# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 07:17:13 2020
#   Inital geometry file: a 38 line input string
#   Ligand name: (2S)-2-chlorobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](Cl)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
 39J  39J  '(2S)-2-chlorobutanoic acid'  ligand  14  7  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_39J
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
 39J  C1    C   C     0   0.590  -1.3534   0.4023  -0.0118
 39J  O1    O   OH1   0  -0.582  -2.1620  -0.2886   0.7728
 39J  C2    C   CH1   0  -0.394   0.0876   0.3210   0.4590
 39J  O2    O   O     0  -0.419  -1.7102   1.0216  -0.9784
 39J  C3    C   CH2   0  -0.413   1.0158   1.2572  -0.2817
 39J  C4    C   CH3   0  -0.664   2.4484   1.2120   0.2259
 39J  CL2   CL  CL    0  -0.131   0.5914  -1.4016   0.2323
 39J  H1    H   HOH1  0   0.489  -3.0732  -0.2373   0.4461
 39J  H2    H   HCH1  0   0.329   0.1294   0.5030   1.5346
 39J  H31C  H   HCH2  0   0.248   0.9784   1.0454  -1.3513
 39J  H32C  H   HCH2  0   0.253   0.6201   2.2676  -0.1473
 39J  H41C  H   HCH3  0   0.242   3.0509   1.9617  -0.2857
 39J  H42C  H   HCH3  0   0.227   2.4986   1.4212   1.2956
 39J  H43C  H   HCH3  0   0.228   2.9113   0.2414   0.0508

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
 39J  C1  O1    single  1.322  0.020  1.322
 39J  C1  C2    single  1.518  0.020  1.518
 39J  C1  O2    double  1.202  0.020  1.202
 39J  C2  C3    single  1.512  0.020  1.512
 39J  C2  CL2   single  1.809  0.020  1.809
 39J  C3  C4    single  1.521  0.020  1.521
 39J  O1  H1    single  0.850  0.020  0.980
 39J  C2  H2    single  0.970  0.020  1.090
 39J  C3  H31C  single  0.970  0.020  1.090
 39J  C3  H32C  single  0.970  0.020  1.090
 39J  C4  H41C  single  0.970  0.020  1.090
 39J  C4  H42C  single  0.970  0.020  1.090
 39J  C4  H43C  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
 39J  O2    C1  C2    123.96  3.000
 39J  O2    C1  O1    124.41  3.000
 39J  C2    C1  O1    111.63  3.000
 39J  H1    O1  C1    110.32  3.000
 39J  H2    C2  CL2   105.76  3.000
 39J  H2    C2  C3    110.85  3.000
 39J  CL2   C2  C3    110.93  3.000
 39J  H2    C2  C1    109.44  3.000
 39J  CL2   C2  C1    106.05  3.000
 39J  C3    C2  C1    113.43  3.000
 39J  H32C  C3  H31C  106.71  3.000
 39J  H32C  C3  C4    109.12  3.000
 39J  H31C  C3  C4    110.72  3.000
 39J  H32C  C3  C2    106.84  3.000
 39J  H31C  C3  C2    109.81  3.000
 39J  C4    C3  C2    113.35  3.000
 39J  H43C  C4  H42C  107.99  3.000
 39J  H43C  C4  H41C  107.61  3.000
 39J  H42C  C4  H41C  107.64  3.000
 39J  H43C  C4  C3    111.91  3.000
 39J  H42C  C4  C3    111.40  3.000
 39J  H41C  C4  C3    110.11  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
 39J  CONST_01  H1    O1  C1  C2   180.00   0.0  0
 39J  Var_01    H41C  C4  C3  C2  -175.36  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
 39J  chir_01  C2  C1  C3  CL2  positiv

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
 39J  plan-1  C1  0.020
 39J  plan-1  O1  0.020
 39J  plan-1  C2  0.020
 39J  plan-1  O2  0.020
 39J  plan-1  H1  0.020

