# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:05:16 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: phosphono (2~{S})-2-oxidanyl-3-phosphonooxy-propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CO[P](O)(O)=O)C(=O)O[P](O)(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
 DG4  DG4  'phosphono (2~{S})-2-oxidanyl-3-phosphonooxy-propanoate'  ligand  19  15  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DG4
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
 DG4  O2P  O  O      0  -0.861  -21.5047  -2.5124  4.5290
 DG4  P1   P  P      0   1.246  -20.3836  -2.7230  5.5251
 DG4  O4P  O  OP    -1  -0.862  -20.1376  -4.1492  5.9733
 DG4  O3P  O  OP    -1  -0.852  -19.1540  -1.8605  5.3499
 DG4  O1P  O  O2     0  -0.590  -21.0427  -1.9269  7.0205
 DG4  C1   C  C      0   0.519  -21.9863  -2.3072  7.8243
 DG4  O1   O  O      0  -0.501  -22.1983  -1.7053  8.8632
 DG4  C2   C  CH1    0  -0.123  -22.8443  -3.5313  7.4924
 DG4  O2   O  OH1    0  -0.682  -22.5381  -4.4919  8.4904
 DG4  C3   C  CH2    0  -0.158  -24.3212  -3.1535  7.5163
 DG4  O5P  O  O2     0  -0.661  -24.5534  -2.0905  6.6448
 DG4  P2   P  P      0   1.210  -25.5143  -2.3616  5.2471
 DG4  O8P  O  OP    -1  -0.890  -25.2402  -1.0846  4.4645
 DG4  O7P  O  OP    -1  -0.900  -26.9353  -2.5030  5.7886
 DG4  O6P  O  O      0  -0.900  -24.9578  -3.6398  4.6237
 DG4  H1   H  HCH1   0   0.214  -22.6058  -3.9114  6.4991
 DG4  H2   H  HOH1   0   0.447  -22.9127  -5.3311  8.2069
 DG4  H4   H  HCH2   0   0.175  -24.9028  -4.0507  7.2633
 DG4  H3   H  HCH2   0   0.170  -24.6010  -2.8794  8.5428

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
 DG4  O2P  P1   deloc   1.514  0.020  1.514
 DG4  O6P  P2   deloc   1.527  0.020  1.527
 DG4  P1   O1P  single  1.818  0.020  1.818
 DG4  P1   O3P  deloc   1.512  0.020  1.512
 DG4  P1   O4P  deloc   1.515  0.020  1.515
 DG4  O7P  P2   deloc   1.527  0.020  1.527
 DG4  O1P  C1   single  1.297  0.020  1.297
 DG4  P2   O8P  deloc   1.523  0.020  1.523
 DG4  P2   O5P  single  1.718  0.020  1.718
 DG4  C1   C2   single  1.531  0.020  1.531
 DG4  C1   O1   double  1.219  0.020  1.219
 DG4  C2   C3   single  1.525  0.020  1.525
 DG4  C2   O2   single  1.419  0.020  1.419
 DG4  O5P  C3   single  1.394  0.020  1.394
 DG4  C2   H1   single  0.970  0.020  1.090
 DG4  O2   H2   single  0.850  0.020  0.980
 DG4  C3   H4   single  0.970  0.020  1.090
 DG4  C3   H3   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
 DG4  O1P  P1   O3P   98.07  3.000
 DG4  O3P  P1   O4P  116.05  3.000
 DG4  O1P  P1   O4P  103.17  3.000
 DG4  O4P  P1   O2P  116.47  3.000
 DG4  O3P  P1   O2P  116.51  3.000
 DG4  O1P  P1   O2P  102.22  3.000
 DG4  C1   O1P  P1   130.20  3.000
 DG4  C2   C1   O1   118.81  3.000
 DG4  O1   C1   O1P  120.66  3.000
 DG4  C2   C1   O1P  120.52  3.000
 DG4  H1   C2   C3   108.21  3.000
 DG4  H1   C2   O2   110.96  3.000
 DG4  C3   C2   O2   111.46  3.000
 DG4  H1   C2   C1   110.72  3.000
 DG4  O2   C2   C1   105.54  3.000
 DG4  C3   C2   C1   109.96  3.000
 DG4  H2   O2   C2   107.43  3.000
 DG4  H3   C3   H4   106.50  3.000
 DG4  H3   C3   O5P  110.57  3.000
 DG4  H4   C3   O5P  112.99  3.000
 DG4  H3   C3   C2   108.85  3.000
 DG4  H4   C3   C2   107.87  3.000
 DG4  O5P  C3   C2   109.90  3.000
 DG4  P2   O5P  C3   118.78  3.000
 DG4  O6P  P2   O7P  113.98  3.000
 DG4  O7P  P2   O8P  115.30  3.000
 DG4  O6P  P2   O8P  115.24  3.000
 DG4  O8P  P2   O5P  100.67  3.000
 DG4  O7P  P2   O5P  104.28  3.000
 DG4  O6P  P2   O5P  105.09  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
 DG4  Var_01  C2   C1  O1P  P1   -7.04  30.0  3
 DG4  Var_02  O6P  P2  O5P  C3  -47.74  30.0  3
 DG4  Var_03  H4   C3  O5P  P2   -7.23  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
 DG4  chir_01  C2  C1  C3  O2  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
 DG4  plan-1  O1P  0.020
 DG4  plan-1  C1   0.020
 DG4  plan-1  O1   0.020
 DG4  plan-1  C2   0.020

