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 strong
SASA done
Strain ΔE
18.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.55, Jaccard 0.52, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.128 kcal/mol/HA)
✓ Good fit quality (FQ -10.40)
✓ Good H-bonds (5 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Moderate strain (18.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-29.338
kcal/mol
LE
-1.128
kcal/mol/HA
Fit Quality
-10.40
FQ (Leeson)
HAC
26
heavy atoms
MW
390
Da
LogP
4.00
cLogP
Interaction summary
HB 5
HY 19
PI 3
CLASH 2
Interaction summary
HB 5
HY 19
PI 3
CLASH 2
| Final rank | 1.958 | Score | -29.338 |
|---|---|---|---|
| Inter norm | -1.074 | Intra norm | -0.055 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ARG97
LEU94
LYS57
LYS95
MET53
NDP301
PHE56
PHE91
THR54
THR83
VAL156
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 | 11 | Native recall | 0.55 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | -0.2908267176309925 | -1.19073 | -29.6003 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 1.8386052021954522 | -1.05981 | -26.1272 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 549 | 1.9584098801368803 | -1.07383 | -29.3381 | 5 | 12 | 11 | 0.55 | 0.40 | - | no | Current |
| 560 | 2.428087883165567 | -0.799576 | -24.0181 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 2.7941902960594462 | -0.966006 | -17.0384 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 3.472283433281198 | -1.06233 | -28.3109 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 3.8612649837231396 | -1.20279 | -31.5508 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 526 | 4.287644089881446 | -1.23726 | -27.9603 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 5.1552079225695575 | -1.06931 | -25.3885 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 550 | 5.633262955142708 | -1.10654 | -23.6606 | 16 | 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
-29.338kcal/mol
Ligand efficiency (LE)
-1.1284kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.396
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
389.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.00
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
49.68kcal/mol
Minimised FF energy
31.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
630.1Ų
Total solvent-accessible surface area of free ligand
BSA total
512.6Ų
Buried surface area upon binding
BSA apolar
355.1Ų
Hydrophobic contacts buried
BSA polar
157.6Ų
Polar contacts buried
Fraction buried
81.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1436.7Ų
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
845.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)