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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
14.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.40, Jaccard 0.33, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.107 kcal/mol/HA)
✓ Good fit quality (FQ -10.20)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (14.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-28.790
kcal/mol
LE
-1.107
kcal/mol/HA
Fit Quality
-10.20
FQ (Leeson)
HAC
26
heavy atoms
MW
354
Da
LogP
2.25
cLogP
Interaction summary
HB 10
HY 22
PI 2
CLASH 2
Interaction summary
HB 10
HY 22
PI 2
CLASH 2
| Final rank | 4.730 | Score | -28.790 |
|---|---|---|---|
| Inter norm | -1.168 | Intra norm | 0.061 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 10 |
| Artifact reason | geometry warning; 9 clashes; 4 protein clashes | ||
| Residues |
ARG92
ARG97
LEU94
LYS57
LYS90
LYS95
MET53
PHE56
PHE91
PRO88
PRO93
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: 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 | 8 | Native recall | 0.40 |
| Jaccard | 0.33 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 644 | 0.07467650484793296 | -1.17551 | -27.9704 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 0.31605851962409415 | -1.3698 | -37.7576 | 13 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 640 | 1.8840439934935043 | -1.06732 | -30.545 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 627 | 1.901340798872262 | -1.02422 | -25.5677 | 8 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 646 | 2.4604224930937084 | -1.26732 | -29.0037 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 639 | 3.296573031191917 | -1.29669 | -29.6725 | 13 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 642 | 3.3256697539250615 | -0.924801 | -16.978 | 8 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 3.947674186548834 | -1.35108 | -30.6177 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 649 | 4.311540670753228 | -1.0456 | -23.7588 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 642 | 4.7302940548873185 | -1.16836 | -28.7896 | 10 | 12 | 8 | 0.40 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.790kcal/mol
Ligand efficiency (LE)
-1.1073kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.202
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
354.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.25
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
96.24kcal/mol
Minimised FF energy
81.50kcal/mol
SASA & burial
✓ computed
SASA (unbound)
607.9Ų
Total solvent-accessible surface area of free ligand
BSA total
490.9Ų
Buried surface area upon binding
BSA apolar
349.7Ų
Hydrophobic contacts buried
BSA polar
141.1Ų
Polar contacts buried
Fraction buried
80.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1458.7Ų
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
814.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)