4-(4-methyl-piperazin-1-ylmethyl)-n-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-benzamide (STI) Summary

METADATA
Parameter Value
Method HamiltonianREMD
Number of MD replicas 16
Length of the MD simulations (ns) 10
Number of steps between exchanges 100
Force Field General Amber Force Field (GAFF)
Charge scheme Semi-Empirical (AM1)
REMD Progression Geometric Progression
Initial (low) temperature (K) / Scaling factor 298 / 1
Final (high) temperature (K) / Scaling factor 498 / 0.59
Molecule number of atoms 69
Molecule charge (simulated) 1
System number of atoms 3078
Box size in simulations (nm) 0.8
Solvent model TIP3P
Box type in simulations Octahedron
MD ensemble NVT
0
1-2 2-3 3-4 4-5 5-6 6-7 7-8 8-9 9-10 10-11 11-12 12-13 13-14 14-15 15-16
Probabilities 0.81 0.81 0.81 0.82 0.82 0.82 0.83 0.83 0.84 0.83 0.84 0.84 0.84 0.84 0.84
# Exchanges 4050 4050 4092 4083 4069 4138 4132 4153 4168 4176 4199 4178 4209 4194 4171
Avg. # Exchanges 0.81 0.81 0.82 0.82 0.81 0.83 0.83 0.83 0.83 0.84 0.84 0.84 0.84 0.84 0.83
RMSd Averages
Reduced chart version
Name Average (Å) Standard deviation (Å)
RMSd_first 2.6363 0.8374
RMSd_exp 2.3728 0.5889
RMSdist_first 1.9023 0.8669
RMSdist_exp 1.5459 0.6779
RMSd Plot
Rgyr Averages
Reduced chart version
Name Average (Å) Standard deviation (Å)
Rgyr 5.9316 0.4394
RgyrX 3.9468 0.1479
RgyrY 5.4368 0.4873
RgyrZ 5.0028 0.5743
Rgyr Plot
Fluctuation Averages
Name Atomic_Fluct
Average (Å) 1.6441
Standard deviation (Å) 0.7848
Atoms list
Atom name Fluctuation (Å)
C 3.151
C1 2.256
C2 1.489
C3 2.377
N 3.329
C4 3.524
C5 0.898
C6 1.732
C7 2.554
N1 2.275
C8 1.125
N2 0.713
N3 0.98
C9 0.651
C10 0.68
C11 0.935
C12 0.954
C13 0.71
C14 0.664
N4 0.842
C15 1.281
C16 1.21
C17 1.701
C18 1.763
C19 1.356
C20 1.768
C21 1.722
C22 1.56
N5 0.901
C23 1.529
C24 2.22
N6 2.342
C25 2.806
C26 2.245
C27 1.552
O 2.182
C28 0.853
3D View
Fluctuation Plot