# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:07:00 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: O-propanoyl-L-serine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)OC[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
 42Y  42Y  'O-propanoyl-L-serine     '  ligand  21  11  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_42Y
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
 42Y  N    N  NH2    0  -0.793   1.3960   1.8914  -0.0871
 42Y  CA   C  CH1    0  -0.253   1.4185   0.5392   0.4349
 42Y  CB   C  CH2    0  -0.173   0.2883  -0.3493  -0.0747
 42Y  OG   O  O2     0  -0.465  -0.9542   0.2389   0.3409
 42Y  C1A  C  C      0   0.599  -2.0873  -0.2824  -0.1115
 42Y  OAC  O  O      0  -0.457  -2.1337  -1.2251  -0.8625
 42Y  C2A  C  CH2    0  -0.573  -3.2858   0.4443   0.4394
 42Y  C    C  C      0   0.400   2.7528  -0.1794   0.1036
 42Y  O    O  O      0  -0.595   3.4736   0.3280  -0.7741
 42Y  C1   C  CH3    0  -0.662  -4.6068  -0.0695  -0.1026
 42Y  O1   O  OC    -1  -0.613   2.9650  -1.2332   0.7348
 42Y  H1   H  HNH2   0   0.330   1.7003   1.8737  -1.0519
 42Y  H2   H  HNH2   0   0.334   0.4538   2.2610  -0.0785
 42Y  H4   H  HCH1   0   0.223   1.3355   0.5836   1.5273
 42Y  H5   H  HCH2   0   0.224   0.3218  -0.4138  -1.1665
 42Y  H6   H  HCH2   0   0.231   0.3704  -1.3573   0.3356
 42Y  H7   H  HCH2   0   0.274  -3.2573   0.3576   1.5295
 42Y  H8   H  HCH2   0   0.271  -3.1687   1.5109   0.2302
 42Y  H9   H  HCH3   0   0.230  -4.6730   0.0501  -1.1836
 42Y  H10  H  HCH3   0   0.231  -4.7552  -1.1235   0.1287
 42Y  H11  H  HCH3   0   0.237  -5.4315   0.4858   0.3426

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
 42Y  C    O    deloc   1.244  0.020  1.244
 42Y  C    CA   single  1.551  0.020  1.551
 42Y  N    CA   single  1.450  0.020  1.450
 42Y  CA   CB   single  1.525  0.020  1.525
 42Y  CB   OG   single  1.436  0.020  1.436
 42Y  OAC  C1A  double  1.206  0.020  1.206
 42Y  OG   C1A  single  1.327  0.020  1.327
 42Y  C1A  C2A  single  1.506  0.020  1.506
 42Y  C2A  C1   single  1.518  0.020  1.518
 42Y  C    O1   deloc   1.247  0.020  1.247
 42Y  N    H1   single  0.890  0.020  1.040
 42Y  N    H2   single  0.890  0.020  1.040
 42Y  CA   H4   single  0.970  0.020  1.090
 42Y  CB   H5   single  0.970  0.020  1.090
 42Y  CB   H6   single  0.970  0.020  1.090
 42Y  C2A  H7   single  0.970  0.020  1.090
 42Y  C2A  H8   single  0.970  0.020  1.090
 42Y  C1   H9   single  0.970  0.020  1.090
 42Y  C1   H10  single  0.970  0.020  1.090
 42Y  C1   H11  single  0.970  0.020  1.090

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
 42Y  H2   N    H1   107.13  3.000
 42Y  H2   N    CA   110.61  3.000
 42Y  H1   N    CA   108.81  3.000
 42Y  H4   CA   C    107.26  3.000
 42Y  H4   CA   CB   107.48  3.000
 42Y  C    CA   CB   107.23  3.000
 42Y  H4   CA   N    108.65  3.000
 42Y  CB   CA   N    114.30  3.000
 42Y  C    CA   N    111.63  3.000
 42Y  H6   CB   H5   108.57  3.000
 42Y  H6   CB   OG   109.55  3.000
 42Y  H5   CB   OG   109.84  3.000
 42Y  H6   CB   CA   110.89  3.000
 42Y  H5   CB   CA   110.18  3.000
 42Y  OG   CB   CA   107.81  3.000
 42Y  C1A  OG   CB   118.64  3.000
 42Y  C2A  C1A  OAC  125.05  3.000
 42Y  C2A  C1A  OG   111.43  3.000
 42Y  OAC  C1A  OG   123.52  3.000
 42Y  H8   C2A  H7   105.38  3.000
 42Y  H8   C2A  C1   110.81  3.000
 42Y  H7   C2A  C1   110.59  3.000
 42Y  H8   C2A  C1A  108.39  3.000
 42Y  H7   C2A  C1A  107.80  3.000
 42Y  C1   C2A  C1A  113.50  3.000
 42Y  O1   C    O    127.12  3.000
 42Y  O1   C    CA   115.46  3.000
 42Y  O    C    CA   117.40  3.000
 42Y  H11  C1   H10  107.66  3.000
 42Y  H11  C1   H9   107.67  3.000
 42Y  H10  C1   H9   107.97  3.000
 42Y  H11  C1   C2A  109.90  3.000
 42Y  H10  C1   C2A  111.74  3.000
 42Y  H9   C1   C2A  111.72  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
 42Y  Var_01  OAC  C1A  OG   CB    -0.36  30.0  3
 42Y  Var_02  C1   C2A  C1A  OG   177.11  30.0  3
 42Y  Var_03  H5   CB   OG   C1A   52.73  30.0  1
 42Y  Var_04  H9   C1   C2A  C1A  -61.29  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
 42Y  chir_01  CA  C  N  CB  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
 42Y  plan-1  CA   0.020
 42Y  plan-1  C    0.020
 42Y  plan-1  O    0.020
 42Y  plan-1  O1   0.020
 42Y  plan-2  OG   0.020
 42Y  plan-2  C1A  0.020
 42Y  plan-2  OAC  0.020
 42Y  plan-2  C2A  0.020

