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 (-0.904 kcal/mol/HA)
✓ Good fit quality (FQ -8.72)
✓ Strong H-bond network (12 bonds)
✗ Very high strain energy (22.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-27.125
kcal/mol
LE
-0.904
kcal/mol/HA
Fit Quality
-8.72
FQ (Leeson)
HAC
30
heavy atoms
MW
426
Da
LogP
3.81
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 22.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 12
Hydrophobic 20
π–π 4
Clashes 10
Severe clashes 1
| Final rank | 7.9199791056897055 | Score | -27.1245 |
|---|---|---|---|
| Inter norm | -0.967789 | Intra norm | 0.0636382 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 12 |
| Artifact reason | excluded; hard geometry fail; 1 severe clash; 1 protein clash; high strain Δ 30.6 | ||
| Residues | A:ALA212;A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL211 | ||
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.50 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2320 | 4.733832512027605 | -0.749109 | -19.6452 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 842 | 5.12868090621561 | -0.672721 | -17.5083 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 840 | 5.430562985145274 | -0.759449 | -19.5022 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1081 | 6.150822673681675 | -1.01065 | -24.5961 | 6 | 15 | 11 | 0.58 | 0.20 | - | no | Open |
| 1535 | 6.340701969272761 | -0.896861 | -21.8457 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 3039 | 6.387591429398569 | -0.795481 | -18.1542 | 13 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 896 | 6.551033378693617 | -1.01922 | -25.7491 | 9 | 16 | 15 | 0.79 | 0.60 | - | no | Open |
| 1388 | 6.782418153234539 | -0.695213 | -22.5111 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 3038 | 7.942117930196553 | -0.674001 | -14.878 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2316 | 5.332628002006268 | -0.868058 | -20.0659 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1532 | 6.083998946279481 | -0.843404 | -20.9054 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1080 | 6.220366681732465 | -1.06851 | -25.4172 | 6 | 16 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1383 | 6.598167365503434 | -0.682163 | -15.7374 | 8 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1387 | 6.776629838576531 | -0.529098 | -10.5191 | 2 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 898 | 7.051474704717249 | -0.870288 | -17.851 | 10 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1538 | 7.171626692757759 | -0.859275 | -24.526 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2319 | 7.225428900990634 | -0.80407 | -18.331 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1539 | 7.527880978032975 | -0.863378 | -26.5491 | 14 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3042 | 7.803879304444552 | -0.781031 | -21.5637 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1085 | 7.88737804889524 | -0.997209 | -30.1388 | 9 | 16 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1079 | 7.9199791056897055 | -0.967789 | -27.1245 | 12 | 14 | 11 | 0.58 | 0.60 | - | yes | Current |
| 899 | 7.9573269696065445 | -0.956018 | -13.3295 | 10 | 14 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1386 | 8.329883020086001 | -0.69776 | -14.9982 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3041 | 8.522111219462987 | -0.620646 | -13.1973 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1084 | 8.62202724252483 | -1.14181 | -32.598 | 6 | 15 | 12 | 0.63 | 0.40 | - | yes | Open |
| 901 | 8.97110738364751 | -0.938366 | -23.1429 | 13 | 15 | 13 | 0.68 | 0.60 | - | yes | Open |
| 843 | 9.049554066120184 | -0.76967 | -19.0359 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1534 | 9.052920689740052 | -0.876852 | -22.1417 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1384 | 9.229102176069318 | -0.644833 | -19.2285 | 8 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3040 | 9.33771504283638 | -0.697682 | -16.7642 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 897 | 9.666190834709859 | -0.991897 | -28.9102 | 10 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1537 | 10.167835793547708 | -0.851087 | -19.5418 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 900 | 10.307363739505979 | -0.858115 | -26.9878 | 10 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2318 | 10.337821320599799 | -0.780804 | -21.2884 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1385 | 10.425827198660368 | -0.702941 | -13.2293 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3043 | 10.563718548236801 | -0.676722 | -16.9382 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1536 | 10.635952226468847 | -0.850561 | -20.6678 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2315 | 10.677094498824093 | -0.79084 | -21.8887 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1078 | 11.020181699390957 | -1.03915 | -23.401 | 7 | 14 | 12 | 0.63 | 0.40 | - | yes | Open |
| 1082 | 11.1631688040782 | -1.40478 | -35.9393 | 10 | 17 | 10 | 0.53 | 0.80 | - | yes | Open |
| 845 | 11.231307470971887 | -0.771748 | -23.2409 | 8 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1533 | 11.316568116311995 | -0.883283 | -22.6526 | 14 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1083 | 11.353956774582517 | -1.41134 | -32.5815 | 8 | 17 | 10 | 0.53 | 0.60 | - | yes | Open |
| 844 | 11.389044557577973 | -0.699434 | -11.3462 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 841 | 11.616586958266717 | -0.814647 | -22.068 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2317 | 13.12860436672826 | -0.838914 | -22.4944 | 6 | 16 | 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
-27.125kcal/mol
Ligand efficiency (LE)
-0.9042kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.722
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
425.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.81
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
84.64kcal/mol
Minimised FF energy
62.59kcal/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.