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 (-0.487 kcal/mol/HA)
✓ Good fit quality (FQ -4.95)
✗ Very high strain energy (40.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-17.546
kcal/mol
LE
-0.487
kcal/mol/HA
Fit Quality
-4.95
FQ (Leeson)
HAC
36
heavy atoms
MW
489
Da
LogP
2.06
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 40.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 0
Clashes 7
Severe clashes 1
| Final rank | 55.86361352782777 | Score | -17.5462 |
|---|---|---|---|
| Inter norm | -0.675154 | Intra norm | 0.187759 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash | ||
| Residues | A:ARG48;A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:SER86;A:TRP47;A:TYR162;A:VAL156;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 | 14 | Native recall | 0.70 |
| Jaccard | 0.56 | 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2024 | 2.6163373679837068 | -0.475481 | -17.0484 | 1 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2027 | 3.4928885063625934 | -0.563652 | -20.526 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2022 | 3.6467519054413224 | -0.529155 | -19.1171 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2026 | 3.8327317138784225 | -0.593881 | -21.194 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2034 | 3.8403771272185705 | -0.571289 | -20.6928 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1593 | 3.845711891364608 | -0.659599 | -22.5774 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 2029 | 3.9675236314669737 | -0.540802 | -15.9912 | 0 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1578 | 4.11210600357286 | -0.68833 | -19.9948 | 1 | 16 | 13 | 0.65 | 0.00 | - | no | Open |
| 2020 | 4.1558378619009915 | -0.579178 | -19.817 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2117 | 4.337823868259857 | -0.539082 | -18.148 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2043 | 4.465568790512528 | -0.644011 | -23.27 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2103 | 4.607453991836869 | -0.662206 | -22.4643 | 2 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 2042 | 4.639213180297254 | -0.658543 | -22.2159 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1579 | 4.6432252304255766 | -0.684326 | -20.4163 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 2017 | 4.748621834292094 | -0.598823 | -18.5389 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2121 | 4.79237879143356 | -0.529856 | -18.6787 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2032 | 4.829681039332907 | -0.582487 | -19.5389 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1595 | 4.884871004956575 | -0.587253 | -20.8029 | 0 | 14 | 12 | 0.60 | 0.00 | - | no | Open |
| 2055 | 4.906581392243264 | -0.524325 | -17.6536 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1597 | 4.92417506720836 | -0.685091 | -23.8902 | 2 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 2052 | 4.954401352935739 | -0.524482 | -16.623 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2033 | 5.022981078201707 | -0.492299 | -13.004 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2101 | 5.11155709729789 | -0.585568 | -17.6736 | 1 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 1591 | 5.124084753602214 | -0.634421 | -18.1472 | 0 | 19 | 15 | 0.75 | 0.00 | - | no | Open |
| 2118 | 5.426853339822896 | -0.623609 | -20.4495 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2108 | 5.53047095297593 | -0.53056 | -18.5361 | 1 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 1588 | 5.556702571159604 | -0.719908 | -26.0581 | 2 | 18 | 18 | 0.90 | 0.20 | - | no | Open |
| 1587 | 5.660487781554783 | -0.676968 | -22.0498 | 2 | 17 | 17 | 0.85 | 0.20 | - | no | Open |
| 2104 | 5.861216494708604 | -0.53385 | -14.3282 | 0 | 15 | 1 | 0.05 | 0.00 | - | no | Open |
| 1580 | 5.9419648427458185 | -0.741494 | -25.6483 | 2 | 18 | 18 | 0.90 | 0.20 | - | no | Open |
| 2050 | 6.062981219002463 | -0.67796 | -20.5511 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2030 | 6.092859177993964 | -0.667293 | -16.2962 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2041 | 6.292989815538051 | -0.540223 | -15.3932 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2111 | 7.190941689273277 | -0.577818 | -19.0597 | 1 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 2115 | 7.465750351073146 | -0.542888 | -18.3604 | 1 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 1583 | 53.60518067486575 | -0.666378 | -18.6167 | 2 | 18 | 17 | 0.85 | 0.00 | - | no | Open |
| 1581 | 53.94516627236904 | -0.725025 | -22.1815 | 1 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1590 | 54.01703522204766 | -0.672758 | -22.6879 | 1 | 16 | 14 | 0.70 | 0.00 | - | no | Open |
| 2038 | 54.225407014079906 | -0.582244 | -18.4704 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2019 | 54.27082013898979 | -0.683853 | -20.6161 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1592 | 54.32474265468863 | -0.692929 | -25.366 | 2 | 16 | 14 | 0.70 | 0.20 | - | no | Open |
