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
19.6 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.65, Jaccard 0.50, H-bond role recall 0.33
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.111 kcal/mol/HA)
✓ Good fit quality (FQ -10.10)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (61%)
✗ Moderate strain (19.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-27.781
kcal/mol
LE
-1.111
kcal/mol/HA
Fit Quality
-10.10
FQ (Leeson)
HAC
25
heavy atoms
MW
404
Da
LogP
0.56
cLogP
Interaction summary
HB 10
HY 16
PI 2
CLASH 3
Interaction summary
HB 10
HY 16
PI 2
CLASH 3
| Final rank | 4.145 | Score | -27.781 |
|---|---|---|---|
| Inter norm | -1.239 | Intra norm | 0.128 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 10 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes; 2 cofactor-context clashes | ||
| Residues |
ALA182
ARG17
ASP181
GLY225
LEU188
LEU226
LEU229
MET183
NDP302
PHE113
SER111
SER112
TYR114
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 | 0.50 | RMSD | - |
| HB strict | 1 | Strict recall | 0.14 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 501 | 1.406540502809502 | -0.776521 | -15.751 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 531 | 1.7669910686618124 | -0.828226 | -19.6464 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 555 | 2.019091271852642 | -0.95225 | -18.4019 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 473 | 4.144549198167141 | -1.23926 | -27.7812 | 10 | 16 | 11 | 0.65 | 0.33 | - | no | Current |
| 504 | 4.245746357076541 | -1.0618 | -22.9763 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 4.7802568935273655 | -0.954752 | -21.8921 | 11 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 487 | 6.7556041603467545 | -1.17079 | -25.4634 | 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
-27.781kcal/mol
Ligand efficiency (LE)
-1.1112kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.102
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
403.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.56
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-185.66kcal/mol
Minimised FF energy
-205.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
611.2Ų
Total solvent-accessible surface area of free ligand
BSA total
523.1Ų
Buried surface area upon binding
BSA apolar
318.8Ų
Hydrophobic contacts buried
BSA polar
204.3Ų
Polar contacts buried
Fraction buried
85.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1512.4Ų
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
1066.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)