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 (-1.094 kcal/mol/HA)
✓ Good fit quality (FQ -9.66)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (35.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.168
kcal/mol
LE
-1.094
kcal/mol/HA
Fit Quality
-9.66
FQ (Leeson)
HAC
23
heavy atoms
MW
347
Da
LogP
2.81
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 35.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 24
π–π 3
Clashes 9
Severe clashes 0
| Final rank | 5.0922701385704325 | Score | -25.1675 |
|---|---|---|---|
| Inter norm | -1.37476 | Intra norm | 0.280524 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 9 protein contact clashes; high strain Δ 48.3 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO167;A:PRO210;A:TRP221;A:TYR174;A:VAL206 | ||
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| 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 | 0.57 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2109 | 2.2817232403148027 | -0.679057 | -19.2757 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1384 | 2.4790994217928746 | -1.25477 | -25.6087 | 10 | 15 | 14 | 0.74 | 0.60 | - | no | Open |
| 2116 | 3.0081850777931063 | -0.599928 | -16.7876 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 3323 | 3.0834435057360547 | -0.906184 | -22.5852 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2112 | 3.1955141570010426 | -0.573236 | -12.7276 | 4 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 2119 | 3.4117311415774165 | -0.569546 | -16.1322 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1389 | 3.489728076230429 | -1.22788 | -23.7259 | 8 | 14 | 13 | 0.68 | 0.40 | - | no | Open |
| 1385 | 3.664719433546682 | -1.25953 | -24.0102 | 11 | 15 | 14 | 0.74 | 0.60 | - | no | Open |
| 1373 | 3.6670062878039307 | -1.32524 | -24.0548 | 10 | 15 | 14 | 0.74 | 0.60 | - | no | Open |
| 1399 | 3.6971470365508363 | -1.22385 | -31.2735 | 9 | 14 | 12 | 0.63 | 0.60 | - | no | Open |
| 3316 | 3.72300503004492 | -0.902301 | -22.4605 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 3328 | 3.756675866591779 | -0.836273 | -20.0222 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2120 | 3.934064561648647 | -0.622792 | -15.0273 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1393 | 3.9906779186315973 | -1.02111 | -20.9101 | 8 | 14 | 13 | 0.68 | 0.40 | - | no | Open |
| 3322 | 3.9913968977460277 | -0.855136 | -21.3275 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2118 | 3.995554465222776 | -0.658135 | -15.1004 | 6 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 2097 | 4.017614336450142 | -0.971659 | -27.5551 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3327 | 4.146932342261554 | -0.823943 | -20.0517 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1400 | 4.2039261022747585 | -1.33055 | -22.1618 | 13 | 15 | 13 | 0.68 | 0.60 | - | no | Open |
| 2106 | 4.2140935958807555 | -0.957124 | -23.5423 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1377 | 4.239719646609262 | -1.2721 | -22.9388 | 8 | 14 | 13 | 0.68 | 0.40 | - | no | Open |
| 1381 | 4.250504728270129 | -1.259 | -21.4587 | 10 | 15 | 14 | 0.74 | 0.60 | - | no | Open |
| 2110 | 4.368245466563768 | -0.613609 | -15.8835 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1397 | 4.4684639282528895 | -1.25769 | -23.2065 | 10 | 15 | 13 | 0.68 | 0.60 | - | no | Open |
| 2092 | 4.526381061160178 | -0.864698 | -21.8592 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2114 | 4.689335990422604 | -0.97976 | -21.6981 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2115 | 4.703718567102414 | -0.987191 | -19.8979 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1388 | 5.0922701385704325 | -1.37476 | -25.1675 | 10 | 14 | 12 | 0.63 | 0.40 | - | no | Current |
| 2113 | 5.094611663606825 | -0.692849 | -14.8715 | 3 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 2106 | 5.181671977122495 | -0.88905 | -18.2955 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2103 | 5.391843343237947 | -1.07928 | -21.4305 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2102 | 5.587357364473357 | -1.00059 | -23.1369 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2101 | 5.698111708307799 | -0.955319 | -19.1876 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2091 | 5.826567961373929 | -1.09338 | -24.1343 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2114 | 5.877202634541105 | -0.803593 | -16.3224 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 2099 | 6.652527695452777 | -0.932214 | -22.0833 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1391 | 4.664114869365893 | -1.2314 | -32.8524 | 7 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 2093 | 4.716820877015008 | -0.965312 | -22.7483 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3319 | 4.734027204020525 | -0.942091 | -22.5059 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3317 | 4.893559535666326 | -0.820032 | -21.8316 | 4 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2094 | 5.092048371122133 | -1.11887 | -19.2752 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1395 | 5.096177319074554 | -1.29947 | -32.8519 | 8 | 14 | 12 | 0.63 | 0.60 | - | yes | Open |
