Wall clock time and date at job start Sat Apr 11 2020 06:28:56
AMSOL-version 7.1
by G. D. Hawkins, D. J. Giesen, G. C. Lynch, C. C. Chambers,
I. Rossi, J. W. Storer, J. Li, J. D. Thompson, P. Winget,
B. J. Lynch, D. Rinaldi, D. A. Liotard, C. J. Cramer, and D. G. Truhlar
Copyright 2004 by Regents of the University of Minnesota.
All rights reserved.
Notice: recipients of this code are asked to comply
with the user agreement in Section 1 of the documentation file.
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* 1SCF - SCF CALCULATION WITHOUT GEOMETRY OPTIMIZATION
* - USE EF ROUTINE FOR MINIMUM SEARCH (DEFAULT)
* GEO-OK - OVERRIDE INTERATOMIC DISTANCE CHECK
* TLIMIT= - A TIME OF 15. SECONDS REQUESTED
* CHARGE - CHARGE ON SYSTEM= -1
* AM1 - THE AM1 HAMILTONIAN TO BE USED
* SM5.42R - SM5.42R CALCULATIONS WILL BE PERFORMED
* - CHARGE MODEL 2 WILL BE USED (CM2A)
* - THE SOLVENT IS WATER
*******************************************************************************
Atom NO. Chemical Bond length Bond angle Dihedral angle
number (k) symbol (angstroms) (degrees) (degrees)
(I) NA:I NB:NA:I NC:NB:NA:I NA NB NC
1 1 N
2 2 C 1.31510 * 1
3 3 Si 1.86808 * 120.00004 * 2 1
4 4 H 1.48507 * 109.46863 * 270.00122 * 3 2 1
5 5 H 1.48503 * 109.47027 * 29.99583 * 3 2 1
6 6 H 1.48493 * 109.47012 * 149.99859 * 3 2 1
7 7 C 1.37877 * 120.00219 * 179.97438 * 2 1 3
8 8 H 1.07997 * 119.99499 * 0.02562 * 7 2 1
9 9 C 1.50697 * 120.00040 * 180.02562 * 7 2 1
10 10 C 1.52997 * 109.47071 * 180.02562 * 9 7 2
11 11 C 1.53005 * 109.46994 * 180.02562 * 10 9 7
12 12 N 1.46502 * 109.46811 * 179.97438 * 11 10 9
13 13 S 1.65600 * 119.99813 * 164.99643 * 12 11 10
14 14 O 1.42093 * 106.40487 * 311.46059 * 13 12 11
15 15 O 1.42102 * 106.40228 * 178.53707 * 13 12 11
16 16 C 1.76199 * 107.21715 * 65.00067 * 13 12 11
17 17 C 1.33619 * 125.10105 * 89.72040 * 16 13 12
18 18 C 1.37931 * 115.09182 * 179.79246 * 17 16 13
19 19 C 1.35058 * 114.65174 * 0.49714 * 18 17 16
20 20 C 1.47209 * 125.28618 * 179.73677 * 19 18 17
21 21 C 1.36066 * 126.61076 * 179.97438 * 20 19 18
22 22 N 1.34123 * 107.49369 * 179.97438 * 21 20 19
23 23 C 1.30346 * 108.94162 * 359.97438 * 22 21 20
24 24 O 1.34102 * 109.08332 * 359.75807 * 23 22 21
25 25 S 1.75854 * 125.10195 * 270.02515 * 16 13 12
26 26 H 0.97004 * 120.00096 * 0.02562 * 1 2 3
27 27 H 1.08996 * 109.47522 * 60.00024 * 9 7 2
28 28 H 1.09001 * 109.46964 * 300.00187 * 9 7 2
29 29 H 1.08999 * 109.47496 * 59.99935 * 10 9 7
30 30 H 1.09001 * 109.47095 * 299.99759 * 10 9 7
31 31 H 1.08999 * 109.47179 * 59.99585 * 11 10 9
32 32 H 1.08993 * 109.47007 * 299.99482 * 11 10 9
33 33 H 0.97005 * 120.00395 * 344.99918 * 12 11 10
34 34 H 1.08002 * 122.45194 * 359.97438 * 17 16 13
35 35 H 1.08005 * 122.67330 * 180.23532 * 18 17 16
36 36 H 1.08005 * 126.25056 * 359.95097 * 21 20 19
37 37 H 1.08007 * 125.45761 * 180.02562 * 23 22 21
Note: An asterisk (*) indicates this parameter was or will be optimized.
