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 (-0.754 kcal/mol/HA)
✓ Good fit quality (FQ -7.34)
✓ Strong H-bond network (13 bonds)
✗ Very high strain energy (22.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.361
kcal/mol
LE
-0.754
kcal/mol/HA
Fit Quality
-7.34
FQ (Leeson)
HAC
31
heavy atoms
MW
442
Da
LogP
3.52
cLogP
Interaction summary
Collapsible panels
H-bonds 13
Hydrophobic 7
π–π 2
Clashes 12
Severe clashes 0
⚠ Hydrophobic exposure 68%
Solvent-exposed hydrophobic surface — desolvation penalty likely
68% of hydrophobic surface is solvent-exposed (13/19 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 19
Buried (contacted) 6
Exposed 13
LogP 3.52
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 6.697741487230212 | Score | -23.3614 |
|---|---|---|---|
| Inter norm | -0.834481 | Intra norm | 0.0808873 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 13 |
| Artifact reason | geometry warning; 15 clashes; 12 protein contact clashes; high strain Δ 24.3 | ||
| Residues | A:ARG141;A:ASN103;A:HIS102;A:MET98;A:TYR94;B:ARG113;B:ASP10;B:CYS69;B:GLY70;B:GLY72;B:GLY74;B:HIS11;B:ILE73;B:MET75;B:PRO12;B:SER71;B:TYR46 | ||
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 16 |
| IFP residues | A:ARG137; A:ARG141; A:ASN103; A:HIS102; A:HIS138; B:ASP10; B:CYS69; B:GLY70; B:GLY74; B:HIS11; B:ILE73; B:PRO12; B:SER71; B:TYR46 | ||
| Current overlap | 12 | Native recall | 0.86 |
| Jaccard | 0.63 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.33 |
| H-bond same residue+role | 4 | Role recall | 0.44 |
| H-bond same residue | 5 | Residue recall | 0.62 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1330 | 4.546058110704963 | -0.682543 | -19.4338 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1741 | 5.0302684532171655 | -0.619505 | -12.9819 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1545 | 5.475804037743344 | -0.858195 | -24.7719 | 14 | 18 | 14 | 1.00 | 0.78 | - | no | Open |
| 2326 | 5.6710136988268705 | -0.837093 | -23.5916 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 3167 | 6.19621727791003 | -0.685976 | -15.3958 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1546 | 6.697741487230212 | -0.834481 | -23.3614 | 13 | 17 | 12 | 0.86 | 0.44 | - | no | Current |
| 1245 | 6.827582501130651 | -0.692988 | -15.2382 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3047 | 6.999599781856376 | -0.77539 | -7.96208 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1247 | 7.034381922465668 | -0.672305 | -15.8863 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1327 | 6.6430406123836665 | -0.797734 | -21.7004 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1742 | 6.910888041166388 | -0.550281 | -17.6747 | 5 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3049 | 6.998896873546217 | -0.646882 | -18.9762 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1541 | 7.131558554810589 | -0.897298 | -26.7563 | 14 | 16 | 11 | 0.79 | 0.44 | - | yes | Open |
| 2322 | 7.664844219982595 | -0.846024 | -22.8803 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1540 | 8.41357608229529 | -0.967822 | -24.7863 | 11 | 17 | 13 | 0.93 | 0.56 | - | yes | Open |
| 1736 | 8.671544433816521 | -0.56961 | -11.0699 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1246 | 9.069527775765122 | -0.759956 | -18.439 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1738 | 9.101550293371464 | -0.650131 | -13.8895 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1543 | 9.159745760417726 | -0.64245 | -17.8971 | 9 | 16 | 12 | 0.86 | 0.56 | - | yes | Open |
| 2325 | 9.322315202086385 | -0.821256 | -21.068 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1737 | 9.351090448136365 | -0.599841 | -18.1504 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1331 | 9.603273683073732 | -0.722889 | -17.7606 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1329 | 9.635185988445942 | -0.679494 | -18.2678 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1739 | 9.682394931482348 | -0.669263 | -11.7161 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1328 | 9.835511068906836 | -0.834962 | -24.8622 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3170 | 9.877092801013724 | -0.725829 | -19.2194 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1248 | 9.891748345386636 | -0.698754 | -15.9964 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2321 | 9.907520125435832 | -0.812969 | -21.0151 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3048 | 10.193644438759188 | -0.810269 | -11.9926 | 11 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1544 | 10.218314395021608 | -0.782423 | -17.0719 | 12 | 16 | 13 | 0.93 | 0.67 | - | yes | Open |
| 3046 | 10.459690023251724 | -0.829698 | -21.2887 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3050 | 10.466104860819398 | -0.683717 | -19.2157 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3171 | 10.66781111009974 | -0.748078 | -18.0424 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3045 | 10.697785973745848 | -0.722622 | -20.0299 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3168 | 10.736235746017124 | -0.720072 | -16.5116 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1542 | 10.756769877726809 | -0.791096 | -19.3139 | 7 | 19 | 13 | 0.93 | 0.44 | - | yes | Open |
| 1332 | 11.485274268108578 | -0.718357 | -21.0061 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3169 | 11.730549864478318 | -0.648128 | -16.6582 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2324 | 11.853554270904706 | -0.790214 | -22.1965 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1740 | 11.870785412133662 | -0.631942 | -7.04487 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1250 | 12.163945104063858 | -0.753395 | -19.1039 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2323 | 13.088444182088494 | -0.860425 | -24.5319 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3044 | 13.201291003737827 | -0.80219 | -16.6917 | 11 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1249 | 13.648523736516637 | -0.779319 | -19.2191 | 9 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3166 | 15.21166044456033 | -0.69508 | -13.6999 | 5 | 16 | 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
-23.361kcal/mol
Ligand efficiency (LE)
-0.7536kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.342
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
441.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.52
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
85.03kcal/mol
Minimised FF energy
62.70kcal/mol
SASA & burial (FreeSASA)
not yet run
SASA has not been computed yet for this pose. It will be calculated automatically
the next time this pose is loaded if a receptor PDB path is stored.