# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 20:14:47 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: S-(carboxymethyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSCC(O)=O)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
 CAY  CAY  S-(carboxymethyl)-L-cysteine  L-peptide  18  11  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CAY
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
 CAY  N    N  NH2    0  -0.799   1.7721  -0.4173   1.8838
 CAY  CA   C  CH1    0  -0.206   0.5128   0.3025   1.9244
 CAY  CB   C  CH2    0  -0.548  -0.4171   0.0088   0.7383
 CAY  CG   C  CH2    0  -0.677  -0.6874  -0.3157  -2.0100
 CAY  SD   S  S2     0  -0.058   0.3403   0.5735  -0.8184
 CAY  CE   C  C      0   0.429  -0.2333  -0.0176  -3.4509
 CAY  C    C  C      0   0.409  -0.2707  -0.0179   3.2217
 CAY  O    O  O      0  -0.602  -0.0189  -1.1016   3.7838
 CAY  OXT  O  OC    -1  -0.615  -1.1205   0.8247   3.5693
 CAY  OF1  O  O      0  -0.598   0.7465   0.7358  -3.5897
 CAY  OF2  O  OC    -1  -0.615  -0.8991  -0.5713  -4.3450
 CAY  HN1  H  HNH2   0   0.329   2.1089  -0.4694   0.9292
 CAY  HN2  H  HNH2   0   0.328   1.5975  -1.3678   2.1865
 CAY  HA   H  HCH1   0   0.210   0.7201   1.3792   1.9247
 CAY  HB1  H  HCH2   0   0.244  -0.5977  -1.0684   0.6738
 CAY  HB2  H  HCH2   0   0.249  -1.3793   0.5052   0.8767
 CAY  HG1  H  HCH2   0   0.261  -0.6269  -1.3910  -1.8192
 CAY  HG2  H  HCH2   0   0.260  -1.7359  -0.0331  -1.8848

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
 CAY  N   CA   single  1.458  0.019  1.458
 CAY  N   HN1  single  0.890  0.020  1.040
 CAY  N   HN2  single  0.890  0.020  1.040
 CAY  CA  CB   single  1.530  0.020  1.530
 CAY  CA  C    single  1.525  0.021  1.525
 CAY  CA  HA   single  0.970  0.020  0.970
 CAY  CB  SD   single  1.821  0.020  1.821
 CAY  CB  HB1  single  0.970  0.020  1.090
 CAY  CB  HB2  single  0.970  0.020  1.090
 CAY  CG  SD   single  1.807  0.020  1.807
 CAY  CG  CE   single  1.540  0.020  1.540
 CAY  CG  HG1  single  0.970  0.020  1.090
 CAY  CG  HG2  single  0.970  0.020  1.090
 CAY  CE  OF1  deloc   1.244  0.020  1.244
 CAY  CE  OF2  deloc   1.245  0.020  1.245
 CAY  C   O    deloc   1.231  0.020  1.231
 CAY  C   OXT  deloc   1.246  0.020  1.246

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
 CAY  HN2  N   HN1  106.89  3.000
 CAY  HN2  N   CA   107.91  3.000
 CAY  HN1  N   CA   109.89  3.000
 CAY  HA   CA  C    109.00  3.000
 CAY  HA   CA  CB   109.00  3.000
 CAY  C    CA  CB   110.10  1.900
 CAY  HA   CA  N    110.00  3.000
 CAY  C    CA  N    111.00  2.800
 CAY  CB   CA  N    110.50  1.700
 CAY  HB2  CB  HB1  108.04  3.000
 CAY  HB2  CB  SD   109.51  3.000
 CAY  HB1  CB  SD   108.88  3.000
 CAY  HB2  CB  CA   110.42  3.000
 CAY  HB1  CB  CA   109.50  3.000
 CAY  SD   CB  CA   110.44  3.000
 CAY  HG2  CG  HG1  106.69  3.000
 CAY  HG2  CG  CE   109.88  3.000
 CAY  HG1  CG  CE   109.71  3.000
 CAY  HG2  CG  SD   110.04  3.000
 CAY  HG1  CG  SD   109.71  3.000
 CAY  CE   CG  SD   110.73  3.000
 CAY  CG   SD  CB   100.05  3.000
 CAY  OF2  CE  OF1  127.64  3.000
 CAY  OF2  CE  CG   115.36  3.000
 CAY  OF1  CE  CG   117.00  3.000
 CAY  OXT  C   O    126.85  3.000
 CAY  OXT  C   CA   116.02  3.000
 CAY  O    C   CA   120.80  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
 CAY  Var_01  CE   CG  SD  CB  -179.34  30.0  1
 CAY  Var_02  OF1  CE  CG  SD     1.32  30.0  3
 CAY  Var_03  HB1  CB  SD  CG    43.70  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
 CAY  chir_01  CA  N  CB  C  negativ

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
 CAY  plan-1  CG   0.020
 CAY  plan-1  CE   0.020
 CAY  plan-1  OF1  0.020
 CAY  plan-1  OF2  0.020
 CAY  plan-2  CA   0.020
 CAY  plan-2  C    0.020
 CAY  plan-2  O    0.020
 CAY  plan-2  OXT  0.020

