# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:59:03 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  23  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   0.560  -2.0474  -0.2236   0.1680
 02X  O1   O  O     0  -0.440  -2.0720   0.7222   0.9167
 02X  C4   C  CH2   0  -0.588  -0.7962  -0.9029  -0.3135
 02X  C5   C  CH1   0  -0.332   0.4786  -0.2710   0.2331
 02X  C6   C  CH1   0  -0.232   1.7362  -0.9503  -0.3599
 02X  C7   C  C     0   0.548   0.4945   1.2008  -0.1128
 02X  O2   O  O     0  -0.449   0.2149   1.6314  -1.2060
 02X  C8   C  CH3   0  -0.662   3.0273  -0.2642   0.0795
 02X  C9   C  CH3   0  -0.664   1.7917  -2.4275   0.0216
 02X  H4   H  HCH2  0   0.304  -0.8566  -1.9538  -0.0224
 02X  H4A  H  HCH2  0   0.288  -0.7926  -0.8978  -1.4073
 02X  H5   H  HCH1  0   0.267   0.5078  -0.3832   1.3207
 02X  H6   H  HCH1  0   0.233   1.6635  -0.8777  -1.4508
 02X  H8   H  HCH3  0   0.223   3.1247  -0.2652   1.1672
 02X  H8A  H  HCH3  0   0.236   3.8874  -0.7955  -0.3295
 02X  H8B  H  HCH3  0   0.234   3.1015   0.7685  -0.2624
 02X  H9   H  HCH3  0   0.236   0.9536  -3.0015  -0.3729
 02X  H9A  H  HCH3  0   0.237   2.7029  -2.8822  -0.3694
 02X  H9B  H  HCH3  0   0.222   1.8015  -2.5492   1.1070
 02X  OXT  O  OH1   0  -0.593  -3.1400  -0.7913  -0.3258
 02X  HXT  H  HOH1  0   0.482  -3.9298  -0.3339  -0.0003
 02X  O3   O  OH1   0  -0.588   0.8937   1.9725   0.8886
 02X  H1   H  HOH1  0   0.476   0.9263   2.8967   0.5981

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   double  1.207  0.020  1.207
 02X  C4   C3   single  1.503  0.020  1.503
 02X  C5   C4   single  1.524  0.020  1.524
 02X  C4   H4   single  0.970  0.020  1.090
 02X  C4   H4A  single  0.970  0.020  1.090
 02X  C7   C5   single  1.512  0.020  1.512
 02X  C5   C6   single  1.547  0.020  1.547
 02X  C5   H5   single  0.970  0.020  1.090
 02X  C6   C8   single  1.527  0.020  1.527
 02X  C6   C9   single  1.527  0.020  1.527
 02X  C6   H6   single  0.970  0.020  1.090
 02X  O2   C7   double  1.208  0.020  1.208
 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  single  1.327  0.020  1.327
 02X  OXT  HXT  single  0.850  0.020  0.980
 02X  C7   O3   single  1.326  0.020  1.326
 02X  O3   H1   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
 02X  OXT  C3   C4   111.90  3.000
 02X  OXT  C3   O1   123.35  3.000
 02X  C4   C3   O1   124.76  3.000
 02X  H4A  C4   H4   105.74  3.000
 02X  H4A  C4   C5   110.73  3.000
 02X  H4   C4   C5   110.46  3.000
 02X  H4A  C4   C3   108.73  3.000
 02X  H4   C4   C3   107.67  3.000
 02X  C5   C4   C3   113.20  3.000
 02X  H5   C5   C7   109.09  3.000
 02X  H5   C5   C6   108.32  3.000
 02X  C7   C5   C6   109.33  3.000
 02X  H5   C5   C4   109.66  3.000
 02X  C6   C5   C4   111.12  3.000
 02X  C7   C5   C4   109.29  3.000
 02X  H6   C6   C9   108.37  3.000
 02X  H6   C6   C8   108.23  3.000
 02X  C9   C6   C8   109.40  3.000
 02X  H6   C6   C5   107.37  3.000
 02X  C9   C6   C5   111.01  3.000
 02X  C8   C6   C5   112.32  3.000
 02X  O3   C7   O2   123.09  3.000
 02X  O3   C7   C5   113.39  3.000
 02X  O2   C7   C5   123.48  3.000
 02X  H8B  C8   H8A  106.87  3.000
 02X  H8B  C8   H8   107.89  3.000
 02X  H8A  C8   H8   107.62  3.000
 02X  H8B  C8   C6   113.13  3.000
 02X  H8A  C8   C6   109.89  3.000
 02X  H8   C8   C6   111.20  3.000
 02X  H9B  C9   H9A  107.59  3.000
 02X  H9B  C9   H9   107.93  3.000
 02X  H9A  C9   H9   107.05  3.000
 02X  H9B  C9   C6   110.88  3.000
 02X  H9A  C9   C6   110.13  3.000
 02X  H9   C9   C6   113.03  3.000
 02X  HXT  OXT  C3   110.14  3.000
 02X  H1   O3   C7   109.80  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  CONST_01  HXT  OXT  C3  O1    0.00   0.0  0
 02X  CONST_02  H1   O3   C7  C5  180.00   0.0  0
 02X  Var_01    C5   C4   C3  O1   -0.39  30.0  2
 02X  Var_02    H8   C8   C6  C5   58.85  30.0  3
 02X  Var_03    H9   C9   C6  C5   62.59  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-1  HXT  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
 02X  plan-2  H1   0.020

