# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 19:32:13 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 2-[hydroxy(4-hydroxybutyl)amino]-2-oxoethyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCCCN(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
 TD3  TD3  '2-[hydroxy(4-hydroxybutyl)amino]-2-oxoethyl dihydrogen phosphate'  ligand  29  15  .  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_TD3
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
 TD3  O01   O  OH1   0  -0.546   0.8200  -1.8134   0.9526
 TD3  N02   N  NT    0  -0.206   0.9718  -1.0099  -0.1482
 TD3  C03   C  CH2   0  -0.284   2.3243  -0.8577  -0.6374
 TD3  C04   C  CH2   0  -0.442   3.2175  -0.0358   0.2828
 TD3  C05   C  CH2   0  -0.462   4.6231   0.0957  -0.2893
 TD3  C06   C  CH2   0  -0.135   5.5228   0.9211   0.6090
 TD3  O07   O  OH1   0  -0.675   6.8111   0.9850   0.0353
 TD3  C12   C  C     0   0.496  -0.0430  -0.1735  -0.4453
 TD3  O13   O  O     0  -0.471   0.0471   0.6964  -1.2902
 TD3  C14   C  CH2   0  -0.270  -1.3244  -0.4195   0.3373
 TD3  O15   O  O2    0  -0.578  -2.2916   0.4870  -0.1669
 TD3  P16   P  P     0   1.456  -3.8356   0.2319   0.1561
 TD3  O17   O  OH1   0  -0.729  -4.3899   1.5459  -0.5512
 TD3  O18   O  OH1   0  -0.740  -4.2836  -1.0279  -0.7185
 TD3  O19   O  O     0  -0.708  -4.1850   0.0015   1.5695
 TD3  HO01  H  HOH1  0   0.482   0.6706  -2.7080   0.6153
 TD3  H103  H  HCH2  0   0.255   2.7402  -1.8568  -0.7873
 TD3  H203  H  HCH2  0   0.255   2.2625  -0.3932  -1.6205
 TD3  H104  H  HCH2  0   0.232   2.7758   0.9554   0.4218
 TD3  H204  H  HCH2  0   0.232   3.2625  -0.5045   1.2694
 TD3  H105  H  HCH2  0   0.226   5.0598  -0.8988  -0.4255
 TD3  H205  H  HCH2  0   0.226   4.5748   0.5583  -1.2801
 TD3  H106  H  HCH2  0   0.191   5.0890   1.9223   0.7332
 TD3  H206  H  HCH2  0   0.188   5.5526   0.4650   1.6078
 TD3  HO07  H  HOH1  0   0.452   7.3598   1.5459   0.5906
 TD3  H114  H  HCH2  0   0.269  -1.6426  -1.4592   0.2154
 TD3  H214  H  HCH2  0   0.282  -1.1591  -0.2452   1.4030
 TD3  H13   H  HOH1  0   0.506  -5.3319   1.7061  -0.4035
 TD3  H14   H  HOH1  0   0.497  -4.1415  -0.9510  -1.6717

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
 TD3  O01  HO01  single  0.850  0.020  0.980
 TD3  N02  C03   single  1.446  0.020  1.446
 TD3  N02  O01   single  1.371  0.020  1.371
 TD3  C03  H103  single  0.970  0.020  1.090
 TD3  C03  H203  single  0.970  0.020  1.090
 TD3  C04  C03   single  1.523  0.020  1.523
 TD3  C04  H104  single  0.970  0.020  1.090
 TD3  C04  H204  single  0.970  0.020  1.090
 TD3  C05  C04   single  1.523  0.020  1.523
 TD3  C05  H105  single  0.970  0.020  1.090
 TD3  C05  H205  single  0.970  0.020  1.090
 TD3  C06  C05   single  1.516  0.020  1.516
 TD3  C06  H106  single  0.970  0.020  1.090
 TD3  C06  H206  single  0.970  0.020  1.090
 TD3  O07  C06   single  1.412  0.020  1.412
 TD3  O07  HO07  single  0.850  0.020  0.980
 TD3  C12  N02   single  1.348  0.020  1.348
 TD3  O13  C12   double  1.216  0.020  1.216
