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 (-0.688 kcal/mol/HA)
✓ Good fit quality (FQ -6.64)
✓ Good H-bonds (5 bonds)
✗ High strain energy (11.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-20.649
kcal/mol
LE
-0.688
kcal/mol/HA
Fit Quality
-6.64
FQ (Leeson)
HAC
30
heavy atoms
MW
398
Da
LogP
3.86
cLogP
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 11
π–π 2
Clashes 15
Severe clashes 0
⚠ Hydrophobic exposure 39%
Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23
Buried (contacted) 14
Exposed 9
LogP 3.86
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 7.366388362828268 | Score | -20.6491 |
|---|---|---|---|
| Inter norm | -0.629821 | Intra norm | -0.0584822 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 5 |
| Artifact reason | geometry warning; 16 clashes; 15 protein contact clashes; moderate strain Δ 15.3 | ||
| Residues | A:ARG116;A:ARG140;A:ARG144;A:ASN106;A:ASP13;A:CYS72;A:GLY73;A:GLY75;A:GLY77;A:HIS105;A:HIS14;A:HIS141;A:LEU101;A:THR74;A:TYR49 | ||
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 16 |
| IFP residues | A:ALA15; A:ARG116; A:ARG140; A:ARG144; A:ASN106; A:ASP13; A:CYS72; A:GLY73; A:GLY75; A:GLY77; A:HIS105; A:HIS14; A:HIS141; A:ILE76; A:LEU101; A:THR74; A:TYR49 | ||
| Current overlap | 15 | Native recall | 0.88 |
| Jaccard | 0.88 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.23 |
| H-bond same residue+role | 4 | Role recall | 0.36 |
| H-bond same residue | 4 | Residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1906 | 4.079634371228655 | -0.565681 | -19.4954 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1904 | 4.708431710135203 | -0.593572 | -18.3879 | 3 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 2552 | 5.837738885508001 | -0.84258 | -26.671 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1374 | 6.9491310065977725 | -1.21986 | -37.7354 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1553 | 7.366388362828268 | -0.629821 | -20.6491 | 5 | 15 | 15 | 0.88 | 0.36 | - | no | Current |
| 1549 | 8.450095171648368 | -0.721285 | -24.1068 | 7 | 16 | 14 | 0.82 | 0.64 | - | no | Open |
| 1900 | 6.1831904129384965 | -0.71915 | -21.2671 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2548 | 6.398582763603283 | -1.07455 | -32.5822 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2553 | 6.594207675159006 | -0.943559 | -27.8785 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2550 | 6.798936814767271 | -0.774692 | -22.9352 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2549 | 6.971189554398788 | -0.915938 | -25.9224 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1905 | 7.018537068616989 | -0.62468 | -21.7228 | 5 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2551 | 7.033853904040928 | -0.845777 | -26.335 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1903 | 7.414535980267811 | -0.629732 | -20.3929 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1901 | 7.816321035401791 | -0.673946 | -21.3884 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1548 | 8.866106778944213 | -0.923782 | -27.0501 | 11 | 19 | 17 | 1.00 | 0.64 | - | yes | Open |
| 1554 | 9.058924025034537 | -0.757065 | -21.7722 | 11 | 18 | 16 | 0.94 | 0.45 | - | yes | Open |
| 1902 | 9.330708255049892 | -0.712915 | -24.4361 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1907 | 9.607718702921597 | -0.633204 | -22.1142 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1547 | 9.80770316554089 | -0.668429 | -17.3057 | 5 | 16 | 14 | 0.82 | 0.27 | - | yes | Open |
| 1552 | 10.005670834294907 | -0.777192 | -26.0641 | 9 | 19 | 15 | 0.88 | 0.36 | - | yes | Open |
| 1550 | 10.24519874536975 | -1.07037 | -31.267 | 12 | 18 | 16 | 0.94 | 0.45 | - | yes | Open |
| 1375 | 10.697110617251491 | -1.12097 | -37.0518 | 10 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1551 | 11.621956666465433 | -0.756254 | -18.4723 | 7 | 15 | 13 | 0.76 | 0.36 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.649kcal/mol
Ligand efficiency (LE)
-0.6883kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.640
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.55kcal/mol
Minimised FF energy
92.80kcal/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.