# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 04:07:54 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: (2R)-2-methylbutanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: 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
 JO3  JO3  '(2R)-2-methylbutanedioic acid'  ligand  17  9  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JO3
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
 JO3  OAN   O  OH1   0  -0.594   2.8137  -0.4899   0.4902
 JO3  CAM   C  C     0   0.574   1.8386   0.3120   0.0783
 JO3  OAO   O  O     0  -0.439   2.0335   1.4374  -0.3087
 JO3  CAL   C  CH1   0  -0.387   0.4908  -0.3703   0.1389
 JO3  CAQ   C  CH3   0  -0.662   0.4449  -1.5029  -0.8936
 JO3  CAK   C  CH2   0  -0.572  -0.6243   0.6432  -0.0766
 JO3  CAJ   C  C     0   0.553  -1.9875   0.1067   0.2681
 JO3  OAP   O  O     0  -0.443  -2.2047  -0.8542   0.9639
 JO3  OAG   O  OH1   0  -0.593  -2.9524   0.8514  -0.2597
 JO3  HAL   H  HCH1  0   0.285   0.3953  -0.8080   1.1368
 JO3  HAQ1  H  HCH3  0   0.249  -0.5138  -2.0171  -0.8518
 JO3  HAQ2  H  HCH3  0   0.235   0.5727  -1.1147  -1.9052
 JO3  HAQ3  H  HCH3  0   0.250   1.2197  -2.2456  -0.7123
 JO3  HAK1  H  HCH2  0   0.303  -0.4734   1.5246   0.5555
 JO3  HAK2  H  HCH2  0   0.279  -0.6277   1.0110  -1.1048
 JO3  HAG   H  HOH1  0   0.480  -3.8184   0.5146   0.0153
 JO3  HAN   H  HOH1  0   0.481   3.6681  -0.0394   0.4133

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
 JO3  OAN  CAM   single  1.328  0.020  1.328
 JO3  CAM  OAO   double  1.206  0.020  1.206
 JO3  CAM  CAL   single  1.512  0.020  1.512
 JO3  CAL  CAQ   single  1.533  0.020  1.533
 JO3  CAL  CAK   single  1.522  0.020  1.522
 JO3  CAK  CAJ   single  1.505  0.020  1.505
 JO3  CAJ  OAP   double  1.206  0.020  1.206
 JO3  CAJ  OAG   single  1.328  0.020  1.328
 JO3  CAL  HAL   single  0.970  0.020  1.090
 JO3  CAQ  HAQ1  single  0.970  0.020  1.090
 JO3  CAQ  HAQ2  single  0.970  0.020  1.090
 JO3  CAQ  HAQ3  single  0.970  0.020  1.090
 JO3  CAK  HAK1  single  0.970  0.020  1.090
 JO3  CAK  HAK2  single  0.970  0.020  1.090
 JO3  OAG  HAG   single  0.850  0.020  0.980
 JO3  OAN  HAN   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
 JO3  HAN   OAN  CAM   110.01  3.000
 JO3  CAL   CAM  OAO   125.32  3.000
 JO3  CAL   CAM  OAN   111.70  3.000
 JO3  OAO   CAM  OAN   122.98  3.000
 JO3  HAL   CAL  CAK   109.37  3.000
 JO3  HAL   CAL  CAQ   108.43  3.000
 JO3  CAK   CAL  CAQ   112.00  3.000
 JO3  HAL   CAL  CAM   107.16  3.000
 JO3  CAK   CAL  CAM   110.30  3.000
 JO3  CAQ   CAL  CAM   109.46  3.000
 JO3  HAQ3  CAQ  HAQ2  108.29  3.000
 JO3  HAQ3  CAQ  HAQ1  107.34  3.000
 JO3  HAQ2  CAQ  HAQ1  107.87  3.000
 JO3  HAQ3  CAQ  CAL   111.75  3.000
 JO3  HAQ2  CAQ  CAL   110.98  3.000
 JO3  HAQ1  CAQ  CAL   110.45  3.000
 JO3  HAK2  CAK  HAK1  105.83  3.000
 JO3  HAK2  CAK  CAJ   109.45  3.000
 JO3  HAK1  CAK  CAJ   106.23  3.000
 JO3  HAK2  CAK  CAL   111.09  3.000
 JO3  HAK1  CAK  CAL   110.68  3.000
 JO3  CAJ   CAK  CAL   113.19  3.000
 JO3  OAG   CAJ  OAP   123.03  3.000
 JO3  OAG   CAJ  CAK   111.54  3.000
 JO3  OAP   CAJ  CAK   125.40  3.000
 JO3  HAG   OAG  CAJ   109.98  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
 JO3  CONST_01  HAN  OAN  CAM  OAO    0.00   0.0  0
 JO3  CONST_02  HAG  OAG  CAJ  CAK  180.00   0.0  0
 JO3  Var_01    OAP  CAJ  CAK  CAL   19.04  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
 JO3  chir_01  CAL  CAM  CAQ  CAK  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
 JO3  plan-1  OAN  0.020
 JO3  plan-1  CAM  0.020
 JO3  plan-1  OAO  0.020
 JO3  plan-1  CAL  0.020
 JO3  plan-1  HAN  0.020
 JO3  plan-2  CAK  0.020
 JO3  plan-2  CAJ  0.020
 JO3  plan-2  OAP  0.020
 JO3  plan-2  OAG  0.020
 JO3  plan-2  HAG  0.020

