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 (-1.147 kcal/mol/HA)
✓ Good fit quality (FQ -10.42)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (24.9 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.663
kcal/mol
LE
-1.147
kcal/mol/HA
Fit Quality
-10.42
FQ (Leeson)
HAC
25
heavy atoms
MW
375
Da
LogP
3.59
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 24.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 1
Clashes 9
Severe clashes 1
| Final rank | 5.531123451872331 | Score | -28.6627 |
|---|---|---|---|
| Inter norm | -1.10461 | Intra norm | -0.0419024 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 7 clashes; 1 protein clash; high strain Δ 28.2 | ||
| Residues | A:ALA32;A:ARG48;A:ASP52;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49 | ||
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 9 |
| IFP residues | A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87 | ||
| Current overlap | 10 | Native recall | 0.50 |
| Jaccard | 0.43 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.14 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2619 | 2.425852643565488 | -1.03891 | -31.6075 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2630 | 2.737183101304363 | -0.908696 | -21.1058 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2610 | 2.87745678336561 | -1.03825 | -27.6698 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2571 | 3.3133375698092387 | -0.781618 | -18.9145 | 4 | 16 | 13 | 0.65 | 0.20 | - | no | Open |
| 2611 | 3.3307698331314484 | -0.909233 | -26.847 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2634 | 3.484222578871666 | -0.90943 | -19.8347 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2631 | 3.6938063235738015 | -0.941899 | -24.2939 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2579 | 3.842818280491077 | -0.824702 | -24.8535 | 3 | 16 | 15 | 0.75 | 0.00 | - | no | Open |
| 2570 | 4.1936771054449995 | -0.920232 | -24.8385 | 6 | 16 | 13 | 0.65 | 0.20 | - | no | Open |
| 2562 | 4.311007225668922 | -0.931678 | -26.7973 | 5 | 16 | 11 | 0.55 | 0.00 | - | no | Open |
| 2585 | 4.386769282679213 | -0.924871 | -23.2719 | 5 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 2583 | 4.405293330625591 | -0.824691 | -22.8843 | 7 | 17 | 14 | 0.70 | 0.20 | - | no | Open |
| 2580 | 4.524655786242075 | -0.883299 | -21.105 | 5 | 16 | 12 | 0.60 | 0.20 | - | no | Open |
| 2561 | 4.755365790853137 | -1.10701 | -22.6931 | 5 | 18 | 15 | 0.75 | 0.20 | - | no | Open |
| 2582 | 5.033596954400377 | -0.851607 | -22.9525 | 4 | 14 | 11 | 0.55 | 0.20 | - | no | Open |
| 2574 | 5.14314487903842 | -1.08683 | -28.6837 | 6 | 14 | 11 | 0.55 | 0.20 | - | no | Open |
| 2576 | 5.8259569356355545 | -0.916168 | -25.2866 | 5 | 17 | 14 | 0.70 | 0.20 | - | no | Open |
| 2618 | 3.0114453068210034 | -0.912672 | -20.9714 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2623 | 4.21471771581715 | -0.820543 | -22.0363 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2639 | 4.248780157815152 | -0.821298 | -20.2188 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2615 | 4.487514418914696 | -0.882147 | -25.0933 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2614 | 4.538070645950707 | -0.878637 | -17.0397 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2626 | 4.689768811513736 | -0.780891 | -21.8388 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2635 | 5.067087900186418 | -0.941108 | -24.0972 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2617 | 5.171769833329963 | -1.09726 | -25.9114 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2591 | 5.285106474641975 | -0.725459 | -21.8758 | 1 | 10 | 10 | 0.50 | 0.20 | - | yes | Open |
| 2586 | 5.531123451872331 | -1.10461 | -28.6627 | 5 | 13 | 10 | 0.50 | 0.20 | - | yes | Current |
| 2564 | 5.6034826234630835 | -0.906807 | -20.5691 | 5 | 16 | 12 | 0.60 | 0.20 | - | yes | Open |
