# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:27:26 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (2S)-2-amino-5-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-5-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(=O)SC[C@H](N)C(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
 CYG  CYG  '(2S)-2-amino-5-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-5-oxopentanoic acid'  L-peptide  28  16  .  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_CYG
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
 CYG  N     N  NH2    0  -0.791  20.8854  50.9266  108.2735
 CYG  CA    C  CH1    0  -0.172  22.1835  51.5349  108.0225
 CYG  C     C  C      0   0.407  22.6029  52.3600  109.2637
 CYG  O     O  O      0  -0.598  23.7184  52.1225  109.7610
 CYG  CB    C  CH2    0  -0.583  22.1488  52.4189  106.7693
 CYG  SG    S  S2     0  -0.019  23.7723  53.1112  106.3492
 CYG  N1    N  NH2    0  -0.808  26.3900  58.1568  106.5666
 CYG  CA1   C  CH1    0  -0.226  26.5983  57.0772  107.5181
 CYG  CB1   C  CH2    0  -0.402  25.3182  56.2600  107.6866
 CYG  CG1   C  CH2    0  -0.531  24.8636  55.6017  106.3836
 CYG  CD1   C  C      0   0.254  23.5724  54.8547  106.5795
 CYG  OE2   O  O      0  -0.389  22.5285  55.3814  106.8725
 CYG  C1    C  C      0   0.409  27.8137  56.1995  107.1158
 CYG  O1    O  O      0  -0.604  27.9001  55.0887  107.6744
 CYG  O2    O  OC    -1  -0.599  28.6232  56.6922  106.3049
 CYG  OXT   O  OC    -1  -0.606  21.7667  53.2020  109.6514
 CYG  H     H  HNH2   0   0.337  20.5327  50.4911  107.4293
 CYG  H2    H  HNH2   0   0.330  20.2301  51.6601  108.5162
 CYG  HA    H  HCH1   0   0.209  22.9118  50.7354  107.8624
 CYG  HB2   H  HCH2   0   0.274  21.8188  51.8378  105.9059
 CYG  HB3   H  HCH2   0   0.273  21.4510  53.2471  106.9030
 CYG  HA1   H  HCH1   0   0.213  26.8453  57.4624  108.5227
 CYG  HB13  H  HCH2   0   0.222  25.4793  55.4967  108.4489
 CYG  HB12  H  HCH2   0   0.222  24.5212  56.9104  108.0572
 CYG  HG13  H  HCH2   0   0.265  24.7020  56.3719  105.6258
 CYG  HG12  H  HCH2   0   0.249  25.6414  54.9319  106.0120
 CYG  HN11  H  HNH2   0   0.335  27.2935  58.4511  106.2207
 CYG  HN12  H  HNH2   0   0.331  25.9685  58.9526  107.0265

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
 CYG  N    CA    single  1.458  0.019  1.458
 CYG  N    H     single  0.860  0.020  0.860
 CYG  N    H2    single  0.890  0.020  1.040
 CYG  CA   C     single  1.525  0.021  1.525
 CYG  CA   CB    single  1.530  0.020  1.530
 CYG  CA   HA    single  0.970  0.020  0.970
 CYG  C    O     deloc   1.231  0.020  1.231
 CYG  C    OXT   deloc   1.248  0.020  1.248
 CYG  CB   SG    single  1.814  0.020  1.814
 CYG  CB   HB2   single  0.970  0.020  1.090
 CYG  CB   HB3   single  0.970  0.020  1.090
 CYG  SG   CD1   single  1.770  0.020  1.770
 CYG  N1   CA1   single  1.454  0.020  1.454
 CYG  N1   HN11  single  0.890  0.020  1.040
 CYG  N1   HN12  single  0.890  0.020  1.040
