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 medium
Native strong
SASA done
Strain ΔE
6.2 kcal/mol
Protein clashes
4
Internal clashes
5
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.50
Reason: no major geometry red flags detected
4 protein-contact clashes
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (6.2 kcal/mol)
✓ Excellent LE (-1.429 kcal/mol/HA)
✓ Good fit quality (FQ -11.96)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-28.578
kcal/mol
LE
-1.429
kcal/mol/HA
Fit Quality
-11.96
FQ (Leeson)
HAC
20
heavy atoms
MW
270
Da
LogP
2.58
cLogP
Interaction summary
HB 8
HY 16
PI 2
CLASH 5
Interaction summary
HB 8
HY 16
PI 2
CLASH 5
| Final rank | 2.771 | Score | -28.578 |
|---|---|---|---|
| Inter norm | -1.456 | Intra norm | 0.028 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; 2 cofactor-context clashes | ||
| Residues |
ARG17
ASP181
GLY225
LEU188
LEU226
LEU229
MET183
NDP302
PHE113
SER111
TYR194
VAL230
ARG287
| ||
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| 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
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 11 | Native recall | 0.65 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 71 | -0.6425912787373339 | -1.5364 | -30.9434 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 69 | 1.694537518369985 | -1.21538 | -22.0621 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 59 | 2.771198386423646 | -1.45638 | -28.5775 | 8 | 13 | 11 | 0.65 | 0.50 | - | no | Current |
| 80 | 3.406183505862583 | -1.22511 | -24.0434 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 45 | 3.6208123248314377 | -1.33156 | -25.6337 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 75 | 4.1092730997855105 | -1.13353 | -20.6307 | 8 | 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
-28.578kcal/mol
Ligand efficiency (LE)
-1.4289kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.957
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
270.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.58
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
6.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.02kcal/mol
Minimised FF energy
59.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
464.3Ų
Total solvent-accessible surface area of free ligand
BSA total
437.8Ų
Buried surface area upon binding
BSA apolar
317.3Ų
Hydrophobic contacts buried
BSA polar
120.5Ų
Polar contacts buried
Fraction buried
94.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1495.6Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1018.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)