# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 02:34:46 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: (6E)-2,6,7-trideoxy-7-phosphono-D-arabino-hept-6-enitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC[C@@H](O)[C@H](O)[C@H](O)\C=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
 D6P  D6P  (6E)-2,6,7-trideoxy-7-phosphono-D-arabino-hept-6-enitol  ligand  28  15  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D6P
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
 D6P  C1   C  CH2    0  -0.135   0.0069  -0.5339   5.1596
 D6P  C2   C  CH2    0  -0.498   0.6094  -0.2981   3.7868
 D6P  C3   C  CH1    0   0.013  -0.4395   0.0569   2.7393
 D6P  C4   C  CH1    0   0.002   0.1807   0.1826   1.3405
 D6P  C5   C  CH1    0  -0.040  -0.8828   0.2313   0.2224
 D6P  C6   C  C1     0  -0.239  -0.2467   0.3940  -1.1322
 D6P  O1   O  OH1    0  -0.676   1.0353  -0.9393   6.0394
 D6P  O3   O  OH1    0  -0.673  -1.1638   1.2252   3.0816
 D6P  O4   O  OH1    0  -0.668   1.0517   1.2921   1.2727
 D6P  O5   O  OH1    0  -0.662  -1.7373  -0.8835   0.3068
 D6P  C7   C  C1     0  -0.577  -0.4397  -0.3821  -2.1970
 D6P  P    P  P      0   1.142   0.3823  -0.1566  -3.8307
 D6P  O1P  O  OP    -1  -0.906   1.1965  -1.4431  -4.0162
 D6P  O2P  O  OP    -1  -0.906  -0.7831  -0.0283  -4.8194
 D6P  O3P  O  O      0  -0.897   1.2339   1.1101  -3.6984
 D6P  H11  H  HCH2   0   0.187  -0.7764  -1.3005   5.0809
 D6P  H12  H  HCH2   0   0.193  -0.4804   0.3808   5.5158
 D6P  H21  H  HCH2   0   0.229   1.3705   0.4877   3.8437
 D6P  H22  H  HCH2   0   0.233   1.1200  -1.2098   3.4627
 D6P  H3   H  HCH1   0   0.229  -1.1765  -0.7503   2.7072
 D6P  H4   H  HCH1   0   0.228   0.8070  -0.7020   1.1692
 D6P  H5   H  HCH1   0   0.229  -1.5234   1.1044   0.4116
 D6P  H6   H  H      0   0.221   0.4329   1.2353  -1.2299
 D6P  HO1  H  HOH1   0   0.452   0.6608  -1.0157   6.9212
 D6P  HO3  H  HOH1   0   0.441  -0.5343   1.9098   3.3327
 D6P  HO4  H  HOH1   0   0.443   0.5259   2.0955   1.1954
 D6P  HO5  H  HOH1   0   0.444  -1.2434  -1.6597   0.0189
 D6P  H7   H  H      0   0.193  -1.1315  -1.2218  -2.1148

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
 D6P  C1  C2   single  1.518  0.020  1.518
 D6P  C1  O1   single  1.413  0.020  1.413
 D6P  C1  H11  single  0.970  0.020  1.090
 D6P  C1  H12  single  0.970  0.020  1.090
 D6P  C2  C3   single  1.524  0.020  1.524
 D6P  C2  H21  single  0.970  0.020  1.090
 D6P  C2  H22  single  0.970  0.020  1.090
 D6P  C3  C4   single  1.535  0.020  1.535
 D6P  C3  O3   single  1.417  0.020  1.417
 D6P  C3  H3   single  0.970  0.020  1.090
 D6P  C4  C5   single  1.544  0.020  1.544
 D6P  C4  O4   single  1.412  0.020  1.412
 D6P  C4  H4   single  0.970  0.020  1.090
 D6P  C5  C6   single  1.505  0.020  1.505
 D6P  C5  O5   single  1.407  0.020  1.407
 D6P  C5  H5   single  0.970  0.020  1.090
 D6P  C6  C7   double  1.332  0.020  1.332
 D6P  C6  H6   single  0.930  0.020  1.080
 D6P  O1  HO1  single  0.850  0.020  0.980
 D6P  O3  HO3  single  0.850  0.020  0.980
 D6P  O4  HO4  single  0.850  0.020  0.980
 D6P  O5  HO5  single  0.850  0.020  0.980
 D6P  C7  P    single  1.843  0.020  1.843
 D6P  C7  H7   single  0.930  0.020  1.080
 D6P  P   O1P  deloc   1.534  0.020  1.534
 D6P  P   O2P  deloc   1.534  0.020  1.534
 D6P  P   O3P  deloc   1.532  0.020  1.532

