[ CH3 ]
    CT3     CE1     MCH3
    CT3     C       MCH3
    CT3     CA      MCH3
    CT3     CC      MCH3
    CT3     CD      MCH3
    CT3     CPB     MCH3
    CT3     CPH1    MCH3
    CT3     CS      MCH3
    CT3     CT1     MCH3
    CT3     CT2     MCH3
    CT3     CT3     MCH3
    CT3     NC2     MCH3
    CT3     NH1     MCH3
    CT3     NH2     MCH3
    CT3     NH3     MCH3
    CT3     OC      MCH3
    CT3     OH1     MCH3
    CT3     OS      MCH3
    CT3     S       MCH3S
    CTL3    CL      MCH3
    CTL3    OSL     MCH3
    CTL3    CTL1    MCH3
    CTL3    CTL2    MCH3
    CTL3    CTL3    MCH3
    CTL3    OHL     MCH3
    CTL3    CEL1    MCH3
    CTL5    NTL     MCH3
[ NH3 ]
    NH3     CT1     MNH3
    NH3     CT2     MNH3
    NH3     CT3     MNH3
    NH3L    CTL2    MNH3
[ NH2 ]
    NH2     planar
    NP      planar
    NC2     planar
; Data for generating dummy aromatic rings.
; Actually we dont need all these bonds and angles,
; but by specifying them here it is easier to improve
; the dummy generation code later.
[ PHE ]
    CG      CD1     0.140
    CG      CD2     0.140
    CD1     CE1     0.140
    CD2     CE2     0.140
    CE1     CZ      0.140
    CE2     CZ      0.140
    CD1     HD1     0.108
    CD2     HD2     0.108
    CE1     HE1     0.108
    CE2     HE2     0.108
    CZ      HZ      0.108
    CG      CD1     CE1     120.0
    CD1     CE1     CZ      120.0
    CE1     CZ      CE2     120.0
    CZ      CE2     CD2     120.0
    CE2     CD2     CG      120.0
    CD2     CG      CD1     120.0
    CG      CD1     HD1     120.0
    CG      CD2     HD2     120.0
    HD1     CD1     CE1     120.0
    CD1     CE1     HE1     120.0
    HE1     CE1     CZ      120.0
    CE1     CZ      HZ      120.0
    HZ      CZ      CE2     120.0
    CZ      CE2     HE2     120.0
    HE2     CE2     CD2     120.0
    HD2     CD2     CG      120.0
[ TYR ]
    CG      CD1     0.140
    CG      CD2     0.140
    CD1     CE1     0.140
    CD2     CE2     0.140
    CE1     CZ      0.140
    CE2     CZ      0.140
    CD1     HD1     0.108
    CD2     HD2     0.108
    CE1     HE1     0.108
    CE2     HE2     0.108
    CZ      OH      0.1364
    OH      HH      0.0945
    CG      CD1     CE1     120.0
    CD1     CE1     CZ      120.0
    CE1     CZ      CE2     120.0
    CZ      CE2     CD2     120.0
    CE2     CD2     CG      120.0
    CD2     CG      CD1     120.0
    CG      CD1     HD1     120.0
    CG      CD2     HD2     120.0
    HD1     CD1     CE1     120.0
    CD1     CE1     HE1     120.0
    HE1     CE1     CZ      120.0
    CE1     CZ      OH      120.0
    CZ      OH      HH      113.0
    OH      CZ      CE2     120.0
    CZ      CE2     HE2     120.0
    HE2     CE2     CD2     120.0
    HD2     CD2     CG      120.0
[ TRP ] ; angles from MD sim, corrected to be perfectly planar
    CB      CG      0.1495
    CG      CD1     0.1352
    CD1     NE1     0.1381
    NE1     CE2     0.138
    CE2     CD2     0.1419
    CD2     CG      0.1459
    CE2     CZ2     0.140
    CZ2     CH2     0.140
    CH2     CZ3     0.140
    CZ3     CE3     0.140
    CE3     CD2     0.1404
