# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 19:41:53 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  22  11  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.778   1.4394   1.8571  -0.1262
 42Y  CA   C  CH1   0  -0.264   1.4616   0.5123   0.3950
 42Y  CB   C  CH2   0  -0.167   0.3343  -0.3979  -0.1058
 42Y  OG   O  O2    0  -0.462  -0.8851   0.2072   0.3212
 42Y  C1A  C  C     0   0.603  -2.0309  -0.3085  -0.1182
 42Y  OAC  O  O     0  -0.449  -2.0860  -1.2564  -0.8597
 42Y  C2A  C  CH2   0  -0.574  -3.2147   0.4378   0.4344
 42Y  C    C  C     0   0.544   2.7971  -0.1359   0.0760
 42Y  O    O  O     0  -0.428   3.6073   0.3095  -0.6931
 42Y  C1   C  CH3   0  -0.662  -4.5467  -0.0830  -0.0730
 42Y  O1   O  OH1   0  -0.592   2.9612  -1.2715   0.7427
 42Y  H1   H  HNH2  0   0.349   1.4274   1.8482  -1.1390
 42Y  H2   H  HNH2  0   0.360   0.5914   2.3214   0.1698
 42Y  H4   H  HCH1  0   0.290   1.3881   0.5680   1.4866
 42Y  H5   H  HCH2  0   0.244   0.3670  -0.4667  -1.1969
 42Y  H6   H  HCH2  0   0.249   0.4131  -1.4056   0.3069
 42Y  H7   H  HCH2  0   0.276  -3.1673   0.3806   1.5256
 42Y  H8   H  HCH2  0   0.275  -3.0947   1.4975   0.1940
 42Y  H9   H  HCH3  0   0.232  -4.6289   0.0074  -1.1557
 42Y  H10  H  HCH3  0   0.232  -4.6976  -1.1292   0.1901
 42Y  H11  H  HCH3  0   0.239  -5.3599   0.4905   0.3697
 42Y  H12  H  HOH1  0   0.485   3.8079  -1.6781   0.5037

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    double  1.203  0.020  1.203
 42Y  C    CA   single  1.518  0.020  1.518
 42Y  N    CA   single  1.442  0.020  1.442
 42Y  CA   CB   single  1.533  0.020  1.533
 42Y  CB   OG   single  1.427  0.020  1.427
 42Y  OAC  C1A  double  1.205  0.020  1.205
 42Y  OG   C1A  single  1.331  0.020  1.331
 42Y  C1A  C2A  single  1.505  0.020  1.505
 42Y  C2A  C1   single  1.518  0.020  1.518
 42Y  C    O1   single  1.327  0.020  1.327
 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
 42Y  O1   H12  single  0.850  0.020  0.980

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   106.67  3.000
 42Y  H2   N    CA   109.58  3.000
 42Y  H1   N    CA   110.69  3.000
 42Y  H4   CA   C    106.86  3.000
 42Y  H4   CA   CB   107.84  3.000
 42Y  C    CA   CB   108.95  3.000
 42Y  H4   CA   N    108.15  3.000
 42Y  CB   CA   N    115.10  3.000
 42Y  C    CA   N    109.61  3.000
 42Y  H6   CB   H5   108.48  3.000
 42Y  H6   CB   OG   109.88  3.000
 42Y  H5   CB   OG   110.54  3.000
 42Y  H6   CB   CA   111.81  3.000
 42Y  H5   CB   CA   109.95  3.000
 42Y  OG   CB   CA   106.19  3.000
 42Y  C1A  OG   CB   118.20  3.000
 42Y  C2A  C1A  OAC  125.47  3.000
 42Y  C2A  C1A  OG   111.33  3.000
 42Y  OAC  C1A  OG   123.19  3.000
 42Y  H8   C2A  H7   105.38  3.000
 42Y  H8   C2A  C1   110.82  3.000
 42Y  H7   C2A  C1   110.71  3.000
 42Y  H8   C2A  C1A  108.28  3.000
 42Y  H7   C2A  C1A  107.85  3.000
 42Y  C1   C2A  C1A  113.43  3.000
 42Y  O1   C    O    123.70  3.000
 42Y  O1   C    CA   111.63  3.000
 42Y  O    C    CA   124.67  3.000
 42Y  H11  C1   H10  107.71  3.000
 42Y  H11  C1   H9   107.68  3.000
 42Y  H10  C1   H9   108.01  3.000
 42Y  H11  C1   C2A  109.81  3.000
 42Y  H10  C1   C2A  111.74  3.000
 42Y  H9   C1   C2A  111.72  3.000
 42Y  H12  O1   C    110.07  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  CONST_01  H12  O1   C    CA   180.00   0.0  0
 42Y  Var_01    OAC  C1A  OG   CB    -0.21  30.0  3
 42Y  Var_02    C1   C2A  C1A  OG   178.11  30.0  3
 42Y  Var_03    H5   CB   OG   C1A   53.26  30.0  1
 42Y  Var_04    H9   C1   C2A  C1A  -61.14  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-1  H12  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