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
 D6P  H12  C1  H11  106.77  3.000
 D6P  H12  C1  O1   111.15  3.000
 D6P  H11  C1  O1   111.30  3.000
 D6P  H12  C1  C2   109.93  3.000
 D6P  H11  C1  C2   109.06  3.000
 D6P  O1   C1  C2   108.60  3.000
 D6P  H22  C2  H21  106.79  3.000
 D6P  H22  C2  C3   108.16  3.000
 D6P  H21  C2  C3   110.28  3.000
 D6P  H22  C2  C1   108.89  3.000
 D6P  H21  C2  C1   109.90  3.000
 D6P  C3   C2  C1   112.62  3.000
 D6P  H3   C3  O3   105.74  3.000
 D6P  H3   C3  C4   107.81  3.000
 D6P  O3   C3  C4   111.05  3.000
 D6P  H3   C3  C2   108.18  3.000
 D6P  O3   C3  C2   112.21  3.000
 D6P  C4   C3  C2   111.55  3.000
 D6P  H4   C4  O4   105.89  3.000
 D6P  H4   C4  C5   107.79  3.000
 D6P  O4   C4  C5   111.43  3.000
 D6P  H4   C4  C3   107.86  3.000
 D6P  O4   C4  C3   110.93  3.000
 D6P  C5   C4  C3   112.59  3.000
 D6P  H5   C5  O5   105.37  3.000
 D6P  H5   C5  C6   108.38  3.000
 D6P  O5   C5  C6   113.34  3.000
 D6P  H5   C5  C4   107.57  3.000
 D6P  O5   C5  C4   110.48  3.000
 D6P  C6   C5  C4   111.34  3.000
 D6P  H6   C6  C7   118.05  3.000
 D6P  H6   C6  C5   115.42  3.000
 D6P  C7   C6  C5   126.53  3.000
 D6P  HO1  O1  C1   108.09  3.000
 D6P  HO3  O3  C3   108.35  3.000
 D6P  HO4  O4  C4   108.81  3.000
 D6P  HO5  O5  C5   107.99  3.000
 D6P  H7   C7  P    116.35  3.000
 D6P  H7   C7  C6   118.70  3.000
 D6P  P    C7  C6   124.96  3.000
 D6P  O3P  P   O2P  114.13  3.000
 D6P  O3P  P   O1P  114.13  3.000
 D6P  O2P  P   O1P  113.31  3.000
 D6P  O3P  P   C7   105.82  3.000
 D6P  O2P  P   C7   104.06  3.000
 D6P  O1P  P   C7   103.97  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
 D6P  Var_01  P    C7  C6  C5  -179.07   0.0  2
 D6P  Var_02  O1   C1  C2  C3   176.26  30.0  1
 D6P  Var_03  O1P  P   C7  C6   117.75  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 D6P  chir_01  C3  C2  C4  O3  positiv
 D6P  chir_02  C4  O4  C3  C5  negativ
 D6P  chir_03  C5  O5  C4  C6  negativ

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
 D6P  plan-1  C5  0.020
 D6P  plan-1  C6  0.020
 D6P  plan-1  C7  0.020
 D6P  plan-1  P   0.020
 D6P  plan-1  H6  0.020
 D6P  plan-1  H7  0.020

