# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 02:50:41 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  12  6  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.805   2.2725   0.1119   0.0667
 PGL  C    C  CH2   0  -0.567   1.1828  -0.6174  -0.5579
 PGL  P    P  P     0   1.355  -0.3757   0.0043   0.1175
 PGL  O1   O  O     0  -0.721  -0.4952  -0.0398   1.5955
 PGL  O2   O  OH1   0  -0.748  -0.5477   1.5255  -0.3765
 PGL  HN1  H  HNH2  0   0.354   2.3948  -0.2022   1.0201
 PGL  HN2  H  HNH2  0   0.366   3.1360  -0.1032  -0.4132
 PGL  H1   H  HCH2  0   0.277   1.1942  -0.4378  -1.6348
 PGL  H2   H  HCH2  0   0.255   1.2093  -1.7064  -0.4212
 PGL  O3   O  OH1   0  -0.748  -1.4359  -0.8811  -0.7062
 PGL  HO2  H  HOH1  0   0.489  -0.5149   1.6577  -1.3327
 PGL  H6   H  HOH1  0   0.493  -2.3532  -0.7786  -0.4184

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  1.452  0.020  1.452
 PGL  N   HN1  single  0.890  0.020  1.040
 PGL  N   HN2  single  0.890  0.020  1.040
 PGL  C   P    single  1.809  0.020  1.809
 PGL  C   H1   single  0.970  0.020  1.090
 PGL  C   H2   single  0.970  0.020  1.090
 PGL  P   O1   double  1.483  0.020  1.483
 PGL  P   O2   single  1.609  0.020  1.609
 PGL  P   O3   single  1.608  0.020  1.608
 PGL  O2  HO2  single  0.850  0.020  0.980
 PGL  O3  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
 PGL  HN2  N   HN1  106.15  3.000
 PGL  HN2  N   C    109.26  3.000
 PGL  HN1  N   C    109.89  3.000
 PGL  H2   C   H1   106.60  3.000
 PGL  H2   C   P    108.38  3.000
 PGL  H1   C   P    108.71  3.000
 PGL  H2   C   N    115.24  3.000
 PGL  H1   C   N    109.50  3.000
 PGL  P    C   N    108.26  3.000
 PGL  O3   P   O2   107.03  3.000
 PGL  O3   P   O1   116.16  3.000
 PGL  O2   P   O1   108.99  3.000
 PGL  O3   P   C    100.81  3.000
 PGL  O2   P   C    107.61  3.000
 PGL  O1   P   C    115.55  3.000
 PGL  HO2  O2  P    115.46  3.000
 PGL  H6   O3  P    114.49  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  -55.26  30.0  3
 PGL  Var_02  HN1  N  C  P   73.90  30.0  3

