# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 03:46:07 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  18  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 OK
;

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  -0.579   0.6781   0.5961   1.0561
 GPF  C2   C  CH2   0  -0.390  -1.5289  -0.2761   0.5587
 GPF  C3   C  C     0   0.524  -2.8856   0.0818   0.0103
 GPF  O1   O  OH1   0  -0.748   1.3365  -1.5312  -0.6012
 GPF  O2   O  O     0  -0.714   1.9941   0.7609  -1.4133
 GPF  O3   O  OH1   0  -0.749   3.1440  -0.2495   0.7195
 GPF  O4   O  O     0  -0.439  -3.2292   1.1911  -0.3087
 GPF  P1   P  P     0   1.360   1.8297  -0.0534  -0.1870
 GPF  O5   O  OH1   0  -0.593  -3.6741  -0.9832  -0.0597
 GPF  N1   N  NH1   0  -0.606  -0.6244   0.8436   0.4729
 GPF  H1   H  HCH2  0   0.260   0.6624  -0.0598   1.9385
 GPF  H1A  H  HCH2  0   0.300   1.1009   1.5470   1.3857
 GPF  H2   H  HCH2  0   0.258  -1.6743  -0.6514   1.5849
 GPF  H2A  H  HCH2  0   0.275  -1.1430  -1.1213  -0.0153
 GPF  HO1  H  HOH1  0   0.490   1.3119  -2.1775   0.1166
 GPF  HO3  H  HOH1  0   0.495   3.9503  -0.4299   0.2171
 GPF  HO5  H  HOH1  0   0.484  -4.5480  -0.7288  -0.3922
 GPF  HN1  H  HNH1  0   0.371  -1.0360   1.6489   0.9232

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  1.815  0.020  1.815
 GPF  C1  N1   single  1.448  0.020  1.448
 GPF  C1  H1   single  0.970  0.020  1.090
 GPF  C1  H1A  single  0.970  0.020  1.090
 GPF  N1  C2   single  1.442  0.020  1.442
 GPF  C2  C3   single  1.507  0.020  1.507
 GPF  C2  H2   single  0.970  0.020  1.090
 GPF  C2  H2A  single  0.970  0.020  1.090
 GPF  O4  C3   double  1.204  0.020  1.204
 GPF  C3  O5   single  1.327  0.020  1.327
 GPF  P1  O1   single  1.612  0.020  1.612
 GPF  O1  HO1  single  0.850  0.020  0.980
 GPF  O2  P1   double  1.481  0.020  1.481
 GPF  O3  P1   single  1.609  0.020  1.609
 GPF  O3  HO3  single  0.850  0.020  0.980
 GPF  O5  HO5  single  0.850  0.020  0.980
 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  106.43  3.000
 GPF  H1A  C1  N1  108.72  3.000
 GPF  H1   C1  N1  114.35  3.000
 GPF  H1A  C1  P1  105.83  3.000
 GPF  H1   C1  P1  110.20  3.000
 GPF  N1   C1  P1  110.86  3.000
 GPF  H2A  C2  H2  105.81  3.000
 GPF  H2A  C2  N1  110.37  3.000
 GPF  H2   C2  N1  113.73  3.000
 GPF  H2A  C2  C3  108.11  3.000
 GPF  H2   C2  C3  107.52  3.000
 GPF  N1   C2  C3  111.02  3.000
 GPF  O5   C3  O4  123.76  3.000
 GPF  O5   C3  C2  111.32  3.000
 GPF  O4   C3  C2  124.91  3.000
 GPF  HO1  O1  P1  115.47  3.000
 GPF  HO3  O3  P1  114.29  3.000
 GPF  O3   P1  O2  116.28  3.000
 GPF  O3   P1  O1  106.44  3.000
 GPF  O2   P1  O1  108.98  3.000
 GPF  O3   P1  C1  100.14  3.000
 GPF  O2   P1  C1  116.16  3.000
 GPF  O1   P1  C1  108.06  3.000
 GPF  HO5  O5  C3  110.08  3.000
 GPF  HN1  N1  C2  109.69  3.000
 GPF  HN1  N1  C1  108.86  3.000
 GPF  C2   N1  C1  114.04  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  CONST_01  HO5  O5  C3  C2  180.00   0.0  0
 GPF  Var_01    C3   C2  N1  C1  176.51  30.0  3
 GPF  Var_02    P1   C1  N1  C2   91.06  30.0  1
 GPF  Var_03    N1   C1  P1  O1  -68.04  30.0  3
 GPF  Var_04    N1   C2  C3  O4   -8.38  30.0  1

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
 GPF  plan-1  HO5  0.020

