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
28.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.35, Jaccard 0.29, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.048 kcal/mol/HA)
✓ Good fit quality (FQ -9.65)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ High strain energy (28.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-27.240
kcal/mol
LE
-1.048
kcal/mol/HA
Fit Quality
-9.65
FQ (Leeson)
HAC
26
heavy atoms
MW
397
Da
LogP
1.61
cLogP
Interaction summary
HB 9
HY 14
PI 2
CLASH 2
Interaction summary
HB 9
HY 14
PI 2
CLASH 2
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
| Final rank | 3.847 | Score | -27.240 |
|---|---|---|---|
| Inter norm | -1.066 | Intra norm | 0.019 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 9 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; moderate strain Δ 28.6 | ||
| Residues |
ARG97
LEU94
LYS57
LYS90
LYS95
MET53
PHE56
PHE91
PRO50
PRO93
THR54
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 7 | Native recall | 0.35 |
| Jaccard | 0.29 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 268 | 0.5548080490475088 | -1.05187 | -27.106 | 10 | 13 | 1 | 0.05 | 0.00 | - | no | Open |
| 279 | 1.180288750449507 | -1.28782 | -33.7615 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 294 | 1.9988238547277395 | -0.906193 | -23.2893 | 3 | 20 | 1 | 0.05 | 0.00 | - | no | Open |
| 359 | 2.152413258275727 | -1.00215 | -26.0228 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 280 | 2.219226374857256 | -1.1531 | -31.621 | 13 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 342 | 3.847482739549202 | -1.0664 | -27.24 | 9 | 11 | 7 | 0.35 | 0.20 | - | no | Current |
| 308 | 4.168474970978635 | -0.789172 | -20.1145 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 331 | 4.964185718646357 | -0.908116 | -24.267 | 11 | 15 | 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
-27.240kcal/mol
Ligand efficiency (LE)
-1.0477kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.653
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
397.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.61
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-85.02kcal/mol
Minimised FF energy
-113.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
637.6Ų
Total solvent-accessible surface area of free ligand
BSA total
483.2Ų
Buried surface area upon binding
BSA apolar
316.0Ų
Hydrophobic contacts buried
BSA polar
167.2Ų
Polar contacts buried
Fraction buried
75.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1433.6Ų
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
1820.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
836.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)