# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:04:10 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: (2S)-2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CS[C@@H](CC(O)=O)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
 CML  CML  '(2S)-2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}butanedioic acid'  L-peptide  23  15  .  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_CML
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
 CML  O5   O  O      0  -0.607  31.0019  -2.3640  26.8708
 CML  C4   C  C      0   0.395  32.2222  -2.1050  26.8206
 CML  O4   O  OC    -1  -0.618  32.9479  -1.7759  27.7831
 CML  C3   C  CH2    0  -0.527  32.8993  -2.2251  25.4435
 CML  C2   C  CH1    0  -0.475  32.2832  -1.3418  24.3618
 CML  C1   C  C      0   0.449  30.8858  -1.8029  23.8830
 CML  O1   O  O      0  -0.598  29.9771  -0.9524  23.8807
 CML  O2   O  OC    -1  -0.611  30.8152  -2.9835  23.4919
 CML  SG   S  S2     0  -0.073  32.1792   0.4135  24.8411
 CML  CB   C  CH2    0  -0.521  33.9314   0.7624  25.2009
 CML  CA   C  CH1    0  -0.231  34.1485   2.2547  25.4341
 CML  C    C  C      0   0.384  33.7895   3.0692  24.1609
 CML  O    O  O      0  -0.616  34.4324   2.7712  23.1327
 CML  N    N  NH2    0  -0.783  33.4967   2.6653  26.6700
 CML  OXT  O  OC    -1  -0.602  32.9147   3.9501  24.2656
 CML  H31  H  HCH2   0   0.220  32.8242  -3.2584  25.0887
 CML  H32  H  HCH2   0   0.203  33.9658  -2.0097  25.5304
 CML  H2   H  HCH1   0   0.249  32.9452  -1.3877  23.4882
 CML  HB1  H  HCH2   0   0.241  34.2405   0.2043  26.0860
 CML  HB2  H  HCH2   0   0.240  34.5381   0.4305  24.3579
 CML  HA   H  HCH1   0   0.224  35.2284   2.3752  25.5884
 CML  H1   H  HNH2   0   0.331  33.6544   3.6574  26.7979
 CML  HN2  H  HNH2   0   0.325  32.4925   2.5877  26.5532

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
 CML  O   C    deloc   1.231  0.020  1.231
 CML  O1  C1   deloc   1.245  0.020  1.245
 CML  C1  O2   deloc   1.246  0.020  1.246
 CML  C1  C2   single  1.547  0.020  1.547
 CML  C2  SG   single  1.823  0.020  1.823
 CML  C2  C3   single  1.526  0.020  1.526
 CML  C   OXT  deloc   1.246  0.020  1.246
 CML  C   CA   single  1.525  0.021  1.525
 CML  SG  CB   single  1.822  0.020  1.822
 CML  CB  CA   single  1.530  0.020  1.530
 CML  C3  C4   single  1.539  0.020  1.539
 CML  CA  N    single  1.458  0.019  1.458
 CML  O5  C4   deloc   1.248  0.020  1.248
 CML  C4  O4   deloc   1.250  0.020  1.250
 CML  C3  H31  single  0.970  0.020  1.090
 CML  C3  H32  single  0.970  0.020  1.090
 CML  C2  H2   single  0.970  0.020  1.090
 CML  CB  HB1  single  0.970  0.020  1.090
 CML  CB  HB2  single  0.970  0.020  1.090
 CML  CA  HA   single  0.970  0.020  0.970
 CML  N   H1   single  0.890  0.020  1.040
 CML  N   HN2  single  0.890  0.020  1.040

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
 CML  C3   C4  O4   117.01  3.000
 CML  O4   C4  O5   126.25  3.000
 CML  C3   C4  O5   116.73  3.000
 CML  H32  C3  H31  106.20  3.000
 CML  H32  C3  C2   109.67  3.000
 CML  H31  C3  C2   106.78  3.000
 CML  H32  C3  C4   110.08  3.000
 CML  H31  C3  C4   109.47  3.000
 CML  C2   C3  C4   114.29  3.000
 CML  H2   C2  SG   106.50  3.000
 CML  H2   C2  C1   106.62  3.000
 CML  SG   C2  C1   108.48  3.000
 CML  H2   C2  C3   107.25  3.000
 CML  SG   C2  C3   113.21  3.000
 CML  C1   C2  C3   114.29  3.000
 CML  O2   C1  O1   127.27  3.000
 CML  O2   C1  C2   115.52  3.000
 CML  O1   C1  C2   117.14  3.000
 CML  CB   SG  C2   100.46  3.000
 CML  HB2  CB  HB1  108.29  3.000
 CML  HB2  CB  CA   109.67  3.000
 CML  HB1  CB  CA   109.63  3.000
 CML  HB2  CB  SG   108.91  3.000
 CML  HB1  CB  SG   109.55  3.000
 CML  CA   CB  SG   110.74  3.000
 CML  HA   CA  N    110.00  3.000
 CML  HA   CA  C    109.00  3.000
 CML  N    CA  C    111.00  2.800
 CML  HA   CA  CB   109.00  3.000
 CML  N    CA  CB   110.50  1.700
 CML  C    CA  CB   110.10  1.900
 CML  OXT  C   O    126.83  3.000
 CML  OXT  C   CA   117.65  3.000
 CML  O    C   CA   120.80  1.700
 CML  HN2  N   H1   104.11  3.000
 CML  HN2  N   CA   108.90  3.000
 CML  H1   N   CA   108.28  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
 CML  Var_01  C2  C3  C4  O5   58.04  30.0  2
 CML  Var_02  CA  CB  SG  C2  171.56  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
 CML  chir_01  C2  C1  SG  C3  negativ
 CML  chir_02  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
 CML  plan-1  O5   0.020
 CML  plan-1  C4   0.020
 CML  plan-1  O4   0.020
 CML  plan-1  C3   0.020
 CML  plan-2  C2   0.020
 CML  plan-2  C1   0.020
 CML  plan-2  O1   0.020
 CML  plan-2  O2   0.020
 CML  plan-3  CA   0.020
 CML  plan-3  C    0.020
 CML  plan-3  O    0.020
 CML  plan-3  OXT  0.020

