# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 05:47:01 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  20  12  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.560   0.6574   0.8841   0.3009
 4NG  CAC  C  CR15  0   0.182   2.0636  -0.9525  -0.2212
 4NG  CAD  C  CH2   0  -0.484   0.6250  -1.4605  -0.2389
 4NG  CAE  C  CR15  0  -0.730  -0.1647  -0.3735   0.5024
 4NG  NAB  N  NR5   0  -0.216   1.8342   0.4768  -0.2215
 4NG  OAF  O  OH1   0  -0.544   2.8882   1.3321  -0.2840
 4NG  OAG  O  O     0  -0.451   0.3304   2.0268   0.5390
 4NG  OAH  O  OH1   0  -0.650   2.7177  -1.3955   0.9260
 4NG  PAI  P  P     0   1.393  -1.8747  -0.2296  -0.0721
 4NG  H1   H  HCR5  0   0.262   2.6109  -1.2271  -1.1267
 4NG  H2   H  HCH2  0   0.280   0.3006  -1.5543  -1.2756
 4NG  H3   H  HCH2  0   0.286   0.5381  -2.4378   0.2286
 4NG  H4   H  HCR5  0   0.357  -0.1944  -0.5849   1.5771
 4NG  H5   H  HOH1  0   0.484   2.9421   1.6287  -1.2027
 4NG  H6   H  HOH1  0   0.465   3.6594  -1.2099   0.8466
 4NG  H7   H  HOH1  0   0.492  -1.5890   1.5038  -1.4129
 4NG  H8   H  HOH1  0   0.499  -3.4488   0.9160   0.9228
 4NG  OAJ  O  OH1   0  -0.747  -1.8210   0.5671  -1.4670
 4NG  OAK  O  O     0  -0.700  -2.5551  -1.5295  -0.2644
 4NG  OAL  O  OH1   0  -0.737  -2.4974   0.7646   1.0166

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  1.212  0.020  1.212
 4NG  CAA  CAE  single  1.516  0.020  1.516
 4NG  CAA  NAB  single  1.350  0.020  1.350
 4NG  CAE  CAD  single  1.535  0.020  1.535
 4NG  CAE  PAI  single  1.810  0.020  1.810
 4NG  OAK  PAI  double  1.480  0.020  1.480
 4NG  CAD  CAC  single  1.526  0.020  1.526
 4NG  NAB  OAF  single  1.359  0.020  1.359
 4NG  NAB  CAC  single  1.448  0.020  1.448
 4NG  PAI  OAL  single  1.600  0.020  1.600
 4NG  PAI  OAJ  single  1.607  0.020  1.607
 4NG  OAH  CAC  single  1.393  0.020  1.393
 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
 4NG  OAJ  H7   single  0.850  0.020  0.980
 4NG  OAL  H8   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  126.54  3.000
 4NG  NAB  CAA  CAE  105.89  3.000
 4NG  OAG  CAA  CAE  127.57  3.000
 4NG  H1   CAC  OAH  111.55  3.000
 4NG  H1   CAC  NAB  109.10  3.000
 4NG  OAH  CAC  NAB  112.87  3.000
 4NG  H1   CAC  CAD  112.26  3.000
 4NG  OAH  CAC  CAD  110.27  3.000
 4NG  NAB  CAC  CAD  100.33  3.000
 4NG  H3   CAD  H2   107.93  3.000
 4NG  H3   CAD  CAE  112.83  3.000
 4NG  H2   CAD  CAE  111.54  3.000
 4NG  H3   CAD  CAC  111.71  3.000
 4NG  H2   CAD  CAC  108.67  3.000
 4NG  CAE  CAD  CAC  104.11  3.000
 4NG  H4   CAE  PAI  107.53  3.000
 4NG  H4   CAE  CAD  110.55  3.000
 4NG  PAI  CAE  CAD  112.91  3.000
 4NG  H4   CAE  CAA  107.76  3.000
 4NG  PAI  CAE  CAA  113.85  3.000
 4NG  CAD  CAE  CAA  104.15  3.000
 4NG  OAF  NAB  CAC  119.91  3.000
 4NG  CAC  NAB  CAA  115.84  3.000
 4NG  OAF  NAB  CAA  120.26  3.000
 4NG  H5   OAF  NAB  106.26  3.000
 4NG  H6   OAH  CAC  109.26  3.000
 4NG  OAL  PAI  OAK  117.08  3.000
 4NG  OAL  PAI  OAJ  107.18  3.000
 4NG  OAK  PAI  OAJ  109.76  3.000
 4NG  OAJ  PAI  CAE  106.46  3.000
 4NG  OAL  PAI  CAE  101.60  3.000
 4NG  OAK  PAI  CAE  113.95  3.000
 4NG  H7   OAJ  PAI  116.10  3.000
 4NG  H8   OAL  PAI  114.44  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_01  CAE  CAA  NAB  CAC    0.00  0.0  0
 4NG  CONST_02  OAG  CAA  NAB  CAC  180.00  0.0  0
 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