 CYG  CA1  CB1   single  1.528  0.020  1.528
 CYG  CA1  C1    single  1.552  0.020  1.552
 CYG  CA1  HA1   single  0.970  0.020  1.090
 CYG  CB1  CG1   single  1.529  0.020  1.529
 CYG  CB1  HB13  single  0.970  0.020  1.090
 CYG  CB1  HB12  single  0.970  0.020  1.090
 CYG  CG1  CD1   single  1.504  0.020  1.504
 CYG  CG1  HG13  single  0.970  0.020  1.090
 CYG  CG1  HG12  single  0.970  0.020  1.090
 CYG  CD1  OE2   double  1.205  0.020  1.205
 CYG  C1   O1    deloc   1.246  0.020  1.246
 CYG  C1   O2    deloc   1.247  0.020  1.247

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
 CYG  H2    N    H     106.60  3.000
 CYG  H2    N    CA    108.40  3.000
 CYG  H     N    CA    114.00  3.000
 CYG  HA    CA   CB    109.00  3.000
 CYG  HA    CA   C     109.00  3.000
 CYG  CB    CA   C     110.10  1.900
 CYG  HA    CA   N     110.00  3.000
 CYG  CB    CA   N     110.50  1.700
 CYG  C     CA   N     111.00  2.800
 CYG  OXT   C    O     127.24  3.000
 CYG  OXT   C    CA    115.27  3.000
 CYG  O     C    CA    120.80  1.700
 CYG  HB3   CB   HB2   107.91  3.000
 CYG  HB3   CB   SG    108.12  3.000
 CYG  HB2   CB   SG    106.88  3.000
 CYG  HB3   CB   CA    110.59  3.000
 CYG  HB2   CB   CA    110.25  3.000
 CYG  SG    CB   CA    112.88  3.000
 CYG  CD1   SG   CB    104.16  3.000
 CYG  HN12  N1   HN11  107.39  3.000
 CYG  HN12  N1   CA1   110.27  3.000
 CYG  HN11  N1   CA1   108.17  3.000
 CYG  HA1   CA1  C1    104.95  3.000
 CYG  HA1   CA1  CB1   105.88  3.000
 CYG  C1    CA1  CB1   112.47  3.000
 CYG  HA1   CA1  N1    111.62  3.000
 CYG  C1    CA1  N1    111.25  3.000
 CYG  CB1   CA1  N1    110.44  3.000
 CYG  HB12  CB1  HB13  106.68  3.000
 CYG  HB12  CB1  CG1   109.16  3.000
 CYG  HB13  CB1  CG1   109.77  3.000
 CYG  HB12  CB1  CA1   109.26  3.000
 CYG  HB13  CB1  CA1   109.12  3.000
 CYG  CG1   CB1  CA1   112.67  3.000
 CYG  HG12  CG1  HG13  107.57  3.000
 CYG  HG12  CG1  CD1   110.56  3.000
 CYG  HG13  CG1  CD1   108.27  3.000
 CYG  HG12  CG1  CB1   110.02  3.000
 CYG  HG13  CG1  CB1   109.36  3.000
 CYG  CD1   CG1  CB1   110.97  3.000
 CYG  OE2   CD1  CG1   123.92  3.000
 CYG  OE2   CD1  SG    124.04  3.000
 CYG  CG1   CD1  SG    112.04  3.000
 CYG  O2    C1   O1    126.76  3.000
 CYG  O2    C1   CA1   116.96  3.000
 CYG  O1    C1   CA1   116.24  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
 CYG  Var_01  CG1  CD1  SG   CB    175.33  30.0  3
 CYG  Var_02  CB1  CG1  CD1  SG   -115.10  30.0  2
 CYG  Var_03  HB2  CB   SG   CD1   124.24  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
 CYG  chir_01  CA   N   C    CB  positiv
 CYG  chir_02  CA1  N1  CB1  C1  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
 CYG  plan-1  CA   0.020
 CYG  plan-1  C    0.020
 CYG  plan-1  O    0.020
 CYG  plan-1  OXT  0.020
 CYG  plan-2  CA1  0.020
 CYG  plan-2  C1   0.020
 CYG  plan-2  O1   0.020
 CYG  plan-2  O2   0.020
 CYG  plan-3  SG   0.020
 CYG  plan-3  CG1  0.020
 CYG  plan-3  CD1  0.020
 CYG  plan-3  OE2  0.020

