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
23.4 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.35, Jaccard 0.29, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.283 kcal/mol/HA)
✓ Good fit quality (FQ -11.32)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ High strain energy (23.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-29.502
kcal/mol
LE
-1.283
kcal/mol/HA
Fit Quality
-11.32
FQ (Leeson)
HAC
23
heavy atoms
MW
338
Da
LogP
-0.31
cLogP
Interaction summary
HB 11
HY 15
PI 2
CLASH 1
Interaction summary
HB 11
HY 15
PI 2
CLASH 1
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 | 2.508 | Score | -29.502 |
|---|---|---|---|
| Inter norm | -1.254 | Intra norm | -0.029 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 11 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes; moderate strain Δ 23.4 | ||
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 272 | 1.0565588024106063 | -1.4079 | -31.3306 | 13 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 283 | 1.0848647482644131 | -1.1194 | -19.7839 | 10 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 326 | 1.1131363785864183 | -0.995394 | -20.8134 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 306 | 1.3109441700977569 | -1.30513 | -28.49 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 338 | 2.507643872441264 | -1.2541 | -29.5019 | 11 | 11 | 7 | 0.35 | 0.20 | - | no | Current |
| 260 | 2.5369634862341512 | -1.09721 | -19.3469 | 9 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 351 | 2.9440503822357695 | -1.14284 | -20.5628 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 271 | 4.247260498455184 | -1.47831 | -27.6122 | 16 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 282 | 4.363777071020779 | -1.0561 | -24.2018 | 7 | 16 | 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
-29.502kcal/mol
Ligand efficiency (LE)
-1.2827kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.321
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
338.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.31
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-153.21kcal/mol
Minimised FF energy
-176.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
543.0Ų
Total solvent-accessible surface area of free ligand
BSA total
441.2Ų
Buried surface area upon binding
BSA apolar
274.0Ų
Hydrophobic contacts buried
BSA polar
167.1Ų
Polar contacts buried
Fraction buried
81.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1345.8Ų
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
835.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)