MOPAC output example from Molecular Modeling Pro and MMP+

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Figure 1. Starting geometry for fluoxetine, the molecule used in the following example.  After the molecule is drawn in, go to the Tools menu and select "MOPAC".  

 

Atom types supported by MOPAC v. 6 methods:

MNDO: H, Li, Be, B, C, N, O, F, Na, Al, Si, P, S, Cl, K, Cr, Zn, Ge, Br, Sn, I, Hg, Pb

MINDO: H, C, N, O, F, P, S, Cl

AM1: H, B, C, N, O, F, Na, Al, Si, P, S, Cl, K, Zn, Ge, Br, I, Hg

PM3: H, C, N, O, F, Na, Mg, Al, Si, P, S, Cl, K, Zn, Ga, Ge, As, Se, Br, Cd, In, Sn, Sb, Te, I, Hg, Tl, Pb, Bi

 

 

 

 

Figure 2.  The MOPAC options panel.  In this example we have checked the PM3 and Force options.  If the keyword does not appear in the checkboxes, type it into the "Other options" text box.  Hit Done after you have selected options.

 

ROT = :  C1 CI CS = 1; C2 C2V C2H = 2; C3 C3V C3H = 3; C4 C4V C4H = 4; C6 C6V C6H = 6; D2 D2D D2H = 4; D3 D3D D3H = 6; D4 D4D D4H = 8; D6 D6D D6H =12; S6 = 3; C(INF)V =1 ; D(INF)H =2; T TD =12; OH = 24.  ROT = the rotational contributions to the thermodynamic quantities of the symmetry number of the molecule.  The symmetry number is the number of equivalent positions attainable by pure rotation.  No reflections or improper rotations are allowed.

 

THEMO (Thermodynamics) calculations require the FORCE and ROT keywords.

 

 

 

 

 

**   32-bit Microsoft Windows, Victor Lobanov, 1996, University of Florida   **

 **     max number of heavy atoms =  50, max number of light atoms = 100      **

 *******************************************************************************

 

                                 PM3 CALCULATION RESULTS

 

 

 *******************************************************************************

 *          MOPAC:  VERSION  6.00               CALC'D.                        

 *   T=      - A TIME OF  3600.0 SECONDS REQUESTED

 *  DUMP=N   - RESTART FILE WRITTEN EVERY  3600.0 SECONDS

 *  FORCE    - FORCE CALCULATION SPECIFIED

 *  PM3      - THE PM3 HAMILTONIAN TO BE USED

 ***********************************************************************050BY100

 PM3   FORCE  T=3600

 fluoxetine

 MOPAC calculations:

 

    ATOM   CHEMICAL  BOND LENGTH    BOND ANGLE     TWIST ANGLE

   NUMBER  SYMBOL    (ANGSTROMS)     (DEGREES)      (DEGREES)

    (I)                  NA:I          NB:NA:I      NC:NB:NA:I     NA   NB   NC

 