Cartesian coordinates (angstroms)
NO. Atom X Y Z
1 7 0.0000 0.0000 0.0000
2 6 1.3151 0.0000 0.0000
3 14 2.2491 1.6178 0.0000
4 1 2.4966 2.0465 -1.4002
5 1 1.4465 2.6528 0.7000
6 1 3.5466 1.4402 0.7000
7 6 2.0045 -1.1940 0.0005
8 1 1.4645 -2.1293 0.0005
9 6 3.5115 -1.1940 0.0011
10 6 4.0215 -2.6364 0.0010
11 6 5.5516 -2.6364 0.0022
12 7 6.0399 -4.0176 0.0027
13 16 7.6222 -4.3365 -0.3672
14 8 7.9076 -3.6198 -1.5605
15 8 7.7869 -5.7428 -0.2470
16 6 8.6103 -3.6099 0.8979
17 6 8.9839 -4.2199 2.0265
18 6 9.7619 -3.4581 2.8732
19 6 10.0160 -2.2072 2.4319
20 6 10.8134 -1.1983 3.1483
21 6 11.0865 0.0672 2.7296
22 7 11.8394 0.6506 3.6739
23 6 12.0352 -0.1984 4.6433
24 8 11.4098 -1.3483 4.3520
25 16 9.2463 -1.9707 0.8681
26 1 -0.4850 0.8401 -0.0004
27 1 3.8745 -0.6800 0.8911
28 1 3.8751 -0.6803 -0.8888
29 1 3.6586 -3.1501 -0.8892
30 1 3.6579 -3.1505 0.8908
31 1 5.9142 -2.1228 0.8926
32 1 5.9156 -2.1223 -0.8873
33 1 5.4364 -4.7454 0.2197
34 1 8.7001 -5.2361 2.2574
35 1 10.1344 -3.8307 3.8160
36 1 10.7573 0.5192 1.8056
37 1 12.6058 -0.0051 5.5398
RHF calculation, no. of doubly occupied orbitals= 57
REFERENCES FOR PARAMETERS IN GAS-PHASE HAMILTONIAN:
H: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
C: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
N: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
O: (AM1): M.J.S. DEWAR ET AL, J. AM. CHEM. SOC. 107 3902-3909 (1985)
Si: (AM1): M.J.S.DEWAR, C. JIE, ORGANOMETALLICS, 6, 1486-1490 (1987).
S: (AM1): M.J.S. DEWAR, Y.-C. YUAN, INORGANIC CHEM., 29, 589 (1990)
REFERENCE FOR CHARGE MODEL 2:
J. Li, J. Xing, C. J. Cramer, and D. G. Truhlar, J. Chem. Phys. 111 (1999) 885.
REFERENCE FOR THE PARAMETERIZATION OF THE SM5.42R SOLVATION MODEL:
