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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.818 kcal/mol/HA)
✓ Good fit quality (FQ -7.89)
✓ Good H-bonds (4 bonds)
✗ High strain energy (15.2 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.543
kcal/mol
LE
-0.818
kcal/mol/HA
Fit Quality
-7.89
FQ (Leeson)
HAC
30
heavy atoms
MW
399
Da
LogP
3.42
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 15.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 5
Clashes 11
Severe clashes 1
| Final rank | 56.984734984948766 | Score | -24.5426 |
|---|---|---|---|
| Inter norm | -0.982329 | Intra norm | 0.164242 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLY205;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:SER207;A:TRP221;A:TYR174;A:VAL164;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 | 14 | Native recall | 0.74 |
| Jaccard | 0.58 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2523 | 2.8912616141868193 | -0.678707 | -21.228 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1787 | 3.541106814497068 | -0.687247 | -20.5018 | 0 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1785 | 3.6428429308409753 | -0.766802 | -21.7252 | 0 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 2521 | 3.957641235179865 | -0.63043 | -18.8248 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1784 | 3.9669495541031314 | -0.759734 | -23.7392 | 0 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 676 | 4.146867383323542 | -0.642742 | -20.231 | 1 | 12 | 10 | 0.53 | 0.20 | - | no | Open |
| 2443 | 4.318783182031566 | -0.739241 | -21.8368 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2516 | 4.668876689509117 | -0.732404 | -23.2317 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1781 | 4.717096058495918 | -0.7534 | -21.7789 | 0 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2444 | 4.724570018391683 | -0.644587 | -19.154 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 679 | 4.80578366293668 | -1.0164 | -29.1006 | 1 | 18 | 14 | 0.74 | 0.00 | - | no | Open |
| 2527 | 5.008532732706648 | -0.659438 | -17.4925 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1792 | 5.102125197510438 | -0.690817 | -18.9181 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2440 | 5.196373221464826 | -0.639136 | -17.9232 | 0 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2519 | 6.473663779578172 | -0.89954 | -27.8107 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2518 | 6.599907344975796 | -0.785215 | -23.1302 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2441 | 54.45144262776451 | -0.713693 | -17.3488 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2526 | 54.45177154363469 | -0.758059 | -22.8641 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2522 | 54.59635575719375 | -0.730208 | -21.3981 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1789 | 54.61054906552604 | -0.703365 | -17.2201 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2446 | 54.711307909049324 | -0.732677 | -21.9606 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2525 | 54.75501543154077 | -0.544067 | -17.3601 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1791 | 54.853267567495166 | -0.741813 | -19.6878 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2447 | 54.87254633563297 | -0.770982 | -22.9984 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2517 | 55.63444881884835 | -0.902055 | -28.1443 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 5.3113548786363225 | -0.637384 | -19.5034 | 3 | 11 | 7 | 0.37 | 0.20 | - | yes | Open |
| 1782 | 7.4938844590395375 | -0.742771 | -18.8053 | 0 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2520 | 55.3621858762145 | -0.697094 | -20.8658 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2442 | 55.58553039289799 | -0.702534 | -20.391 | 1 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 680 | 55.96299572129093 | -1.09423 | -31.9513 | 1 | 16 | 13 | 0.68 | 0.00 | - | yes | Open |
| 2445 | 56.17945021700643 | -0.545783 | -13.9951 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1790 | 56.39061612048332 | -0.827149 | -21.4923 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2524 | 56.70336184582236 | -0.69982 | -15.3237 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 677 | 56.708239477829665 | -0.927271 | -25.469 | 1 | 18 | 14 | 0.74 | 0.00 | - | yes | Open |
| 673 | 56.984734984948766 | -0.982329 | -24.5426 | 4 | 19 | 14 | 0.74 | 0.20 | - | yes | Current |
| 1783 | 57.08674454100152 | -0.918668 | -20.1928 | 1 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1786 | 57.40835755441452 | -0.743678 | -23.4507 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 678 | 57.94532316397163 | -0.951664 | -22.2206 | 2 | 19 | 14 | 0.74 | 0.20 | - | yes | Open |
| 1788 | 57.98501067398691 | -0.719014 | -17.6395 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 674 | 61.892979508413646 | -0.971799 | -22.2846 | 2 | 18 | 13 | 0.68 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.543kcal/mol
Ligand efficiency (LE)
-0.8181kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.892
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
398.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.42
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.03kcal/mol
Minimised FF energy
83.83kcal/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.