# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 03:30:45 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  15  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 PERFECT
;

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  OC    -1  -0.632   2.8483  -0.5081   0.4037
 JO3  CAM   C  C      0   0.419   1.9042   0.2761   0.1613
 JO3  OAO   O  O      0  -0.609   2.0182   1.4969  -0.0724
 JO3  CAL   C  CH1    0  -0.361   0.4906  -0.3461   0.1574
 JO3  CAQ   C  CH3    0  -0.659   0.4241  -1.4711  -0.8759
 JO3  CAK   C  CH2    0  -0.532  -0.6297   0.6641  -0.0550
 JO3  CAJ   C  C      0   0.394  -2.0447   0.1017   0.1494
 JO3  OAP   O  O      0  -0.624  -2.2251  -0.6470   1.1345
 JO3  OAG   O  OC    -1  -0.630  -2.9267   0.4624  -0.6603
 JO3  HAL   H  HCH1   0   0.203   0.3445  -0.8018   1.1433
 JO3  HAQ1  H  HCH3   0   0.214  -0.5325  -1.9950  -0.8371
 JO3  HAQ2  H  HCH3   0   0.203   0.5416  -1.0801  -1.8904
 JO3  HAQ3  H  HCH3   0   0.217   1.2100  -2.2071  -0.7112
 JO3  HAK1  H  HCH2   0   0.213  -0.5021   1.4913   0.6529
 JO3  HAK2  H  HCH2   0   0.183  -0.5496   1.1087  -1.0510

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   deloc   1.251  0.020  1.251
 JO3  CAM  OAO   deloc   1.248  0.020  1.248
 JO3  CAM  CAL   single  1.544  0.020  1.544
 JO3  CAL  CAQ   single  1.529  0.020  1.529
 JO3  CAL  CAK   single  1.523  0.020  1.523
 JO3  CAK  CAJ   single  1.536  0.020  1.536
 JO3  CAJ  OAP   deloc   1.250  0.020  1.250
 JO3  CAJ  OAG   deloc   1.250  0.020  1.250
 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

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  CAL   CAM  OAO   118.50  3.000
 JO3  CAL   CAM  OAN   116.02  3.000
 JO3  OAO   CAM  OAN   125.48  3.000
 JO3  HAL   CAL  CAK   107.64  3.000
 JO3  HAL   CAL  CAQ   107.23  3.000
 JO3  CAK   CAL  CAQ   111.21  3.000
 JO3  HAL   CAL  CAM   106.69  3.000
 JO3  CAK   CAL  CAM   113.97  3.000
 JO3  CAQ   CAL  CAM   109.75  3.000
 JO3  HAQ3  CAQ  HAQ2  107.71  3.000
 JO3  HAQ3  CAQ  HAQ1  107.62  3.000
 JO3  HAQ2  CAQ  HAQ1  107.38  3.000
 JO3  HAQ3  CAQ  CAL   111.32  3.000
 JO3  HAQ2  CAQ  CAL   111.05  3.000
 JO3  HAQ1  CAQ  CAL   111.55  3.000
 JO3  HAK2  CAK  HAK1  105.83  3.000
 JO3  HAK2  CAK  CAJ   109.72  3.000
 JO3  HAK1  CAK  CAJ   107.31  3.000
 JO3  HAK2  CAK  CAL   110.04  3.000
 JO3  HAK1  CAK  CAL   108.95  3.000
 JO3  CAJ   CAK  CAL   114.58  3.000
 JO3  OAG   CAJ  OAP   125.53  3.000
 JO3  OAG   CAJ  CAK   117.25  3.000
 JO3  OAP   CAJ  CAK   117.18  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  Var_01  OAP  CAJ  CAK  CAL  43.08  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-2  CAK  0.020
 JO3  plan-2  CAJ  0.020
 JO3  plan-2  OAP  0.020
 JO3  plan-2  OAG  0.020

