# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 01:59:52 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: (2R)-2,3-dihydroxypropyl (2S)-2,3-dihydroxypropyl hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H](O)CO[P](O)(=O)OC[C@H](O)CO
#
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
 CU7  CU7  '(2R)-2,3-dihydroxypropyl (2S)-2,3-dihydroxypropyl hydrogen phosphate'  ligand  30  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_CU7
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
 CU7  C12  C  CH2   0  -0.165   4.8836  -0.1824  -0.0428
 CU7  O1   O  OH1   0  -0.666  -5.7062  -1.3126  -0.4388
 CU7  O6   O  O2    0  -0.578  -1.2039   0.2196  -0.2434
 CU7  C2   C  CH2   0  -0.167  -4.9032  -0.2034  -0.1217
 CU7  C3   C  CH1   0  -0.045  -3.4431  -0.6098  -0.2414
 CU7  C5   C  CH2   0  -0.182  -2.5627   0.6086  -0.0199
 CU7  O4   O  OH1   0  -0.654  -3.1000  -1.6700   0.6143
 CU7  O15  O  OH1   0  -0.743   0.0179   2.4136  -0.7995
 CU7  P7   P  P     0   1.472  -0.0124   1.1737   0.2092
 CU7  O14  O  O     0  -0.709  -0.0329   1.6708   1.5973
 CU7  O8   O  O2    0  -0.578   1.1799   0.1985  -0.1947
 CU7  C9   C  CH2   0  -0.183   2.5220   0.5289   0.1766
 CU7  C10  C  CH1   0  -0.046   3.4455  -0.5368  -0.3893
 CU7  O13  O  OH1   0  -0.666   5.7390  -1.1106  -0.6611
 CU7  O11  O  OH1   0  -0.653   3.0857  -1.8271   0.0351
 CU7  H1   H  HCH2  0   0.205   5.0844   0.8432  -0.3778
 CU7  H2   H  HCH2  0   0.199   5.0002  -0.1861   1.0510
 CU7  H3   H  HOH1  0   0.457  -6.6262  -1.0480  -0.3524
 CU7  H5   H  HCH2  0   0.199  -5.0949   0.1595   0.8990
 CU7  H6   H  HCH1  0   0.243  -3.2701  -0.9766  -1.2585
 CU7  H7   H  HCH2  0   0.239  -2.6883   0.9896   0.9985
 CU7  H8   H  HCH2  0   0.244  -2.8405   1.4051  -0.7150
 CU7  H9   H  HOH1  0   0.446  -3.3106  -1.4190   1.5207
 CU7  H10  H  HOH1  0   0.496   0.0323   2.1926  -1.7405
 CU7  H11  H  HCH2  0   0.244   2.7996   1.5080  -0.2225
 CU7  H12  H  HCH2  0   0.240   2.6064   0.5697   1.2671
 CU7  H13  H  HCH1  0   0.243   3.3411  -0.5403  -1.4792
 CU7  H14  H  HOH1  0   0.457   6.6420  -0.8937  -0.4133
 CU7  H15  H  HOH1  0   0.446   3.2176  -1.8911   0.9879
 CU7  H4   H  HCH2  0   0.205  -5.0898   0.6410  -0.7970

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
 CU7  O13  C12  single  1.406  0.020  1.406
 CU7  C12  C10  single  1.521  0.020  1.521
 CU7  C10  C9   single  1.519  0.020  1.519
 CU7  C10  O11  single  1.405  0.020  1.405
 CU7  C9   O8   single  1.431  0.020  1.431
 CU7  O8   P7   single  1.592  0.020  1.592
 CU7  O14  P7   double  1.475  0.020  1.475
 CU7  P7   O6   single  1.592  0.020  1.592
 CU7  P7   O15  single  1.599  0.020  1.599
 CU7  O4   C3   single  1.405  0.020  1.405
 CU7  O6   C5   single  1.431  0.020  1.431
 CU7  C5   C3   single  1.519  0.020  1.519
