#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 LYS LYS 'LYSINE                              ' L-peptide 22 9 . 2009-08-12 2012-12-06
;
Copy of CCP4 Monomer Library entry with added rotamer_info.
Added neutron distances
;
#
data_comp_LYS
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
 LYS           N      N    NH1      -0.204
 LYS           H      H    HNH1      0.204
 LYS           CA     C    CH1       0.058
 LYS           HA     H    HCH1      0.046
 LYS           CB     C    CH2      -0.076
 LYS           HB1    H    HCH2      0.038
 LYS           HB2    H    HCH2      0.038
 LYS           CG     C    CH2      -0.076
 LYS           HG1    H    HCH2      0.038
 LYS           HG2    H    HCH2      0.038
 LYS           CD     C    CH2      -0.076
 LYS           HD1    H    HCH2      0.038
 LYS           HD2    H    HCH2      0.038
 LYS           CE     C    CH2      -0.013
 LYS           HE1    H    HCH2      0.098
 LYS           HE2    H    HCH2      0.098
 LYS           NZ     N    NT3      -0.506
 LYS           HZ1    H    HNT3      0.441
 LYS           HZ2    H    HNT3      0.441
 LYS           HZ3    H    HNT3      0.441
 LYS           C      C    C         0.318
 LYS           O      O    O        -0.422
loop_
_chem_comp_tree.comp_id
_chem_comp_tree.atom_id
_chem_comp_tree.atom_back
_chem_comp_tree.atom_forward
_chem_comp_tree.connect_type
 LYS      N      n/a    CA     START
 LYS      H      N      .      .
 LYS      CA     N      C      .
 LYS      HA     CA     .      .
 LYS      CB     CA     CG     .
 LYS      HB1    CB     .      .
 LYS      HB2    CB     .      .
 LYS      CG     CB     CD     .
 LYS      HG1    CG     .      .
 LYS      HG2    CG     .      .
 LYS      CD     CG     CE     .
 LYS      HD1    CD     .      .
 LYS      HD2    CD     .      .
 LYS      CE     CD     NZ     .
 LYS      HE1    CE     .      .
 LYS      HE2    CE     .      .
 LYS      NZ     CE     HZ3    .
 LYS      HZ1    NZ     .      .
 LYS      HZ2    NZ     .      .
 LYS      HZ3    NZ     .      .
 LYS      C      CA     .      END
 LYS      O      C      .      .
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 LYS      N      H         coval       0.860    0.020    1.020
 LYS      N      CA        coval       1.458    0.019    1.458
 LYS      CA     HA        coval       0.970    0.020    1.090
 LYS      CA     CB        coval       1.530    0.020    1.530
 LYS      CB     HB1       coval       0.970    0.020    1.090
 LYS      CB     HB2       coval       0.970    0.020    1.090
 LYS      CB     CG        coval       1.520    0.030    1.520
 LYS      CG     HG1       coval       0.970    0.020    1.090
 LYS      CG     HG2       coval       0.970    0.020    1.090
 LYS      CG     CD        coval       1.520    0.030    1.520
 LYS      CD     HD1       coval       0.970    0.020    1.090
 LYS      CD     HD2       coval       0.970    0.020    1.090
 LYS      CD     CE        coval       1.520    0.030    1.520
 LYS      CE     HE1       coval       0.970    0.020    1.090
 LYS      CE     HE2       coval       0.970    0.020    1.090
 LYS      CE     NZ        coval       1.489    0.030    1.489
 LYS      NZ     HZ1       coval       0.890    0.020    1.040
 LYS      NZ     HZ2       coval       0.890    0.020    1.040
 LYS      NZ     HZ3       coval       0.890    0.020    1.040
 LYS      CA     C         coval       1.525    0.021    1.525
 LYS      C      O         coval       1.231    0.020    1.231
loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 LYS      H      N      CA      114.000    3.000
 LYS      HA     CA     CB      109.000    3.000
