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 (-1.141 kcal/mol/HA)
✓ Good fit quality (FQ -9.73)
✗ High strain energy (13.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.964
kcal/mol
LE
-1.141
kcal/mol/HA
Fit Quality
-9.73
FQ (Leeson)
HAC
21
heavy atoms
MW
288
Da
LogP
-0.67
cLogP
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 15
π–π 1
Clashes 2
Severe clashes 0
| Final rank | 1.662312667078168 | Score | -23.9637 |
|---|---|---|---|
| Inter norm | -1.11875 | Intra norm | -0.0223829 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 2 |
| Artifact reason | geometry warning; 7 clashes; 2 protein contact clashes; moderate strain Δ 19.9 | ||
| Residues | A:ARG14;A:ASP161;A:GLY205;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:TRP221;A:TYR174;A:VAL206 | ||
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| Residue summary | LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | H-bonds | 6 |
| IFP residues | A:ARG14; A:ASP161; A:CYS168; A:GLY205; A:LEU208; A:LEU209; A:LYS178; A:MET213; A:NAP301; A:PHE171; A:PHE97; A:PRO210; A:PRO99; A:SER207; A:SER95; A:TRP221; A:TYR174; A:TYR98; A:VAL206 | ||
| Current overlap | 12 | Native recall | 0.63 |
| Jaccard | 0.63 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 24 | 1.662312667078168 | -1.11875 | -23.9637 | 2 | 12 | 12 | 0.63 | 0.20 | - | no | Current |
| 22 | 1.7233050905436884 | -1.25431 | -26.5951 | 5 | 14 | 12 | 0.63 | 0.20 | - | no | Open |
| 48 | 1.866414483308465 | -1.23511 | -26.0846 | 5 | 14 | 12 | 0.63 | 0.20 | - | no | Open |
| 57 | 1.874320548740702 | -1.02289 | -20.1842 | 1 | 15 | 14 | 0.74 | 0.00 | - | no | Open |
| 40 | 1.9208733552596937 | -1.10354 | -23.3674 | 2 | 12 | 12 | 0.63 | 0.20 | - | no | Open |
| 52 | 2.051962080173818 | -1.23641 | -25.7429 | 2 | 15 | 13 | 0.68 | 0.20 | - | no | Open |
| 25 | 51.6276199905179 | -1.26532 | -25.4374 | 3 | 13 | 12 | 0.63 | 0.20 | - | no | Open |
| 39 | 51.671671478313236 | -1.1965 | -25.1441 | 2 | 13 | 12 | 0.63 | 0.00 | - | no | Open |
| 44 | 51.88196694817234 | -1.24288 | -26.344 | 4 | 13 | 11 | 0.58 | 0.00 | - | no | Open |
| 28 | 51.96137106207113 | -1.42769 | -28.3757 | 5 | 14 | 12 | 0.63 | 0.40 | - | no | Open |
| 32 | 51.978180482209424 | -1.10491 | -23.521 | 4 | 12 | 12 | 0.63 | 0.20 | - | no | Open |
| 23 | 52.28649569674507 | -0.98994 | -21.0496 | 2 | 14 | 13 | 0.68 | 0.20 | - | no | Open |
| 33 | 52.316183645348474 | -1.18039 | -25.4541 | 2 | 15 | 13 | 0.68 | 0.00 | - | no | Open |
| 11 | 52.33756189826127 | -1.50174 | -30.8162 | 6 | 13 | 13 | 0.68 | 0.60 | - | no | Open |
| 29 | 52.57140542473638 | -1.2123 | -25.8053 | 2 | 14 | 13 | 0.68 | 0.20 | - | no | Open |
| 41 | 52.84172032042223 | -1.32457 | -27.9437 | 6 | 13 | 13 | 0.68 | 0.80 | - | no | Open |
| 26 | 52.89119334802034 | -1.25898 | -26.4911 | 4 | 13 | 9 | 0.47 | 0.00 | - | no | Open |
| 30 | 52.91464472426016 | -1.2216 | -25.452 | 2 | 16 | 14 | 0.74 | 0.20 | - | no | Open |
| 16 | 53.12321513999725 | -1.06779 | -22.7208 | 3 | 12 | 12 | 0.63 | 0.60 | - | no | Open |
| 18 | 53.291383298518014 | -1.19356 | -25.0437 | 4 | 14 | 13 | 0.68 | 0.20 | - | no | Open |