    CD1     HD1     0.108
    NE1     HE1     0.101
    CE3     HE3     0.108
    CZ2     HZ2     0.108
    CZ3     HZ3     0.108
    CH2     HH2     0.108
    CB      CG      CD1     125.6
    CB      CG      CD2     128.7
    CG      CD1     NE1     109.7
    CD1     NE1     CE2     111.7
    NE1     CE2     CD2     104.3
    CE2     CD2     CG      108.5
    CD2     CG      CD1     105.7
    NE1     CE2     CZ2     135.7
    CE2     CZ2     CH2     120.0
    CZ2     CH2     CZ3     120.0
    CH2     CZ3     CE3     120.0
    CZ3     CE3     CD2     120.0
    CE2     CD2     CE3     120.0
    CD2     CE2     CZ2     120.0
    CE3     CD2     CG      131.5
    CG      CD1     HD1     124.6
    HD1     CD1     NE1     125.7
    CD1     NE1     HE1     122.7
    HE1     NE1     CE2     125.6
    CZ3     CE3     HE3     120.0
    HE3     CE3     CD2     120.0
    CE2     CZ2     HZ2     120.0
    HZ2     CZ2     CH2     120.0
    CH2     CZ3     HZ3     120.0
    HZ3     CZ3     CE3     120.0
    CZ2     CH2     HH2     120.0
    HH2     CH2     CZ3     120.0
[ HISA ] ; angles from MD sim, corrected to be perfectly planar
    CG      ND1     0.1381
    ND1     CE1     0.1343
    CE1     NE2     0.1335
    NE2     CD2     0.1394
    CD2     CG      0.137
    ND1     HD1     0.101
    CE1     HE1     0.108
    CD2     HD2     0.108
    CG      ND1     CE1     107.4
    ND1     CE1     NE2     113.1
    CE1     NE2     CD2     104.5
    NE2     CD2     CG      109.3
    CD2     CG      ND1     105.7
    CG      ND1     HD1     127.7
    HD1     ND1     CE1     124.9
    ND1     CE1     HE1     122.9
    HE1     CE1     NE2     124.0
    CG      CD2     HD2     129.0
    HD2     CD2     NE2     121.7
[ HISB ] ; angles from MD sim, corrected to be perfectly planar
    CG      ND1     0.1394
    ND1     CE1     0.1335
    CE1     NE2     0.1343
    NE2     CD2     0.1381
    CD2     CG      0.137
    CD2     HD2     0.108
    CE1     HE1     0.108
    NE2     HE2     0.101
    CG      ND1     CE1     104.9
    ND1     CE1     NE2     112.9
    CE1     NE2     CD2     107.3
    NE2     CD2     CG      106.4
    CD2     CG      ND1     108.5
    NE2     CD2     HD2     122.4
    HD2     CD2     CG      131.2
    ND1     CE1     HE1     123.8
    HE1     CE1     NE2     123.3
    CE1     NE2     HE2     125.9
    HE2     NE2     CD2     126.8
[ HISH ] ; angles from MD sim, corrected to be perfectly planar
    CG      ND1     0.1381
    ND1     CE1     0.1343
    CE1     NE2     0.1343
    NE2     CD2     0.1381
    CD2     CG      0.137
    ND1     HD1     0.101
    CE1     HE1     0.108
    CD2     HD2     0.108
    NE2     HE2     0.101
    CG      ND1     CE1     107.4
    ND1     CE1     NE2     111.4
    CE1     NE2     CD2     107.2
    NE2     CD2     CG      107.4
    CD2     CG      ND1     106.6
    CG      ND1     HD1     127.4
    HD1     ND1     CE1     125.2
    ND1     CE1     HE1     124.3
    HE1     CE1     NE2     124.3
    CE1     NE2     HE2     126.4
    HE2     NE2     CD2     126.4
    NE2     CD2     HD2     120.8
    HD2     CD2     CG      131.8