 LYS      CB     CA     C       110.100    1.900
 LYS      HA     CA     C       109.000    3.000
 LYS      N      CA     HA      110.000    3.000
 LYS      N      CA     CB      110.500    1.700
 LYS      HB1    CB     HB2     110.000    3.000
 LYS      HB2    CB     CG      108.000    3.000
 LYS      HB1    CB     CG      108.000    3.000
 LYS      CA     CB     HB1     109.000    3.000
 LYS      CA     CB     HB2     109.000    3.000
 LYS      CA     CB     CG      114.100    2.000
 LYS      HG1    CG     HG2     110.000    3.000
 LYS      HG2    CG     CD      108.000    3.000
 LYS      HG1    CG     CD      108.000    3.000
 LYS      CB     CG     HG1     109.000    3.000
 LYS      CB     CG     HG2     109.000    3.000
 LYS      CB     CG     CD      111.300    2.300
 LYS      HD1    CD     HD2     110.000    3.000
 LYS      HD2    CD     CE      108.000    3.000
 LYS      HD1    CD     CE      108.000    3.000
 LYS      CG     CD     HD1     109.000    3.000
 LYS      CG     CD     HD2     109.000    3.000
 LYS      CG     CD     CE      111.300    2.300
 LYS      HE1    CE     HE2     110.000    3.000
 LYS      HE2    CE     NZ      108.000    3.000
 LYS      HE1    CE     NZ      108.000    3.000
 LYS      CD     CE     HE1     109.000    3.000
 LYS      CD     CE     HE2     109.000    3.000
 LYS      CD     CE     NZ      111.900    3.200
 LYS      HZ1    NZ     HZ2     109.000    3.000
 LYS      HZ2    NZ     HZ3     109.000    3.000
 LYS      HZ1    NZ     HZ3     109.000    3.000
 LYS      CE     NZ     HZ1     110.000    3.000
 LYS      CE     NZ     HZ2     110.000    3.000
 LYS      CE     NZ     HZ3     110.000    3.000
 LYS      N      CA     C       111.000    2.800
 LYS      CA     C      O       120.800    1.700
loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 LYS      chi1     N      CA     CB     CG       180.000   15.000   3
 LYS      chi2     CA     CB     CG     CD       180.000   15.000   3
 LYS      chi3     CB     CG     CD     CE       180.000   15.000   3
 LYS      chi4     CG     CD     CE     NZ       180.000   15.000   3
 LYS      hh       CD     CE     NZ     HZ3       60.000   30.000   3
loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 LYS      chir_01  CA     N      CB     C         negativ
loop_
  _chem_comp_rotamer_info.comp_id
  _chem_comp_rotamer_info.phil_str
  LYS  
;
tor_ids = chi1 chi2 chi3 chi4 hh
tor_atom_ids = chi1 N CA CB CG
tor_atom_ids = chi2 CA CB CG CD
tor_atom_ids = chi3 CB CG CD CE
tor_atom_ids = chi4 CG CD CE NZ
rotamer {
 id = pttm
 frequency_annotation = "<1%"
 frequency = 0.0078
 angles = 64.3 -177.6 -178.9 -67.1 60
}
rotamer {
 id = ptpt
 frequency_annotation = "<1%"
 frequency = 0.0044
 angles = 64.8 179.1 73.0 174.5 60
}
rotamer {
 id = ptmt
 frequency_annotation = "<1%"
 frequency = 0.0053
 angles = 66.7 -175.9 -71.4 -175.8 60
}
rotamer {
 id = pttt
 frequency = 0.0399
 angles = 65.4 -178.1 -179.3 -179.7 60
}
rotamer {
 id = pmtt
 frequency_annotation = "<1%"
 frequency = 0.0003
 angles = 73.2 -74.1 -168.0 -174.6 60
}
rotamer {
 id = pttp
 frequency_annotation = "<1%"
 frequency = 0.0069
 angles = 67.6 -179.1 178.3 66.7 60
}
rotamer {
 id = pmmt
 frequency_annotation = "<1%"
 frequency = 0.0001
 angles = 77.9 -73.7 -71.4 179.1 60
}
rotamer {
 id = ptpp
 frequency_annotation = "<1%"
 frequency = 0.0026
 angles = 65.3 178.4 72.0 66.0 60
}
rotamer {
 id = pptt
 frequency_annotation = "<1%"
 frequency = 0.0007
 angles = 64.2 89.9 175.6 179.1 60
}
rotamer {
 id = ptmm
 frequency_annotation = "<1%"
 frequency = 0.0023
 angles = 66.6 -177.9 -69.6 -66.1 60
}
rotamer {
 id = tppt
