# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 05:29:45 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  25  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 OK
;

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  -0.444  -2.1532  -0.5377  -1.9155
 G88  C6    C  C     0   0.554  -1.1579   0.1151  -1.7196
 G88  O7    O  OH1   0  -0.593  -1.0763   1.4124  -1.9912
 G88  C5    C  CH2   0  -0.607   0.1103  -0.4099  -1.1043
 G88  C4    C  CH2   0  -0.417   0.2523  -1.9241  -1.1475
 G88  C2    C  CH1   0  -0.385   0.2819  -2.5488  -2.5532
 G88  C3    C  C     0   0.552   1.3413  -1.8548  -3.3803
 G88  O5    O  OH1   0  -0.587   0.8253  -0.9656  -4.2179
 G88  O4    O  O     0  -0.440   2.5260  -2.0356  -3.2482
 G88  C1    C  CH2   0  -0.745   0.5778  -4.0444  -2.4371
 G88  P1    P  P     0   1.373   0.3884  -4.8846  -4.0163
 G88  O2    O  O     0  -0.712   1.0443  -4.2353  -5.1811
 G88  O3    O  OH1   0  -0.747  -1.2125  -4.9971  -4.1491
 G88  O1    O  OH1   0  -0.741   0.9157  -6.3626  -3.6712
 G88  H7    H  HOH1  0   0.479  -1.9223   1.7327  -2.3389
 G88  H5C1  H  HCH2  0   0.277   0.9725   0.0954  -1.5438
 G88  H5C2  H  HCH2  0   0.309   0.1041  -0.0920  -0.0561
 G88  H4C1  H  HCH2  0   0.261  -0.5658  -2.3888  -0.5947
 G88  H4C2  H  HCH2  0   0.257   1.1720  -2.1913  -0.6231
 G88  H2    H  HCH1  0   0.287  -0.6946  -2.3990  -3.0162
 G88  H1C1  H  HCH2  0   0.305  -0.0891  -4.5002  -1.7024
 G88  H1C2  H  HCH2  0   0.297   1.5980  -4.2024  -2.0825
 G88  H5    H  HOH1  0   0.480   1.5341  -0.5004  -4.6882
 G88  H3    H  HOH1  0   0.492  -1.5224  -5.0890  -5.0602
 G88  H1    H  HOH1  0   0.494   1.0952  -6.9073  -4.4498

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    double  1.206  0.020  1.206
 G88  C6  O7    single  1.328  0.020  1.328
 G88  C6  C5    single  1.504  0.020  1.504
 G88  O7  H7    single  0.850  0.020  0.980
 G88  C5  H5C1  single  0.970  0.020  1.090
 G88  C5  H5C2  single  0.970  0.020  1.090
 G88  C5  C4    single  1.521  0.020  1.521
 G88  C4  H4C1  single  0.970  0.020  1.090
 G88  C4  H4C2  single  0.970  0.020  1.090
 G88  C4  C2    single  1.539  0.020  1.539
 G88  C2  H2    single  0.970  0.020  1.090
 G88  C2  C1    single  1.529  0.020  1.529
 G88  C2  C3    single  1.513  0.020  1.513
 G88  C3  O5    single  1.326  0.020  1.326
 G88  C3  O4    double  1.206  0.020  1.206
 G88  O5  H5    single  0.850  0.020  0.980
 G88  C1  H1C1  single  0.970  0.020  1.090
 G88  C1  H1C2  single  0.970  0.020  1.090
 G88  C1  P1    single  1.799  0.020  1.799
 G88  P1  O1    single  1.607  0.020  1.607
 G88  P1  O2    double  1.486  0.020  1.486
 G88  P1  O3    single  1.610  0.020  1.610
 G88  O3  H3    single  0.850  0.020  0.980
 G88  O1  H1    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
 G88  C5    C6  O7    111.89  3.000
 G88  C5    C6  O6    124.97  3.000
 G88  O7    C6  O6    123.11  3.000
 G88  H7    O7  C6    110.04  3.000
 G88  H5C2  C5  H5C1  104.80  3.000
 G88  H5C2  C5  C4    108.45  3.000
 G88  H5C1  C5  C4    112.05  3.000
 G88  C4    C5  C6    114.48  3.000
 G88  H5C2  C5  C6    106.58  3.000
 G88  H5C1  C5  C6    109.86  3.000
 G88  H4C2  C4  H4C1  106.50  3.000
 G88  H4C2  C4  C2    108.86  3.000
 G88  H4C1  C4  C2    107.71  3.000
 G88  C2    C4  C5    115.58  3.000
 G88  H4C2  C4  C5    107.97  3.000
 G88  H4C1  C4  C5    109.85  3.000
 G88  H2    C2  C1    109.86  3.000
 G88  C1    C2  C3    110.78  3.000
 G88  H2    C2  C3    109.38  3.000
 G88  C3    C2  C4    109.07  3.000
 G88  C1    C2  C4    109.36  3.000
 G88  H2    C2  C4    108.35  3.000
 G88  O4    C3  O5    123.51  3.000
 G88  O4    C3  C2    124.02  3.000
 G88  O5    C3  C2    112.37  3.000
 G88  H5    O5  C3    110.10  3.000
 G88  H1C2  C1  H1C1  106.97  3.000
 G88  H1C2  C1  P1    108.42  3.000
 G88  H1C1  C1  P1    109.36  3.000
 G88  P1    C1  C2    111.70  3.000
 G88  H1C2  C1  C2    110.31  3.000
 G88  H1C1  C1  C2    109.95  3.000
 G88  O1    P1  O3    106.25  3.000
 G88  O3    P1  O2    113.87  3.000
 G88  O1    P1  O2    115.17  3.000
 G88  O3    P1  C1    102.11  3.000
 G88  O2    P1  C1    115.95  3.000
 G88  O1    P1  C1    101.92  3.000
 G88  H3    O3  P1    113.78  3.000
 G88  H1    O1  P1    113.96  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  CONST_01  H7  O7  C6  O6    0.00   0.0  0
 G88  CONST_02  H5  O5  C3  C2  180.00   0.0  0
 G88  Var_01    C4  C5  C6  O6   19.32  30.0  3
 G88  Var_02    C2  C4  C5  C6   61.25  30.0  3
 G88  Var_03    O1  P1  C1  C2  173.49  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-1  H7  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
 G88  plan-2  H5  0.020