 CU7  C3   C2   single  1.520  0.020  1.520
 CU7  O1   C2   single  1.406  0.020  1.406
 CU7  C12  H1   single  0.970  0.020  1.090
 CU7  C12  H2   single  0.970  0.020  1.090
 CU7  O1   H3   single  0.850  0.020  0.980
 CU7  C2   H4   single  0.970  0.020  1.090
 CU7  C2   H5   single  0.970  0.020  1.090
 CU7  C3   H6   single  0.970  0.020  1.090
 CU7  C5   H7   single  0.970  0.020  1.090
 CU7  C5   H8   single  0.970  0.020  1.090
 CU7  O4   H9   single  0.850  0.020  0.980
 CU7  O15  H10  single  0.850  0.020  0.980
 CU7  C9   H11  single  0.970  0.020  1.090
 CU7  C9   H12  single  0.970  0.020  1.090
 CU7  C10  H13  single  0.970  0.020  1.090
 CU7  O13  H14  single  0.850  0.020  0.980
 CU7  O11  H15  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
 CU7  H2   C12  H1   106.70  3.000
 CU7  H2   C12  O13  111.76  3.000
 CU7  H1   C12  O13  111.81  3.000
 CU7  H2   C12  C10  109.02  3.000
 CU7  H1   C12  C10  108.73  3.000
 CU7  O13  C12  C10  108.74  3.000
 CU7  H3   O1   C2   108.01  3.000
 CU7  P7   O6   C5   120.22  3.000
 CU7  H5   C2   H4   106.71  3.000
 CU7  H5   C2   C3   109.18  3.000
 CU7  H4   C2   C3   108.70  3.000
 CU7  H5   C2   O1   111.72  3.000
 CU7  H4   C2   O1   111.80  3.000
 CU7  C3   C2   O1   108.66  3.000
 CU7  H6   C3   O4   105.92  3.000
 CU7  H6   C3   C5   108.21  3.000
 CU7  O4   C3   C5   112.01  3.000
 CU7  H6   C3   C2   108.32  3.000
 CU7  C5   C3   C2   109.31  3.000
 CU7  O4   C3   C2   112.85  3.000
 CU7  H8   C5   H7   107.99  3.000
 CU7  H8   C5   C3   110.15  3.000
 CU7  H7   C5   C3   110.38  3.000
 CU7  H8   C5   O6   109.88  3.000
 CU7  H7   C5   O6   110.42  3.000
 CU7  C3   C5   O6   108.03  3.000
 CU7  H9   O4   C3   108.84  3.000
 CU7  H10  O15  P7   115.92  3.000
 CU7  O8   P7   O14  117.11  3.000
 CU7  O14  P7   O15  109.43  3.000
 CU7  O8   P7   O15  107.50  3.000
 CU7  O15  P7   O6   107.43  3.000
 CU7  O14  P7   O6   117.34  3.000
 CU7  O8   P7   O6    96.97  3.000
 CU7  C9   O8   P7   119.67  3.000
 CU7  H12  C9   H11  108.11  3.000
 CU7  H12  C9   C10  110.51  3.000
 CU7  H11  C9   C10  109.74  3.000
 CU7  H12  C9   O8   109.84  3.000
 CU7  H11  C9   O8   110.50  3.000
 CU7  C10  C9   O8   108.15  3.000
 CU7  H13  C10  O11  105.86  3.000
 CU7  H13  C10  C9   108.36  3.000
 CU7  O11  C10  C9   112.08  3.000
 CU7  H13  C10  C12  108.52  3.000
 CU7  O11  C10  C12  112.78  3.000
 CU7  C9   C10  C12  109.05  3.000
 CU7  H14  O13  C12  108.02  3.000
 CU7  H15  O11  C10  108.93  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
 CU7  Var_01  O8   P7  O6  C5   176.44  30.0  1
 CU7  Var_02  C10  C9  O8  P7  -177.49  30.0  1

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
 CU7  chir_01  C3   O4   C5  C2   positiv
 CU7  chir_02  C10  C12  C9  O11  positiv

