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 (-0.988 kcal/mol/HA)
✓ Good fit quality (FQ -9.10)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (29.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.674
kcal/mol
LE
-0.988
kcal/mol/HA
Fit Quality
-9.10
FQ (Leeson)
HAC
26
heavy atoms
MW
435
Da
LogP
1.98
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 29.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 4
Clashes 9
Severe clashes 3
| Final rank | 9.876834433836482 | Score | -25.6738 |
|---|---|---|---|
| Inter norm | -1.03363 | Intra norm | 0.0461731 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 13 clashes; 3 protein clashes; high strain Δ 39.7 | ||
| Residues | A:ARG14;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;A:TRP221;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 | 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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1287 | 3.9347902390586915 | -1.09217 | -23.2921 | 7 | 16 | 15 | 0.79 | 0.60 | - | no | Open |
| 1072 | 4.010485004591458 | -0.904747 | -10.8948 | 6 | 14 | 14 | 0.74 | 0.40 | - | no | Open |
| 1052 | 5.0871382403698275 | -1.27975 | -30.8194 | 7 | 18 | 14 | 0.74 | 0.60 | - | no | Open |
| 1288 | 5.399741877780713 | -0.828004 | -17.114 | 4 | 15 | 11 | 0.58 | 0.00 | - | no | Open |
| 1277 | 5.401195410350391 | -1.07172 | -29.8618 | 7 | 17 | 15 | 0.79 | 0.60 | - | no | Open |
| 1265 | 5.500832315539352 | -1.01026 | -27.0815 | 7 | 16 | 14 | 0.74 | 0.60 | - | no | Open |
| 1271 | 5.748479112895801 | -1.19752 | -25.7368 | 8 | 18 | 14 | 0.74 | 0.60 | - | no | Open |
| 1289 | 6.44087622679251 | -0.994892 | -25.129 | 8 | 14 | 12 | 0.63 | 0.60 | - | no | Open |
| 1276 | 5.35569648620121 | -0.906162 | -21.3171 | 5 | 12 | 9 | 0.47 | 0.00 | - | yes | Open |
| 1266 | 5.710883256197661 | -1.11171 | -25.4735 | 2 | 15 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1285 | 6.153381041682635 | -1.15416 | -29.6549 | 8 | 15 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1074 | 6.308025739988558 | -0.975439 | -21.9046 | 1 | 13 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1259 | 6.680941343857131 | -1.41825 | -32.4838 | 10 | 20 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1282 | 6.705917080408783 | -1.03361 | -28.017 | 3 | 17 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1048 | 6.707626050865905 | -1.15117 | -24.8216 | 7 | 19 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1269 | 6.709108062547374 | -1.07757 | -33.0639 | 8 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1279 | 6.718796974617663 | -1.1957 | -29.3041 | 10 | 18 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1275 | 6.7246142682149666 | -1.20898 | -27.4873 | 9 | 16 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1283 | 6.785852290369973 | -1.12755 | -24.353 | 8 | 17 | 16 | 0.84 | 0.60 | - | yes | Open |
| 1067 | 6.821254752248905 | -1.25115 | -32.5421 | 8 | 17 | 17 | 0.89 | 0.60 | - | yes | Open |
| 1264 | 7.106353181932397 | -0.788376 | -19.0246 | 7 | 13 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1060 | 7.254473248808168 | -1.21448 | -24.2478 | 9 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1055 | 7.261360406673291 | -1.23383 | -26.9383 | 7 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1068 | 7.301059177682515 | -1.18621 | -26.6271 | 7 | 19 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1078 | 7.37149058938099 | -0.952978 | -21.6056 | 1 | 13 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1066 | 7.50777521369321 | -0.909599 | -26.1817 | 7 | 16 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1267 | 7.673665709212381 | -1.3591 | -33.1608 | 10 | 20 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1064 | 7.733427607157031 | -1.09376 | -20.6444 | 10 | 19 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1270 | 7.797656133864394 | -1.03339 | -26.0823 | 1 | 17 | 14 | 0.74 | 0.00 | - | yes | Open |
