pm3 force thermo rot=1 nomm charge=-2
thymidine nucleotide
                                                                                
  C    0.000000  0    0.000000  0    0.000000  0    0   0   0
  C    1.348663  1    0.000000  0    0.000000  0    1   0   0
  C    2.794174  1   57.199600  1    0.000000  0    1   2   0
  N    1.368454  1   58.670120  1  177.674957  1    3   1   2
  C    1.482681  1  117.960968  1    2.002060  1    1   2   3
  O    1.221268  1  124.841431  1  179.162949  1    5   1   2
  O    1.206284  1  118.053635  1  184.295639  1    3   4   5
  C    1.506714  1  122.860336  1  180.315979  1    1   2   5
  N    1.353790  1  124.710281  1    0.000000  1    2   1   5
  C    5.719116  1   13.428696  1   70.811905  1    1   2   9
  C    1.526779  1   13.460175  1   81.850357  1   10   1   2
  C    1.474335  1  120.053955  1  179.451462  1    9   2   1
  O    1.422470  1  116.042831  1  165.456238  1   12   9   2
  C    1.519882  1  103.998962  1  352.537277  1   10  11  12
  O    1.428513  1  110.524475  1  111.026306  1   10  11  12
  C    1.519394  1  113.236450  1  220.595078  1   14  10  11
  O    1.419296  1  109.672943  1  185.991700  1   16  14  10
  P    1.628128  1  118.892929  1  163.945511  1   17  16  14
  O    1.482117  1  108.408752  1   49.327728  1   18  17  16
  O    1.483841  1  106.056992  1  282.076828  1   18  17  16
  O    1.737061  1  107.999603  1  166.330505  1   18  17  16
  H    1.100372  1  118.127075  1  179.552872  1    2   1   5
  H    1.006973  1  116.215942  1    2.192657  1    4   3   7
  H    1.113525  1  110.160782  1  240.049210  1    8   1   2
  H    1.113678  1  110.048874  1  120.517319  1    8   1   2
  H    1.112793  1  112.654190  1    0.316483  1    8   1   2
  H    1.113449  1  111.445953  1  230.974350  1   10  11  12
  H    1.113098  1  112.314972  1  229.947952  1   11  10  14
  H    1.116348  1  109.330231  1  109.382690  1   11  10  14
  H    1.118149  1  107.510010  1  285.182220  1   12   9   2
  H    1.117722  1  109.980682  1   97.980530  1   14  10  11
  H    0.942230  1  107.183044  1  183.902222  1   15  10  11
  H    1.114441  1  110.762268  1   65.127441  1   16  14  10
  H    1.115707  1  108.242645  1  305.382965  1   16  14  10