 frequency_annotation = "<1%"
 frequency = 0.0078
 angles = -178.2 63.5 69.5 177.4 60
}
rotamer {
 id = ttmm
 frequency_annotation = "<1%"
 frequency = 0.0058
 angles = -174.1 179.7 -71.0 -67.0 60
}
rotamer {
 id = tptt
 frequency = 0.0349
 angles = -178.9 69.1 175.6 177.2 60
}
rotamer {
 id = ttpm
 frequency_annotation = "<1%"
 frequency = 0.0001
 angles = -176.9 175.3 87.1 -84.4 60
}
rotamer {
 id = tmtp
 frequency_annotation = "<1%"
 frequency = 0.0003
 angles = -176.6 -98.0 -178.4 65.1 60
}
rotamer {
 id = tmtt
 frequency_annotation = "<1%"
 frequency = 0.0023
 angles = -172.7 -91.1 -176.9 -178.5 60
}
rotamer {
 id = tmmt
 frequency_annotation = "<1%"
 frequency = 0.0009
 angles = -179.2 -93.4 -70.4 -179.5 60
}
rotamer {
 id = tttm
 frequency = 0.0332
 angles = -176.4 177.8 -176.2 -67.4 60
}
rotamer {
 id = tmmm
 frequency_annotation = "<1%"
 frequency = 0.0002
 angles = -177.5 -81.8 -63.1 -64.5 60
}
rotamer {
 id = tttt
 frequency = 0.1440
 angles = -175.5 176.6 179.7 -179.9 60
}
rotamer {
 id = tptm
 frequency_annotation = "<1%"
 frequency = 0.0055
 angles = -177.9 67.2 -179.4 -66.2 60
}
rotamer {
 id = tptp
 frequency = 0.0118
 angles = -179.9 67.4 173.6 66.2 60
}
rotamer {
 id = ttmt
 frequency = 0.0196
 angles = -174.6 -177.3 -73.5 -175.1 60
}
rotamer {
 id = tmtm
 frequency_annotation = "<1%"
 frequency = 0.0005
 angles = -172.2 -90.5 -172.5 -64.9 60
}
rotamer {
 id = tttp
 frequency = 0.0351
 angles = -177.6 175.4 173.9 65.9 60
}
rotamer {
 id = ttpt
 frequency = 0.0254
 angles = -178.3 174.6 73.0 175.1 60
}
rotamer {
 id = ttpp
 frequency_annotation = "<1%"
 frequency = 0.0064
 angles = -178.4 174.1 71.6 68.2 60
}
rotamer {
 id = tppp
 frequency_annotation = "<1%"
 frequency = 0.0010
 angles = -177.9 62.3 65.5 67.9 60
}
rotamer {
 id = ttmp
 frequency_annotation = "<1%"
 frequency = 0.0003
 angles = -174.2 -179.4 -95.7 76.7 60
}
rotamer {
 id = mtpt
 frequency = 0.0386
 angles = -69.2 174.2 70.5 175.2 60
}
rotamer {
 id = mtpp
 frequency = 0.0113
 angles = -68.5 177.0 70.5 67.7 60
}
rotamer {
 id = mtpm
 frequency_annotation = "<1%"
 frequency = 0.0006
 angles = -70.3 174.8 90.6 -70.0 60
}
rotamer {
 id = mmpt
 frequency_annotation = "<1%"
 frequency = 0.0009
 angles = -60.4 -70.6 93.6 175.5 60
}
rotamer {
 id = mtmp
 frequency_annotation = "<1%"
 frequency = 0.0003
 angles = -67.5 -175.8 -95.8 73.5 60
}
rotamer {
 id = mmtp
 frequency = 0.0135
 angles = -61.5 -68.6 179.7 67.9 60
}
rotamer {
 id = mtmt
 frequency = 0.0382
 angles = -66.8 -173.3 -73.7 -175.4 60
}
rotamer {
 id = mmtt
 frequency = 0.0898
 angles = -61.7 -67.2 -176.8 -178.2 60
}
rotamer {
 id = mtmm
 frequency = 0.0122
 angles = -63.9 -177.2 -70.4 -66.0 60
}
rotamer {
 id = mmtm
 frequency = 0.0208
 angles = -60.2 -65.6 -173.1 -68.9 60
}
rotamer {
 id = mptt
 frequency_annotation = "<1%"
 frequency = 0.0038
 angles = -79.9 73.0 176.1 175.1 60
}
rotamer {
 id = mptp
 frequency_annotation = "<1%"
 frequency = 0.0007
 angles = -74.9 86.6 171.6 65.2 60
}
rotamer {
 id = mmmt
 frequency = 0.0161
 angles = -62.7 -64.1 -70.7 -176.8 60
}
rotamer {
 id = mppt
 frequency_annotation = "<1%"
 frequency = 0.0009
 angles = -82.6 73.5 69.2 177.4 60
}
rotamer {
 id = mmmm
 frequency_annotation = "<1%"
 frequency = 0.0025
 angles = -61.4 -61.8 -66.9 -64.7 60
}
rotamer {
 id = mptm
 frequency_annotation = "<1%"
 frequency = 0.0004
 angles = -91.7 61.2 -173.7 -61.0 60
}
rotamer {
 id = mttm
 frequency = 0.0531
 angles = -66.9 -177.8 -176.7 -67.4 60
}
rotamer {
 id = mttp
 frequency = 0.0404
 angles = -65.9 -179.4 176.3 66.7 60
}
rotamer {
 id = mttt
 frequency = 0.2473
 angles = -67.7 -178.8 -179.1 179.5 60
}
;
