O S O O N N H + N H N N O N
Ligand: Ligand from 1XP0(A) > VDN(A-201) Reference receptor: 2CHM(A)

Rank: 1
IFP Score: 2.7
# clusters: 1
Selected Traj ClusID: 0
Major Clusters (> 5% of trajectory)
Cluster Size <MMPBSA>a,b <iBintScore>a
0 98% -52.1 ± 0.2 -46.4 ± 0.5
Otherc 2% -52.9 ± 1.1 -46.8 ± 4.7
aEnsemble average ± 2*StdErr. bkcal/mol. c"Other" includes Minor clusters as well as Outliers from the clustering.

Clustering Details:
- 500 frames aligned by active site Cαs
- Ligand RMSD clustering with DBSCAN
- Produced 2 clusters with 3 Outliers
- 1 Major cluster (>5% of trajectory)

IFP Step2 MD Results Summary

Interactions O S O O N N H + N H N N O N TYR 612A HIS 613A HIS 617A LEU 725A ASP 764A LEU 765A ALA 767A ILE 768A GLN 775A ILE 778A ALA 779A VAL 782A ALA 783A PHE 786A LEU 804A ILE 813A MET 816A GLN 817A PHE 820A ILE 824A 2nd 501th 59.6% 74.8% 91.2% 8.2% 91.6% 8.0% 50.8% 13.2% Legend side-chain backbone & side-chain ligand acceptor ligand donor contact only stacking Residue Styles Interaction Styles Legend Torsion Fluctuation 0 45 90 135 180 225 270 315 O S O O N N H + N H N N O N TYR 612A HIS 613A HIS 617A LEU 725A ASP 764A LEU 765A ALA 767A ILE 768A GLN 775A ILE 778A ALA 779A VAL 782A ALA 783A PHE 786A LEU 804A ILE 813A MET 816A GLN 817A PHE 820A ILE 824A Legend rigid flexible Legend B-factor O S O O N N H + N H N N O N TYR 612A HIS 613A HIS 617A LEU 725A ASP 764A LEU 765A ALA 767A ILE 768A GLN 775A ILE 778A ALA 779A VAL 782A ALA 783A PHE 786A LEU 804A ILE 813A MET 816A GLN 817A PHE 820A ILE 824A 0.0 10.0 25.0 50.0 100.0 26.70 Contact Map O S O O N N H + N H N N O N TYR 612A HIS 613A HIS 617A LEU 725A ASP 764A LEU 765A ALA 767A ILE 768A GLN 775A ILE 778A ALA 779A VAL 782A ALA 783A PHE 786A LEU 804A ILE 813A MET 816A GLN 817A PHE 820A ILE 824A
Interactions O S O O N N H + N H N N O N TYR 612A HIS 613A HIS 617A LEU 725A ASP 764A LEU 765A ALA 767A ILE 768A GLN 775A ILE 778A ALA 779A VAL 782A ALA 783A PHE 786A LEU 804A ILE 813A MET 816A GLN 817A PHE 820A ILE 824A 2nd 493th 59.6% 74.6% 91.3% 8.1% 92.1% 7.5% 50.8% 12.8% Legend side-chain backbone & side-chain ligand acceptor ligand donor contact only stacking Residue Styles Interaction Styles Legend Torsion Fluctuation 0 45 90 135 180 225 270 315 O S O O N N H + N H N N O N TYR 612A HIS 613A HIS 617A LEU 725A ASP 764A LEU 765A ALA 767A ILE 768A GLN 775A ILE 778A ALA 779A VAL 782A ALA 783A PHE 786A LEU 804A ILE 813A MET 816A GLN 817A PHE 820A ILE 824A Legend rigid flexible Legend B-factor O S O O N N H + N H N N O N TYR 612A HIS 613A HIS 617A LEU 725A ASP 764A LEU 765A ALA 767A ILE 768A GLN 775A ILE 778A ALA 779A VAL 782A ALA 783A PHE 786A LEU 804A ILE 813A MET 816A GLN 817A PHE 820A ILE 824A 0.0 10.0 25.0 50.0 100.0 26.67 Contact Map O S O O N N H + N H N N O N TYR 612A HIS 613A HIS 617A LEU 725A ASP 764A LEU 765A ALA 767A ILE 768A GLN 775A ILE 778A ALA 779A VAL 782A ALA 783A PHE 786A LEU 804A ILE 813A MET 816A GLN 817A PHE 820A ILE 824A
O S O O N N H + N H N N O N TYR 612A HIS 617A LEU 725A ASP 764A ALA 767A ILE 768A GLN 775A ILE 778A ALA 779A VAL 782A PHE 786A LEU 804A ILE 813A MET 816A GLN 817A PHE 820A Legend backbone side-chain backbone & side-chain ligand acceptor ligand donor contact only stacking Residue Styles Interaction Styles Legend

Ligand Clustering based on Active Site Alignment


Cluster membership of ligand by Trajectory frame

2023-06-15T03:28:13.709899 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Trajectory Active Site Side Chain RMSD to the Input Reference Receptor

2023-06-15T04:09:04.285073 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/

Trajectory Active Site Side Chain TFD to the Input Reference Receptor

2023-06-15T04:09:04.623235 image/svg+xml Matplotlib v3.3.2, https://matplotlib.org/


Cluster Results by Starting Pose


How much time did each starting pose's trajectory spend in each major cluster?
How close is each ligand cluster to each starting pose?


Cluster RMSD AS SC RMSD AS SC TFD Cluster Percent Cluster 0 1.40 ± 0.01 Å 1.30 ± 0.03 Å 0.12 ± 0.00 98% Other 1.70 ± 0.09 Å 1.02 ± 0.25 Å 0.13 ± 0.01 2%

This Table tells us (1) how far each major cluster pose lies from each starting pose by computing the ensemble average RMSD (in Å) between them; and (2) the active site side chain RMSD and the TFD (torsion fingerprint deviation) of each major cluster protein from the input reference receptor. The "Other" category includes minor clusters as well as Outliers from the clustering.