[ 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