# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:24:20 2022
#   Inital geometry file: a 61 line input string
#   Ligand name: S-[(acetylamino)methyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCSC[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
 CY1  CY1  S-[(acetylamino)methyl]-L-cysteine  L-peptide  23  12  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_CY1
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
 CY1  N    N  NH2    0  -0.801  22.1091  25.8411  28.6358
 CY1  CA   C  CH1    0  -0.218  22.5498  24.4697  28.4506
 CY1  CB   C  CH2    0  -0.531  22.9850  23.8934  29.7881
 CY1  SG   S  S2     0  -0.036  21.6338  24.0803  30.9957
 CY1  CD   C  CH2    0  -0.428  21.8388  22.5766  31.9968
 CY1  NE   N  NH1    0  -0.596  21.5203  21.3702  31.2890
 CY1  CZ   C  C      0   0.518  22.4255  20.4351  30.9313
 CY1  OAC  O  O      0  -0.495  23.5961  20.4658  31.2823
 CY1  CM   C  CH3    0  -0.773  21.8890  19.3365  30.0480
 CY1  C    C  C      0   0.416  21.4543  23.6037  27.7721
 CY1  O    O  O      0  -0.598  20.5219  24.2115  27.2120
 CY1  OXT  O  OC    -1  -0.603  21.6332  22.3707  27.8017
 CY1  H    H  HNH2   0   0.337  21.5476  26.1090  27.8390
 CY1  H2   H  HNH2   0   0.334  22.9049  26.4647  28.6712
 CY1  HA   H  HCH1   0   0.219  23.4312  24.3999  27.7889
 CY1  HB2  H  HCH2   0   0.265  23.2305  22.8395  29.6798
 CY1  HB3  H  HCH2   0   0.254  23.8696  24.4108  30.1647
 CY1  HD2  H  HCH2   0   0.279  22.8529  22.5052  32.3822
 CY1  HD3  H  HCH2   0   0.285  21.1655  22.7056  32.8453
 CY1  HE   H  HNH1   0   0.399  20.5900  21.3042  30.9079
 CY1  HM1  H  HCH3   0   0.266  22.3145  19.4484  29.0499
 CY1  HM2  H  HCH3   0   0.260  22.2065  18.3685  30.4320
 CY1  HM3  H  HCH3   0   0.248  20.8046  19.3394  29.9560

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
 CY1  N   CA   single  1.458  0.019  1.458
 CY1  N   H    single  0.860  0.020  0.860
 CY1  N   H2   single  0.890  0.020  1.040
 CY1  CA  CB   single  1.530  0.020  1.530
 CY1  CA  C    single  1.525  0.021  1.525
 CY1  CA  HA   single  0.970  0.020  0.970
 CY1  CB  SG   single  1.822  0.020  1.822
 CY1  CB  HB2  single  0.970  0.020  1.090
 CY1  CB  HB3  single  0.970  0.020  1.090
 CY1  SG  CD   single  1.818  0.020  1.818
 CY1  CD  NE   single  1.435  0.020  1.435
 CY1  CD  HD2  single  0.970  0.020  1.090
 CY1  CD  HD3  single  0.970  0.020  1.090
 CY1  NE  CZ   single  1.350  0.020  1.350
 CY1  NE  HE   single  0.860  0.020  1.020
 CY1  CZ  OAC  double  1.222  0.020  1.222
 CY1  CZ  CM   single  1.508  0.020  1.508
 CY1  CM  HM1  single  0.970  0.020  1.090
 CY1  CM  HM2  single  0.970  0.020  1.090
 CY1  CM  HM3  single  0.970  0.020  1.090
 CY1  C   O    deloc   1.231  0.020  1.231
 CY1  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
 CY1  H2   N   H    107.53  3.000
 CY1  H2   N   CA   110.35  3.000
 CY1  H    N   CA   114.00  3.000
 CY1  HA   CA  C    109.00  3.000
 CY1  HA   CA  CB   109.00  3.000
 CY1  C    CA  CB   110.10  1.900
 CY1  HA   CA  N    110.00  3.000
 CY1  C    CA  N    111.00  2.800
 CY1  CB   CA  N    110.50  1.700
 CY1  HB3  CB  HB2  108.10  3.000
 CY1  HB3  CB  SG   108.89  3.000
 CY1  HB2  CB  SG   109.44  3.000
 CY1  HB3  CB  CA   110.84  3.000
 CY1  HB2  CB  CA   110.14  3.000
 CY1  SG   CB  CA   109.39  3.000
 CY1  CD   SG  CB   101.33  3.000
 CY1  HD3  CD  HD2  107.92  3.000
 CY1  HD3  CD  NE   110.26  3.000
 CY1  HD2  CD  NE   109.07  3.000
 CY1  HD3  CD  SG   105.12  3.000
 CY1  HD2  CD  SG   110.77  3.000
 CY1  NE   CD  SG   113.51  3.000
 CY1  HE   NE  CZ   118.27  3.000
 CY1  HE   NE  CD   116.53  3.000
 CY1  CZ   NE  CD   124.37  3.000
 CY1  CM   CZ  OAC  121.81  3.000
 CY1  CM   CZ  NE   114.91  3.000
 CY1  OAC  CZ  NE   123.28  3.000
 CY1  HM3  CM  HM2  108.83  3.000
 CY1  HM3  CM  HM1  108.12  3.000
 CY1  HM2  CM  HM1  107.47  3.000
 CY1  HM3  CM  CZ   113.70  3.000
 CY1  HM2  CM  CZ   109.72  3.000
 CY1  HM1  CM  CZ   108.81  3.000
 CY1  OXT  C   O    126.92  3.000
 CY1  OXT  C   CA   116.11  3.000
 CY1  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
 CY1  CONST_01  OAC  CZ  NE  CD     0.00   0.0  0
 CY1  CONST_02  CM   CZ  NE  CD   180.00   0.0  0
 CY1  CONST_03  HE   NE  CZ  OAC  180.00   0.0  0
 CY1  Var_01    NE   CD  SG  CB   -68.67  30.0  3
 CY1  Var_02    CZ   NE  CD  SG   111.52  30.0  3
 CY1  Var_03    HB2  CB  SG  CD    25.06  30.0  1
 CY1  Var_04    HM1  CM  CZ  NE   110.25  30.0  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
 CY1  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
 CY1  plan-1  CD   0.020
 CY1  plan-1  NE   0.020
 CY1  plan-1  CZ   0.020
 CY1  plan-1  OAC  0.020
 CY1  plan-1  CM   0.020
 CY1  plan-1  HE   0.020
 CY1  plan-2  CA   0.020
 CY1  plan-2  C    0.020
 CY1  plan-2  O    0.020
 CY1  plan-2  OXT  0.020

