# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 03:53:34 2020
#   Inital geometry file: a 60 line input string
#   Ligand name: (2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[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
 KSV  KSV  '(2R)-2,3-dihydroxypropyl ethyl hydrogen (S)-phosphate'  ligand  25  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KSV
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
 KSV  C2   C  CH2   0  -0.176  -3.6065  -0.4031   0.1360
 KSV  C3   C  CH2   0  -0.183   1.3941   0.6223   0.0530
 KSV  O3   O  O     0  -0.712  -1.3084   1.2077   1.6284
 KSV  C4   C  CH1   0  -0.045   2.5207  -0.3663  -0.1937
 KSV  C5   C  CH2   0  -0.165   3.8535   0.3601  -0.0980
 KSV  P1   P  P     0   1.472  -1.2123   0.6702   0.2581
 KSV  C1   C  CH3   0  -0.686  -4.3080  -1.5629  -0.5245
 KSV  O1   O  O2    0  -0.581  -2.1942  -0.5170  -0.1350
 KSV  O2   O  OH1   0  -0.745  -1.4423   1.8533  -0.7936
 KSV  O4   O  O2    0  -0.580   0.1495  -0.0584  -0.1372
 KSV  O5   O  OH1   0  -0.654   2.4447  -1.4790   0.6612
 KSV  O6   O  OH1   0  -0.667   4.8795  -0.5321  -0.4557
 KSV  H1   H  HCH2  0   0.236  -3.9865   0.5438  -0.2550
 KSV  H2   H  HCH2  0   0.241  -3.7675  -0.4141   1.2153
 KSV  H3   H  HCH2  0   0.239   1.4548   1.0246   1.0694
 KSV  H4   H  HCH2  0   0.243   1.4711   1.4581  -0.6472
 KSV  H5   H  HCH1  0   0.243   2.4157  -0.7607  -1.2098
 KSV  H6   H  HCH2  0   0.204   3.8269   1.2347  -0.7608
 KSV  H7   H  HCH2  0   0.200   3.9853   0.7428   0.9249
 KSV  H8   H  HCH3  0   0.240  -5.3763  -1.4971  -0.3202
 KSV  H9   H  HCH3  0   0.238  -4.1714  -1.5481  -1.6055
 KSV  H10  H  HCH3  0   0.239  -3.9512  -2.5174  -0.1384
 KSV  H11  H  HOH1  0   0.496  -1.4104   1.6009  -1.7261
 KSV  H12  H  HOH1  0   0.446   2.5981  -1.1860   1.5665
 KSV  H13  H  HOH1  0   0.457   5.7176  -0.0687  -0.3735

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
 KSV  O5  C4   single  1.405  0.020  1.405
 KSV  C4  C3   single  1.519  0.020  1.519
 KSV  C4  C5   single  1.521  0.020  1.521
 KSV  O3  P1   double  1.475  0.020  1.475
 KSV  O6  C5   single  1.406  0.020  1.406
 KSV  C3  O4   single  1.431  0.020  1.431
 KSV  O2  P1   single  1.600  0.020  1.600
 KSV  P1  O4   single  1.594  0.020  1.594
 KSV  P1  O1   single  1.590  0.020  1.590
 KSV  O1  C2   single  1.443  0.020  1.443
 KSV  C2  C1   single  1.508  0.020  1.508
 KSV  C2  H1   single  0.970  0.020  1.090
 KSV  C2  H2   single  0.970  0.020  1.090
 KSV  C3  H3   single  0.970  0.020  1.090
 KSV  C3  H4   single  0.970  0.020  1.090
 KSV  C4  H5   single  0.970  0.020  1.090
 KSV  C5  H6   single  0.970  0.020  1.090
 KSV  C5  H7   single  0.970  0.020  1.090
 KSV  C1  H8   single  0.970  0.020  1.090
 KSV  C1  H9   single  0.970  0.020  1.090
 KSV  C1  H10  single  0.970  0.020  1.090
 KSV  O2  H11  single  0.850  0.020  0.980
 KSV  O5  H12  single  0.850  0.020  0.980
 KSV  O6  H13  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
 KSV  H2   C2  H1  108.14  3.000
 KSV  H2   C2  O1  109.23  3.000
 KSV  H1   C2  O1  109.98  3.000
 KSV  H2   C2  C1  110.91  3.000
 KSV  H1   C2  C1  110.37  3.000
 KSV  O1   C2  C1  108.20  3.000
 KSV  H4   C3  H3  108.05  3.000
 KSV  H4   C3  O4  109.87  3.000
 KSV  H3   C3  O4  110.26  3.000
 KSV  H4   C3  C4  109.96  3.000
 KSV  H3   C3  C4  110.42  3.000
 KSV  O4   C3  C4  108.29  3.000
 KSV  H5   C4  O5  105.91  3.000
 KSV  H5   C4  C5  108.33  3.000
 KSV  O5   C4  C5  112.79  3.000
 KSV  H5   C4  C3  108.30  3.000
 KSV  C5   C4  C3  109.20  3.000
 KSV  O5   C4  C3  112.11  3.000
 KSV  H7   C5  H6  106.69  3.000
 KSV  H7   C5  O6  111.71  3.000
 KSV  H6   C5  O6  111.70  3.000
 KSV  H7   C5  C4  109.25  3.000
 KSV  H6   C5  C4  108.74  3.000
 KSV  O6   C5  C4  108.69  3.000
 KSV  O4   P1  O2  107.32  3.000
 KSV  O4   P1  O1   97.18  3.000
 KSV  O2   P1  O1  107.51  3.000
 KSV  O1   P1  O3  117.49  3.000
 KSV  O4   P1  O3  116.90  3.000
 KSV  O2   P1  O3  109.38  3.000
 KSV  H10  C1  H9  108.80  3.000
 KSV  H10  C1  H8  107.90  3.000
 KSV  H9   C1  H8  107.94  3.000
 KSV  H10  C1  C2  111.49  3.000
 KSV  H9   C1  C2  111.46  3.000
 KSV  H8   C1  C2  109.12  3.000
 KSV  P1   O1  C2  119.94  3.000
 KSV  H11  O2  P1  115.88  3.000
 KSV  P1   O4  C3  119.51  3.000
 KSV  H12  O5  C4  108.79  3.000
 KSV  H13  O6  C5  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
 KSV  Var_01  O3  P1  O1  C2   49.68  30.0  1
 KSV  Var_02  C1  C2  O1  P1  171.45  30.0  3
 KSV  Var_03  H3  C3  O4  P1   50.32  30.0  1
 KSV  Var_04  H8  C1  C2  O1  179.42  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
 KSV  chir_01  C4  O5  C3  C5  negativ
 KSV  chir_02  P1  O2  O4  O1  both

