# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 04:27:29 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[C@@H](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
 2JD  2JD  '(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoic acid'  ligand  27  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2JD
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
 2JD  C16  C  C     0   0.514   3.5245   0.0411   0.1552
 2JD  O3   O  O     0  -0.436   4.1472  -0.5196  -0.7122
 2JD  C17  C  CH1   0  -0.032   2.1472  -0.4215   0.6108
 2JD  O4   O  OH1   0  -0.654   2.0842  -1.8185   0.5293
 2JD  C18  C  CT    0  -0.186   0.9989   0.2842  -0.1657
 2JD  C19  C  CH2   0  -0.131  -0.2893  -0.2193   0.4930
 2JD  C20  C  CH3   0  -0.653   1.1004   1.8030  -0.0080
 2JD  C21  C  CH3   0  -0.668   1.0154  -0.0883  -1.6490
 2JD  P    P  P     0   1.456  -2.8783  -0.2007   0.0709
 2JD  O1P  O  O     0  -0.711  -3.0485  -1.6510  -0.1358
 2JD  O2P  O  O2    0  -0.589  -1.4146   0.3906  -0.1470
 2JD  O3P  O  OH1   0  -0.732  -3.6296   0.7867  -0.9298
 2JD  H15  H  HCH1  0   0.277   2.0343  -0.1683   1.6699
 2JD  H16  H  HOH1  0   0.451   2.3851  -2.0982  -0.3430
 2JD  H17  H  HCH2  0   0.249  -0.3586  -1.3057   0.4091
 2JD  H18  H  HCH2  0   0.243  -0.2918   0.0427   1.5562
 2JD  H19  H  HCH3  0   0.238   1.9603   2.2081  -0.5411
 2JD  H20  H  HCH3  0   0.246   0.2172   2.2886  -0.4213
 2JD  H21  H  HCH3  0   0.234   1.1820   2.1000   1.0398
 2JD  H22  H  HCH3  0   0.231   0.9069  -1.1626  -1.8072
 2JD  H23  H  HCH3  0   0.250   0.1935   0.3978  -2.1738
 2JD  H24  H  HCH3  0   0.241   1.9376   0.2332  -2.1333
 2JD  OXT  O  OH1   0  -0.744  -3.3221   0.1804   1.5589
 2JD  H27  H  HOH1  0   0.495  -3.2932   1.1212   1.7789
 2JD  H4   H  HOH1  0   0.504  -4.5599   0.5673  -1.0742
 2JD  O1   O  OH1   0  -0.578   3.9665   1.0950   0.8180
 2JD  HXT  H  HOH1  0   0.486   4.8342   1.3667   0.4796

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
 2JD  O3   C16  double  1.206  0.020  1.206
 2JD  C16  C17  single  1.523  0.020  1.523
 2JD  O4   C17  single  1.401  0.020  1.401
 2JD  C17  C18  single  1.555  0.020  1.555
 2JD  O3P  P    single  1.594  0.020  1.594
 2JD  O2P  C19  single  1.431  0.020  1.431
 2JD  O2P  P    single  1.594  0.020  1.594
 2JD  C20  C18  single  1.530  0.020  1.530
 2JD  C18  C19  single  1.532  0.020  1.532
 2JD  C18  C21  single  1.529  0.020  1.529
 2JD  P    O1P  double  1.475  0.020  1.475
 2JD  C17  H15  single  0.970  0.020  1.090
 2JD  O4   H16  single  0.850  0.020  0.980
 2JD  C19  H17  single  0.970  0.020  1.090
 2JD  C19  H18  single  0.970  0.020  1.090
 2JD  C20  H19  single  0.970  0.020  1.090
 2JD  C20  H20  single  0.970  0.020  1.090
 2JD  C20  H21  single  0.970  0.020  1.090
 2JD  C21  H22  single  0.970  0.020  1.090
 2JD  C21  H23  single  0.970  0.020  1.090
 2JD  C21  H24  single  0.970  0.020  1.090
 2JD  P    OXT  single  1.599  0.020  1.599
 2JD  OXT  H27  single  0.850  0.020  0.980
 2JD  O3P  H4   single  0.850  0.020  0.980
 2JD  C16  O1   single  1.321  0.020  1.321
 2JD  O1   HXT  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
 2JD  O1   C16  C17  113.25  3.000
 2JD  O1   C16  O3   123.99  3.000
 2JD  C17  C16  O3   122.75  3.000
 2JD  H15  C17  C18  107.57  3.000
 2JD  H15  C17  O4   106.39  3.000
 2JD  C18  C17  O4   112.96  3.000
 2JD  H15  C17  C16  108.21  3.000
 2JD  C18  C17  C16  112.37  3.000
 2JD  O4   C17  C16  109.04  3.000
 2JD  H16  O4   C17  109.14  3.000
 2JD  C21  C18  C20  109.93  3.000
 2JD  C21  C18  C19  110.24  3.000
 2JD  C20  C18  C19  109.73  3.000
 2JD  C21  C18  C17  111.45  3.000
 2JD  C19  C18  C17  104.89  3.000
 2JD  C20  C18  C17  110.48  3.000
 2JD  H18  C19  H17  108.21  3.000
 2JD  H18  C19  O2P  109.29  3.000
 2JD  H17  C19  O2P  109.87  3.000
 2JD  H18  C19  C18  109.92  3.000
 2JD  H17  C19  C18  110.33  3.000
 2JD  O2P  C19  C18  109.20  3.000
 2JD  H21  C20  H20  107.66  3.000
 2JD  H21  C20  H19  108.01  3.000
 2JD  H20  C20  H19  106.76  3.000
 2JD  H21  C20  C18  111.95  3.000
 2JD  H20  C20  C18  110.46  3.000
 2JD  H19  C20  C18  111.77  3.000
 2JD  H24  C21  H23  107.02  3.000
 2JD  H24  C21  H22  108.06  3.000
 2JD  H23  C21  H22  107.12  3.000
 2JD  H24  C21  C18  111.60  3.000
 2JD  H23  C21  C18  110.51  3.000
 2JD  H22  C21  C18  112.28  3.000
 2JD  OXT  P    O3P  107.80  3.000
 2JD  OXT  P    O2P  107.08  3.000
 2JD  O3P  P    O2P   96.73  3.000
 2JD  OXT  P    O1P  109.44  3.000
 2JD  O2P  P    O1P  116.86  3.000
 2JD  O3P  P    O1P  117.82  3.000
 2JD  P    O2P  C19  120.19  3.000
 2JD  H4   O3P  P    114.00  3.000
 2JD  H27  OXT  P    115.82  3.000
 2JD  HXT  O1   C16  110.34  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
 2JD  CONST_01  HXT  O1   C16  O3      0.00   0.0  0
 2JD  Var_01    O2P  C19  C18  C17   179.32  30.0  3
 2JD  Var_02    O3P  P    O2P  C19  -176.18  30.0  3
 2JD  Var_03    H19  C20  C18  C17    69.87  30.0  3
 2JD  Var_04    H22  C21  C18  C17    59.31  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
 2JD  chir_01  C17  C16  O4  C18  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
 2JD  plan-1  C16  0.020
 2JD  plan-1  O3   0.020
 2JD  plan-1  C17  0.020
 2JD  plan-1  O1   0.020
 2JD  plan-1  HXT  0.020