      1      C      

      2      C         1.40000  *                                  1

      3      C         1.40000  *     120.04090  *                 2    1

      4      C         1.40000  *     120.00010  *     .00000  *   3    2    1

      5      C         1.40087  *     119.93860  *     .00000  *   1    2    3

      6      H         1.08400  *     120.03070  *  180.00000  *   1    2    3

      7      O         1.36000  *     119.97960  *  180.00000  *   2    3    4

      8      C         1.40000  *     120.02040  *     .00000  *   5    1    2

      9      H         1.08400  *     119.98980  *  180.00000  *   5    1    2

     10      H         1.08400  *     120.00000  *  180.00000  *   3    2    1

     11      C         1.42600  *     109.47120  *     .00000  *   7    2    3

     12      C         1.50500  *     120.00000  *  180.00000  *   8    5    1

     13      H         1.08400  *     120.00010  *  180.00000  *   4    3    2

     14      C         1.51000  *     109.47120  *  180.00000  *  11    7    2

     15      C         1.54450  *     109.47120  *   59.99978  *  11    7    2

     16      H         1.09100  *     109.47120  *  -59.99980  *  11    7    2

     17      C         1.40000  *     120.03070  *  180.00000  *  14   11    7

     18      C         1.40087  *     120.03070  *     .00000  *  14   11    7

     19      C         1.40000  *     120.04090  *  180.00000  *  17   14   11

     20      H         1.08400  *     119.97950  *     .00000  *  17   14   11

     21      C         1.40000  *     120.02050  *  180.00000  *  18   14   11

     22      H         1.08400  *     119.98980  *     .00000  *  18   14   11

     23      C         1.40000  *     120.00000  *     .00000  *  19   17   14

     24      H         1.08400  *     120.00000  *  180.00000  *  19   17   14

     25      H         1.08400  *     120.00000  *  180.00000  *  21   18   14

     26      H         1.08400  *     120.00000  *  180.00000  *  23   19   17

     27      C         1.53700  *     109.47120  *  180.00000  *  15   11    7

     28      H         1.09100  *     109.47120  *   59.99978  *  15   11    7

     29      H         1.09100  *     109.47120  *  -59.99980  *  15   11    7

     30      N         1.47200  *     108.00000  *  180.00000  *  27   15   11

     31      H         1.09100  *     109.83780  *   60.22756  *  27   15   11

     32      H         1.09100  *     110.32770  *  -59.34290  *  27   15   11

     33      C         1.47200  *     108.00000  *  180.00000  *  30   27   15

     34      H         1.00800  *     109.83770  *   60.22758  *  30   27   15

     35      H         1.09100  *     109.47120  *  180.00000  *  33   30   27

     36      H         1.09100  *     109.47130  *   59.99981  *  33   30   27

     37      H         1.09100  *     109.47120  *  -59.99980  *  33   30   27

     38      F         1.33300  *     109.47120  *  180.00000  *  12    8    5

     39      F         1.33300  *     109.47120  *   59.99978  *  12    8    5

     40      F         1.33300  *     109.47130  *  -59.99970  *  12    8    5

 

 

          CARTESIAN COORDINATES

 

    NO.       ATOM         X         Y         Z

 

     1         C         .0000     .0000     .0000

     2         C        1.4000     .0000     .0000

     3         C        2.1009    1.2119     .0000

     4         C        1.4017    2.4249     .0000

     5         C        -.6991    1.2139     .0000

     6         H        -.5425    -.9385     .0000

     7         O        2.0796   -1.1780     .0000

     8         C         .0017    2.4259     .0000

     9         H       -1.7831    1.2149     .0000

    10         H        3.1849    1.2112     .0000

    11         C        3.4817    -.9180     .0000

    12         C        -.7498    3.7298     .0000

    13         H        1.9444    3.3633     .0000

    14         C        4.2362   -2.2259     .0000

    15         C        3.8551    -.1082    1.2611

    16         H        3.7454    -.3460    -.8908

    17         C        5.6362   -2.2272     .0000

    18         C        3.5360   -3.4392     .0000

    19         C        6.3360   -3.4397     .0000

    20         H        6.1787   -1.2887     .0000

    21         C        4.2358   -4.6518     .0000

    22         H        2.4520   -3.4392     .0000

    23         C        5.6358   -4.6521     .0000

    24         H        7.4200   -3.4399     .0000

    25         H        3.6936   -5.5905     .0000

    26         H        6.1776   -5.5909     .0000

    27         C        5.3663     .1721    1.2611

    28         H        3.5913    -.6802    2.1519

    29         H        3.3099     .8368    1.2611

    30         N        5.6859     .9433    2.4735

    31         H        5.6361     .7476     .3744

    32         H        5.9255    -.7646    1.2493

    33         C        7.1332    1.2118    2.4735

    34         H        5.4366     .4116    3.2927

    35         H        7.3970    1.7838    3.3643

    36         H        7.3970    1.7838    1.5827

    37         H        7.6784     .2668    2.4735

    38         F         .1171    4.7423     .0000

    39         F       -1.5161    3.8009    1.0884

    40         F       -1.5162    3.8009   -1.0884

  H: (PM3): J. J. P. STEWART, J. COMP. CHEM.     10, 209 (1989).               

  C: (PM3): J. J. P. STEWART, J. COMP. CHEM.     10, 209 (1989).               

  N: (PM3): J. J. P. STEWART, J. COMP. CHEM.     10, 209 (1989).               

  O: (PM3): J. J. P. STEWART, J. COMP. CHEM.     10, 209 (1989).               

  F: (PM3): J. J. P. STEWART, J. COMP. CHEM.     10, 209 (1989).             

Figure 3.  The first part of the MOPAC output contains the header with the keywords used and the original starting geometry.  Here we specified the PM3 and FORCE keywords.

 

 

CYCLE:  54 TIME:    .71 TIME LEFT:   3582.6 GRAD.:     1.984 HEAT:-148.5333   

 

 

          HERBERTS TEST SATISFIED - GEOMETRY OPTIMIZED

Figure 4.  Make sure that you see the word "satisfied" somewhere in the section describing optimization of geometry in the print-out.  Otherwise you may want to re-run the job with a different starting geometry or use the GEO-OK keyword.

