# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 22:36:51 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-{hydroxy[(phosphonooxy)acetyl]amino}butyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ON(CCCCO[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
 TD4  TD4  '4-{hydroxy[(phosphonooxy)acetyl]amino}butyl dihydrogen phosphate'  ligand  34  19  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TD4
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
 TD4  O01   O  OH1   0  -0.546  -1.4397  -2.0129   0.8703
 TD4  N02   N  NT    0  -0.208  -1.1875  -1.0745  -0.0959
 TD4  C03   C  CH2   0  -0.271   0.1117  -1.1522  -0.7243
 TD4  C04   C  CH2   0  -0.457   1.2387  -0.6830   0.1872
 TD4  C05   C  CH2   0  -0.468   2.5873  -0.8057  -0.5120
 TD4  C06   C  CH2   0  -0.153   3.7076  -0.3075   0.3738
 TD4  O07   O  O2    0  -0.592   4.9532  -0.5297  -0.3081
 TD4  P08   P  P     0   1.451   6.2651   0.2335   0.1774
 TD4  O09   O  O     0  -0.713   6.4971   0.2937   1.6330
 TD4  O10   O  OH1   0  -0.732   7.3027  -0.5880  -0.7122
 TD4  O11   O  OH1   0  -0.741   6.1898   1.7191  -0.4090
 TD4  C12   C  C     0   0.494  -2.2211  -0.3233  -0.5244
 TD4  O13   O  O     0  -0.471  -2.1275   0.4709  -1.4404
 TD4  C14   C  CH2   0  -0.270  -3.5201  -0.5381   0.2386
 TD4  O15   O  O2    0  -0.579  -4.4654   0.3693  -0.3021
 TD4  P16   P  P     0   1.458  -5.9882   0.2730   0.1753
 TD4  O17   O  OH1   0  -0.729  -6.4969   1.5783  -0.5809
 TD4  O18   O  OH1   0  -0.740  -6.6235  -0.9982  -0.5541
 TD4  O19   O  O     0  -0.708  -6.2143   0.1745   1.6286
 TD4  HO01  H  HOH1  0   0.483  -1.1446  -1.6350   1.7108
 TD4  H03   H  HCH2  0   0.254   0.2829  -2.1841  -1.0431
 TD4  H03A  H  HCH2  0   0.259   0.0753  -0.5371  -1.6217
 TD4  H04   H  HCH2  0   0.240   1.0555   0.3544   0.4801
 TD4  H04A  H  HCH2  0   0.234   1.2523  -1.2797   1.1037
 TD4  H05   H  HCH2  0   0.241   2.7705  -1.8507  -0.7772
 TD4  H05A  H  HCH2  0   0.240   2.5784  -0.2305  -1.4418
 TD4  H06   H  HCH2  0   0.233   3.5691   0.7562   0.5883
 TD4  H06A  H  HCH2  0   0.238   3.7184  -0.8455   1.3243
 TD4  HO10  H  HOH1  0   0.503   8.2271  -0.3482  -0.5632
 TD4  HO11  H  HOH1  0   0.495   6.0724   1.7862  -1.3662
 TD4  H14   H  HCH2  0   0.275  -3.8502  -1.5747   0.1228
 TD4  H14A  H  HCH2  0   0.277  -3.3753  -0.3509   1.3054
 TD4  HO17  H  HOH1  0   0.506  -7.4251   1.7941  -0.4176
 TD4  HO18  H  HOH1  0   0.497  -6.5625  -1.0028  -1.5190

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
 TD4  N02  O01   single  1.370  0.020  1.370
 TD4  O01  HO01  single  0.850  0.020  0.980
 TD4  C03  N02   single  1.445  0.020  1.445
 TD4  N02  C12   single  1.348  0.020  1.348
 TD4  C03  C04   single  1.524  0.020  1.524
 TD4  C03  H03   single  0.970  0.020  1.090
 TD4  C03  H03A  single  0.970  0.020  1.090
 TD4  C05  C04   single  1.524  0.020  1.524
 TD4  C04  H04   single  0.970  0.020  1.090
 TD4  C04  H04A  single  0.970  0.020  1.090
 TD4  C06  C05   single  1.513  0.020  1.513
 TD4  C05  H05   single  0.970  0.020  1.090
 TD4  C05  H05A  single  0.970  0.020  1.090
 TD4  O07  C06   single  1.437  0.020  1.437
 TD4  C06  H06   single  0.970  0.020  1.090
 TD4  C06  H06A  single  0.970  0.020  1.090
 TD4  O07  P08   single  1.594  0.020  1.594
 TD4  O09  P08   double  1.475  0.020  1.475
 TD4  O11  P08   single  1.599  0.020  1.599
 TD4  P08  O10   single  1.595  0.020  1.595