J. Li, T. Zhu, G. D. Hawkins, P. Winget, D. A. Liotard, C. J. Cramer, and
D. G. Truhlar, Theor. Chem. Acc. 103 (1999) 9-63
P. Winget, J. D. Thompson C. J. Cramer,and D. G. Truhlar, J. Phys. Chem. B. submitted.
CHARGE=-1 AM1 1SCF TLIMIT=15 GEO-OK SM5.42R
& SOLVNT=WATER
ZINC001260000246.mol2 37
1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED
SCF FIELD WAS ACHIEVED
Wall clock time and date at job start Sat Apr 11 2020 06:28:56
Heat of formation + Delta-G solvation = -50.792512 kcal
Electronic energy + Delta-G solvation = -23904.180490 eV
Core-core repulsion = 20093.877588 eV
Total energy + Delta-G solvation = -3810.302902 eV
No. of doubly occupied orbitals = 57
Molecular weight
(most abundant/longest-lived isotopes) = 342.054 amu
Computer time = 0.37 seconds
Orbital eigenvalues (eV)
-44.40885 -39.11628 -38.38788 -37.44282 -37.08280 -35.95205 -35.11994 -33.21483
-32.96916 -29.58084 -28.55273 -26.01423 -24.49641 -23.96992 -23.27255 -22.19204
-21.37272 -20.34134 -19.75938 -18.97634 -18.49573 -18.21828 -17.76721 -17.38964
-17.01419 -16.46613 -16.20565 -16.10478 -15.54248 -15.43316 -14.97510 -14.80454
-14.56453 -14.18985 -14.05085 -13.83537 -13.63484 -13.33274 -13.31354 -13.27227
-12.79293 -12.72783 -12.66758 -12.60784 -12.12541 -11.82079 -11.81392 -11.63769
-11.54281 -11.38379 -11.28793 -10.73065 -10.51997 -9.80212 -9.45644 -8.26224
-6.30270 -1.19621 -0.74885 -0.02269 0.40617 0.43086 1.31697 1.40499
1.41240 1.52831 1.67007 1.68268 1.95424 2.39448 2.58239 3.10019
3.17773 3.36459 3.38223 3.76657 3.98812 4.04885 4.18231 4.25265
4.39678 4.42929 4.52517 4.64277 4.66769 4.83876 4.92497 5.07685
5.09045 5.10697 5.17033 5.55106 5.62495 5.69734 6.02545 6.31710
6.48322 6.78804 7.34485 8.90556
Molecular weight = 342.05amu
Principal moments of inertia in cm(-1)
A = 0.009489 B = 0.003277 C = 0.002588
Principal moments of inertia in units of 10**(-40)*gram-cm**2
A = 2950.017920 B = 8542.837888 C =10818.324195
Net atomic charges, atomic populations, and dipole contributions
calculated with CM2
Atom NO. Type Charge No. of electrons
1 N -0.955 5.955
2 C 0.001 3.999
3 Si 0.948 3.052
4 H -0.268 1.268
5 H -0.288 1.288
6 H -0.238 1.238
7 C -0.531 4.531
8 H 0.033 0.967
9 C -0.016 4.016
10 C -0.102 4.102
11 C 0.113 3.887
12 N -1.104 6.104
13 S 2.738 3.262
14 O -0.979 6.979
15 O -0.971 6.971
16 C -0.809 4.809
17 C 0.019 3.981
18 C -0.143 4.143
19 C -0.090 4.090
20 C -0.007 4.007
21 C -0.011 4.011
22 N -0.520 5.520
23 C 0.210 3.790
24 O -0.197 6.197
25 S 0.274 5.726
26 H 0.265 0.735
27 H 0.029 0.971
28 H 0.023 0.977
29 H 0.058 0.942
30 H 0.066 0.934
31 H 0.081 0.919
32 H 0.080 0.920
33 H 0.429 0.571
34 H 0.182 0.818
35 H 0.175 0.825
36 H 0.198 0.802
37 H 0.305 0.695
For the charges calculated by CM2:
Dipole moment (debyes) X Y Z Total
from point charges 28.116 -5.063 10.055 30.286
Note: The Mulliken population analysis charges presented below were not
used in the solvation calculation but are provided for completeness.
The chosen solvation model uses CM2 partial charges for calculating
solvation energies.
