# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 00:39:34 2020
#   Inital geometry file: a 46 line input string
#   Ligand name: S-(methylselanyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se]SC[C@H](N)C(O)=O
#
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
 CSK  CSK  S-(methylselanyl)-L-cysteine  L-peptide  18  9  .  2022-07-24  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CSK
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 CSK  N     N   NH2   0  -0.756   1.2814   1.3632   1.0475
 CSK  CA    C   CH1   0  -0.188   1.8488   0.0952   0.6816
 CSK  C     C   C     0   0.522   3.0019   0.1980  -0.3148
 CSK  O     O   O     0  -0.433   3.2910   1.1973  -0.9216
 CSK  CB    C   CH2   0  -0.579   0.7865  -0.8462   0.1040
 CSK  SG    S   S2    0  -0.073  -0.5624  -1.1733   1.2725
 CSK  SE    SE  SE    0   0.031  -1.9185   0.5282   1.0270
 CSK  CM    C   CH3   0  -0.795  -3.3103  -0.3469  -0.0363
 CSK  OXT   O   OH1   0  -0.592   3.6518  -0.9523  -0.4426
 CSK  HN1   H   HNH2  0   0.360   1.9731   1.9368   1.5118
 CSK  HN2   H   HNH2  0   0.347   0.9807   1.8756   0.2278
 CSK  HA    H   HCH1  0   0.282   2.2475  -0.3749   1.5862
 CSK  HB1C  H   HCH2  0   0.289   0.3743  -0.4618  -0.8306
 CSK  HB2C  H   HCH2  0   0.301   1.2180  -1.8258  -0.1079
 CSK  HXT   H   HOH1  0   0.483   4.3675  -0.8639  -1.0903
 CSK  HM1C  H   HCH3  0   0.266  -2.9173  -0.6590  -1.0019
 CSK  HM2C  H   HCH3  0   0.268  -3.7212  -1.2034   0.4937
 CSK  HM3C  H   HCH3  0   0.268  -4.1036   0.3851  -0.1952

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
 CSK  N    CA    single  1.458  0.019  1.458
 CSK  CA   C     single  1.525  0.021  1.525
 CSK  CA   CB    single  1.521  0.033  1.521
 CSK  C    O     double  1.231  0.020  1.231
 CSK  C    OXT   single  1.327  0.020  1.327
 CSK  CB   SG    single  1.814  0.020  1.814
 CSK  SG   SE    single  2.190  0.020  2.190
 CSK  SE   CM    single  1.958  0.020  1.958
 CSK  N    HN1   single  0.890  0.020  1.040
 CSK  N    HN2   single  0.890  0.020  1.040
 CSK  CA   HA    single  0.970  0.020  0.970
 CSK  CB   HB1C  single  0.970  0.020  1.090
 CSK  CB   HB2C  single  0.970  0.020  1.090
 CSK  OXT  HXT   single  0.850  0.020  0.980
 CSK  CM   HM1C  single  0.970  0.020  1.090
 CSK  CM   HM2C  single  0.970  0.020  1.090
 CSK  CM   HM3C  single  0.970  0.020  1.090

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
 CSK  HN2   N    HN1   106.72  3.000
 CSK  HN2   N    CA    110.96  3.000
 CSK  HN1   N    CA    110.32  3.000
 CSK  HA    CA   CB    109.00  3.000
 CSK  HA    CA   C     110.00  3.000
 CSK  CB    CA   C     110.50  1.500
 CSK  HA    CA   N     110.00  3.000
 CSK  CB    CA   N     110.40  1.500
 CSK  C     CA   N     111.00  2.800
 CSK  OXT   C    O     123.58  3.000
 CSK  OXT   C    CA    120.80  1.700
 CSK  O     C    CA    120.80  1.700
 CSK  HB2C  CB   HB1C  107.42  3.000
 CSK  HB2C  CB   SG    104.90  3.000
 CSK  HB1C  CB   SG    109.52  3.000
 CSK  HB2C  CB   CA    110.53  3.000
 CSK  HB1C  CB   CA    111.60  3.000
 CSK  SG    CB   CA    112.54  3.000
 CSK  SE    SG   CB    104.37  3.000
 CSK  CM    SE   SG     98.85  3.000
 CSK  HM3C  CM   HM2C  108.94  3.000
 CSK  HM3C  CM   HM1C  109.01  3.000
 CSK  HM2C  CM   HM1C  110.06  3.000
 CSK  HM3C  CM   SE    107.22  3.000
 CSK  HM2C  CM   SE    110.84  3.000
 CSK  HM1C  CM   SE    110.70  3.000
 CSK  HXT   OXT  C     110.29  3.000

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
 CSK  CONST_01  HXT   OXT  C   CA  180.00   0.0  0
 CSK  Var_01    HM1C  CM   SE  SG  -64.26  30.0  3
 CSK  Var_02    HB1C  CB   SG  SE  -41.24  30.0  1

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
 CSK  chir_01  CA  N  C  CB  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 CSK  plan-1  CA   0.020
 CSK  plan-1  C    0.020
 CSK  plan-1  O    0.020
 CSK  plan-1  OXT  0.020
 CSK  plan-1  HXT  0.020

