Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native mixed
SASA done
Strain ΔE
24.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.52, Jaccard 0.46, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.581 kcal/mol/HA)
✓ Good fit quality (FQ -5.81)
✓ Good H-bonds (5 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (24.4 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (19)
Score
-19.751
kcal/mol
LE
-0.581
kcal/mol/HA
Fit Quality
-5.81
FQ (Leeson)
HAC
34
heavy atoms
MW
474
Da
LogP
4.20
cLogP
Interaction summary
HB 5
HY 24
PI 2
CLASH 3
Interaction summary
HB 5
HY 24
PI 2
CLASH 3
| Final rank | 2.050 | Score | -19.751 |
|---|---|---|---|
| Inter norm | -0.787 | Intra norm | 0.206 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 19 clashes; 5 protein contact clashes; 1 severe cofactor-context clash; moderate strain Δ 24.4 | ||
| Residues |
NDP301
ARG97
GLU43
ILE45
LEU94
LYS95
MET53
PHE56
PHE91
PRO88
SER44
SER86
THR83
VAL87
| ||
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
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: strict.
| Name | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
NDP301
ALA32
ARG97
ASP52
GLY157
ILE45
LEU94
LYS57
MET53
PHE55
PHE56
PHE91
PRO88
SER86
THR180
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 11 | Native recall | 0.52 |
| Jaccard | 0.46 | 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: strict. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 435 | 1.9301717756467363 | -0.72761 | -23.752 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 334 | 2.0263869649204853 | -0.930222 | -27.1777 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 395 | 2.0501377984473983 | -0.787007 | -19.7508 | 5 | 14 | 11 | 0.52 | 0.00 | - | no | Current |
| 397 | 2.752858282721569 | -0.800489 | -23.9414 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 396 | 2.7601535713818413 | -0.591573 | -16.9942 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 381 | 2.9359635508409108 | -0.793642 | -19.3973 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 3.1523302745872246 | -0.760382 | -22.134 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 379 | 3.2188609293194674 | -0.712407 | -23.9203 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 418 | 3.4321465037133247 | -0.816749 | -26.4904 | 4 | 18 | 1 | 0.05 | 0.00 | - | no | Open |
| 407 | 3.5524489581677203 | -0.633858 | -18.4382 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 370 | 3.7807067079968997 | -0.979467 | -27.5375 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 493 | 3.8486675627744926 | -0.726729 | -19.7364 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 4.10912935177256 | -0.834923 | -27.5266 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 336 | 4.160825631036783 | -0.993151 | -30.1156 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 464 | 5.0362869852581325 | -0.819442 | -25.2435 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.751kcal/mol
Ligand efficiency (LE)
-0.5809kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.812
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
474.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.20
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
82.99kcal/mol
Minimised FF energy
58.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
737.5Ų
Total solvent-accessible surface area of free ligand
BSA total
569.4Ų
Buried surface area upon binding
BSA apolar
403.5Ų
Hydrophobic contacts buried
BSA polar
165.9Ų
Polar contacts buried
Fraction buried
77.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3286.2Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1686.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)