# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 10:01:54 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-{hydroxy[(phosphonooxy)acetyl]amino}propyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON(CCCO[P](O)(O)=O)C(=O)CO[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
 PH4  PH4  '3-{hydroxy[(phosphonooxy)acetyl]amino}propyl dihydrogen phosphate'  ligand  31  18  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PH4
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
 PH4  N3    N  NT    0  -0.204  -0.6335  -1.1305  -0.0611
 PH4  C4    C  CH2   0  -0.293   0.6675  -1.1445  -0.6879
 PH4  C5    C  CH2   0  -0.481   1.7148  -0.3824   0.1174
 PH4  C6    C  CH2   0  -0.161   3.0641  -0.4657  -0.5629
 PH4  O62   O  OH1   0  -0.732   6.0570   1.2150   0.9937
 PH4  P6    P  P     0   1.452   5.5661   0.0707  -0.0009
 PH4  O63   O  O     0  -0.711   6.0591   0.1029  -1.3903
 PH4  O61   O  OH1   0  -0.741   5.9284  -1.3398   0.6591
 PH4  O6    O  O2    0  -0.589   4.0010   0.2928   0.2143
 PH4  O3    O  OH1   0  -0.545  -0.8478  -2.0560   0.9244
 PH4  C2    C  C     0   0.498  -1.6554  -0.3297  -0.4200
 PH4  O2    O  O     0  -0.470  -1.5612   0.4947  -1.3085
 PH4  C1    C  CH2   0  -0.270  -2.9407  -0.5415   0.3667
 PH4  O1    O  O2    0  -0.578  -3.8655   0.4295  -0.0921
 PH4  P1    P  P     0   1.454  -5.4263   0.2001   0.1640
 PH4  O12   O  O     0  -0.707  -5.8182  -0.2035   1.5264
 PH4  O13   O  OH1   0  -0.729  -5.9067   1.6219  -0.3672
 PH4  O11   O  OH1   0  -0.738  -5.9056  -0.9082  -0.8816
 PH4  H4    H  HCH2  0   0.267   0.9619  -2.1875  -0.8222
 PH4  H4A   H  HCH2  0   0.264   0.5619  -0.7120  -1.6819
 PH4  H5    H  HCH2  0   0.254   1.4102   0.6624   0.2126
 PH4  H5A   H  HCH2  0   0.244   1.7952  -0.7994   1.1243
 PH4  H6    H  HCH2  0   0.236   3.3802  -1.5103  -0.6405
 PH4  H6A   H  HCH2  0   0.244   3.0147  -0.0542  -1.5736
 PH4  HO62  H  HOH1  0   0.504   7.0042   1.4012   0.9444
 PH4  HO61  H  HOH1  0   0.495   5.6894  -1.4421   1.5902
 PH4  HO3   H  HOH1  0   0.481  -0.5242  -1.6709   1.7516
 PH4  H1    H  HCH2  0   0.276  -3.3021  -1.5614   0.2034
 PH4  H1A   H  HCH2  0   0.277  -2.7679  -0.4183   1.4381
 PH4  HO13  H  HOH1  0   0.506  -6.8540   1.7843  -0.2613
 PH4  HO11  H  HOH1  0   0.497  -5.7344  -0.7114  -1.8126

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
 PH4  C4   N3    single  1.444  0.020  1.444
 PH4  C2   N3    single  1.347  0.020  1.347
 PH4  N3   O3    single  1.369  0.020  1.369
 PH4  C4   C5    single  1.525  0.020  1.525
 PH4  C4   H4    single  0.970  0.020  1.090
 PH4  C4   H4A   single  0.970  0.020  1.090
 PH4  C6   C5    single  1.513  0.020  1.513
 PH4  C5   H5    single  0.970  0.020  1.090
 PH4  C5   H5A   single  0.970  0.020  1.090
 PH4  O6   C6    single  1.434  0.020  1.434
 PH4  C6   H6    single  0.970  0.020  1.090
 PH4  C6   H6A   single  0.970  0.020  1.090
 PH4  O62  P6    single  1.594  0.020  1.594
 PH4  O62  HO62  single  0.850  0.020  0.980
 PH4  O63  P6    double  1.475  0.020  1.475
 PH4  P6   O61   single  1.599  0.020  1.599
 PH4  P6   O6    single  1.595  0.020  1.595
