# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:24:07 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: (2S)-2-(phosphonomethyl)pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CC[C@H](C[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
 G88  G88  '(2S)-2-(phosphonomethyl)pentanedioic acid'  ligand  21  14  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G88
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
 G88  O6    O  O      0  -0.618  -2.2544  -0.6512  -1.5493
 G88  C6    C  C      0   0.410  -1.2849   0.1322  -1.6223
 G88  O7    O  OC    -1  -0.639  -1.3266   1.3064  -2.0515
 G88  C5    C  CH2    0  -0.577   0.0670  -0.3563  -1.0806
 G88  C4    C  CH2    0  -0.385   0.3094  -1.8582  -1.1425
 G88  C2    C  CH1    0  -0.298   0.3608  -2.4637  -2.5512
 G88  C3    C  C      0   0.423   1.4084  -1.7139  -3.3842
 G88  O5    O  OC    -1  -0.640   1.0080  -0.9788  -4.3118
 G88  O4    O  O      0  -0.647   2.6032  -1.8344  -3.0272
 G88  C1    C  CH2    0  -0.700   0.6367  -3.9629  -2.4749
 G88  P1    P  P      0   1.156   0.3696  -4.9213  -4.0408
 G88  O2    O  O      0  -0.905   1.3506  -4.3607  -5.0798
 G88  O3    O  OP    -1  -0.925  -1.1087  -4.7028  -4.4098
 G88  O1    O  OP    -1  -0.931   0.6778  -6.3809  -3.6511
 G88  H5C1  H  HCH2   0   0.201   0.8751   0.1826  -1.5814
 G88  H5C2  H  HCH2   0   0.212   0.1203  -0.0388  -0.0300
 G88  H4C1  H  HCH2   0   0.184  -0.4719  -2.3678  -0.5709
 G88  H4C2  H  HCH2   0   0.179   1.2531  -2.0860  -0.6353
 G88  H2    H  HCH1   0   0.170  -0.6204  -2.3179  -3.0083
 G88  H1C1  H  HCH2   0   0.163  -0.0087  -4.3995  -1.7001
 G88  H1C2  H  HCH2   0   0.168   1.6626  -4.1132  -2.1208

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
 G88  O6  C6    deloc   1.249  0.020  1.249
 G88  C6  O7    deloc   1.251  0.020  1.251
 G88  C6  C5    single  1.536  0.020  1.536
 G88  C5  H5C1  single  0.970  0.020  1.090
 G88  C5  H5C2  single  0.970  0.020  1.090
 G88  C5  C4    single  1.523  0.020  1.523
 G88  C4  H4C1  single  0.970  0.020  1.090
 G88  C4  H4C2  single  0.970  0.020  1.090
 G88  C4  C2    single  1.534  0.020  1.534
 G88  C2  H2    single  0.970  0.020  1.090
 G88  C2  C1    single  1.526  0.020  1.526
 G88  C2  C3    single  1.534  0.020  1.534
 G88  C3  O5    deloc   1.249  0.020  1.249
 G88  C3  O4    deloc   1.253  0.020  1.253
 G88  C1  H1C1  single  0.970  0.020  1.090
 G88  C1  H1C2  single  0.970  0.020  1.090
 G88  C1  P1    single  1.855  0.020  1.855
 G88  P1  O1    deloc   1.542  0.020  1.542
 G88  P1  O2    deloc   1.535  0.020  1.535
 G88  P1  O3    deloc   1.539  0.020  1.539

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
 G88  C5    C6  O7    116.67  3.000
 G88  C5    C6  O6    117.59  3.000
 G88  O7    C6  O6    125.67  3.000
 G88  H5C2  C5  H5C1  105.06  3.000
 G88  H5C2  C5  C4    108.43  3.000
 G88  H5C1  C5  C4    110.49  3.000
 G88  C4    C5  C6    116.07  3.000
 G88  H5C2  C5  C6    106.74  3.000
 G88  H5C1  C5  C6    109.41  3.000
 G88  H4C2  C4  H4C1  106.05  3.000
 G88  H4C2  C4  C2    108.31  3.000
 G88  H4C1  C4  C2    108.65  3.000
 G88  C2    C4  C5    115.59  3.000
 G88  H4C2  C4  C5    108.87  3.000
 G88  H4C1  C4  C5    108.94  3.000
 G88  H2    C2  C1    108.32  3.000
 G88  C1    C2  C3    112.57  3.000
 G88  H2    C2  C3    108.72  3.000
 G88  C3    C2  C4    109.18  3.000
 G88  C1    C2  C4    110.36  3.000
 G88  H2    C2  C4    107.54  3.000
 G88  O4    C3  O5    125.01  3.000
 G88  O4    C3  C2    116.71  3.000
 G88  O5    C3  C2    118.16  3.000
 G88  H1C2  C1  H1C1  105.51  3.000
 G88  H1C2  C1  P1    109.68  3.000
 G88  H1C1  C1  P1    107.77  3.000
 G88  P1    C1  C2    116.06  3.000
 G88  H1C2  C1  C2    108.67  3.000
 G88  H1C1  C1  C2    108.63  3.000
 G88  O1    P1  O3    112.77  3.000
 G88  O3    P1  O2    113.56  3.000
 G88  O1    P1  O2    112.90  3.000
 G88  O3    P1  C1    105.50  3.000
 G88  O2    P1  C1    106.89  3.000
 G88  O1    P1  C1    104.30  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
 G88  Var_01  C4  C5  C6  O6    28.98  30.0  3
 G88  Var_02  C2  C4  C5  C6    63.72  30.0  3
 G88  Var_03  O1  P1  C1  C2  -178.28  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
 G88  chir_01  C2  C4  C1  C3  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
 G88  plan-1  O6  0.020
 G88  plan-1  C6  0.020
 G88  plan-1  O7  0.020
 G88  plan-1  C5  0.020
 G88  plan-2  C2  0.020
 G88  plan-2  C3  0.020
 G88  plan-2  O5  0.020
 G88  plan-2  O4  0.020