| 2106 | 54.34351585520999 | -0.517885 | -16.8477 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2023 | 54.51761680697442 | -0.615697 | -22.7562 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2025 | 54.5504332723274 | -0.700134 | -22.423 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2016 | 54.56861517971585 | -0.642851 | -20.1613 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2035 | 54.64292276207239 | -0.486915 | -15.9519 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2037 | 54.70442086450687 | -0.570538 | -22.5871 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2120 | 54.824810003280305 | -0.464971 | -15.6665 | 2 | 12 | 1 | 0.05 | 0.00 | - | no | Open |
| 2036 | 54.839280872714156 | -0.611319 | -21.9237 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2039 | 54.902038495601 | -0.625934 | -22.2033 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2040 | 55.16068785439058 | -0.525451 | -18.5236 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1586 | 55.226130951055794 | -0.647077 | -18.1187 | 1 | 15 | 14 | 0.70 | 0.20 | - | no | Open |
| 2122 | 55.27072465510055 | -0.55801 | -20.9679 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2048 | 55.30009342554581 | -0.612143 | -18.7004 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2046 | 55.52316687698773 | -0.471934 | -13.6649 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2028 | 5.814537516115726 | -0.451253 | -17.1767 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2053 | 54.35653394853977 | -0.497156 | -17.2232 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2051 | 54.812840320296125 | -0.578085 | -18.6726 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2044 | 55.46849333103313 | -0.657518 | -19.4207 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2054 | 55.72440581649079 | -0.454059 | -17.0965 | 0 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2116 | 55.76375103801218 | -0.493854 | -18.2418 | 2 | 16 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1598 | 55.77108923636941 | -0.677819 | -22.7851 | 2 | 19 | 14 | 0.70 | 0.20 | - | yes | Open |
| 2105 | 55.79730841562623 | -0.541155 | -19.3678 | 0 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1594 | 55.86361352782777 | -0.675154 | -17.5462 | 1 | 19 | 14 | 0.70 | 0.20 | - | yes | Current |
| 2100 | 55.8891579558789 | -0.475004 | -14.239 | 3 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2119 | 55.893116686505614 | -0.612591 | -19.834 | 3 | 14 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2107 | 56.02483498883145 | -0.516179 | -18.0325 | 0 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2112 | 56.028493397490074 | -0.639203 | -21.2063 | 1 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2110 | 56.11658908957474 | -0.575265 | -16.8079 | 2 | 17 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2123 | 56.23028610614121 | -0.599977 | -19.9603 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2109 | 56.270864216080824 | -0.574174 | -13.2812 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1582 | 56.29779856372032 | -0.640856 | -20.8737 | 2 | 15 | 13 | 0.65 | 0.20 | - | yes | Open |
| 2049 | 56.314780141210385 | -0.556315 | -18.5881 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2114 | 56.473010910276855 | -0.552235 | -18.9966 | 0 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2021 | 56.54202741386497 | -0.501882 | -16.6833 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2113 | 56.58503913826052 | -0.646471 | -22.8869 | 1 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 1589 | 56.61765100753739 | -0.657869 | -23.1366 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1577 | 56.89894148985696 | -0.750792 | -21.36 | 2 | 16 | 14 | 0.70 | 0.20 | - | yes | Open |
| 1600 | 56.94171451477686 | -0.670943 | -20.4638 | 1 | 16 | 12 | 0.60 | 0.00 | - | yes | Open |
| 1596 | 57.21426940452754 | -0.719943 | -23.7315 | 2 | 19 | 14 | 0.70 | 0.20 | - | yes | Open |
| 2018 | 57.2750138654006 | -0.604609 | -20.2327 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2045 | 57.367431785210385 | -0.584256 | -11.2855 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1585 | 57.551590262051164 | -0.68564 | -20.0425 | 1 | 15 | 14 | 0.70 | 0.20 | - | yes | Open |
| 2047 | 57.8560831635867 | -0.528427 | -18.1744 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1584 | 57.873996237507995 | -0.694137 | -21.4757 | 2 | 18 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1599 | 58.02651076084146 | -0.518317 | -16.6413 | 1 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 2102 | 58.53968462892805 | -0.580672 | -15.3338 | 3 | 14 | 1 | 0.05 | 0.00 | - | yes | Open |
| 2031 | 59.438586238108655 | -0.534984 | -18.1274 | 1 | 17 | 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
-17.546kcal/mol
Ligand efficiency (LE)
-0.4874kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.954
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
488.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.06
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
212.81kcal/mol
Minimised FF energy
172.14kcal/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.