[ None ]
[ COO- ]
    [ replace ]
        C       C       CC      12.011  0.34
        O       OT1     OC      15.9994 -0.67
        OXT     OT2     OC      15.9994 -0.67
    [ add ]
        2       8       OT      C       CA      N
        OC      15.9994 -0.67   -1
    [ impropers ]
        C       CA      OT2     OT1
[ COOH ]
    [ replace ]
        C       C       CD      12.011  0.72
        O       OT1     OB      15.9994 -0.55
        OXT     OT2     OH      15.9994 -0.61
    [ add ]
        2       8       OT      C       CA      N
        OB      15.9994 -0.55   -1
        1       2       HT2     OT2     C       CA
        H       1.008   0.44    -1
    [ replace ]
        OT2     OT2     OH1     15.9994 -0.61
    [ impropers ]
        C       CA      OT2     OT1
[ CT2 ]
    [ replace ]
        C       CC      12.011  0.55
        O       O       15.9994 -0.55
    [ add ]
        1       2       NT      C       CA      N
        NH2     14.0027 -0.62   -1
        2       3       HT      NT      C       CA
        H       1.008   0.00    -1
    [ replace ]
        HT1     H       1.008   0.30    ; this one is trans to O
        HT2     H       1.008   0.32    ; this one is cis to O
    [ impropers ]
        C       NT      CA      O
        C       CA      NT      O
        NT      C       HT1     HT2
        NT      C       HT2     HT1
[ CT3 ]
    ; N-Methylamide C-terminus
    ;
    ; |
    ; C=O
    ; |
    ; NT-HNT
    ; |
    ; HT1-CAT-HT3
    ; |
    ; HT2
    ;
    [ delete ]
        OXT
    [ add ]
        1       8       NT      C       CA      N
        NH1     14.0027 -0.47   -1
        1       2       HNT     NT      C       O
        H       1.008   0.31    -1
        1       8       CAT     NT      C       O
        CT3     12.011  -0.11   -1
        3       4       HT      CAT     NT      C
        HA      1.008   0.09    -1
    [ bonds ]
        NT      CAT     ; otherwise CAT does not get bonded to other atoms...
    [ impropers ]
        NT      C       CAT     HNT
        C       CA      NT      O
