# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Nov 23 06:42:06 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: (2S)-2-hydroxy-2-[2-oxo-2-(phosphonooxy)ethyl]butanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@](O)(CC(=O)O[P](O)(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
 Y2A  Y2A  "(2S)-2-hydroxy-2-[2-oxo-2-(phosphonooxy)ethyl]butanedioic acid"  ligand  26  17  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y2A
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
 Y2A  CA   C  CH2   0  -0.600  86.9044  105.7447  128.5679
 Y2A  CB   C  CT    0   0.117  87.8236  105.4974  127.3682
 Y2A  OB1  O  O     0  -0.411  88.5640  106.9879  125.6121
 Y2A  OB2  O  OH1   0  -0.590  88.6243  107.6969  127.7308
 Y2A  CG   C  CH2   0  -0.563  89.0329  104.6114  127.7564
 Y2A  OG1  O  O     0  -0.401  90.9916  105.8140  128.4613
 Y2A  OG2  O  O2    0  -0.575  89.5995  105.0348  130.0193
 Y2A  CAC  C  C     0   0.566  85.7398  106.6279  128.2148
 Y2A  CBC  C  C     0   0.525  88.3628  106.8103  126.7818
 Y2A  CGC  C  C     0   0.571  89.9855  105.2270  128.7422
 Y2A  O1   O  OH1   0  -0.720  91.8009  105.1545  131.3468
 Y2A  O3   O  OH1   0  -0.712  89.6871  105.0721  132.4877
 Y2A  O4   O  O     0  -0.670  90.2551  107.2752  131.1646
 Y2A  OA1  O  O     0  -0.441  85.5370  107.0728  127.1094
 Y2A  OA2  O  OH1   0  -0.581  84.9628  106.8667  129.2560
 Y2A  OHB  O  OH1   0  -0.649  87.1788  104.7636  126.3711
 Y2A  P    P  P     0   1.452  90.3634  105.8137  131.2647
 Y2A  H1   H  HCH2  0   0.316  86.5251  104.7820  128.9238
 Y2A  H2   H  HCH2  0   0.305  87.4269  106.1897  129.4151
 Y2A  H3   H  HOH1  0   0.488  89.0180  108.4980  127.3500
 Y2A  H4   H  HCH2  0   0.307  88.6415  103.6731  128.1554
 Y2A  H5   H  HCH2  0   0.309  89.5921  104.3875  126.8473
 Y2A  H6   H  HOH1  0   0.507  92.4847  105.6075  130.8335
 Y2A  H7   H  HOH1  0   0.511  88.8574  105.4664  132.7918
 Y2A  H8   H  HOH1  0   0.484  84.2180  107.4333  129.0000
 Y2A  H9   H  HOH1  0   0.454  86.4475  105.2849  126.0184

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
 Y2A  OB1  CBC  double  1.200  0.020  1.200
 Y2A  CBC  OB2  single  1.325  0.020  1.325
 Y2A  CBC  CB   single  1.536  0.020  1.536
 Y2A  OHB  CB   single  1.396  0.020  1.396
 Y2A  CB   CG   single  1.549  0.020  1.549
 Y2A  CB   CA   single  1.531  0.020  1.531
 Y2A  OA1  CAC  double  1.209  0.020  1.209
 Y2A  CG   CGC  single  1.503  0.020  1.503
 Y2A  CAC  CA   single  1.504  0.020  1.504
 Y2A  CAC  OA2  single  1.321  0.020  1.321
 Y2A  OG1  CGC  double  1.198  0.020  1.198
 Y2A  CGC  OG2  single  1.348  0.020  1.348
 Y2A  OG2  P    single  1.656  0.020  1.656
 Y2A  P    O4   double  1.469  0.020  1.469
 Y2A  P    O1   single  1.584  0.020  1.584
 Y2A  P    O3   single  1.582  0.020  1.582
 Y2A  CA   H1   single  0.970  0.020  1.090
 Y2A  CA   H2   single  0.970  0.020  1.090
 Y2A  OB2  H3   single  0.850  0.020  0.980
 Y2A  CG   H4   single  0.970  0.020  1.090
 Y2A  CG   H5   single  0.970  0.020  1.090
 Y2A  O1   H6   single  0.850  0.020  0.980
 Y2A  O3   H7   single  0.850  0.020  0.980