| 1281 | 8.089507438939714 | -1.14599 | -33.1643 | 9 | 15 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1273 | 8.243512782890457 | -0.988646 | -26.6643 | 9 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1261 | 8.442454067474745 | -1.1071 | -29.7202 | 3 | 17 | 14 | 0.74 | 0.00 | - | yes | Open |
| 1062 | 8.500941060235188 | -1.07983 | -29.3445 | 9 | 17 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1059 | 8.692108167370677 | -1.2265 | -32.5437 | 8 | 17 | 17 | 0.89 | 0.60 | - | yes | Open |
| 1076 | 8.92712206735579 | -1.0551 | -18.0095 | 9 | 20 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1058 | 8.928748461342215 | -0.967743 | -27.6246 | 8 | 17 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1073 | 9.068509901582944 | -0.875479 | -21.3439 | 3 | 15 | 11 | 0.58 | 0.00 | - | yes | Open |
| 1056 | 9.217332786089234 | -1.15172 | -31.1582 | 9 | 19 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1079 | 9.673002038376433 | -1.25746 | -32.2559 | 11 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1049 | 9.708229859491125 | -1.05423 | -22.3448 | 7 | 18 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1063 | 9.876834433836482 | -1.03363 | -25.6738 | 6 | 14 | 13 | 0.68 | 0.40 | - | yes | Current |
| 1054 | 10.123116171188725 | -0.979268 | -22.3481 | 7 | 15 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1262 | 10.36830997356805 | -1.0482 | -27.4088 | 3 | 18 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1070 | 10.443920457711686 | -1.02407 | -28.6792 | 9 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1286 | 10.468292940729203 | -1.02319 | -27.6041 | 4 | 18 | 14 | 0.74 | 0.00 | - | yes | Open |
| 1051 | 10.812574592521296 | -1.35258 | -35.2318 | 12 | 16 | 16 | 0.84 | 0.60 | - | yes | Open |
| 1274 | 11.587228868677006 | -1.04768 | -27.5955 | 3 | 19 | 14 | 0.74 | 0.00 | - | yes | Open |
| 1071 | 13.905701161889505 | -1.03121 | -23.3672 | 11 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1263 | 55.60157700388984 | -1.4176 | -33.951 | 9 | 18 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1278 | 56.25270818621046 | -1.10285 | -30.5608 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1065 | 57.20483236660184 | -0.804768 | -22.3064 | 3 | 17 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1075 | 57.86985222199679 | -1.19579 | -31.5225 | 10 | 17 | 17 | 0.89 | 0.60 | - | yes | Open |
| 1061 | 58.26966126926524 | -0.913697 | -20.3522 | 7 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1280 | 58.762853138969916 | -0.961509 | -26.1931 | 7 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1290 | 59.03272213555162 | -1.06472 | -27.4732 | 10 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1053 | 59.631438582898824 | -0.819121 | -19.1323 | 4 | 12 | 9 | 0.47 | 0.00 | - | yes | Open |
| 1077 | 59.9174331428899 | -0.784755 | -19.0099 | 5 | 12 | 10 | 0.53 | 0.00 | - | yes | Open |
| 1050 | 62.593533502382456 | -1.1386 | -28.9329 | 2 | 18 | 15 | 0.79 | 0.00 | - | yes | Open |
| 1284 | 63.541179566703974 | -0.865491 | -22.726 | 8 | 17 | 11 | 0.58 | 0.20 | - | yes | Open |
| 1268 | 63.65740605954292 | -1.02844 | -24.3589 | 9 | 20 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1272 | 63.813481781377554 | -0.920539 | -28.3275 | 10 | 21 | 15 | 0.79 | 0.60 | - | yes | Open |
| 1069 | 64.49152462931427 | -1.13915 | -24.0612 | 4 | 18 | 9 | 0.47 | 0.20 | - | yes | Open |
| 1057 | 66.50720886933654 | -1.11943 | -29.1661 | 7 | 18 | 11 | 0.58 | 0.20 | - | yes | Open |
| 1260 | 67.38431273537378 | -0.85647 | -17.618 | 3 | 18 | 12 | 0.63 | 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
-25.674kcal/mol
Ligand efficiency (LE)
-0.9875kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.098
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
435.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.98
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
119.49kcal/mol
Minimised FF energy
90.12kcal/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.