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 mixed
SASA done
Strain ΔE
35.2 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.40
Reason: 8 internal clashes
8 protein-contact clashes
8 intramolecular clashes
55% of hydrophobic surface appears solvent-exposed (12/22 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 (-0.685 kcal/mol/HA)
✓ Good fit quality (FQ -6.54)
✓ Good H-bonds (3 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Very high strain energy (35.2 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (10)
✗ Many internal clashes (16)
Score
-19.861
kcal/mol
LE
-0.685
kcal/mol/HA
Fit Quality
-6.54
FQ (Leeson)
HAC
29
heavy atoms
MW
380
Da
LogP
3.75
cLogP
Final rank
2.5020
rank score
Inter norm
-0.824
normalised
Contacts
13
H-bonds 7
Interaction summary
HBA 3
HY 4
PI 0
CLASH 8
Interaction summary
HBA 3
HY 4
PI 0
CLASH 8
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
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: permissive.
| 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 | 8 | Native recall | 0.53 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 421 | 1.5107380157589754 | -1.19651 | -31.5511 | 12 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 392 | 2.0393466344051294 | -1.14197 | -32.3388 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 422 | 2.5020325984158265 | -0.824247 | -19.8611 | 7 | 13 | 8 | 0.53 | 0.40 | - | no | Current |
| 384 | 2.5226772709928533 | -1.15055 | -33.5848 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 448 | 2.9849378761319296 | -0.983949 | -31.4423 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 438 | 3.4416752268468827 | -1.00556 | -28.7569 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 510 | 4.634483626967154 | -0.856266 | -26.3288 | 4 | 10 | 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
-19.861kcal/mol
Ligand efficiency (LE)
-0.6849kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.538
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
380.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.75
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.20kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
128.93kcal/mol
Minimised FF energy
93.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
635.8Ų
Total solvent-accessible surface area of free ligand
BSA total
499.7Ų
Buried surface area upon binding
BSA apolar
428.6Ų
Hydrophobic contacts buried
BSA polar
71.1Ų
Polar contacts buried
Fraction buried
78.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2499.7Ų
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
1394.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)