 Y2A  OA2  H8   single  0.850  0.020  0.980
 Y2A  OHB  H9   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
 Y2A  H2   CA   H1   105.82  3.000
 Y2A  H2   CA   CAC  108.29  3.000
 Y2A  H1   CA   CAC  108.94  3.000
 Y2A  H2   CA   CB   112.77  3.000
 Y2A  H1   CA   CB   108.71  3.000
 Y2A  CAC  CA   CB   112.07  3.000
 Y2A  OHB  CB   CBC  109.81  3.000
 Y2A  OHB  CB   CG   103.83  3.000
 Y2A  CBC  CB   CG   108.10  3.000
 Y2A  CG   CB   CA   111.39  3.000
 Y2A  OHB  CB   CA   111.55  3.000
 Y2A  CBC  CB   CA   111.83  3.000
 Y2A  H3   OB2  CBC  110.57  3.000
 Y2A  H5   CG   H4   108.18  3.000
 Y2A  H5   CG   CGC  107.81  3.000
 Y2A  H4   CG   CGC  109.84  3.000
 Y2A  H5   CG   CB   107.99  3.000
 Y2A  H4   CG   CB   107.65  3.000
 Y2A  CGC  CG   CB   115.16  3.000
 Y2A  P    OG2  CGC  120.89  3.000
 Y2A  OA2  CAC  OA1  123.75  3.000
 Y2A  OA2  CAC  CA   112.13  3.000
 Y2A  OA1  CAC  CA   124.12  3.000
 Y2A  OB2  CBC  OB1  124.48  3.000
 Y2A  OB2  CBC  CB   111.59  3.000
 Y2A  OB1  CBC  CB   123.88  3.000
 Y2A  OG2  CGC  OG1  122.17  3.000
 Y2A  OG2  CGC  CG   112.43  3.000
 Y2A  OG1  CGC  CG   125.39  3.000
 Y2A  H6   O1   P    114.78  3.000
 Y2A  H7   O3   P    114.73  3.000
 Y2A  H8   OA2  CAC  110.44  3.000
 Y2A  H9   OHB  CB   109.10  3.000
 Y2A  O4   P    O3   119.18  3.000
 Y2A  O3   P    O1    98.79  3.000
 Y2A  O4   P    O1   118.99  3.000
 Y2A  O3   P    OG2   99.42  3.000
 Y2A  O1   P    OG2  105.19  3.000
 Y2A  O4   P    OG2  112.51  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
 Y2A  CONST_01  H8   OA2  CAC  CA    180.00   0.0  0
 Y2A  CONST_02  H3   OB2  CBC  CB    180.00   0.0  0
 Y2A  CONST_03  H3   OB2  CBC  OB1     0.00   0.0  0
 Y2A  CONST_04  H8   OA2  CAC  OA1     0.00   0.0  0
 Y2A  Var_01    OG1  CGC  CG   CB    -95.47  30.0  3
 Y2A  Var_02    OG2  CGC  CG   CB     85.42  30.0  3
 Y2A  Var_03    OA1  CAC  CA   CB      1.22  30.0  2
 Y2A  Var_04    OA2  CAC  CA   CB   -178.57  30.0  2
 Y2A  Var_05    P    OG2  CGC  CG   -170.68  30.0  3
 Y2A  Var_06    P    OG2  CGC  OG1    10.18  30.0  3
 Y2A  Var_07    O4   P    OG2  CGC    61.20  30.0  3
 Y2A  Var_08    O1   P    OG2  CGC   -69.80  30.0  3
 Y2A  Var_09    O3   P    OG2  CGC  -171.66  30.0  3
 Y2A  Var_10    H4   CG   CGC  OG1   142.81  30.0  1
 Y2A  Var_11    H5   CG   CGC  OG1    25.15  30.0  1
 Y2A  Var_12    H4   CG   CGC  OG2   -36.29  30.0  1
 Y2A  Var_13    H5   CG   CGC  OG2  -153.96  30.0  1
 Y2A  Var_14    H1   CA   CAC  OA1  -119.11  30.0  3
 Y2A  Var_15    H2   CA   CAC  OA1   126.24  30.0  3
 Y2A  Var_16    H1   CA   CAC  OA2    61.10  30.0  3
 Y2A  Var_17    H2   CA   CAC  OA2   -53.55  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
 Y2A  chir_01  CB  OHB  CG  CA  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
 Y2A  plan-1  CA   0.020
 Y2A  plan-1  CAC  0.020
 Y2A  plan-1  OA1  0.020
 Y2A  plan-1  OA2  0.020
 Y2A  plan-1  H8   0.020
 Y2A  plan-2  CB   0.020
 Y2A  plan-2  OB1  0.020
 Y2A  plan-2  OB2  0.020
 Y2A  plan-2  CBC  0.020
 Y2A  plan-2  H3   0.020
 Y2A  plan-3  CG   0.020
 Y2A  plan-3  OG1  0.020
 Y2A  plan-3  OG2  0.020
 Y2A  plan-3  CGC  0.020

