When I open the simple .xyz file:
2
Test NO molecule
N 0.0 0.5685 0.0
O 0.0 -0.5685 0.0
with IQmol and use the “Translate To Center” tool and open the QChem set up window, it shifts the coordinates to
$molecule
0 2
N 0.0000000 0.6064000 0.0000000
O 0.0000000 -0.5306000 0.0000000
$end
If I calculate the CoM myself and shift the molecule accordingly using the IUPAC average atomic masses (2023 Atomic Weights, N = 14.007, 15.999), I get that the N atom should be a distance of 0.60625 away from the origin. If I use the most common isotope masses (N = 14.003, O = 15.995), I get 0.60624.
After rounding for significant digits, I get either 0.6063 or 0.6062. Why is IQmol giving 0.6064?
This is a small example and small difference but I am trying to understand some discrepancies I am finding for larger, more complex systems. For example, I have translated this molecule
28
DPP-2T, translated to CM (average masses)
C -1.606120 1.904536 0.185881
C -2.009744 0.593827 0.089622
C -0.200620 2.041485 0.176647
C 0.456413 0.836753 0.076801
C 1.882187 0.615699 0.055681
C 4.140265 1.247639 0.062340
C 4.008270 -0.213228 0.014639
C 2.607420 -0.542360 0.009152
C 2.468565 -1.993216 -0.031153
C 4.714647 -1.368318 -0.018754
C -3.372619 0.072749 0.076959
C -3.818184 -1.142534 0.524814
C -5.221517 -1.313702 0.356215
C -5.816020 -0.228180 -0.213718
S -0.665275 -0.489442 -0.027171
S -4.680060 1.018157 -0.570308
N 2.785127 1.673284 0.089146
N 3.819989 -2.425233 -0.045218
H 0.305161 2.999894 0.258386
H 4.065727 -3.404803 -0.077973
H 2.544030 2.654079 0.102371
H -2.298890 2.735468 0.284571
H 5.784505 -1.542090 -0.025200
H -3.163473 -1.881981 0.978953
H -5.764685 -2.205274 0.654199
H -6.864789 -0.090239 -0.450708
O 5.090845 1.994114 0.077656
O 1.504148 -2.732699 -0.052343
manually to its center of mass. When I use the “Translate to Center” tool the coordinates change rather significantly to:
$molecule
0 1
C -1.5897281 1.9070096 0.1802596
C -1.9933521 0.5963006 0.0840006
C -0.1842281 2.0439586 0.1710256
C 0.4728049 0.8392266 0.0711796
C 1.8985789 0.6181726 0.0500596
C 4.1566569 1.2501126 0.0567186
C 4.0246619 -0.2107544 0.0090176
C 2.6238119 -0.5398864 0.0035306
C 2.4849569 -1.9907424 -0.0367744
C 4.7310389 -1.3658444 -0.0243754
C -3.3562271 0.0752226 0.0713376
C -3.8017921 -1.1400604 0.5191926
C -5.2051251 -1.3112284 0.3505936
C -5.7996281 -0.2257064 -0.2193394
S -0.6488831 -0.4869684 -0.0327924
S -4.6636681 1.0206306 -0.5759294
N 2.8015189 1.6757576 0.0835246
N 3.8363809 -2.4227594 -0.0508394
H 0.3215529 3.0023676 0.2527646
H 4.0821189 -3.4023294 -0.0835944
H 2.5604219 2.6565526 0.0967496
H -2.2824981 2.7379416 0.2789496
H 5.8008969 -1.5396164 -0.0308214
H -3.1470811 -1.8795074 0.9733316
H -5.7482931 -2.2028004 0.6485776
H -6.8483971 -0.0877654 -0.4563294
O 5.1072369 1.9965876 0.0720346
O 1.5205399 -2.7302254 -0.0579644
$end