Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
No SASA yet
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA missing
Strain ΔE
24.1 kcal/mol
Protein clashes
9
Internal clashes
10
Native overlap
contact recall 0.65, Jaccard 0.57, H-bond role recall 0.00
Reason: 9 protein-contact clashes, 10 internal clashes
9 protein-contact clashes
10 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.861 kcal/mol/HA)
✓ Good fit quality (FQ -8.46)
✗ High strain energy (24.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (9)
✗ Many internal clashes (10)
ℹ SASA not computed
Score
-27.536
kcal/mol
LE
-0.861
kcal/mol/HA
Fit Quality
-8.46
FQ (Leeson)
HAC
32
heavy atoms
MW
478
Da
LogP
3.61
cLogP
Interaction summary
HB 1
HY 24
PI 1
CLASH 0
Interaction summary
HB 1
HY 24
PI 1
CLASH 0
| Final rank | 4.958 | Score | -27.536 |
|---|---|---|---|
| Inter norm | -0.772 | Intra norm | -0.089 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 10 clashes; 9 protein contact clashes; high strain Δ 24.1 | ||
| Residues |
ARG48
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
SER86
THR83
TRP47
VAL156
VAL49
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 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:NDP301
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 | HB | 0 |
| IFP residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR180
THR54
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 13 | Native recall | 0.65 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 539 | 4.578051279948418 | -0.836441 | -23.7077 | 1 | 21 | 18 | 0.90 | 0.20 | - | no | Open |
| 531 | 4.873103504307923 | -0.755991 | -21.9113 | 1 | 21 | 18 | 0.90 | 0.20 | - | no | Open |
| 544 | 4.957947154718397 | -0.77194 | -27.5356 | 1 | 16 | 13 | 0.65 | 0.00 | - | no | Current |
| 424 | 4.9786679789210915 | -0.607541 | -14.4757 | 3 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 547 | 5.35220158640997 | -0.788979 | -23.0974 | 2 | 19 | 17 | 0.85 | 0.20 | - | no | Open |
| 418 | 5.503663179548383 | -0.591602 | -15.7788 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 536 | 5.592270017366477 | -0.760386 | -20.7067 | 1 | 16 | 14 | 0.70 | 0.00 | - | no | Open |
| 421 | 6.130453196567059 | -0.634935 | -20.8308 | 3 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 416 | 55.392362047497045 | -0.680698 | -16.8839 | 5 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 422 | 56.08470595499364 | -0.652427 | -20.7805 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 5.351274929047857 | -0.708091 | -23.2492 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 428 | 54.92680923743816 | -0.612277 | -17.4971 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 542 | 54.93402315854781 | -0.805458 | -25.2612 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 543 | 55.11394031842511 | -0.719767 | -20.2266 | 1 | 15 | 13 | 0.65 | 0.00 | - | yes | Open |
| 538 | 55.320432949481805 | -0.847022 | -26.2041 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 554 | 55.44674008211802 | -0.826456 | -27.7497 | 1 | 17 | 16 | 0.80 | 0.00 | - | yes | Open |
| 425 | 55.634847078930164 | -0.69617 | -22.5042 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 426 | 55.978226159919124 | -0.653399 | -24.2595 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 419 | 56.099292180823014 | -0.726868 | -22.5368 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 550 | 56.15369218492761 | -0.823781 | -27.1051 | 2 | 15 | 12 | 0.60 | 0.00 | - | yes | Open |
| 417 | 56.17706705702731 | -0.608003 | -12.7259 | 4 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
| 549 | 56.491681708803526 | -0.740201 | -25.7463 | 3 | 10 | 9 | 0.45 | 0.20 | - | yes | Open |
| 541 | 56.59007578258512 | -0.764635 | -20.806 | 1 | 18 | 15 | 0.75 | 0.00 | - | yes | Open |
| 420 | 56.64458233008418 | -0.722115 | -24.8227 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 545 | 56.76538553890124 | -0.749641 | -23.9649 | 1 | 20 | 16 | 0.80 | 0.00 | - | yes | Open |
| 430 | 56.8614587127542 | -0.587938 | -18.1571 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 534 | 56.898701725433426 | -0.808824 | -25.7914 | 1 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 552 | 56.90385083398705 | -0.809357 | -17.8446 | 3 | 13 | 11 | 0.55 | 0.20 | - | yes | Open |
| 535 | 57.056440842723944 | -0.775288 | -21.1576 | 1 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 537 | 57.14621584789709 | -0.765841 | -16.9705 | 2 | 16 | 13 | 0.65 | 0.00 | - | yes | Open |
| 540 | 57.43980407676235 | -0.676081 | -18.3247 | 1 | 19 | 18 | 0.90 | 0.00 | - | yes | Open |
| 548 | 57.858147270023764 | -0.720473 | -17.1943 | 1 | 16 | 14 | 0.70 | 0.00 | - | yes | Open |
| 533 | 58.61620205238415 | -0.770822 | -25.5399 | 1 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 553 | 59.357423973642355 | -0.702808 | -22.5276 | 2 | 17 | 13 | 0.65 | 0.00 | - | yes | Open |
| 427 | 59.49085344586227 | -0.705055 | -24.2427 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 429 | 60.01765742426803 | -0.678756 | -20.4807 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 551 | 60.04628309910173 | -0.822051 | -24.2471 | 1 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 546 | 60.6066765495306 | -0.925317 | -25.6492 | 3 | 14 | 12 | 0.60 | 0.20 | - | yes | Open |
| 431 | 61.29124134893323 | -0.652682 | -23.0277 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 423 | 61.42540633024061 | -0.656692 | -19.582 | 4 | 15 | 1 | 0.05 | 0.00 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-27.536kcal/mol
Ligand efficiency (LE)
-0.8605kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.462
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
478.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.61
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.88kcal/mol
Minimised FF energy
35.75kcal/mol
SASA & burial
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate SASA burial metrics without blocking the page.