Net atomic charges, atomic populations, and dipole contributions
using Mulliken population analysis
Atom NO. Type Charge No. of electrons
1 N -0.596 5.596
2 C -0.195 4.195
3 Si 0.771 3.229
4 H -0.193 1.193
5 H -0.214 1.214
6 H -0.161 1.161
7 C -0.569 4.569
8 H 0.051 0.949
9 C -0.054 4.054
10 C -0.141 4.141
11 C -0.013 4.013
12 N -0.867 5.867
13 S 2.825 3.175
14 O -0.969 6.969
15 O -0.961 6.961
16 C -1.011 5.011
17 C -0.016 4.016
18 C -0.174 4.174
19 C -0.210 4.210
20 C -0.061 4.061
21 C -0.152 4.152
22 N -0.247 5.247
23 C -0.015 4.015
24 O -0.085 6.085
25 S 0.543 5.457
26 H 0.074 0.926
27 H 0.048 0.952
28 H 0.042 0.958
29 H 0.077 0.923
30 H 0.085 0.915
31 H 0.099 0.901
32 H 0.098 0.902
33 H 0.266 0.734
34 H 0.200 0.800
35 H 0.193 0.807
36 H 0.214 0.786
37 H 0.319 0.681
Dipole moment (debyes) X Y Z Total
from point charges 28.545 -3.474 8.237 29.912
hybrid contribution -0.720 -0.985 1.606 2.017
sum 27.825 -4.460 9.843 29.850
Atomic orbital electron populations
1.70075 1.08441 1.28098 1.52937 1.26046 0.95584 1.03656 0.94250
0.85696 0.79820 0.78158 0.79242 1.19306 1.21399 1.16129 1.21515
0.92278 0.93070 1.50052 0.94875 1.19538 0.93812 0.94785 0.97286
1.21497 0.92438 0.97979 1.02181 1.21503 0.96198 0.80746 1.02818
1.55262 1.27505 1.15618 1.88292 1.00442 0.72058 0.72323 0.72693
1.93578 1.84601 1.75013 1.43700 1.93569 1.85869 1.29613 1.87053
1.35936 1.29500 1.11630 1.24080 1.20135 0.91105 1.01466 0.88845
1.20841 1.01354 0.92059 1.03176 1.22347 1.02677 0.96483 0.99522
1.20179 1.03197 0.95660 0.87095 1.23770 0.99287 0.90906 1.01245
1.70424 1.17519 1.33495 1.03236 1.29486 0.94568 0.76708 1.00731
1.84546 1.52510 1.39955 1.31453 1.84259 1.43873 1.06225 1.11296
0.92620 0.95225 0.95833 0.92348 0.91549 0.90109 0.90213 0.73356
0.80044 0.80719 0.78554 0.68052
Number of geometries 1
Number of calculations of the screened coulomb radii 1
The total number of SCF iterations 15.
Note: The number of geometries may not
correspond to the number of cycles due to rejected geometry changes.
In the following table subtotal= G_P + SS G_CDS.
Atom Chem. CM2 G_P Area Sigma k SS G_CDS Subtotal M
number symbol chg. (kcal) (Ang**2) cal/(Ang**2) (kcal) (kcal) value
1 N -0.95 -59.47 13.96 21.45 0.30 -59.17 16
2 C 0.00 0.06 5.47 84.66 0.46 0.52 16
3 Si 0.95 42.97 27.47 68.60 1.88 44.86 16
4 H -0.27 -11.75 7.11 99.48 0.71 -11.05 16
5 H -0.29 -12.97 7.11 99.48 0.71 -12.27 16
6 H -0.24 -9.69 6.54 99.48 0.65 -9.04 16
7 C -0.53 -29.65 9.66 25.60 0.25 -29.40 16
8 H 0.03 2.04 7.99 -2.91 -0.02 2.01 16
9 C -0.02 -0.69 4.04 29.85 0.12 -0.57 16
10 C -0.10 -3.48 5.29 30.59 0.16 -3.32 16
11 C 0.11 2.98 6.22 86.38 0.54 3.52 16
12 N -1.10 -24.75 6.00 -187.49 -1.12 -25.88 16
