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 (-1.198 kcal/mol/HA)
✓ Good fit quality (FQ -9.82)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (12.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-22.762
kcal/mol
LE
-1.198
kcal/mol/HA
Fit Quality
-9.82
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
-0.53
cLogP
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 0
π–π 0
Clashes 4
Severe clashes 0
⚠ Hydrophobic exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (12/12 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 12
Buried (contacted) 0
Exposed 12
LogP -0.53
H-bonds 8
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.026871902667413 | Score | -22.7618 |
|---|---|---|---|
| Inter norm | -1.14291 | Intra norm | -0.0550831 |
| Top1000 | no | Excluded | no |
| Contacts | 8 | H-bonds | 8 |
| Artifact reason | geometry warning; 4 clashes; 4 protein contact clashes; high strain Δ 22.3 | ||
| Residues | A:ARG337;A:ASP243;A:ASP385;A:GLU384;A:LEU339;A:MET386;A:PHE383;A:VAL336 | ||
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 7 |
| IFP residues | A:ARG22; A:ARG242; A:ARG337; A:ARG342; A:ASP243; A:ASP385; A:GLN341; A:GLU384; A:LEU25; A:LEU339; A:LEU382; A:PRO340; A:PRO344; A:SER282; A:THR241 | ||
| Current overlap | 5 | Native recall | 0.33 |
| Jaccard | 0.28 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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
No hydrophobic contacts detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2218 | 2.026871902667413 | -1.14291 | -22.7618 | 8 | 8 | 5 | 0.33 | 0.40 | - | no | Current |
| 2240 | 2.6603027078915193 | -1.13227 | -21.2646 | 10 | 9 | 7 | 0.47 | 0.40 | - | no | Open |
| 2225 | 2.926559441366489 | -0.984292 | -18.1629 | 6 | 8 | 5 | 0.33 | 0.20 | - | no | Open |
| 2244 | 2.9994837867102038 | -1.06455 | -18.2589 | 7 | 9 | 7 | 0.47 | 0.20 | - | no | Open |
| 2033 | 3.005426615928177 | -1.10122 | -24.3358 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2233 | 3.0305860436455854 | -0.967732 | -18.5018 | 6 | 10 | 7 | 0.47 | 0.20 | - | no | Open |
| 2031 | 3.439757743207278 | -1.23837 | -22.0394 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2219 | 3.6736360702498603 | -1.23432 | -16.3059 | 8 | 11 | 7 | 0.47 | 0.20 | - | no | Open |
| 2232 | 3.7109895108672033 | -1.38009 | -23.3596 | 8 | 10 | 7 | 0.47 | 0.20 | - | no | Open |
| 2239 | 3.7301979323386565 | -1.16731 | -21.1186 | 10 | 11 | 8 | 0.53 | 0.40 | - | no | Open |
| 2224 | 3.8131917456090445 | -1.31688 | -21.5211 | 8 | 10 | 7 | 0.47 | 0.40 | - | no | Open |
| 2006 | 3.938484542984906 | -1.47514 | -23.7311 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2241 | 4.0573841509592175 | -0.956382 | -19.1841 | 6 | 11 | 5 | 0.33 | 0.20 | - | no | Open |
| 2009 | 3.64336835867456 | -1.23336 | -23.2299 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2023 | 3.8576950139824273 | -1.28078 | -22.0359 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2217 | 3.8614512475870413 | -1.25539 | -20.7896 | 6 | 9 | 5 | 0.33 | 0.20 | - | yes | Open |
| 2015 | 4.045196438237178 | -1.26347 | -21.3339 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2235 | 4.061172695494321 | -0.908576 | -12.0235 | 5 | 9 | 7 | 0.47 | 0.20 | - | yes | Open |
| 2229 | 4.184803569541945 | -1.2042 | -21.0722 | 5 | 10 | 5 | 0.33 | 0.20 | - | yes | Open |
| 2035 | 4.490157721600345 | -1.12032 | -18.8623 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2221 | 4.518052043509275 | -1.38391 | -21.9055 | 7 | 10 | 6 | 0.40 | 0.20 | - | yes | Open |
| 2236 | 4.702686246712027 | -0.995458 | -20.7366 | 7 | 11 | 8 | 0.53 | 0.60 | - | yes | Open |
| 2029 | 4.803072175671976 | -1.12471 | -19.6841 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2013 | 4.866254858817714 | -1.33469 | -23.7553 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2222 | 4.868191230149295 | -1.1976 | -22.6408 | 11 | 9 | 5 | 0.33 | 0.20 | - | yes | Open |
| 2223 | 4.915543641676009 | -1.44788 | -26.1058 | 7 | 10 | 8 | 0.53 | 0.40 | - | yes | Open |
