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
12.8 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.50, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.354 kcal/mol/HA)
✓ Good fit quality (FQ -10.30)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Moderate strain (12.8 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
Score
-21.659
kcal/mol
LE
-1.354
kcal/mol/HA
Fit Quality
-10.30
FQ (Leeson)
HAC
16
heavy atoms
MW
254
Da
LogP
1.80
cLogP
Interaction summary
HB 6
HY 13
PI 2
CLASH 2
Interaction summary
HB 6
HY 13
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 | -0.686 | Score | -21.659 |
|---|---|---|---|
| Inter norm | -1.573 | Intra norm | 0.220 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 6 |
| Artifact reason | geometry warning; 4 clashes; 2 protein contact clashes; 1 severe cofactor-context clash | ||
| Residues |
ARG17
HIS241
LEU18
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
SER111
TYR194
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 10 | Native recall | 0.53 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 494 | -0.6860410761604958 | -1.57326 | -21.6586 | 6 | 11 | 10 | 0.53 | 0.20 | - | no | Current |
| 513 | 0.923740226137635 | -1.55587 | -22.3636 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 493 | 2.2497935265458597 | -1.61594 | -24.5796 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 467 | 2.89061770523603 | -2.02262 | -29.942 | 5 | 13 | 9 | 0.47 | 0.20 | - | no | Open |
| 500 | 3.1916782193520294 | -1.74067 | -25.2459 | 7 | 13 | 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
-21.659kcal/mol
Ligand efficiency (LE)
-1.3537kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.304
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
16HA
Physicochemical properties
Molecular weight
254.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
50.18kcal/mol
Minimised FF energy
37.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
454.6Ų
Total solvent-accessible surface area of free ligand
BSA total
405.5Ų
Buried surface area upon binding
BSA apolar
250.9Ų
Hydrophobic contacts buried
BSA polar
154.6Ų
Polar contacts buried
Fraction buried
89.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1449.4Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1023.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)