# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:47:51 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: N-(phosphonomethyl)glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC[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
 GPF  GPF  N-(phosphonomethyl)glycine  ligand  15  10  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GPF
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
 GPF  C1   C  CH2    0  -0.559   0.6599   0.7326   0.9970
 GPF  C2   C  CH2    0  -0.387  -1.4465  -0.2570   0.2777
 GPF  C3   C  C      0   0.380  -2.9478   0.0458   0.1421
 GPF  O1   O  OP    -1  -0.906   1.4076  -1.6067  -0.2193
 GPF  O2   O  O      0  -0.918   2.1392   0.6125  -1.2864
 GPF  O3   O  OP    -1  -0.924   3.1722  -0.1486   0.9398
 GPF  O4   O  O      0  -0.615  -3.3428   1.1852   0.4669
 GPF  P1   P  P      0   1.150   1.9461  -0.1865   0.0096
 GPF  O5   O  OC    -1  -0.632  -3.6648  -0.9002  -0.2458
 GPF  N1   N  NH1    0  -0.597  -0.6312   0.9315   0.3583
 GPF  H1   H  HCH2   0   0.140   0.5530   0.2279   1.9778
 GPF  H1A  H  HCH2   0   0.182   1.0704   1.7242   1.2204
 GPF  H2   H  HCH2   0   0.166  -1.3376  -0.8982   1.1751
 GPF  H2A  H  HCH2   0   0.204  -1.1227  -0.8874  -0.5519
 GPF  HN1  H  HNH1   0   0.315  -1.1662   1.6132   0.8806

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
 GPF  P1  C1   single  1.864  0.020  1.864
 GPF  C1  N1   single  1.454  0.020  1.454
 GPF  C1  H1   single  0.970  0.020  1.090
 GPF  C1  H1A  single  0.970  0.020  1.090
 GPF  N1  C2   single  1.444  0.020  1.444
 GPF  C2  C3   single  1.538  0.020  1.538
 GPF  C2  H2   single  0.970  0.020  1.090
 GPF  C2  H2A  single  0.970  0.020  1.090
 GPF  O4  C3   deloc   1.249  0.020  1.249
 GPF  C3  O5   deloc   1.249  0.020  1.249
 GPF  P1  O1   deloc   1.536  0.020  1.536
 GPF  O2  P1   deloc   1.535  0.020  1.535
 GPF  O3  P1   deloc   1.540  0.020  1.540
 GPF  N1  HN1  single  0.890  0.020  1.040

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
 GPF  H1A  C1  H1  105.53  3.000
 GPF  H1A  C1  N1  107.35  3.000
 GPF  H1   C1  N1  111.44  3.000
 GPF  H1A  C1  P1  107.19  3.000
 GPF  H1   C1  P1  108.12  3.000
 GPF  N1   C1  P1  116.58  3.000
 GPF  H2A  C2  H2  104.60  3.000
 GPF  H2A  C2  N1  110.52  3.000
 GPF  H2   C2  N1  112.07  3.000
 GPF  H2A  C2  C3  109.66  3.000
 GPF  H2   C2  C3  106.34  3.000
 GPF  N1   C2  C3  113.22  3.000
 GPF  O5   C3  O4  126.18  3.000
 GPF  O5   C3  C2  116.03  3.000
 GPF  O4   C3  C2  117.75  3.000
 GPF  O3   P1  O2  113.40  3.000
 GPF  O3   P1  O1  113.08  3.000
 GPF  O2   P1  O1  113.56  3.000
 GPF  O3   P1  C1  102.55  3.000
 GPF  O2   P1  C1  106.11  3.000
 GPF  O1   P1  C1  107.03  3.000
 GPF  HN1  N1  C2  106.55  3.000
 GPF  HN1  N1  C1  109.57  3.000
 GPF  C2   N1  C1  114.41  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
 GPF  Var_01  C3  C2  N1  C1  156.89  30.0  3
 GPF  Var_02  P1  C1  N1  C2   73.54  30.0  1
 GPF  Var_03  N1  C1  P1  O1  -63.52  30.0  3
 GPF  Var_04  N1  C2  C3  O4  -18.66  30.0  2

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
 GPF  plan-1  C2  0.020
 GPF  plan-1  C3  0.020
 GPF  plan-1  O4  0.020
 GPF  plan-1  O5  0.020

