# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 18:06:09 2020
#   Inital geometry file: a 34 line input string
#   Ligand name: (aminomethyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[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
 PGL  PGL  '(aminomethyl)phosphonic acid'  peptide  10  6  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PGL
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
 PGL  N    N  NH2    0  -0.810   2.3284   0.1178  -0.0040
 PGL  C    C  CH2    0  -0.565   1.1945  -0.5351  -0.6571
 PGL  P    P  P      0   1.146  -0.4331   0.0600   0.0291
 PGL  O1   O  O      0  -0.915  -0.2888  -0.1633   1.5450
 PGL  O2   O  OP    -1  -0.913  -0.5623   1.5369  -0.3619
 PGL  HN1  H  HNH2   0   0.316   2.1596   0.0884   0.9943
 PGL  HN2  H  HNH2   0   0.324   3.1736  -0.4191  -0.1543
 PGL  H1   H  HCH2   0   0.176   1.2402  -0.3395  -1.7351
 PGL  H2   H  HCH2   0   0.157   1.2224  -1.6318  -0.5530
 PGL  O3   O  OP    -1  -0.915  -1.4788  -0.8470  -0.6361

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
 PGL  N  C    single  1.462  0.020  1.462
 PGL  N  HN1  single  0.890  0.020  1.040
 PGL  N  HN2  single  0.890  0.020  1.040
 PGL  C  P    single  1.864  0.020  1.864
 PGL  C  H1   single  0.970  0.020  1.090
 PGL  C  H2   single  0.970  0.020  1.090
 PGL  P  O1   deloc   1.539  0.020  1.539
 PGL  P  O2   deloc   1.533  0.020  1.533
 PGL  P  O3   deloc   1.536  0.020  1.536

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
 PGL  HN2  N  HN1  105.66  3.000
 PGL  HN2  N  C    110.13  3.000
 PGL  HN1  N  C    107.34  3.000
 PGL  H2   C  H1   105.62  3.000
 PGL  H2   C  P    107.76  3.000
 PGL  H1   C  P    109.96  3.000
 PGL  H2   C  N    112.49  3.000
 PGL  H1   C  N    109.09  3.000
 PGL  P    C  N    111.73  3.000
 PGL  O3   P  O2   113.65  3.000
 PGL  O3   P  O1   113.88  3.000
 PGL  O2   P  O1   113.50  3.000
 PGL  O3   P  C    104.28  3.000
 PGL  O2   P  C    106.69  3.000
 PGL  O1   P  C    103.56  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
 PGL  Var_01  O1   P  C  N  -53.70  30.0  3
 PGL  Var_02  HN1  N  C  P   46.59  30.0  3