| 2108 | 5.19797635369277 | -0.615794 | -17.1083 | 7 | 6 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2105 | 5.366856212704486 | -0.765928 | -17.8553 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3320 | 5.426867484682479 | -0.901688 | -20.6603 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2110 | 5.474317811137535 | -1.0787 | -26.2047 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3324 | 5.48858270460473 | -0.873917 | -18.7532 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1379 | 5.521915815724084 | -1.39896 | -34.5245 | 8 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1386 | 5.686116133705395 | -1.314 | -31.543 | 7 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2098 | 5.7040931822828265 | -1.1076 | -25.194 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2109 | 5.78732357110473 | -0.939823 | -24.1535 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3315 | 6.3011881760692035 | -1.03323 | -20.7724 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3330 | 6.3729646161153815 | -0.930746 | -23.4739 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1403 | 6.390644189895468 | -1.21181 | -28.4889 | 8 | 14 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1383 | 6.444852216192885 | -1.25351 | -31.7246 | 6 | 16 | 16 | 0.84 | 0.60 | - | yes | Open |
| 1372 | 6.489311564518409 | -1.28061 | -29.3135 | 7 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2090 | 6.623552548199285 | -1.11374 | -18.6588 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1382 | 6.66919791935104 | -1.31161 | -32.5385 | 7 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 3325 | 6.671002579865375 | -0.88808 | -22.929 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2105 | 7.178981615177039 | -0.999044 | -20.3546 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1376 | 7.3019115717677625 | -1.30982 | -17.9547 | 9 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1374 | 7.77223503653453 | -1.34885 | -33.5406 | 10 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1402 | 7.82131201751168 | -1.42985 | -34.0305 | 11 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 2107 | 7.8756787369303165 | -1.01789 | -20.3399 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2086 | 8.233159239020857 | -1.1628 | -20.1503 | 10 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1394 | 8.233386799490189 | -1.24205 | -30.2453 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2095 | 8.400478474589676 | -0.88741 | -21.5237 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2087 | 8.508800281760102 | -1.00178 | -21.004 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1396 | 8.732202156231997 | -1.2755 | -26.7201 | 6 | 15 | 9 | 0.47 | 0.40 | - | yes | Open |
| 2113 | 9.342500673624961 | -0.880015 | -14.2893 | 9 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2085 | 11.509261434721678 | -1.00948 | -13.144 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2112 | 11.963503035092673 | -0.991524 | -26.1158 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2100 | 54.359611551879205 | -0.934704 | -23.6809 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1387 | 54.560128014171255 | -1.21231 | -30.9496 | 5 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1378 | 55.20187882979501 | -1.44592 | -30.2395 | 6 | 14 | 12 | 0.63 | 0.40 | - | yes | Open |
| 2089 | 55.40540882047909 | -0.892494 | -20.0869 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2117 | 55.51969399681993 | -0.754919 | -17.2917 | 9 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1390 | 55.53025956530544 | -1.36664 | -32.1924 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 3326 | 55.585034003335075 | -1.00091 | -24.4226 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3321 | 55.59056900055058 | -0.912881 | -22.9746 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1380 | 55.741272368153616 | -1.39793 | -23.129 | 14 | 16 | 14 | 0.74 | 0.80 | - | yes | Open |
| 3318 | 55.80565761683176 | -1.01534 | -25.9406 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3329 | 56.49665759520963 | -0.920598 | -23.4678 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2115 | 56.54179439865516 | -0.665181 | -16.0545 | 5 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2107 | 56.73661195276771 | -0.621801 | -17.4872 | 5 | 8 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2111 | 57.462710660153405 | -0.56109 | -16.6275 | 5 | 6 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1392 | 58.62937376505696 | -1.25522 | -27.0824 | 10 | 13 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1375 | 59.099908242275916 | -1.30418 | -30.1739 | 3 | 16 | 14 | 0.74 | 0.20 | - | yes | Open |
| 2116 | 60.52662575739957 | -0.870654 | -21.8222 | 9 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1398 | 61.9935744345689 | -1.18069 | -28.978 | 11 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2088 | 62.12806704342215 | -0.951496 | -24.6835 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2111 | 62.30915048839577 | -0.859914 | -22.1044 | 10 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1401 | 62.38168301258153 | -1.15392 | -23.2157 | 5 | 13 | 9 | 0.47 | 0.00 | - | yes | Open |
| 2108 | 62.98756790404555 | -0.850343 | -22.2836 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2096 | 63.31017956514508 | -0.958468 | -25.9733 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2104 | 64.65676214125594 | -0.93009 | -24.3738 | 11 | 14 | 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
-25.168kcal/mol
Ligand efficiency (LE)
-1.0942kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.658
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.81
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
92.81kcal/mol
Minimised FF energy
57.66kcal/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.