# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 04:25:53 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: carboxy-N-(phosphonomethyl)methanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[NH2+]C[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
 GPJ  GPJ  carboxy-N-(phosphonomethyl)methanaminium  ligand  19  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_GPJ
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
 GPJ  P1    P  P     0   1.380  -2.0543   0.1687   0.0674
 GPJ  O1    O  O     0  -0.683  -2.0110   1.0887   1.2223
 GPJ  O2    O  OH1   0  -0.731  -2.1250   0.9997  -1.2957
 GPJ  O3    O  OH1   0  -0.727  -3.1560  -0.9766   0.0229
 GPJ  O4    O  OH1   0  -0.572   4.2119  -0.6379  -0.0504
 GPJ  O5    O  O     0  -0.420   3.0243   1.2491   0.1945
 GPJ  C1    C  CH2   0  -0.601  -0.5645  -0.8799  -0.0552
 GPJ  C2    C  CH2   0  -0.402   1.8978  -0.8445  -0.0648
 GPJ  C3    C  C     0   0.547   3.1025   0.0592   0.0436
 GPJ  N1    N  NT2   1  -0.667   0.6570  -0.0392  -0.0011
 GPJ  HO2   H  HOH1  0   0.502  -2.2648   0.4948  -2.1089
 GPJ  HO3   H  HOH1  0   0.511  -4.0711  -0.6854   0.1487
 GPJ  HO4   H  HOH1  0   0.500   4.9891  -0.0615   0.0216
 GPJ  H11   H  HCH2  0   0.349  -0.5457  -1.4539  -0.9799
 GPJ  H12   H  HCH2  0   0.350  -0.5332  -1.5690   0.7875
 GPJ  H21   H  HCH2  0   0.352   1.9038  -1.3904  -1.0078
 GPJ  H22   H  HCH2  0   0.353   1.8823  -1.5637   0.7535
 GPJ  HN    H  HNT2  0   0.480   0.6544   0.6352  -0.7705
 GPJ  HN11  H  HNT2  0   0.479   0.6527   0.5200   0.8567

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
 GPJ  P1  O1    double  1.477  0.020  1.477
 GPJ  P1  O2    single  1.598  0.020  1.598
 GPJ  P1  O3    single  1.590  0.020  1.590
 GPJ  P1  C1    single  1.826  0.020  1.826
 GPJ  O2  HO2   single  0.850  0.020  0.980
 GPJ  O3  HO3   single  0.850  0.020  0.980
 GPJ  O4  C3    single  1.314  0.020  1.314
 GPJ  O4  HO4   single  0.850  0.020  0.980
 GPJ  O5  C3    double  1.202  0.020  1.202
 GPJ  C1  N1    single  1.484  0.020  1.484
 GPJ  C1  H11   single  0.970  0.020  1.090
 GPJ  C1  H12   single  0.970  0.020  1.090
 GPJ  C2  C3    single  1.510  0.020  1.510
 GPJ  C2  N1    single  1.481  0.020  1.481
 GPJ  C2  H21   single  0.970  0.020  1.090
 GPJ  C2  H22   single  0.970  0.020  1.090
 GPJ  N1  HN    single  0.890  0.020  1.040
 GPJ  N1  HN11  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
 GPJ  C1    P1  O3    98.62  3.000
 GPJ  C1    P1  O2   106.11  3.000
 GPJ  O3    P1  O2   108.67  3.000
 GPJ  C1    P1  O1   112.72  3.000
 GPJ  O3    P1  O1   119.39  3.000
 GPJ  O2    P1  O1   110.14  3.000
 GPJ  HO2   O2  P1   116.87  3.000
 GPJ  HO3   O3  P1   115.75  3.000
 GPJ  HO4   O4  C3   110.85  3.000
 GPJ  H12   C1  H11  108.85  3.000
 GPJ  H12   C1  N1   107.86  3.000
 GPJ  H11   C1  N1   108.39  3.000
 GPJ  H12   C1  P1   109.56  3.000
 GPJ  H11   C1  P1   111.96  3.000
 GPJ  N1    C1  P1   110.11  3.000
 GPJ  H22   C2  H21  108.62  3.000
 GPJ  H22   C2  N1   108.35  3.000
 GPJ  H21   C2  N1   108.33  3.000
 GPJ  H22   C2  C3   110.64  3.000
 GPJ  H21   C2  C3   110.95  3.000
 GPJ  N1    C2  C3   109.88  3.000
 GPJ  C2    C3  O5   123.34  3.000
 GPJ  C2    C3  O4   110.56  3.000
 GPJ  O5    C3  O4   126.11  3.000
 GPJ  HN11  N1  HN   105.66  3.000
 GPJ  HN11  N1  C2   109.67  3.000
 GPJ  HN    N1  C2   109.17  3.000
 GPJ  HN11  N1  C1   109.66  3.000
 GPJ  HN    N1  C1   110.12  3.000
 GPJ  C2    N1  C1   112.34  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
 GPJ  CONST_01  HO4  O4  C3  O5     0.00   0.0  0
 GPJ  Var_01    C2   N1  C1  P1   178.66  30.0  3
 GPJ  Var_02    N1   C1  P1  O1   -51.58  30.0  3
 GPJ  Var_03    N1   C2  C3  O4  -178.18  30.0  2
 GPJ  Var_04    C3   C2  N1  C1  -178.00  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
 GPJ  plan-1  O4   0.020
 GPJ  plan-1  O5   0.020
 GPJ  plan-1  C2   0.020
 GPJ  plan-1  C3   0.020
 GPJ  plan-1  HO4  0.020

