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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
53.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.80, Jaccard 0.57, H-bond role recall 0.40
Reason: strain 53.5 kcal/mol
strain ΔE 53.5 kcal/mol
1 protein-contact clashes
37% of hydrophobic surface appears solvent-exposed (10/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.464 kcal/mol/HA)
✓ Good fit quality (FQ -4.71)
✓ Good H-bonds (4 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Extreme strain energy (53.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-16.691
kcal/mol
LE
-0.464
kcal/mol/HA
Fit Quality
-4.71
FQ (Leeson)
HAC
36
heavy atoms
MW
499
Da
LogP
1.32
cLogP
Final rank
3.8458
rank score
Inter norm
-0.612
normalised
Contacts
18
H-bonds 5
Interaction summary
HBD 3
HBA 1
HY 5
PI 0
CLASH 1
Interaction summary
HBD 3
HBA 1
HY 5
PI 0
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 12 | Native recall | 0.80 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
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:ORX602
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 314 | 1.8403910590171513 | -0.854739 | -30.533 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 265 | 3.2535200232590507 | -0.957853 | -29.2182 | 11 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 236 | 3.7004113748811287 | -0.679853 | -25.4528 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 273 | 3.8458234271104295 | -0.611894 | -16.691 | 5 | 18 | 12 | 0.80 | 0.40 | - | no | Current |
| 276 | 3.866792565577019 | -0.639361 | -14.0366 | 8 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 196 | 4.975403539515579 | -0.770765 | -16.315 | 12 | 20 | 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
-16.691kcal/mol
Ligand efficiency (LE)
-0.4636kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.712
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
498.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.32
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
53.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
75.65kcal/mol
Minimised FF energy
22.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
851.2Ų
Total solvent-accessible surface area of free ligand
BSA total
603.3Ų
Buried surface area upon binding
BSA apolar
519.1Ų
Hydrophobic contacts buried
BSA polar
84.2Ų
Polar contacts buried
Fraction buried
70.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2701.2Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1368.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)