# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 02:56:21 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: [(3S,5S)-1,5-dihydroxy-2-oxopyrrolidin-3-yl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1C[C@@H](C(=O)N1O)[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
 4NG  4NG  '[(3S,5S)-1,5-dihydroxy-2-oxopyrrolidin-3-yl]phosphonic acid'  ligand  18  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4NG
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
 4NG  CAA  C  CR5    0   0.513   0.6780   0.8933   0.2571
 4NG  CAC  C  CR15   0   0.142   1.9984  -0.9540  -0.3937
 4NG  CAD  C  CH2    0  -0.504   0.5797  -1.4565  -0.1529
 4NG  CAE  C  CR15   0  -0.645  -0.1587  -0.3096   0.5463
 4NG  NAB  N  NR5    0  -0.068   1.7530   0.4631  -0.4702
 4NG  OAF  O  OH1    0  -0.593   2.7733   1.3126  -0.7841
 4NG  OAG  O  O      0  -0.570   0.5017   2.0541   0.5756
 4NG  OAH  O  OH1    0  -0.716   2.8344  -1.2999   0.6808
 4NG  PAI  P  P      0   1.176  -1.9299  -0.1165  -0.0741
 4NG  H1   H  HCR5   0   0.264   2.4232  -1.3057  -1.3382
 4NG  H2   H  HCH2   0   0.231   0.1183  -1.6727  -1.1169
 4NG  H3   H  HCH2   0   0.236   0.5858  -2.3803   0.4233
 4NG  H4   H  HCR5   0   0.266  -0.1787  -0.4536   1.6312
 4NG  H5   H  HOH1   0   0.507   3.2501   1.5068   0.0360
 4NG  H6   H  HOH1   0   0.438   3.7519  -1.1694   0.4217
 4NG  OAJ  O  OP    -1  -0.956  -1.7537   0.3661  -1.5167
 4NG  OAK  O  O      0  -0.851  -2.4970  -1.5340   0.0466
 4NG  OAL  O  OP    -1  -0.870  -2.5861   0.8975   0.8620

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
 4NG  OAG  CAA  double  1.217  0.020  1.217
 4NG  CAA  CAE  single  1.494  0.020  1.494
 4NG  CAA  NAB  single  1.367  0.020  1.367
 4NG  CAE  CAD  single  1.533  0.020  1.533
 4NG  CAE  PAI  single  1.887  0.020  1.887
 4NG  OAK  PAI  deloc   1.532  0.020  1.532
 4NG  CAD  CAC  single  1.524  0.020  1.524
 4NG  NAB  OAF  single  1.364  0.020  1.364
 4NG  NAB  CAC  single  1.440  0.020  1.440
 4NG  PAI  OAL  deloc   1.528  0.020  1.528
 4NG  PAI  OAJ  deloc   1.531  0.020  1.531
 4NG  OAH  CAC  single  1.405  0.020  1.405
 4NG  CAC  H1   single  0.970  0.020  1.090
 4NG  CAD  H2   single  0.970  0.020  1.090
 4NG  CAD  H3   single  0.970  0.020  1.090
 4NG  CAE  H4   single  0.970  0.020  1.090
 4NG  OAF  H5   single  0.850  0.020  0.980
 4NG  OAH  H6   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
 4NG  OAG  CAA  NAB  123.60  3.000
 4NG  NAB  CAA  CAE  106.86  3.000
 4NG  OAG  CAA  CAE  129.54  3.000
 4NG  H1   CAC  OAH  110.50  3.000
 4NG  H1   CAC  NAB  109.68  3.000
 4NG  OAH  CAC  NAB  112.61  3.000
 4NG  H1   CAC  CAD  113.07  3.000
 4NG  OAH  CAC  CAD  110.61  3.000
 4NG  NAB  CAC  CAD  100.03  3.000
 4NG  H3   CAD  H2   107.58  3.000
 4NG  H3   CAD  CAE  113.34  3.000
 4NG  H2   CAD  CAE  110.35  3.000
 4NG  H3   CAD  CAC  110.98  3.000
 4NG  H2   CAD  CAC  108.64  3.000
 4NG  CAE  CAD  CAC  105.89  3.000
 4NG  H4   CAE  PAI  108.80  3.000
 4NG  H4   CAE  CAD  111.25  3.000
 4NG  PAI  CAE  CAD  112.26  3.000
 4NG  H4   CAE  CAA  107.94  3.000
 4NG  PAI  CAE  CAA  112.32  3.000
 4NG  CAD  CAE  CAA  104.15  3.000
 4NG  OAF  NAB  CAC  119.83  3.000
 4NG  CAC  NAB  CAA  114.54  3.000
 4NG  OAF  NAB  CAA  120.96  3.000
 4NG  H5   OAF  NAB  107.35  3.000
 4NG  H6   OAH  CAC  109.15  3.000
 4NG  OAL  PAI  OAK  114.00  3.000
 4NG  OAL  PAI  OAJ  114.67  3.000
 4NG  OAK  PAI  OAJ  114.12  3.000
 4NG  OAJ  PAI  CAE  103.53  3.000
 4NG  OAL  PAI  CAE  105.65  3.000
 4NG  OAK  PAI  CAE  103.12  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
 4NG  CONST_03  OAF  NAB  CAA  CAE  180.00  0.0  0
 4NG  CONST_04  OAG  CAA  NAB  OAF    0.00  0.0  0

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
 4NG  chir_01  CAC  CAD  NAB  OAH  negativ
 4NG  chir_02  CAE  PAI  CAD  CAA  negativ

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
 4NG  plan-1  CAA  0.020
 4NG  plan-1  CAC  0.020
 4NG  plan-1  CAE  0.020
 4NG  plan-1  NAB  0.020
 4NG  plan-1  OAF  0.020
 4NG  plan-1  OAG  0.020

