# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:28:32 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  13  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 GRAND
;

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   0.433  -1.3498   0.2605  -0.0402
 39J  O1    O   OC    -1  -0.601  -2.1460   0.5858   0.8591
 39J  C2    C   CH1    0  -0.358   0.1270   0.1385   0.3992
 39J  O2    O   O      0  -0.596  -1.5916   0.0703  -1.2427
 39J  C3    C   CH2    0  -0.417   0.9805   1.2509  -0.1811
 39J  C4    C   CH3    0  -0.660   2.4304   1.2413   0.2763
 39J  CL2   CL  CL     0  -0.205   0.7707  -1.4746  -0.1446
 39J  H2    H   HCH1   0   0.264   0.2091   0.1236   1.4860
 39J  H31C  H   HCH2   0   0.231   0.9173   1.2178  -1.2705
 39J  H32C  H   HCH2   0   0.236   0.5143   2.1925   0.1278
 39J  H41C  H   HCH3   0   0.232   2.9685   2.0962  -0.1341
 39J  H42C  H   HCH3   0   0.220   2.5020   1.2979   1.3639
 39J  H43C  H   HCH3   0   0.222   2.9488   0.3385  -0.0466

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    deloc   1.244  0.020  1.244
 39J  C1  C2    single  1.546  0.020  1.546
 39J  C1  O2    deloc   1.241  0.020  1.241
 39J  C2  C3    single  1.517  0.020  1.517
 39J  C2  CL2   single  1.820  0.020  1.820
 39J  C3  C4    single  1.520  0.020  1.520
 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    116.71  3.000
 39J  O2    C1  O1    127.99  3.000
 39J  C2    C1  O1    115.25  3.000
 39J  H2    C2  CL2   105.02  3.000
 39J  H2    C2  C3    110.42  3.000
 39J  CL2   C2  C3    109.67  3.000
 39J  H2    C2  C1    110.89  3.000
 39J  CL2   C2  C1    108.84  3.000
 39J  C3    C2  C1    111.76  3.000
 39J  H32C  C3  H31C  106.44  3.000
 39J  H32C  C3  C4    109.06  3.000
 39J  H31C  C3  C4    110.80  3.000
 39J  H32C  C3  C2    106.44  3.000
 39J  H31C  C3  C2    109.08  3.000
 39J  C4    C3  C2    114.62  3.000
 39J  H43C  C4  H42C  107.88  3.000
 39J  H43C  C4  H41C  107.65  3.000
 39J  H42C  C4  H41C  107.58  3.000
 39J  H43C  C4  C3    111.70  3.000
 39J  H42C  C4  C3    111.22  3.000
 39J  H41C  C4  C3    110.64  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  Var_01  H41C  C4  C3  C2  -176.86  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

