

[ 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       MCH3
  CT3     SM      MCH3
  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