 TD4  O10  HO10  single  0.850  0.020  0.980
 TD4  O11  HO11  single  0.850  0.020  0.980
 TD4  C14  C12   single  1.522  0.020  1.522
 TD4  C12  O13   double  1.216  0.020  1.216
 TD4  C14  O15   single  1.417  0.020  1.417
 TD4  C14  H14   single  0.970  0.020  1.090
 TD4  C14  H14A  single  0.970  0.020  1.090
 TD4  P16  O15   single  1.599  0.020  1.599
 TD4  O19  P16   double  1.474  0.020  1.474
 TD4  P16  O18   single  1.597  0.020  1.597
 TD4  P16  O17   single  1.592  0.020  1.592
 TD4  O17  HO17  single  0.850  0.020  0.980
 TD4  O18  HO18  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
 TD4  HO01  O01  N02  106.80  3.000
 TD4  C12   N02  C03  125.53  3.000
 TD4  C12   N02  O01  117.69  3.000
 TD4  C03   N02  O01  115.80  3.000
 TD4  H03A  C03  H03  107.35  3.000
 TD4  H03A  C03  C04  110.12  3.000
 TD4  H03   C03  C04  110.44  3.000
 TD4  H03A  C03  N02  107.34  3.000
 TD4  H03   C03  N02  108.56  3.000
 TD4  C04   C03  N02  112.85  3.000
 TD4  H04A  C04  H04  107.17  3.000
 TD4  H04A  C04  C05  109.24  3.000
 TD4  H04   C04  C05  110.34  3.000
 TD4  H04A  C04  C03  110.03  3.000
 TD4  H04   C04  C03  109.18  3.000
 TD4  C05   C04  C03  110.81  3.000
 TD4  H05A  C05  H05  107.33  3.000
 TD4  H05A  C05  C06  109.31  3.000
 TD4  H05   C05  C06  109.43  3.000
 TD4  H05A  C05  C04  109.92  3.000
 TD4  H05   C05  C04  109.66  3.000
 TD4  C06   C05  C04  111.11  3.000
 TD4  H06A  C06  H06  108.03  3.000
 TD4  H06A  C06  O07  109.15  3.000
 TD4  H06   C06  O07  110.68  3.000
 TD4  H06A  C06  C05  110.77  3.000
 TD4  H06   C06  C05  109.96  3.000
 TD4  O07   C06  C05  108.25  3.000
 TD4  P08   O07  C06  119.66  3.000
 TD4  O11   P08  O10  107.74  3.000
 TD4  O10   P08  O09  117.98  3.000
 TD4  O11   P08  O09  109.35  3.000
 TD4  O10   P08  O07   96.83  3.000
 TD4  O11   P08  O07  107.13  3.000
 TD4  O09   P08  O07  116.72  3.000
 TD4  HO10  O10  P08  114.11  3.000
 TD4  HO11  O11  P08  115.68  3.000
 TD4  C14   C12  O13  122.39  3.000
 TD4  O13   C12  N02  122.99  3.000
 TD4  C14   C12  N02  114.62  3.000
 TD4  H14A  C14  H14  107.79  3.000
 TD4  H14A  C14  O15  110.55  3.000
 TD4  H14   C14  O15  111.41  3.000
 TD4  H14A  C14  C12  110.62  3.000
 TD4  H14   C14  C12  109.77  3.000
 TD4  O15   C14  C12  106.72  3.000
 TD4  P16   O15  C14  118.86  3.000
 TD4  O19   P16  O18  109.63  3.000
 TD4  O18   P16  O17  107.97  3.000
 TD4  O19   P16  O17  118.29  3.000
 TD4  O17   P16  O15   96.50  3.000
 TD4  O18   P16  O15  106.89  3.000
 TD4  O19   P16  O15  116.39  3.000
 TD4  HO17  O17  P16  114.18  3.000
 TD4  HO18  O18  P16  115.75  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
 TD4  CONST_01  C14  C12  N02  O01    0.00   0.0  0
 TD4  CONST_02  O13  C12  N02  O01  180.00   0.0  0
 TD4  CONST_03  C14  C12  N02  C03  180.00   0.0  0
 TD4  CONST_04  O13  C12  N02  C03    0.00   0.0  0
 TD4  Var_01    C04  C03  N02  O01  -72.91  30.0  1
 TD4  Var_02    C05  C04  C03  N02  179.07  30.0  3
 TD4  Var_03    O15  C14  C12  N02  177.32  30.0  1
 TD4  Var_04    C06  C05  C04  C03  178.50  30.0  1
 TD4  Var_05    O07  C06  C05  C04  176.36  30.0  1
 TD4  Var_06    O09  P08  O07  C06   43.75  30.0  3
 TD4  Var_07    O19  P16  O15  C14   47.40  30.0  2

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
 TD4  plan-1  O01  0.020
 TD4  plan-1  N02  0.020
 TD4  plan-1  C03  0.020
 TD4  plan-1  C12  0.020
 TD4  plan-1  O13  0.020
 TD4  plan-1  C14  0.020

