Molecular metrics status: done
Cached molecular metrics are available for this pose.
Metrics cached · SASA missing
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
No SASA yet
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA missing
Strain ΔE
37.6 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.85, Jaccard 0.85, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.510 kcal/mol/HA)
✓ Good fit quality (FQ -5.11)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (37.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
✗ Excluded by docking heuristics
ℹ SASA not computed
Score
-17.359
kcal/mol
LE
-0.510
kcal/mol/HA
Fit Quality
-5.11
FQ (Leeson)
HAC
34
heavy atoms
MW
463
Da
LogP
1.38
cLogP
Interaction summary
HB 3
HY 24
PI 2
CLASH 2
Interaction summary
HB 3
HY 24
PI 2
CLASH 2
| Final rank | 55.728 | Score | -17.359 |
|---|---|---|---|
| Inter norm | -0.582 | Intra norm | 0.072 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 12 clashes; 1 protein clash | ||
| Residues |
ALA32
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
Protein summary
225 residues
| Protein target | T03 | Atoms | 3428 |
|---|---|---|---|
| Residues | 225 | Chains | 2 |
| Residue summary | LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:NDP301
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 3CL9 | Contacts | 20 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA32
ARG97
ASP52
ILE45
LEU94
LYS57
MET53
NDP301
PHE56
PHE91
PRO88
SER86
THR180
THR54
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 17 | Native recall | 0.85 |
| Jaccard | 0.85 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
HB · H-bonds
Mode: permissive. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1176 | 3.402864701018557 | -0.663813 | -18.2776 | 0 | 19 | 16 | 0.80 | 0.00 | - | no | Open |
| 1263 | 3.9990604149423805 | -0.711846 | -22.53 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1260 | 4.4753230285021495 | -0.712311 | -22.4158 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1264 | 5.159523238865605 | -0.662175 | -20.6769 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1204 | 5.477112655515728 | -0.691578 | -22.6745 | 1 | 18 | 13 | 0.65 | 0.20 | - | no | Open |
| 1184 | 5.541202272118075 | -0.659492 | -17.8819 | 0 | 17 | 13 | 0.65 | 0.00 | - | no | Open |
| 1177 | 5.566946121226586 | -0.751676 | -23.4419 | 2 | 18 | 16 | 0.80 | 0.20 | - | no | Open |
| 1199 | 5.631111653167176 | -0.625717 | -20.0399 | 1 | 16 | 11 | 0.55 | 0.20 | - | no | Open |
| 1190 | 5.678718160062305 | -0.713346 | -18.3026 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1198 | 6.254957794951255 | -0.778277 | -25.0414 | 1 | 22 | 18 | 0.90 | 0.20 | - | no | Open |
| 1188 | 6.325771420887529 | -0.587341 | -16.9229 | 0 | 18 | 14 | 0.70 | 0.00 | - | no | Open |
| 1178 | 6.36188162765554 | -0.659512 | -12.7139 | 2 | 20 | 18 | 0.90 | 0.20 | - | no | Open |
| 1191 | 6.56750148961188 | -0.668599 | -18.9567 | 1 | 16 | 15 | 0.75 | 0.20 | - | no | Open |
| 1175 | 6.794888250722963 | -0.748457 | -20.9639 | 0 | 20 | 16 | 0.80 | 0.00 | - | no | Open |
| 1257 | 53.872438886812105 | -0.582816 | -18.3348 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1183 | 54.341520696096715 | -0.652059 | -19.5408 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 1182 | 54.41382869599642 | -0.640632 | -21.134 | 0 | 20 | 17 | 0.85 | 0.00 | - | no | Open |
| 1258 | 54.490932092442215 | -0.680854 | -18.9453 | 0 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1185 | 54.53606804760635 | -0.579419 | -15.016 | 2 | 11 | 9 | 0.45 | 0.00 | - | no | Open |
| 1181 | 54.67552439964703 | -0.663086 | -20.4531 | 0 | 21 | 17 | 0.85 | 0.00 | - | no | Open |
| 1180 | 55.078895244555575 | -0.714419 | -18.4452 | 0 | 15 | 13 | 0.65 | 0.00 | - | no | Open |
| 1179 | 55.569919695452114 | -0.548479 | -14.7052 | 1 | 16 | 15 | 0.75 | 0.00 | - | no | Open |
| 1201 | 6.106456679136357 | -0.635301 | -21.5905 | 0 | 19 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1200 | 6.373871250571508 | -0.678999 | -21.1536 | 1 | 21 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1202 | 6.8209671570146355 | -0.697339 | -21.9246 | 0 | 16 | 11 | 0.55 | 0.00 | - | yes | Open |
| 1173 | 7.527546456074216 | -0.599193 | -23.0442 | 1 | 17 | 17 | 0.85 | 0.00 | - | yes | Open |
| 1192 | 55.18249394600299 | -0.676298 | -19.0891 | 0 | 18 | 14 | 0.70 | 0.00 | - | yes | Open |
| 1262 | 55.442316641919334 | -0.676484 | -19.3769 | 1 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1187 | 55.72764713393109 | -0.582275 | -17.3587 | 1 | 17 | 17 | 0.85 | 0.00 | - | yes | Current |
| 1197 | 56.31646235955749 | -0.703132 | -22.4177 | 0 | 22 | 18 | 0.90 | 0.00 | - | yes | Open |
| 1259 | 56.358462552788836 | -0.687859 | -22.5573 | 1 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1189 | 56.372576900626385 | -0.734814 | -22.0573 | 0 | 22 | 18 | 0.90 | 0.00 | - | yes | Open |
| 1193 | 56.79629875755536 | -0.612258 | -16.3708 | 2 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1196 | 56.89139187650238 | -0.769657 | -24.7178 | 0 | 18 | 16 | 0.80 | 0.00 | - | yes | Open |
| 1261 | 57.14118150611999 | -0.671137 | -19.4895 | 0 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1203 | 57.36959418637549 | -0.739535 | -19.4651 | 1 | 20 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1174 | 57.40147018454787 | -0.730569 | -18.7216 | 1 | 18 | 16 | 0.80 | 0.20 | - | yes | Open |
| 1194 | 58.223153835087224 | -0.642037 | -18.5372 | 1 | 19 | 15 | 0.75 | 0.20 | - | yes | Open |
| 1195 | 58.37196833807934 | -0.587214 | -14.7791 | 1 | 14 | 13 | 0.65 | 0.20 | - | yes | Open |
| 1186 | 58.786068888430485 | -0.615115 | -19.4548 | 3 | 17 | 17 | 0.85 | 0.20 | - | yes | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.359kcal/mol
Ligand efficiency (LE)
-0.5105kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.109
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
462.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.38
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
236.40kcal/mol
Minimised FF energy
198.84kcal/mol
SASA & burial
not yet run
SASA has not been computed yet for this pose. Queue a background recompute to populate SASA burial metrics without blocking the page.