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 (-0.733 kcal/mol/HA)
✓ Good fit quality (FQ -7.33)
✗ Very high strain energy (20.2 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.917
kcal/mol
LE
-0.733
kcal/mol/HA
Fit Quality
-7.33
FQ (Leeson)
HAC
34
heavy atoms
MW
464
Da
LogP
2.62
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 20.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 2
Clashes 5
Severe clashes 1
| Final rank | 56.22693303779636 | Score | -24.9168 |
|---|---|---|---|
| Inter norm | -0.793334 | Intra norm | 0.0604857 |
| Top1000 | no | Excluded | yes |
| Contacts | 22 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 20 clashes; 1 protein clash | ||
| Residues | A:ALA32;A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER86;A:THR83;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49;A:VAL87 | ||
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 | 18 | Native recall | 0.90 |
| Jaccard | 0.75 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 980 | 4.2667967127332425 | -0.647076 | -18.8906 | 1 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 964 | 4.4375082130399335 | -0.666507 | -20.7389 | 1 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 963 | 4.8283277279898265 | -0.818882 | -26.4773 | 0 | 22 | 18 | 0.90 | 0.00 | - | no | Open |
| 976 | 4.861076246789533 | -0.717485 | -23.0849 | 3 | 19 | 14 | 0.70 | 0.20 | - | no | Open |
| 1020 | 5.608822815282937 | -0.559562 | -18.2789 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 975 | 5.658661119979025 | -0.72701 | -19.9178 | 3 | 16 | 15 | 0.75 | 0.60 | - | no | Open |
| 972 | 5.872917234042555 | -0.66726 | -10.5276 | 2 | 16 | 12 | 0.60 | 0.20 | - | no | Open |
| 1017 | 5.943411109675365 | -0.558633 | -16.3741 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1013 | 6.307109152626905 | -0.591976 | -22.2418 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 998 | 6.617839771151886 | -0.692384 | -24.2271 | 4 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 1005 | 7.263428324635448 | -0.598723 | -20.9956 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1001 | 8.518952245362764 | -0.512154 | -10.4528 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 965 | 54.268108346420284 | -0.680293 | -21.6517 | 1 | 15 | 12 | 0.60 | 0.20 | - | no | Open |
| 969 | 54.730108154157584 | -0.83792 | -26.6193 | 2 | 19 | 16 | 0.80 | 0.20 | - | no | Open |
| 966 | 54.90998971603653 | -0.681929 | -20.9942 | 2 | 18 | 14 | 0.70 | 0.20 | - | no | Open |
| 974 | 55.25225600517029 | -0.712966 | -21.7259 | 2 | 17 | 13 | 0.65 | 0.20 | - | no | Open |
| 957 | 55.33920843725555 | -0.601959 | -15.7833 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 961 | 55.34723382073465 | -0.695261 | -21.8508 | 1 | 19 | 15 | 0.75 | 0.20 | - | no | Open |
| 1018 | 55.577770402172845 | -0.615158 | -14.106 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 970 | 56.763655045820364 | -0.680825 | -21.5861 | 1 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1015 | 55.7401178962693 | -0.644859 | -23.9105 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 979 | 56.22693303779636 | -0.793334 | -24.9168 | 1 | 22 | 18 | 0.90 | 0.20 | - | yes | Current |
| 959 | 56.22887233234621 | -0.657743 | -14.235 | 6 | 18 | 15 | 0.75 | 0.60 | - | yes | Open |
| 971 | 56.25495307434291 | -0.857331 | -26.9352 | 1 | 21 | 18 | 0.90 | 0.20 | - | yes | Open |
| 1014 | 56.3140252935371 | -0.690966 | -20.8452 | 2 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 999 | 56.37188078468921 | -0.631895 | -19.5435 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 973 | 56.56725214004422 | -0.623201 | -24.1552 | 1 | 15 | 13 | 0.65 | 0.20 | - | yes | Open |
| 968 | 56.7475004943868 | -0.581465 | -19.5245 | 6 | 18 | 14 | 0.70 | 0.20 | - | yes | Open |
| 967 | 56.759649217372015 | -0.676006 | -18.7339 | 3 | 20 | 17 | 0.85 | 0.40 | - | yes | Open |
| 978 | 57.32083151732589 | -0.712682 | -25.1394 | 4 | 20 | 18 | 0.90 | 0.60 | - | yes | Open |
| 997 | 57.3249242113801 | -0.604676 | -18.5954 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1009 | 57.394715812575434 | -0.52356 | -11.3693 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1002 | 57.4808605706708 | -0.617815 | -16.9265 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1000 | 57.625401861715766 | -0.674365 | -18.6906 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1019 | 57.800249436248784 | -0.723992 | -26.6835 | 1 | 24 | 0 | 0.00 | 0.00 | - | yes | Open |
| 958 | 57.93847770081955 | -0.710876 | -22.6368 | 2 | 17 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1003 | 58.20546004129062 | -0.675781 | -24.2705 | 2 | 24 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1006 | 58.38086441393017 | -0.693607 | -24.2081 | 5 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 977 | 58.49646276358023 | -0.732312 | -24.1209 | 2 | 15 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1012 | 58.925483999481 | -0.743273 | -20.6742 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1016 | 59.78910891302541 | -0.540698 | -18.6917 | 4 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1011 | 59.83248892398216 | -0.718821 | -24.3108 | 3 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1004 | 59.87167927601356 | -0.603058 | -21.4062 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 962 | 59.872548927288754 | -0.784707 | -24.1046 | 2 | 16 | 12 | 0.60 | 0.20 | - | yes | Open |
| 1008 | 60.23140483524128 | -0.615151 | -10.199 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1007 | 60.38065659113832 | -0.565567 | -15.815 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1010 | 60.75011301860987 | -0.623404 | -16.21 | 1 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 960 | 62.283215330865104 | -0.611563 | -6.28831 | 4 | 22 | 15 | 0.75 | 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
-24.917kcal/mol
Ligand efficiency (LE)
-0.7328kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.333
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
463.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.62
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
93.37kcal/mol
Minimised FF energy
73.15kcal/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.