| 2577 | 5.787533909719497 | -0.867791 | -19.3597 | 6 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2569 | 5.939339394584405 | -1.05752 | -26.1362 | 6 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2589 | 5.961852564681067 | -1.03278 | -23.4073 | 7 | 17 | 14 | 0.70 | 0.20 | - | yes | Open |
| 2637 | 6.013216276604863 | -1.04969 | -24.6266 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2590 | 6.246007748002172 | -1.09916 | -25.639 | 5 | 12 | 9 | 0.45 | 0.20 | - | yes | Open |
| 2566 | 6.4159852919523415 | -0.92184 | -23.0593 | 4 | 15 | 12 | 0.60 | 0.20 | - | yes | Open |
| 2565 | 6.8779477086832745 | -0.861715 | -8.98491 | 3 | 16 | 13 | 0.65 | 0.00 | - | yes | Open |
| 2573 | 7.071720201343002 | -1.00754 | -25.7949 | 6 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2627 | 7.165461485168329 | -0.783173 | -20.7324 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2563 | 7.321944936097866 | -0.931319 | -24.031 | 6 | 15 | 12 | 0.60 | 0.20 | - | yes | Open |
| 2587 | 7.445411535384595 | -0.951119 | -28.2282 | 6 | 13 | 10 | 0.50 | 0.20 | - | yes | Open |
| 2625 | 7.466015995483927 | -1.1276 | -29.6913 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2620 | 7.548605335236438 | -1.1016 | -25.6395 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2629 | 7.633404417074706 | -1.15662 | -26.6108 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2633 | 7.835610140824386 | -1.01254 | -25.2893 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2609 | 7.846804034211145 | -1.20209 | -29.4824 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2572 | 8.011985383395809 | -1.00543 | -25.9321 | 6 | 17 | 14 | 0.70 | 0.20 | - | yes | Open |
| 2621 | 8.076562930939367 | -1.07006 | -25.4363 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2613 | 8.176528115055714 | -1.1272 | -24.2878 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2636 | 8.991496445453414 | -1.01403 | -21.282 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2578 | 54.66175885189302 | -1.16716 | -32.1084 | 6 | 13 | 10 | 0.50 | 0.20 | - | yes | Open |
| 2581 | 54.67641370366 | -1.07019 | -26.8344 | 5 | 16 | 13 | 0.65 | 0.20 | - | yes | Open |
| 2616 | 55.79303577917653 | -1.1278 | -23.8755 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2622 | 56.22232862251494 | -0.826567 | -18.8031 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2588 | 56.28636613620056 | -0.955578 | -22.3954 | 7 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 2575 | 56.40314607127925 | -0.895951 | -25.702 | 9 | 13 | 9 | 0.45 | 0.20 | - | yes | Open |
| 2567 | 56.54258500303558 | -1.02927 | -28.823 | 6 | 13 | 10 | 0.50 | 0.20 | - | yes | Open |
| 2624 | 56.63748302183652 | -0.98823 | -24.9264 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2568 | 56.75493169541731 | -0.954994 | -25.9646 | 5 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 2608 | 57.47118739606409 | -1.05092 | -28.298 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2584 | 58.183634883560416 | -0.92506 | -22.6169 | 6 | 19 | 14 | 0.70 | 0.20 | - | yes | Open |
| 2638 | 58.259456206206714 | -0.787239 | -10.6807 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2632 | 58.32206888940812 | -0.928968 | -20.9409 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2628 | 58.40696538999711 | -0.937958 | -23.6188 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2612 | 58.85513005734401 | -1.01283 | -24.2861 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2560 | 59.13082926094182 | -0.910745 | -22.5104 | 8 | 20 | 14 | 0.70 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.663kcal/mol
Ligand efficiency (LE)
-1.1465kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.423
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
375.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.59
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
91.94kcal/mol
Minimised FF energy
67.06kcal/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.