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 medium
Native strong
SASA done
Strain ΔE
32.8 kcal/mol
Protein clashes
3
Internal clashes
5
Native overlap
contact recall 0.59, Jaccard 0.53, H-bond role recall 0.50
Reason: no major geometry red flags detected
3 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.200 kcal/mol/HA)
✓ Good fit quality (FQ -11.06)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (32.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-31.209
kcal/mol
LE
-1.200
kcal/mol/HA
Fit Quality
-11.06
FQ (Leeson)
HAC
26
heavy atoms
MW
350
Da
LogP
2.71
cLogP
Interaction summary
HB 6
HY 20
PI 2
CLASH 5
Interaction summary
HB 6
HY 20
PI 2
CLASH 5
| Final rank | 2.630 | Score | -31.209 |
|---|---|---|---|
| Inter norm | -1.145 | Intra norm | -0.056 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 6 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; 1 severe cofactor-context clash; high strain Δ 32.8 | ||
| Residues |
ARG17
HIS241
LEU188
LEU226
LEU229
NDP302
PHE113
SER111
SER112
TYR114
TYR194
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 | 10 | Native recall | 0.59 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 4 | Strict recall | 0.57 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 619 | 1.3467696206102813 | -0.991354 | -27.6349 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 1.6273533240198839 | -0.996887 | -27.9479 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 609 | 2.417857911312347 | -1.02629 | -28.7645 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 2.630175173364487 | -1.14452 | -31.2089 | 6 | 12 | 10 | 0.59 | 0.50 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.209kcal/mol
Ligand efficiency (LE)
-1.2003kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.059
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
350.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.71
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-116.07kcal/mol
Minimised FF energy
-148.85kcal/mol
SASA & burial
✓ computed
SASA (unbound)
623.5Ų
Total solvent-accessible surface area of free ligand
BSA total
486.1Ų
Buried surface area upon binding
BSA apolar
386.0Ų
Hydrophobic contacts buried
BSA polar
100.1Ų
Polar contacts buried
Fraction buried
78.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1637.3Ų
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
1063.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)