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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.091 kcal/mol/HA)
✓ Good fit quality (FQ -10.41)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (25.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-31.630
kcal/mol
LE
-1.091
kcal/mol/HA
Fit Quality
-10.41
FQ (Leeson)
HAC
29
heavy atoms
MW
432
Da
LogP
2.46
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 25.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 24
π–π 3
Clashes 5
Severe clashes 0
| Final rank | 3.934851688206675 | Score | -31.6298 |
|---|---|---|---|
| Inter norm | -1.05437 | Intra norm | -0.0364235 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 9 |
| Artifact reason | geometry warning; 10 clashes; 5 protein contact clashes; high strain Δ 31.8 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:LYS13;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;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 | 13 | Native recall | 0.68 |
| Jaccard | 0.65 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 911 | 3.934851688206675 | -1.05437 | -31.6298 | 9 | 14 | 13 | 0.68 | 0.40 | - | no | Current |
| 713 | 3.9952709474174926 | -0.8634 | -22.2003 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2183 | 4.043627968636792 | -0.859714 | -25.8903 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 928 | 4.3710461106631335 | -0.949537 | -27.6882 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1020 | 5.530663825124199 | -0.977961 | -26.5705 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1484 | 5.860901488190194 | -0.679928 | -19.1693 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2913 | 5.999895760686788 | -0.86261 | -26.0656 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2262 | 6.180708760204886 | -0.975157 | -27.1958 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1149 | 6.195156783362302 | -0.786786 | -21.6311 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1486 | 6.26390379358215 | -0.796843 | -23.2709 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2181 | 6.4835609116488335 | -1.01887 | -29.87 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 890 | 8.841099049291712 | -0.628314 | -19.5849 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1147 | 5.336013607163179 | -0.785829 | -22.6412 | 5 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1485 | 6.30169603271199 | -0.818891 | -24.2435 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2184 | 6.5658627872834385 | -0.88894 | -26.8146 | 8 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2915 | 6.688314927464544 | -0.806719 | -25.3999 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1146 | 6.786019890627314 | -0.889455 | -25.7264 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2914 | 6.810923746743246 | -0.891399 | -26.3856 | 9 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2917 | 6.880224321858031 | -0.75114 | -22.1025 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 913 | 6.881381309286566 | -0.973006 | -23.2418 | 11 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1483 | 6.915602690039133 | -0.721704 | -22.8575 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 923 | 7.204354901833299 | -0.931422 | -27.2184 | 10 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 712 | 7.312982770588979 | -0.760361 | -18.9109 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 924 | 7.317543103212255 | -1.07461 | -31.2436 | 10 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 927 | 7.341732199324325 | -1.00125 | -30.8889 | 11 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2182 | 7.4556040238988 | -0.92785 | -25.7284 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 715 | 7.4657525629182055 | -0.75441 | -20.4943 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2919 | 7.909740169116287 | -0.680535 | -18.9306 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1014 | 7.964194681009658 | -1.04643 | -29.5377 | 11 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2918 | 7.9663078587874985 | -0.890191 | -27.138 | 8 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1482 | 8.150873362949012 | -0.767383 | -22.3089 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 714 | 8.583898417534163 | -0.764349 | -22.7592 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1015 | 8.80397856710363 | -0.998746 | -28.3842 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1017 | 9.221594405994194 | -0.957393 | -22.5083 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 914 | 9.369176783365493 | -1.10036 | -23.287 | 13 | 17 | 11 | 0.58 | 0.40 | - | yes | Open |
| 2916 | 9.505600578657544 | -0.762079 | -21.0175 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1148 | 9.516971621030477 | -0.837204 | -23.9706 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 912 | 9.598812723078094 | -1.05341 | -28.2515 | 7 | 17 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1019 | 10.236441904016148 | -1.01641 | -28.7939 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 925 | 10.349770435110718 | -1.02237 | -26.6499 | 12 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1018 | 10.616758952888329 | -1.0997 | -26.5256 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 926 | 12.44656996526837 | -1.10832 | -27.6439 | 13 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1016 | 12.849199331135889 | -0.882225 | -25.3172 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 891 | 13.461127199669205 | -0.79909 | -20.9919 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1481 | 13.632396890366213 | -0.716655 | -21.4595 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2261 | 16.67959401097733 | -0.842933 | -23.5451 | 5 | 18 | 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
-31.630kcal/mol
Ligand efficiency (LE)
-1.0907kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.411
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
431.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.46
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-0.11kcal/mol
Minimised FF energy
-25.77kcal/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.