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
18.5 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.58, Jaccard 0.55, H-bond role recall 0.20
Reason: no major geometry red flags detected
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.033 kcal/mol/HA)
✓ Good fit quality (FQ -9.51)
✓ Good H-bonds (3 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (18.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-26.846
kcal/mol
LE
-1.033
kcal/mol/HA
Fit Quality
-9.51
FQ (Leeson)
HAC
26
heavy atoms
MW
399
Da
LogP
4.85
cLogP
Interaction summary
HB 3
HY 17
PI 3
CLASH 1
Interaction summary
HB 3
HY 17
PI 3
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 | 1.164 | Score | -26.846 |
|---|---|---|---|
| Inter norm | -1.119 | Intra norm | 0.087 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 3 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; 2 cofactor-context clashes | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
MET233
NDP302
PHE113
SER111
TYR194
VAL237
ARG287
| ||
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.55 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 415 | 0.7067403089329425 | -1.2582 | -30.6077 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 1.0913425355892699 | -0.855067 | -20.4389 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 414 | 1.1639069284048813 | -1.1191 | -26.8464 | 3 | 12 | 11 | 0.58 | 0.20 | - | no | Current |
| 462 | 1.841593328223823 | -0.854383 | -22.2042 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 1.97218672047719 | -1.08105 | -22.5838 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 2.322335104540528 | -0.789116 | -18.7871 | 5 | 12 | 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
-26.846kcal/mol
Ligand efficiency (LE)
-1.0326kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.513
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
398.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
45.24kcal/mol
Minimised FF energy
26.77kcal/mol
SASA & burial
✓ computed
SASA (unbound)
656.9Ų
Total solvent-accessible surface area of free ligand
BSA total
477.1Ų
Buried surface area upon binding
BSA apolar
324.0Ų
Hydrophobic contacts buried
BSA polar
153.2Ų
Polar contacts buried
Fraction buried
72.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1590.0Ų
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
1046.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)