 

 

 

          FINAL HEAT OF FORMATION =       -148.53332 KCAL

 

 

          TOTAL ENERGY            =      -4068.76037 EV

          ELECTRONIC ENERGY       =     -26504.69534 EV

          CORE-CORE REPULSION     =      22435.93497 EV

 

          IONIZATION POTENTIAL    =          9.43788

          NO. OF FILLED LEVELS    =         59

          MOLECULAR WEIGHT        =    309.331

 

 

          SCF CALCULATIONS  =               70

          COMPUTATION TIME =  17.520 SECONDS

 

Figure 5. Some molecular properties are calculated and listed in the MOPAC output.  Total energy is obtained by adding the electronic and nuclear (core-core repulsion) terms.

 

 

                 EIGENVALUES

 

 -42.13589 -40.07828 -37.73502 -36.18697 -33.31150 -32.15972 -30.38707 -29.91798

 -29.17670 -27.80775 -25.52086 -24.43056 -24.11096 -22.89517 -22.55156 -22.03164

 -21.91026 -21.17663 -20.35929 -20.11519 -19.29631 -18.92290 -18.84656 -18.73410

 -18.53598 -17.30181 -16.89974 -16.87843 -16.78064 -16.53757 -16.40417 -16.16978

 -16.02944 -15.88430 -15.81132 -15.72932 -15.56671 -15.29560 -15.23757 -15.13248

 -14.90351 -14.63184 -14.29400 -14.05873 -13.83685 -13.56941 -13.32018 -13.18359

 -13.05904 -12.91737 -12.65500 -12.48564 -12.29419 -11.98834 -10.39627 -10.01499

  -9.88280  -9.70706  -9.43788   -.38791   -.16249    .01144    .15362   1.28122

   1.69908   2.07155   2.38452   2.44376   2.54428   2.67768   2.76329   2.83535

   2.94947   3.06670   3.08419   3.11271   3.17194   3.20430   3.31893   3.36635

   3.43797   3.52969   3.57431   3.64486   3.70275   3.78035   3.84691   3.94869

   4.13230   4.15338   4.25532   4.31244   4.38297   4.45546   4.68703   4.73059

   4.76490   4.93038   5.00820   5.08249   5.38298   5.45135   5.55310   5.84846

   5.91692   6.08812

Figure 6.  From the Eigenvalue table you can obtain the HOMO and LUMO values of the molecule in EV.  Usually there is an obvious break point in the eigenvalues, typically where the number goes from positive to negative.  However above these numbers are both negative (HOMO = -9.43788 EV, LUMO = -0.16249 EV)(HOMO = highest occupied molecular orbital, LUMO = lowest unoccupied molecular orbital).  These eigenvalues are solutions of the Shrodinger equation.

 

 

              NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS

 

         ATOM NO.   TYPE          CHARGE        ATOM  ELECTRON DENSITY

           1          C           -.1519          4.1519

           2          C            .1339          3.8661

           3          C           -.2006          4.2006

           4          C            .0045          3.9955

           5          C           -.0083          4.0083

           6          H            .1280           .8720

           7          O           -.1804          6.1804

           8          C           -.2287          4.2287

           9          H            .1160           .8840

          10          H            .1272           .8728

          11          C            .1087          3.8913

          12          C            .4084          3.5916

          13          H            .1177           .8823

          14          C           -.0991          4.0991

          15          C           -.1349          4.1349

          16          H            .0706           .9294

          17          C           -.1110          4.1110

          18          C           -.0726          4.0726

          19          C           -.0989          4.0989

          20          H            .1107           .8893

          21          C           -.1016          4.1016

          22          H            .1180           .8820

          23          C           -.0965          4.0965

          24          H            .1045           .8955

          25          H            .1052           .8948

          26          H            .1048           .8952

          27          C           -.1022          4.1022

          28          H            .0703           .9297

          29          H            .0787           .9213

          30          N           -.0561          5.0561

          31          H            .0548           .9452

          32          H            .0409           .9591

          33          C           -.0998          4.0998

          34          H            .0474           .9526

          35          H            .0483           .9517

          36          H            .0463           .9537

          37          H            .0199           .9801

          38          F           -.1386          7.1386

          39          F           -.1417          7.1417

          40          F           -.1419          7.1419

 DIPOLE           X         Y         Z       TOTAL

 POINT-CHG.     2.380    -2.468      .174     3.433

 HYBRID         1.255     -.742     -.647     1.595

 SUM            3.636    -3.209     -.473     4.873

 

Figure 7. The calculated dipole moment is 4.873 debyes.  If you line the molecule up so that its maximum length is along the x axis and maximum width along the y axis, then comparison of the X, Y and Z components of this molecule to other similarly oriented molecules becomes meaningful.  The point charges and electron densities for each atom are also listed.  Note the relationship between position on the periodic table, electron density and partial charge (e.g. positive core charge [H=1, C=4, O=6 etc.] - number of valence electrons [electron density number]  = partial charge in electrons).

