# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:11:42 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: 3-[(2-hydroxyethyl)disulfanyl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CSSCCO)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
 CME  CME  3-[(2-hydroxyethyl)disulfanyl]-L-alanine  L-peptide  21  11  .  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_CME
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
 CME  N    N  NH2    0  -0.788  12.8667  20.5602  16.1934
 CME  CA   C  CH1    0  -0.210  14.0057  21.2524  15.6256
 CME  CB   C  CH2    0  -0.557  13.6807  22.1359  14.4136
 CME  SG   S  S2     0  -0.080  12.6384  23.5639  14.9097
 CME  SD   S  S2     0  -0.065  11.6726  24.0460  13.1629
 CME  CE   C  CH2    0  -0.573  10.0721  23.1887  13.3208
 CME  CZ   C  CH2    0  -0.150  10.1601  21.6893  13.4659
 CME  OH   O  OH1    0  -0.657  10.8315  21.1399  12.3592
 CME  C    C  C      0   0.402  14.7273  22.1174  16.6885
 CME  O    O  O      0  -0.593  14.0098  22.5879  17.5936
 CME  OXT  O  OC    -1  -0.599  15.9429  22.3117  16.5079
 CME  H    H  HNH2   0   0.332  12.2793  21.2292  16.6743
 CME  H2   H  HNH2   0   0.338  12.3048  20.1456  15.4593
 CME  HA   H  HCH1   0   0.229  14.7136  20.5037  15.2540
 CME  HB2  H  HCH2   0   0.265  14.5963  22.5162  13.9597
 CME  HB3  H  HCH2   0   0.275  13.1313  21.5716  13.6598
 CME  HE2  H  HCH2   0   0.276   9.5276  23.6035  14.1689
 CME  HE3  H  HCH2   0   0.278   9.5289  23.4651  12.4131
 CME  HZ2  H  HCH2   0   0.201  10.6625  21.4489  14.4108
 CME  HZ3  H  HCH2   0   0.222   9.1331  21.3086  13.5500
 CME  HH   H  HOH1   0   0.455  10.9084  20.1915  12.4976

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
 CME  N   CA   single  1.458  0.019  1.458
 CME  N   H    single  0.860  0.020  0.860
 CME  N   H2   single  0.890  0.020  1.040
 CME  CA  CB   single  1.530  0.020  1.530
 CME  CA  C    single  1.525  0.021  1.525
 CME  CA  HA   single  0.970  0.020  0.970
 CME  CB  SG   single  1.836  0.020  1.836
 CME  CB  HB2  single  0.970  0.020  1.090
 CME  CB  HB3  single  0.970  0.020  1.090
 CME  SG  SD   single  2.053  0.020  2.053
 CME  SD  CE   single  1.823  0.020  1.823
 CME  CE  CZ   single  1.509  0.020  1.509
 CME  CE  HE2  single  0.970  0.020  1.090
 CME  CE  HE3  single  0.970  0.020  1.090
 CME  CZ  OH   single  1.406  0.020  1.406
 CME  CZ  HZ2  single  0.970  0.020  1.090
 CME  CZ  HZ3  single  0.970  0.020  1.090
 CME  OH  HH   single  0.850  0.020  0.980
 CME  C   O    deloc   1.231  0.020  1.231
 CME  C   OXT  deloc   1.244  0.020  1.244

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
 CME  H2   N   H    107.03  3.000
 CME  H2   N   CA   110.34  3.000
 CME  H    N   CA   114.00  3.000
 CME  HA   CA  C    109.00  3.000
 CME  HA   CA  CB   109.00  3.000
 CME  C    CA  CB   110.10  1.900
 CME  HA   CA  N    110.00  3.000
 CME  C    CA  N    111.00  2.800
 CME  CB   CA  N    110.50  1.700
 CME  HB3  CB  HB2  108.41  3.000
 CME  HB3  CB  SG   107.65  3.000
 CME  HB2  CB  SG   108.53  3.000
 CME  HB3  CB  CA   110.78  3.000
 CME  HB2  CB  CA   110.59  3.000
 CME  SG   CB  CA   110.77  3.000
 CME  SD   SG  CB   102.70  3.000
 CME  CE   SD  SG   103.23  3.000
 CME  HE3  CE  HE2  107.56  3.000
 CME  HE3  CE  CZ   111.11  3.000
 CME  HE2  CE  CZ   109.42  3.000
 CME  HE3  CE  SD   104.21  3.000
 CME  HE2  CE  SD   109.09  3.000
 CME  CZ   CE  SD   115.12  3.000
 CME  HZ3  CZ  HZ2  106.64  3.000
 CME  HZ3  CZ  OH   111.79  3.000
 CME  HZ2  CZ  OH   111.94  3.000
 CME  HZ3  CZ  CE   107.29  3.000
 CME  HZ2  CZ  CE   109.11  3.000
 CME  OH   CZ  CE   109.90  3.000
 CME  HH   OH  CZ   108.07  3.000
 CME  OXT  C   O    127.48  3.000
 CME  OXT  C   CA   116.28  3.000
 CME  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
 CME  Var_01  CZ   CE  SD  SG  -60.07  30.0  3
 CME  Var_02  OH   CZ  CE  SD  -58.24  30.0  3
 CME  Var_03  HB2  CB  SG  SD   83.11  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
 CME  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
 CME  plan-1  CA   0.020
 CME  plan-1  C    0.020
 CME  plan-1  O    0.020
 CME  plan-1  OXT  0.020