 TD3  C14  C12   single  1.521  0.020  1.521
 TD3  C14  H114  single  0.970  0.020  1.090
 TD3  C14  H214  single  0.970  0.020  1.090
 TD3  O15  C14   single  1.418  0.020  1.418
 TD3  P16  O15   single  1.598  0.020  1.598
 TD3  P16  O19   double  1.474  0.020  1.474
 TD3  O17  P16   single  1.592  0.020  1.592
 TD3  O18  P16   single  1.598  0.020  1.598
 TD3  O17  H13   single  0.850  0.020  0.980
 TD3  O18  H14   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
 TD3  HO01  O01  N02   106.20  3.000
 TD3  C12   N02  C03   124.34  3.000
 TD3  C12   N02  O01   117.20  3.000
 TD3  C03   N02  O01   115.89  3.000
 TD3  H203  C03  H103  106.72  3.000
 TD3  H203  C03  C04   110.40  3.000
 TD3  H103  C03  C04   110.68  3.000
 TD3  C04   C03  N02   113.63  3.000
 TD3  H203  C03  N02   107.28  3.000
 TD3  H103  C03  N02   107.82  3.000
 TD3  H204  C04  H104  106.88  3.000
 TD3  H204  C04  C05   109.75  3.000
 TD3  H104  C04  C05   110.00  3.000
 TD3  C05   C04  C03   111.15  3.000
 TD3  H204  C04  C03   109.76  3.000
 TD3  H104  C04  C03   109.20  3.000
 TD3  H205  C05  H105  106.79  3.000
 TD3  H205  C05  C06   109.42  3.000
 TD3  H105  C05  C06   109.37  3.000
 TD3  C06   C05  C04   111.85  3.000
 TD3  H205  C05  C04   109.62  3.000
 TD3  H105  C05  C04   109.66  3.000
 TD3  H206  C06  H106  106.64  3.000
 TD3  H206  C06  O07   111.33  3.000
 TD3  H106  C06  O07   111.42  3.000
 TD3  O07   C06  C05   108.99  3.000
 TD3  H206  C06  C05   109.20  3.000
 TD3  H106  C06  C05   109.20  3.000
 TD3  HO07  O07  C06   108.21  3.000
 TD3  C14   C12  O13   122.38  3.000
 TD3  C14   C12  N02   114.85  3.000
 TD3  O13   C12  N02   122.76  3.000
 TD3  H214  C14  H114  107.72  3.000
 TD3  H214  C14  O15   110.36  3.000
 TD3  H114  C14  O15   111.68  3.000
 TD3  O15   C14  C12   106.75  3.000
 TD3  H214  C14  C12   110.40  3.000
 TD3  H114  C14  C12   109.96  3.000
 TD3  P16   O15  C14   119.02  3.000
 TD3  O19   P16  O18   109.58  3.000
 TD3  O18   P16  O17   108.06  3.000
 TD3  O19   P16  O17   118.20  3.000
 TD3  O18   P16  O15   106.63  3.000
 TD3  O17   P16  O15    96.60  3.000
 TD3  O19   P16  O15   116.61  3.000
 TD3  H13   O17  P16   114.09  3.000
 TD3  H14   O18  P16   115.84  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
 TD3  CONST_01  O13  C12  N02  O01   180.00   0.0  0
 TD3  CONST_02  C14  C12  N02  O01     0.00   0.0  0
 TD3  CONST_03  O13  C12  N02  C03     0.00   0.0  0
 TD3  CONST_04  C14  C12  N02  C03   180.00   0.0  0
 TD3  Var_01    C04  C03  N02  O01   -70.21  30.0  3
 TD3  Var_02    C05  C04  C03  N02  -179.65  30.0  1
 TD3  Var_03    O15  C14  C12  N02  -176.29  30.0  1
 TD3  Var_04    C06  C05  C04  C03   179.53  30.0  1
 TD3  Var_05    O07  C06  C05  C04   179.02  30.0  1
 TD3  Var_06    O19  P16  O15  C14    50.60  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
 TD3  plan-1  O01  0.020
 TD3  plan-1  N02  0.020
 TD3  plan-1  C03  0.020
 TD3  plan-1  C12  0.020
 TD3  plan-1  O13  0.020
 TD3  plan-1  C14  0.020

