[ None ]

[ GLY-NH3+ ]
[ replace ]
 N  N   NH3     14.0070 -0.3
 CA CA  CT2     12.011  0.13
[ Add ]
 3  4   H   N   CA  C
    HC  1.008   0.33    -1
[ delete ]
 HN

[ NH3+ ]
[ replace ]
 N    N NH3     14.0070 -0.3
 CA   CA    CT1     12.011  0.21
 HA   HA    HB1     1.008    0.10
[ Add ]
 3       4       H       N       CA      C
         HC      1.008   0.33    -1
[ delete ]
 HN

[ PRO-NH2+ ]
[ replace ]
 N    N NP       14.0070 -0.07
 CA   CA    CP1      12.011  0.16
 CD   CD    CP3      12.011  0.16
[ add ]
 2       4       HN      N       CA      C
         HC      1.008   0.24    -1

; Created by Michel Cuendet
[ NH2 ]
[ replace ]
 N      NH2     14.0070 -0.96
 CA     CT1     12.011  0.19
 HA     HB1     1.008   0.09
[ add ]
 2  4   HT  N   CA  C
    H   1.008   0.34    -1
[ delete ]
 HN


; Created by Bjelkmar 
[ GLY-NH2 ]
[ replace ]
 N      NH2     14.0070 -0.96
 CA     CT2     12.011  0.10
[ add ]
 2  4   HT  N   CA  C
    H   1.008   0.34    -1
[ delete ]
 HN


; Created by Bjelkmar 
[ PRO-NH ]
[ replace ]
 N      NP  14.0070 -0.40
 CA     CP1 12.011  -0.08
 CD     CP3 12.011  -0.10
[ add ]
 1  4   H   N   CA  C
 HC 1.008   0.31    -1

; added by Justin Lemkul 
[ 5TER ]
[ replace ]
 O5'    ON5  15.9994 -0.66
 C5'    CN8B 12.011   0.05
[ add ]
 1  2  H5T  O5'  C5'  C4'
    HN5  1.008  0.43    -1
[ delete ]
 P
 O1P
 O2P