# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 10:34:07 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (2S)-2-(propan-2-yl)butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](CC(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
 02X  02X  '(2S)-2-(propan-2-yl)butanedioic acid'  ligand  21  11  .  2021-07-27  2021-07-27  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_02X
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
 02X  C3   C  C      0   0.405  -2.1471  -0.2075   0.1355
 02X  O1   O  O      0  -0.612  -2.1504   0.4554   1.1925
 02X  C4   C  CH2    0  -0.562  -0.8345  -0.8860  -0.2761
 02X  C5   C  CH1    0  -0.283   0.4323  -0.2388   0.2724
 02X  C6   C  CH1    0  -0.220   1.6969  -0.8967  -0.3175
 02X  C7   C  C      0   0.420   0.4418   1.2696  -0.0307
 02X  O2   O  O      0  -0.628   0.0742   1.6091  -1.1774
 02X  C8   C  CH3    0  -0.652   2.9859  -0.2356   0.1666
 02X  C9   C  CH3    0  -0.658   1.7626  -2.3918  -0.0087
 02X  H4   H  HCH2   0   0.215  -0.8996  -1.9285   0.0592
 02X  H4A  H  HCH2   0   0.193  -0.7814  -0.9342  -1.3672
 02X  H5   H  HCH1   0   0.170   0.4652  -0.3735   1.3598
 02X  H6   H  HCH1   0   0.196   1.6454  -0.7788  -1.4073
 02X  H8   H  HCH3   0   0.204   3.0723  -0.2992   1.2544
 02X  H8A  H  HCH3   0   0.210   3.8571  -0.7363  -0.2611
 02X  H8B  H  HCH3   0   0.225   3.0470   0.8172  -0.1052
 02X  H9   H  HCH3   0   0.225   0.9226  -2.9455  -0.4280
 02X  H9A  H  HCH3   0   0.218   2.6763  -2.8335  -0.4127
 02X  H9B  H  HCH3   0   0.206   1.7659  -2.5630   1.0713
 02X  OXT  O  OC    -1  -0.640  -3.1372  -0.4087  -0.6037
 02X  O3   O  OC    -1  -0.633   0.8525   2.0467   0.8573

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
 02X  O1  C3   deloc   1.248  0.020  1.248
 02X  C4  C3   single  1.534  0.020  1.534
 02X  C5  C4   single  1.525  0.020  1.525
 02X  C4  H4   single  0.970  0.020  1.090
 02X  C4  H4A  single  0.970  0.020  1.090
 02X  C7  C5   single  1.539  0.020  1.539
 02X  C5  C6   single  1.543  0.020  1.543
 02X  C5  H5   single  0.970  0.020  1.090
 02X  C6  C8   single  1.527  0.020  1.527
 02X  C6  C9   single  1.528  0.020  1.528
 02X  C6  H6   single  0.970  0.020  1.090
 02X  O2  C7   deloc   1.251  0.020  1.251
 02X  C8  H8   single  0.970  0.020  1.090
 02X  C8  H8A  single  0.970  0.020  1.090
 02X  C8  H8B  single  0.970  0.020  1.090
 02X  C9  H9   single  0.970  0.020  1.090
 02X  C9  H9A  single  0.970  0.020  1.090
 02X  C9  H9B  single  0.970  0.020  1.090
 02X  C3  OXT  deloc   1.252  0.020  1.252
 02X  C7  O3   deloc   1.249  0.020  1.249

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
 02X  OXT  C3  C4   116.57  3.000
 02X  OXT  C3  O1   125.70  3.000
 02X  C4   C3  O1   117.69  3.000
 02X  H4A  C4  H4   105.42  3.000
 02X  H4A  C4  C5   109.71  3.000
 02X  H4   C4  C5   110.04  3.000
 02X  H4A  C4  C3   109.20  3.000
 02X  H4   C4  C3   106.71  3.000
 02X  C5   C4  C3   115.26  3.000
 02X  H5   C5  C7   108.40  3.000
 02X  H5   C5  C6   107.59  3.000
 02X  C7   C5  C6   109.74  3.000
 02X  H5   C5  C4   109.25  3.000
 02X  C6   C5  C4   111.26  3.000
 02X  C7   C5  C4   110.51  3.000
 02X  H6   C6  C9   107.93  3.000
 02X  H6   C6  C8   107.93  3.000
 02X  C9   C6  C8   108.85  3.000
 02X  H6   C6  C5   107.18  3.000
 02X  C9   C6  C5   112.04  3.000
 02X  C8   C6  C5   112.71  3.000
 02X  O3   C7  O2   125.39  3.000
 02X  O3   C7  C5   118.15  3.000
 02X  O2   C7  C5   116.41  3.000
 02X  H8B  C8  H8A  107.50  3.000
 02X  H8B  C8  H8   107.47  3.000
 02X  H8A  C8  H8   107.46  3.000
 02X  H8B  C8  C6   112.75  3.000
 02X  H8A  C8  C6   110.53  3.000
 02X  H8   C8  C6   110.91  3.000
 02X  H9B  C9  H9A  107.43  3.000
 02X  H9B  C9  H9   107.62  3.000
 02X  H9A  C9  H9   107.27  3.000
 02X  H9B  C9  C6   110.67  3.000
 02X  H9A  C9  C6   110.90  3.000
 02X  H9   C9  C6   112.71  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
 02X  Var_01  C5  C4  C3  O1  -24.90  30.0  2
 02X  Var_02  H8  C8  C6  C5   60.16  30.0  3
 02X  Var_03  H9  C9  C6  C5   61.13  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
 02X  chir_01  C5  C4  C7  C6  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
 02X  plan-1  C3   0.020
 02X  plan-1  O1   0.020
 02X  plan-1  C4   0.020
 02X  plan-1  OXT  0.020
 02X  plan-2  C5   0.020
 02X  plan-2  C7   0.020
 02X  plan-2  O2   0.020
 02X  plan-2  O3   0.020

