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 (-0.540 kcal/mol/HA)
✓ Good fit quality (FQ -5.41)
✓ Strong H-bond network (12 bonds)
✗ Very high strain energy (53.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-18.368
kcal/mol
LE
-0.540
kcal/mol/HA
Fit Quality
-5.41
FQ (Leeson)
HAC
34
heavy atoms
MW
464
Da
LogP
0.01
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 53.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 12
Hydrophobic 24
π–π 2
Clashes 11
Severe clashes 1
| Final rank | 9.555464824002463 | Score | -18.368 |
|---|---|---|---|
| Inter norm | -0.77606 | Intra norm | 0.235825 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash; high strain Δ 55.0 | ||
| Residues | A:ALA10;A:ASP22;A:GLU31;A:ILE61;A:ILE8;A:LEU23;A:LEU68;A:NAP201;A:PHE135;A:PHE180;A:PHE35;A:PRO62;A:SER60;A:THR137;A:THR57;A:TYR122;A:TYR34;A:VAL116;A:VAL136;A:VAL9 | ||
Protein summary
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 5 |
| IFP residues | A:ALA10; A:ASN65; A:ASP22; A:GLN36; A:GLU31; A:GLY117; A:GLY21; A:ILE61; A:ILE8; A:LEU23; A:LEU68; A:NAP201; A:PHE32; A:PHE35; A:PRO62; A:SER60; A:THR137; A:THR57; A:TYR122; A:VAL116; A:VAL9 | ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.64 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.20 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
Hydrogen bonds
Mode: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1672 | 6.553287637562716 | -0.469225 | -14.31 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2374 | 7.0277155750997125 | -0.801565 | -19.3286 | 5 | 18 | 16 | 0.76 | 0.40 | - | no | Open |
| 1128 | 8.279679784249446 | -1.10835 | -35.3116 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 2389 | 8.932020653140293 | -0.72534 | -20.9136 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2375 | 7.998985302388609 | -0.680797 | -19.3308 | 5 | 21 | 16 | 0.76 | 0.20 | - | yes | Open |
| 2377 | 8.293207856549127 | -0.73836 | -18.1077 | 6 | 23 | 16 | 0.76 | 0.20 | - | yes | Open |
| 2378 | 8.720141502228294 | -0.68369 | -21.8797 | 4 | 20 | 17 | 0.81 | 0.40 | - | yes | Open |
| 1670 | 8.782437359823664 | -0.50038 | -15.2619 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1132 | 9.271157550842759 | -1.09843 | -28.4821 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1671 | 9.338314851942613 | -0.525663 | -12.6315 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2376 | 9.555464824002463 | -0.77606 | -18.368 | 6 | 20 | 16 | 0.76 | 0.20 | - | yes | Current |
| 2388 | 9.83579067852548 | -0.735619 | -17.9182 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1127 | 10.032142465531289 | -0.811542 | -19.6774 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2390 | 10.168211503698725 | -0.753227 | -20.2765 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1130 | 10.277260042986192 | -0.912664 | -19.3283 | 6 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2391 | 10.535621536011838 | -0.713232 | -23.5757 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1669 | 11.267807890877943 | -0.628624 | -16.1568 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1131 | 12.024236004679132 | -0.721658 | -17.7021 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1129 | 14.93735397991637 | -1.11311 | -25.0349 | 9 | 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
-18.368kcal/mol
Ligand efficiency (LE)
-0.5402kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.406
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
463.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.01
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
53.34kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
134.02kcal/mol
Minimised FF energy
80.67kcal/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.