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 high
Native mixed
SASA done
Strain ΔE
20.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.38, H-bond role recall 0.20
Reason: no major geometry red flags detected
2 protein-contact clashes
100% of hydrophobic surface is solvent-exposed (18/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.005 kcal/mol/HA)
✓ Good fit quality (FQ -9.26)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ High strain energy (20.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-26.127
kcal/mol
LE
-1.005
kcal/mol/HA
Fit Quality
-9.26
FQ (Leeson)
HAC
26
heavy atoms
MW
390
Da
LogP
4.00
cLogP
Interaction summary
HB 6
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
Interaction summary
HB 6
HY 0
PI 0
CLASH 2
⚠ Exposure 100%
Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (18/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 18
Buried (contacted) 0
Exposed 18
LogP 4.0
H-bonds 6
Exposed fragments:
phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 1.839 | Score | -26.127 |
|---|---|---|---|
| Inter norm | -1.060 | Intra norm | 0.055 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; moderate strain Δ 20.6 | ||
| Residues |
ALA283
ARG242
ARG337
ARG50
ASP243
ASP385
ASP44
ASP47
GLU384
LEU339
PHE383
SER282
THR241
VAL336
| ||
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
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 | 8 | Native recall | 0.53 |
| Jaccard | 0.38 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | -0.2908267176309925 | -1.19073 | -29.6003 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 1.8386052021954522 | -1.05981 | -26.1272 | 6 | 14 | 8 | 0.53 | 0.20 | - | no | Current |
| 549 | 1.9584098801368803 | -1.07383 | -29.3381 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 560 | 2.428087883165567 | -0.799576 | -24.0181 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 552 | 2.7941902960594462 | -0.966006 | -17.0384 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 3.472283433281198 | -1.06233 | -28.3109 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 516 | 3.8612649837231396 | -1.20279 | -31.5508 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 526 | 4.287644089881446 | -1.23726 | -27.9603 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 530 | 5.1552079225695575 | -1.06931 | -25.3885 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 550 | 5.633262955142708 | -1.10654 | -23.6606 | 16 | 15 | 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
-26.127kcal/mol
Ligand efficiency (LE)
-1.0049kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.258
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
389.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.00
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.70kcal/mol
Minimised FF energy
32.06kcal/mol
SASA & burial
✓ computed
SASA (unbound)
589.2Ų
Total solvent-accessible surface area of free ligand
BSA total
455.6Ų
Buried surface area upon binding
BSA apolar
331.6Ų
Hydrophobic contacts buried
BSA polar
124.1Ų
Polar contacts buried
Fraction buried
77.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2371.0Ų
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
1401.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)