Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
23.0 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.48, Jaccard 0.40, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.078 kcal/mol/HA)
✓ Good fit quality (FQ -9.19)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ High strain energy (23.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-22.631
kcal/mol
LE
-1.078
kcal/mol/HA
Fit Quality
-9.19
FQ (Leeson)
HAC
21
heavy atoms
MW
330
Da
LogP
1.27
cLogP
Interaction summary
HB 10
HY 23
PI 1
CLASH 2
Interaction summary
HB 10
HY 23
PI 1
CLASH 2
| Final rank | 1.583 | Score | -22.631 |
|---|---|---|---|
| Inter norm | -1.209 | Intra norm | 0.131 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 10 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; 1 severe cofactor-context clash; moderate strain Δ 23.0 | ||
| Residues |
NDP301
ALA32
ARG48
ASP52
ILE45
MET53
PHE56
PRO50
TRP47
TYR162
VAL156
VAL30
VAL31
VAL49
| ||
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 | 10 | Native recall | 0.48 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 568 | 1.583129999457927 | -1.20878 | -22.6312 | 10 | 14 | 10 | 0.48 | 0.33 | - | no | Current |
| 581 | 2.8930255084694276 | -1.28328 | -25.8698 | 5 | 14 | 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
-22.631kcal/mol
Ligand efficiency (LE)
-1.0777kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.192
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
330.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.27
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-104.11kcal/mol
Minimised FF energy
-127.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
523.1Ų
Total solvent-accessible surface area of free ligand
BSA total
450.2Ų
Buried surface area upon binding
BSA apolar
287.0Ų
Hydrophobic contacts buried
BSA polar
163.2Ų
Polar contacts buried
Fraction buried
86.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3072.6Ų
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
1715.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)