| 2017 | 5.1515721798021765 | -1.10403 | -18.7275 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2032 | 5.328442844841178 | -1.14634 | -22.1108 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2238 | 5.40584278815577 | -1.03792 | -20.3077 | 9 | 11 | 6 | 0.40 | 0.20 | - | yes | Open |
| 2230 | 5.68916261214194 | -1.31052 | -24.1428 | 8 | 11 | 6 | 0.40 | 0.20 | - | yes | Open |
| 2024 | 5.761255144045803 | -1.27891 | -19.7006 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2215 | 5.782772674582591 | -1.44079 | -25.3918 | 7 | 10 | 8 | 0.53 | 0.40 | - | yes | Open |
| 2246 | 5.823329495083621 | -1.36096 | -24.4997 | 10 | 11 | 6 | 0.40 | 0.20 | - | yes | Open |
| 2019 | 5.890182783520056 | -1.3051 | -17.7785 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2037 | 5.894511591378404 | -1.12067 | -21.8113 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2025 | 5.978723121372389 | -1.06654 | -22.662 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2026 | 6.002792951217877 | -1.37637 | -24.056 | 11 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2245 | 6.085644639233802 | -0.996695 | -16.3884 | 5 | 10 | 6 | 0.40 | 0.20 | - | yes | Open |
| 2016 | 6.118152948823159 | -1.09185 | -18.5692 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2012 | 6.125664527902213 | -1.27859 | -20.6399 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2234 | 6.147505467060259 | -1.11666 | -20.1522 | 5 | 10 | 6 | 0.40 | 0.20 | - | yes | Open |
| 2027 | 6.282088696229935 | -1.24298 | -22.9085 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2010 | 6.3285950573094745 | -1.53038 | -22.5993 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2007 | 6.375508283178409 | -1.36617 | -21.9488 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2227 | 6.442677896213871 | -1.26053 | -20.4678 | 7 | 12 | 6 | 0.40 | 0.40 | - | yes | Open |
| 2036 | 6.541446118972117 | -1.21648 | -20.0421 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2018 | 7.3119849345106305 | -1.27495 | -21.1875 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2021 | 7.602828333694626 | -1.14254 | -22.8145 | 8 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2226 | 54.35881857057994 | -1.14038 | -20.5263 | 6 | 10 | 6 | 0.40 | 0.20 | - | yes | Open |
| 2008 | 54.84243709664221 | -1.39776 | -22.4524 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2231 | 55.099938857539584 | -1.30828 | -20.4055 | 6 | 9 | 7 | 0.47 | 0.20 | - | yes | Open |
| 2030 | 55.374439016037485 | -1.3945 | -25.7136 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2228 | 55.66950002303142 | -1.13288 | -18.9641 | 7 | 8 | 5 | 0.33 | 0.20 | - | yes | Open |
| 2011 | 55.71464406906111 | -1.45556 | -25.2589 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2028 | 55.82138655876557 | -1.16562 | -19.7479 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2220 | 55.86528566775287 | -1.30055 | -22.6264 | 7 | 10 | 7 | 0.47 | 0.20 | - | yes | Open |
| 2022 | 55.95191748638111 | -1.40855 | -23.5316 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2242 | 55.974407454042655 | -1.11278 | -22.2904 | 5 | 11 | 6 | 0.40 | 0.20 | - | yes | Open |
| 2034 | 56.21764766101079 | -1.25071 | -14.3425 | 12 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2014 | 56.30159903302769 | -1.34144 | -24.6298 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2237 | 56.43784972685953 | -1.08522 | -18.4297 | 8 | 11 | 7 | 0.47 | 0.20 | - | yes | Open |
| 2216 | 56.58339452851141 | -1.25857 | -20.7031 | 8 | 11 | 6 | 0.40 | 0.20 | - | yes | Open |
| 2243 | 56.702632901700554 | -1.02299 | -16.3893 | 7 | 9 | 5 | 0.33 | 0.20 | - | yes | Open |
| 2020 | 57.45909968129073 | -1.14936 | -20.3795 | 6 | 13 | 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
-22.762kcal/mol
Ligand efficiency (LE)
-1.1980kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.820
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.53
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
83.88kcal/mol
Minimised FF energy
71.46kcal/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.