artifact reason | excluded; geometry warning; 6 clashes; 4 protein clashes; high strain Δ 31.5 | ||
| Residues | A:ALA67;A:ARG277;A:ASP332;A:ASP88;A:GLU274;A:GLY199;A:GLY236;A:GLY237;A:GLY276;A:HIS197;A:HIS333;A:LYS69;A:SER200;A:TYR331;A:TYR389 | ||
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 10 |
| IFP residues | A:ALA111; A:ALA67; A:ARG154; A:ARG277; A:ASP332; A:ASP88; A:CYS70; A:GLU274; A:GLY236; A:GLY237; A:GLY276; A:HIS197; A:LYS69; A:PHE238; A:PRO275; A:SER200; A:TYR278; A:TYR331; A:TYR389 | ||
| Current overlap | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | RMSD | - |
| H-bond strict | 5 | Strict recall | 0.56 |
| H-bond same residue+role | 4 | Role recall | 0.57 |
| H-bond same residue | 5 | Residue recall | 0.71 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 822 | 1.7651825253178435 | -1.54473 | -29.5498 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 804 | 1.7814656416736707 | -1.54385 | -29.6147 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1101 | 2.451736318244695 | -1.22209 | -22.957 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1099 | 2.751730486354672 | -1.2615 | -23.9145 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 770 | 2.912457314165155 | -1.0945 | -22.0785 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 824 | 2.9572062989000787 | -1.58614 | -29.0417 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2973 | 2.958631931911466 | -1.35838 | -25.6607 | 9 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 724 | 2.958792498600509 | -1.19931 | -21.6886 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2954 | 2.981482915776274 | -1.32647 | -25.5936 | 9 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 2818 | 3.073606886422904 | -1.1316 | -21.8999 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2200 | 3.1894039718698437 | -1.40229 | -26.0771 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2838 | 3.209712360742235 | -1.16054 | -20.1799 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 785 | 3.371986881492304 | -1.44392 | -27.8137 | 14 | 18 | 15 | 0.79 | 0.43 | - | no | Open |
| 772 | 3.4610727815057416 | -1.20072 | -21.8379 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 823 | 3.513058973892604 | -1.45659 | -26.4354 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2817 | 3.5148101262244955 | -1.34198 | -25.4179 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 806 | 3.5200046885906664 | -1.57638 | -29.017 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 725 | 3.657543007624825 | -1.18038 | -21.8508 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2816 | 3.7496605103873684 | -1.22427 | -23.475 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2976 | 3.8993722559434802 | -0.996862 | -21.3146 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2955 | 3.9047540819396707 | -1.32016 | -24.533 | 11 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 805 | 4.233728072955784 | -1.3742 | -25.5985 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2209 | 4.335538708389735 | -1.28094 | -23.6878 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2837 | 4.471999308101291 | -1.29246 | -24.4616 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2819 | 4.509559112160315 | -1.18635 | -22.4397 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1100 | 4.532198986214107 | -1.30203 | -24.5606 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 825 | 4.551399586390781 | -1.38019 | -25.7894 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 723 | 4.221287024700854 | -1.11783 | -21.1668 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2975 | 5.043363479944811 | -0.979852 | -17.9419 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2956 | 5.1289243130459905 | -1.06611 | -20.5302 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2836 | 5.189952954981379 | -1.25436 | -24.4355 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2839 | 5.2281491444919235 | -1.20309 | -22.6846 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 771 | 5.269168263680848 | -1.19091 | -21.9458 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2201 | 5.412711748212557 | -1.4146 | -26.5109 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 773 | 5.470576026124684 | -1.17562 | -21.6957 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 722 | 7.11719285334885 | -1.08093 | -21.2818 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2957 | 7.95279810263039 | -1.24603 | -22.8766 | 9 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2974 | 8.479483345283569 | -1.00809 | -19.2111 | 10 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2199 | 8.507687583879294 | -1.17628 | -21.9315 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 784 | 9.42692754453209 | -1.37134 | -26.8779 | 13 | 16 | 14 | 0.74 | 0.71 | - | yes | Open |
| 782 | 9.542291570199374 | -1.33149 | -26.616 | 13 | 15 | 13 | 0.68 | 0.57 | - | yes | Current |
| 2210 | 9.96613238288551 | -1.21135 | -22.4258 | 8 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2211 | 10.220336031702155 | -1.22577 | -23.9789 | 9 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 783 | 10.98940917383317 | -1.35565 | -26.1193 | 13 | 15 | 13 | 0.68 | 0.43 | - | yes | Open |
| 807 | 13.168104140684166 | -1.46486 | -27.2197 | 8 | 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
-26.616kcal/mol
Ligand efficiency (LE)
-1.3308kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.136
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
296.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.27
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-7.30kcal/mol
Minimised FF energy
-27.43kcal/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.