| 35 | 56.67226378574871 | -1.13086 | -23.4311 | 9 | 10 | 8 | 0.42 | 0.60 | - | no | Open |
| 55 | 56.85019849179166 | -1.18688 | -24.3044 | 8 | 10 | 8 | 0.42 | 0.60 | - | no | Open |
| 36 | 53.01571260029264 | -1.29786 | -27.5005 | 4 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 46 | 53.596763449687025 | -1.20544 | -25.4255 | 7 | 13 | 12 | 0.63 | 0.40 | - | yes | Open |
| 12 | 53.64299692290468 | -1.55452 | -32.7305 | 7 | 13 | 12 | 0.63 | 0.40 | - | yes | Open |
| 43 | 53.67017243217007 | -1.53207 | -32.2299 | 6 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 42 | 53.84339344891555 | -1.46465 | -30.7446 | 5 | 13 | 12 | 0.63 | 0.40 | - | yes | Open |
| 54 | 53.92540685962988 | -1.47784 | -30.5183 | 5 | 15 | 13 | 0.68 | 0.60 | - | yes | Open |
| 15 | 53.968295411625036 | -1.04374 | -22.3688 | 1 | 14 | 12 | 0.63 | 0.00 | - | yes | Open |
| 34 | 53.98551636967701 | -1.44464 | -29.8703 | 5 | 13 | 12 | 0.63 | 0.60 | - | yes | Open |
| 50 | 54.07148931752043 | -1.20339 | -25.4392 | 7 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 38 | 54.370352169277254 | -1.26276 | -26.8338 | 10 | 14 | 12 | 0.63 | 0.40 | - | yes | Open |
| 37 | 54.45594865809728 | -1.29766 | -27.8656 | 10 | 13 | 11 | 0.58 | 0.40 | - | yes | Open |
| 13 | 54.46419188347337 | -1.23894 | -25.5577 | 3 | 13 | 11 | 0.58 | 0.40 | - | yes | Open |
| 19 | 54.5162563111974 | -1.35994 | -28.8809 | 9 | 13 | 12 | 0.63 | 0.40 | - | yes | Open |
| 58 | 54.742087145431725 | -1.55072 | -32.5676 | 5 | 14 | 13 | 0.68 | 0.40 | - | yes | Open |
| 20 | 54.81036627725986 | -1.50189 | -31.4962 | 9 | 13 | 12 | 0.63 | 0.40 | - | yes | Open |
| 47 | 55.26506311624412 | -1.49047 | -30.9951 | 8 | 13 | 12 | 0.63 | 0.40 | - | yes | Open |
| 53 | 55.32317152273487 | -1.0076 | -20.3708 | 2 | 13 | 13 | 0.68 | 0.00 | - | yes | Open |
| 56 | 55.45807563679888 | -1.30038 | -27.6413 | 8 | 14 | 12 | 0.63 | 0.40 | - | yes | Open |
| 31 | 55.479921792595015 | -1.12874 | -23.8267 | 3 | 13 | 13 | 0.68 | 0.20 | - | yes | Open |
| 51 | 55.505935658257165 | -1.36485 | -28.4855 | 8 | 10 | 9 | 0.47 | 0.60 | - | yes | Open |
| 17 | 55.584957425645634 | -1.231 | -25.996 | 4 | 16 | 14 | 0.74 | 0.20 | - | yes | Open |
| 49 | 56.104202193582154 | -1.04877 | -22.0849 | 6 | 12 | 11 | 0.58 | 0.40 | - | yes | Open |
| 21 | 56.238213984312274 | -1.1227 | -23.522 | 2 | 12 | 10 | 0.53 | 0.00 | - | yes | Open |
| 27 | 56.89876702178748 | -1.34654 | -25.9541 | 8 | 10 | 9 | 0.47 | 0.60 | - | yes | Open |
| 45 | 59.17291208703662 | -1.04464 | -22.055 | 2 | 10 | 8 | 0.42 | 0.00 | - | yes | Open |
| 14 | 61.41724755659753 | -1.3385 | -24.8031 | 9 | 9 | 9 | 0.47 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.964kcal/mol
Ligand efficiency (LE)
-1.1411kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.733
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
288.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.67
Lipinski: ≤ 5
Rotatable bonds
0
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
75.09kcal/mol
Minimised FF energy
61.78kcal/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.