# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 17:28:55 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: bis[(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
 X3X  X3X  'bis[(2S)-2,3-dihydroxypropyl] hydrogen phosphate'  ligand  29  15  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X3X
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
 X3X  O3   O  OH1    0  -0.669  -5.6965  -1.1541  -0.6925
 X3X  C3   C  CH2    0  -0.164  -4.8673  -0.1057  -0.2530
 X3X  C2   C  CH1    0  -0.041  -3.4398  -0.6158  -0.1392
 X3X  O2   O  OH1    0  -0.659  -3.3242  -1.6842   0.7708
 X3X  C1   C  CH2    0  -0.159  -2.5094   0.5373   0.2034
 X3X  O1   O  O2     0  -0.614  -1.1791   0.0631   0.2396
 X3X  PAO  P  P      0   1.331   0.0157   1.1775   0.0898
 X3X  OAF  O  OP    -1  -0.795   0.0782   1.6771  -1.3217
 X3X  OAA  O  O      0  -0.802  -0.0417   2.1633   1.2172
 X3X  O6   O  O2     0  -0.613   1.1972   0.0715   0.3557
 X3X  C6   C  CH2    0  -0.157   2.5300   0.5367   0.3670
 X3X  C5   C  CH1    0  -0.045   3.4684  -0.6352   0.1251
 X3X  O5   O  OH1    0  -0.657   3.2281  -1.2651  -1.1103
 X3X  C4   C  CH2    0  -0.163   4.9104  -0.1752   0.2730
 X3X  O4   O  OH1    0  -0.669   5.7613  -1.2879   0.1401
 X3X  H1   H  HOH1   0   0.455  -6.5992  -0.8255  -0.7225
 X3X  H2   H  HCH2   0   0.199  -4.8834   0.7428  -0.9493
 X3X  H3   H  HCH2   0   0.194  -5.1888   0.2825   0.7245
 X3X  H4   H  HCH1   0   0.230  -3.1382  -1.0196  -1.1117
 X3X  H5   H  HOH1   0   0.442  -3.6110  -1.3792   1.6389
 X3X  H6   H  HCH2   0   0.210  -2.6353   1.3238  -0.5500
 X3X  H7   H  HCH2   0   0.209  -2.7911   0.9689   1.1727
 X3X  H9   H  HCH2   0   0.205   2.6949   1.2985  -0.4068
 X3X  H10  H  HCH2   0   0.213   2.7708   0.9984   1.3308
 X3X  H11  H  HCH1   0   0.230   3.2722  -1.3964   0.8882
 X3X  H12  H  HOH1   0   0.441   3.3826  -0.6271  -1.8158
 X3X  H13  H  HCH2   0   0.194   5.1259   0.5929  -0.4847
 X3X  H14  H  HCH2   0   0.199   5.0251   0.3084   1.2520
 X3X  H15  H  HOH1   0   0.455   6.6685  -0.9764   0.2000

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
 X3X  O5   C5   single  1.407  0.020  1.407
 X3X  O2   C2   single  1.408  0.020  1.408
 X3X  C6   C5   single  1.521  0.020  1.521
 X3X  C6   O6   single  1.412  0.020  1.412
 X3X  OAA  PAO  deloc   1.499  0.020  1.499
 X3X  C5   C4   single  1.521  0.020  1.521
 X3X  O1   PAO  single  1.641  0.020  1.641
 X3X  O1   C1   single  1.413  0.020  1.413
 X3X  C2   C1   single  1.521  0.020  1.521
 X3X  C2   C3   single  1.520  0.020  1.520
 X3X  PAO  O6   single  1.640  0.020  1.640
 X3X  PAO  OAF  deloc   1.499  0.020  1.499
 X3X  C3   O3   single  1.407  0.020  1.407
 X3X  C4   O4   single  1.407  0.020  1.407
 X3X  O3   H1   single  0.850  0.020  0.980
 X3X  C3   H2   single  0.970  0.020  1.090
 X3X  C3   H3   single  0.970  0.020  1.090
 X3X  C2   H4   single  0.970  0.020  1.090
 X3X  O2   H5   single  0.850  0.020  0.980
 X3X  C1   H6   single  0.970  0.020  1.090
 X3X  C1   H7   single  0.970  0.020  1.090
 X3X  C6   H9   single  0.970  0.020  1.090
 X3X  C6   H10  single  0.970  0.020  1.090
 X3X  C5   H11  single  0.970  0.020  1.090
 X3X  O5   H12  single  0.850  0.020  0.980
 X3X  C4   H13  single  0.970  0.020  1.090
 X3X  C4   H14  single  0.970  0.020  1.090
 X3X  O4   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
 X3X  H1   O3   C3   107.97  3.000
 X3X  H3   C3   H2   106.65  3.000
 X3X  H3   C3   C2   109.05  3.000
 X3X  H2   C3   C2   108.70  3.000
 X3X  H3   C3   O3   111.61  3.000
 X3X  H2   C3   O3   111.67  3.000
 X3X  C2   C3   O3   109.07  3.000
 X3X  H4   C2   C1   108.13  3.000
 X3X  H4   C2   O2   105.76  3.000
 X3X  C1   C2   O2   112.31  3.000
 X3X  H4   C2   C3   108.40  3.000
 X3X  C1   C2   C3   109.69  3.000
 X3X  O2   C2   C3   112.34  3.000
 X3X  H5   O2   C2   108.52  3.000
 X3X  H7   C1   H6   107.17  3.000
 X3X  H7   C1   O1   110.55  3.000
 X3X  H6   C1   O1   111.50  3.000
 X3X  H7   C1   C2   109.88  3.000
 X3X  H6   C1   C2   108.60  3.000
 X3X  O1   C1   C2   109.11  3.000
 X3X  PAO  O1   C1   117.09  3.000
 X3X  O6   PAO  OAA  110.44  3.000
 X3X  O6   PAO  OAF  110.33  3.000
 X3X  OAA  PAO  OAF  119.40  3.000
 X3X  OAF  PAO  O1   110.04  3.000
 X3X  O6   PAO  O1    92.97  3.000
 X3X  OAA  PAO  O1   110.50  3.000
 X3X  C6   O6   PAO  117.33  3.000
 X3X  H10  C6   H9   107.13  3.000
 X3X  H10  C6   C5   109.21  3.000
 X3X  H9   C6   C5   109.25  3.000
 X3X  H10  C6   O6   110.70  3.000
 X3X  H9   C6   O6   111.39  3.000
 X3X  C5   C6   O6   109.11  3.000
 X3X  H11  C5   C4   108.19  3.000
 X3X  H11  C5   O5   105.65  3.000
 X3X  C4   C5   O5   112.50  3.000
 X3X  H11  C5   C6   108.31  3.000
 X3X  C4   C5   C6   109.67  3.000
 X3X  O5   C5   C6   112.28  3.000
 X3X  H12  O5   C5   108.60  3.000
 X3X  H14  C4   H13  106.62  3.000
 X3X  H14  C4   O4   111.68  3.000
 X3X  H13  C4   O4   111.63  3.000
 X3X  H14  C4   C5   108.60  3.000
 X3X  H13  C4   C5   109.26  3.000
 X3X  O4   C4   C5   108.97  3.000
 X3X  H15  O4   C4   107.98  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
 X3X  Var_01  OAA  PAO  O1  C1     61.56  30.0  3
 X3X  Var_02  C5   C6   O6  PAO  -159.87  30.0  1
 X3X  Var_03  H6   C1   O1  PAO    40.14  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
 X3X  chir_01  C2  O2  C1  C3  positiv
 X3X  chir_02  C5  O5  C6  C4  positiv