 

          CARTESIAN COORDINATES

 

    NO.       ATOM               X         Y         Z

 

     1         C                   .0000     .0000     .0000

     2         C                  1.4062     .0000     .0000

     3         C                  2.1172    1.2070     .0000

     4         C                  1.4261    2.4115     .0035

     5         C                  -.6763    1.2091     .0005

     6         H                  -.5565    -.9447    -.0029

     7         O                  1.9643   -1.2542    -.0312

     8         C                   .0345    2.4118     .0043

     9         H                 -1.7727    1.2274    -.0006

    10         H                  3.2177    1.1984    -.0042

    11         C                  3.3870   -1.3492     .1285

    12         C                  -.7617    3.7114     .0089

    13         H                  1.9866    3.3539     .0051

    14         C                  3.8672   -2.5610    -.6357

    15         C                  3.7380   -1.4650    1.6267

    16         H                  3.8757    -.4350    -.3081

    17         C                  5.2370   -2.6539    -.9039

    18         C                  3.0163   -3.5780   -1.0664

    19         C                  5.7445   -3.7352   -1.6108

    20         H                  5.9136   -1.8725    -.5234

    21         C                  3.5296   -4.6602   -1.7763

    22         H                  1.9411   -3.5401    -.8573

    23         C                  4.8888   -4.7394   -2.0538

    24         H                  6.8177   -3.7969   -1.8185

    25         H                  2.8551   -5.4530   -2.1172

    26         H                  5.2868   -5.5903   -2.6163

    27         C                  5.1214    -.8800    1.8915

    28         H                  3.6858   -2.5267    1.9418

    29         H                  2.9802    -.9370    2.2412

    30         N                  5.5156   -1.0773    3.3083

    31         H                  5.1193     .2128    1.6985

    32         H                  5.8607   -1.3166    1.1727

    33         C                  6.8645    -.5674    3.6064

    34         H                  5.4588   -2.0468    3.5411

    35         H                  7.0849    -.7459    4.6664

    36         H                  6.8922     .5161    3.4301

    37         H                  7.6633   -1.0287    3.0047

    38         F                  -.0272    4.8472     .0127

    39         F                 -1.5828    3.8430    1.0779

    40         F                 -1.5828    3.8502   -1.0592

 

Figure 8.  The coordinates of the optimized molecular geometry.  These are the coordinates that are read back into Molecular Modeling Pro and Molecular Modeling Pro Plus.

 

 

          ATOMIC ORBITAL ELECTRON POPULATIONS

 

   1.17777    .93382    .98517   1.05514   1.17027    .92239    .85530    .91812

   1.18126    .99733    .93329   1.08871   1.16830    .92037    .97230    .93454

   1.17148    .98254    .91515    .93913    .87198   1.83669   1.21582   1.25008

   1.87786   1.18511    .96280    .93826   1.14257    .88397    .87284   1.17043

    .81764    .96052    .94267   1.15914    .80623    .84733    .77887    .88229

   1.18551    .95183    .96277    .99895   1.17177    .97993   1.03218    .95104

    .92937   1.18149    .94734    .98787    .99432   1.17574    .98706    .93688

    .97294   1.17824    .98281    .95239    .98544    .88930   1.18042    .95770

    .97703    .98644    .88202   1.17971    .94726    .97903    .99051    .89554

    .89478    .89521   1.18210    .96264   1.00971    .94776    .92975    .92134

   1.47891   1.23345   1.18742   1.15628    .94515    .95907   1.15078    .93273

   1.00868   1.00757    .95256    .95172    .95372    .98014   1.77175   1.82297

   1.57213   1.97180   1.77394   1.76453   1.96898   1.63421   1.77398   1.76468

   1.96829   1.63497

 

Figure 9.  The atomic orbital electron populations in electrons.

 

 

 

           PRINCIPAL MOMENTS OF INERTIA IN CM(-1)

 

          A =     .014222   B =     .003855   C =     .003252

 

 

 

           PRINCIPAL MOMENTS OF INERTIA IN UNITS OF 10**(-40)*GRAM-CM**2

 

          A = 1968.332005   B = 7260.768676   C = 8606.615691

 

Figure 10.  Since we specified the FORCE keyword, the moments of inertia are printed out.  Following these number are the matrices and vibrational contributions from which the moments of inertia are derived.

 

 

NOTICE of the Public Domain nature of MOPAC version 6:

the MOPAC computer program is a work of the United States Government and as such is not subject to protection by copyright.  You may freely distribute the MOPAC.EXE file packaged with this program.