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
25.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.65, Jaccard 0.58, H-bond role recall 0.33
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.662 kcal/mol/HA)
✓ Good fit quality (FQ -6.73)
✓ Good H-bonds (5 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (25.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-23.838
kcal/mol
LE
-0.662
kcal/mol/HA
Fit Quality
-6.73
FQ (Leeson)
HAC
36
heavy atoms
MW
487
Da
LogP
4.95
cLogP
Interaction summary
HB 5
HY 22
PI 1
CLASH 3
Interaction summary
HB 5
HY 22
PI 1
CLASH 3
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 | 4.018 | Score | -23.838 |
|---|---|---|---|
| Inter norm | -0.810 | Intra norm | 0.147 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 16 clashes; 2 protein clashes; 2 cofactor-context clashes; moderate strain Δ 25.8 | ||
| Residues |
ARG17
ASP232
HIS241
LEU188
LEU229
MET233
NDP302
PHE113
PRO115
TYR114
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 | 11 | Native recall | 0.65 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 196 | 1.7019758963377631 | -0.730653 | -21.3575 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 360 | 2.9347810964604713 | -0.848876 | -24.4387 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 274 | 3.7376633077853794 | -0.6017 | -16.0766 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 249 | 3.875488679018085 | -0.721187 | -22.5888 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 228 | 4.017761737308767 | -0.809853 | -23.8385 | 5 | 13 | 11 | 0.65 | 0.33 | - | no | Current |
| 216 | 4.031433399399227 | -0.748275 | -22.4575 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 175 | 5.581316289847065 | -0.820513 | -24.5642 | 13 | 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
-23.838kcal/mol
Ligand efficiency (LE)
-0.6622kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.730
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
486.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.95
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
140.06kcal/mol
Minimised FF energy
114.30kcal/mol
SASA & burial
✓ computed
SASA (unbound)
786.0Ų
Total solvent-accessible surface area of free ligand
BSA total
553.2Ų
Buried surface area upon binding
BSA apolar
441.0Ų
Hydrophobic contacts buried
BSA polar
112.2Ų
Polar contacts buried
Fraction buried
70.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1791.6Ų
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
1043.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)