 PH4  O61  HO61  single  0.850  0.020  0.980
 PH4  O3   HO3   single  0.850  0.020  0.980
 PH4  C1   C2    single  1.522  0.020  1.522
 PH4  C2   O2    double  1.216  0.020  1.216
 PH4  C1   O1    single  1.417  0.020  1.417
 PH4  C1   H1    single  0.970  0.020  1.090
 PH4  C1   H1A   single  0.970  0.020  1.090
 PH4  P1   O1    single  1.598  0.020  1.598
 PH4  O12  P1    double  1.474  0.020  1.474
 PH4  O13  P1    single  1.592  0.020  1.592
 PH4  P1   O11   single  1.597  0.020  1.597
 PH4  O13  HO13  single  0.850  0.020  0.980
 PH4  O11  HO11  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
 PH4  C2    N3   O3   118.36  3.000
 PH4  O3    N3   C4   116.55  3.000
 PH4  C2    N3   C4   125.00  3.000
 PH4  H4A   C4   H4   107.05  3.000
 PH4  H4A   C4   C5   110.49  3.000
 PH4  H4    C4   C5   110.92  3.000
 PH4  H4A   C4   N3   107.75  3.000
 PH4  H4    C4   N3   107.78  3.000
 PH4  C5    C4   N3   112.62  3.000
 PH4  H5A   C5   H5   107.77  3.000
 PH4  H5A   C5   C6   109.13  3.000
 PH4  H5    C5   C6   109.90  3.000
 PH4  H5A   C5   C4   110.26  3.000
 PH4  H5    C5   C4   109.42  3.000
 PH4  C6    C5   C4   110.32  3.000
 PH4  H6A   C6   H6   107.89  3.000
 PH4  H6A   C6   O6   109.37  3.000
 PH4  H6    C6   O6   110.77  3.000
 PH4  H6A   C6   C5   110.78  3.000
 PH4  H6    C6   C5   110.00  3.000
 PH4  O6    C6   C5   108.04  3.000
 PH4  HO62  O62  P6   114.10  3.000
 PH4  O6    P6   O61  106.82  3.000
 PH4  O6    P6   O63  116.87  3.000
 PH4  O61   P6   O63  109.42  3.000
 PH4  O6    P6   O62   96.78  3.000
 PH4  O61   P6   O62  107.82  3.000
 PH4  O63   P6   O62  117.99  3.000
 PH4  HO61  O61  P6   115.78  3.000
 PH4  P6    O6   C6   119.61  3.000
 PH4  HO3   O3   N3   107.09  3.000
 PH4  C1    C2   O2   122.53  3.000
 PH4  O2    C2   N3   122.62  3.000
 PH4  C1    C2   N3   114.85  3.000
 PH4  H1A   C1   H1   107.69  3.000
 PH4  H1A   C1   O1   110.09  3.000
 PH4  H1    C1   O1   112.01  3.000
 PH4  H1A   C1   C2   110.96  3.000
 PH4  H1    C1   C2   109.36  3.000
 PH4  O1    C1   C2   106.76  3.000
 PH4  P1    O1   C1   119.15  3.000
 PH4  O11   P1   O13  108.10  3.000
 PH4  O11   P1   O12  109.59  3.000
 PH4  O13   P1   O12  118.22  3.000
 PH4  O11   P1   O1   106.72  3.000
 PH4  O13   P1   O1    96.49  3.000
 PH4  O12   P1   O1   116.55  3.000
 PH4  HO13  O13  P1   114.15  3.000
 PH4  HO11  O11  P1   115.85  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
 PH4  CONST_01  C1   C2  N3  C4  180.00   0.0  0
 PH4  CONST_02  O2   C2  N3  C4    0.00   0.0  0
 PH4  CONST_03  C1   C2  N3  O3    0.00   0.0  0
 PH4  CONST_04  O2   C2  N3  O3  180.00   0.0  0
 PH4  Var_01    C6   C5  C4  N3  178.28  30.0  3
 PH4  Var_02    O1   C1  C2  N3  176.71  30.0  1
 PH4  Var_03    O6   C6  C5  C4  178.55  30.0  1
 PH4  Var_04    C2   N3  C4  C5  100.98  30.0  3
 PH4  Var_05    O62  P6  O6  C6  175.64  30.0  1
 PH4  Var_06    O12  P1  O1  C1   47.17  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
 PH4  plan-1  N3  0.020
 PH4  plan-1  C4  0.020
 PH4  plan-1  O3  0.020
 PH4  plan-1  C2  0.020
 PH4  plan-1  O2  0.020
 PH4  plan-1  C1  0.020