13 S 2.74 64.81 5.88 -56.49 -0.33 64.47 16
14 O -0.98 -28.99 17.37 -128.00 -2.22 -31.21 16
15 O -0.97 -25.89 17.80 -128.00 -2.28 -28.16 16
16 C -0.81 -16.25 6.54 66.77 0.44 -15.81 16
17 C 0.02 0.31 9.82 21.15 0.21 0.52 16
18 C -0.14 -2.19 10.10 21.46 0.22 -1.97 16
19 C -0.09 -1.60 6.42 23.90 0.15 -1.44 16
20 C -0.01 -0.11 7.18 24.12 0.17 0.06 16
21 C -0.01 -0.19 11.67 83.84 0.98 0.79 16
22 N -0.52 -8.81 11.27 -314.75 -3.55 -12.35 16
23 C 0.21 2.11 13.22 130.46 1.72 3.83 16
24 O -0.20 -2.83 10.80 -9.33 -0.10 -2.93 16
25 S 0.27 5.27 22.97 -56.49 -1.30 3.97 16
26 H 0.27 15.43 8.31 -92.71 -0.77 14.66 16
27 H 0.03 1.22 7.20 -2.39 -0.02 1.20 16
28 H 0.02 0.98 7.57 -2.39 -0.02 0.96 16
29 H 0.06 2.06 8.14 -2.39 -0.02 2.04 16
30 H 0.07 2.20 8.14 -2.39 -0.02 2.19 16
31 H 0.08 1.84 8.14 -2.39 -0.02 1.82 16
32 H 0.08 2.11 7.75 -2.39 -0.02 2.09 16
33 H 0.43 8.16 8.65 -96.74 -0.84 7.32 16
34 H 0.18 2.11 8.05 -2.91 -0.02 2.09 16
35 H 0.18 1.87 8.06 -2.91 -0.02 1.84 16
36 H 0.20 2.82 8.06 -2.91 -0.02 2.79 16
37 H 0.30 -0.66 8.06 -2.91 -0.02 -0.68 16
Total: -1.00 -78.62 354.02 -3.07 -81.70
By element:
Atomic # 1 Polarization: 7.76 SS G_CDS: 0.23 Total: 7.99 kcal
Atomic # 6 Polarization: -48.69 SS G_CDS: 5.42 Total: -43.27 kcal
Atomic # 7 Polarization: -93.03 SS G_CDS: -4.37 Total: -97.40 kcal
Atomic # 8 Polarization: -57.71 SS G_CDS: -4.60 Total: -62.31 kcal
Atomic # 14 Polarization: 42.97 SS G_CDS: 1.88 Total: 44.86 kcal
Atomic # 16 Polarization: 70.08 SS G_CDS: -1.63 Total: 68.45 kcal
Total: -78.62 -3.07 -81.70 kcal
The number of atoms in the molecule is 37
The average number of expansion shells was 16.00
The maximum number of expansion shells was 16
The minimum number of expansion shells was 16
**** NOTA BENE ****
This is the net solvation energy for this exact molecular structure
(nuclear and electronic)! The standard-state solvation energy should be
obtained as the difference between the heat of formation plus delta-G solvation
for the relaxed solvated system and that for the relaxed gas-phase system.
ZINC001260000246.mol2 37
1SCF run
This is a breakdown of the solvation energy calculated
without geometric relaxation in solution:
(1) E-EN(sol) electronic-nuclear energy of solute 30.903 kcal
(2) G-P(sol) polarization free energy of solvation -78.624 kcal
(3) G-ENP(sol) elect.-nuc.-pol. free energy of system -47.722 kcal
(4) G-CDS(sol) cavity-dispersion-solvent structure free energy -3.071 kcal
(5) G-P-CDS(sol) = G-P(sol) + G-CDS(sol) = (2) + (4) -81.695 kcal
(6) G-S(sol) free energy of system = (1) + (5) -50.793 kcal
1SCF WAS SPECIFIED, SO GEOMETRY OPTIMIZATION WAS NOT USED
Total computer time = 0.37 seconds