Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
21.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.71, Jaccard 0.71, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.742 kcal/mol/HA)
✓ Good fit quality (FQ -6.92)
✓ Good H-bonds (5 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ High strain energy (21.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-20.030
kcal/mol
LE
-0.742
kcal/mol/HA
Fit Quality
-6.92
FQ (Leeson)
HAC
27
heavy atoms
MW
389
Da
LogP
1.65
cLogP
Interaction summary
HB 5
HY 18
PI 2
CLASH 1
Interaction summary
HB 5
HY 18
PI 2
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 | 2.800 | Score | -20.030 |
|---|---|---|---|
| Inter norm | -1.060 | Intra norm | 0.318 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes; 1 severe cofactor-context clash; moderate strain Δ 21.9 | ||
| Residues |
ARG17
HIS241
LEU188
LEU229
MET233
NDP302
PHE113
SER111
SER227
TYR191
TYR194
VAL230
| ||
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.71 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 382 | 1.1856817848753087 | -1.2299 | -36.6954 | 12 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 410 | 1.5492191472670493 | -1.06094 | -32.6346 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 431 | 1.6558929653522128 | -0.885977 | -23.8179 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 392 | 1.7134426677175625 | -1.06546 | -26.3867 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 346 | 2.08459079571292 | -1.28056 | -31.9367 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 331 | 2.799827702615812 | -1.05953 | -20.0297 | 5 | 12 | 12 | 0.71 | 0.33 | - | no | Current |
| 363 | 2.9071394399987356 | -1.09378 | -35.5375 | 7 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 392 | 3.4571126202015106 | -1.01023 | -31.045 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 374 | 4.317628293699705 | -0.87843 | -27.1637 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 4.388836339845029 | -1.195 | -30.9661 | 12 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 359 | 5.916636608464641 | -1.03551 | -21.5961 | 9 | 18 | 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
-20.030kcal/mol
Ligand efficiency (LE)
-0.7418kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.921
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
389.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.65
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.92kcal/mol
Minimised FF energy
14.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
662.2Ų
Total solvent-accessible surface area of free ligand
BSA total
515.1Ų
Buried surface area upon binding
BSA apolar
338.4Ų
Hydrophobic contacts buried
BSA polar
176.7Ų
Polar contacts buried
Fraction buried
77.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1627.3Ų
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
1024.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)