# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 22:45:34 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (2R)-2,3-dibutoxypropyl hydrogen (S)-propylphosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCOC[C@H](CO[P](O)(=O)CCC)OCCCC
#
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
 HY4  HY4  '(2R)-2,3-dibutoxypropyl hydrogen (S)-propylphosphonate'  ligand  50  20  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HY4
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
 HY4  O11  O  O      0  -0.814  -3.2984   0.2330   1.9479
 HY4  P13  P  P      0   1.275  -3.2585   0.6955   0.5132
 HY4  C3   C  CH2    0  -0.705  -4.1346  -0.4960  -0.5555
 HY4  C2   C  CH2    0  -0.430  -5.6410  -0.4709  -0.3045
 HY4  C1   C  CH3    0  -0.655  -6.3969  -1.4757  -1.1628
 HY4  O5   O  O2     0  -0.624  -1.7299   0.4604  -0.0893
 HY4  C6   C  CH2    0  -0.127  -0.7143   1.3399   0.3345
 HY4  C7   C  CH1    0  -0.033   0.6255   0.7777  -0.1045
 HY4  O50  O  O2     0  -0.499   0.8517  -0.4550   0.5418
 HY4  C33  C  CH2    0  -0.116   0.9669  -1.5721  -0.3061
 HY4  C30  C  CH2    0  -0.460   1.2285  -2.8071   0.5323
 HY4  C31  C  CH2    0  -0.429   1.3146  -4.0677  -0.3202
 HY4  C32  C  CH3    0  -0.660   1.5530  -5.3198   0.5116
 HY4  C8   C  CH2    0  -0.128   1.7533   1.7338   0.2380
 HY4  O9   O  O2     0  -0.486   2.9489   1.2334  -0.2986
 HY4  C26  C  CH2    0  -0.121   4.0919   1.9064   0.1717
 HY4  C27  C  CH2    0  -0.456   5.3308   1.3015  -0.4569
 HY4  C28  C  CH2    0  -0.430   6.6083   1.9470   0.0662
 HY4  C29  C  CH3    0  -0.660   7.8633   1.3557  -0.5597
 HY4  H2   H  HCH2   0   0.230  -3.9340  -0.2639  -1.6055
 HY4  H3   H  HCH2   0   0.231  -3.7451  -1.5024  -0.3754
 HY4  H4   H  HCH2   0   0.216  -5.8375  -0.6735   0.7517
 HY4  H5   H  HCH2   0   0.217  -6.0217   0.5349  -0.4991
 HY4  H6   H  HCH3   0   0.225  -7.4718  -1.4254  -0.9825
 HY4  H7   H  HCH3   0   0.215  -6.2307  -1.2919  -2.2259
 HY4  H8   H  HCH3   0   0.216  -6.0740  -2.4967  -0.9515
 HY4  H9   H  HCH2   0   0.199  -0.8498   2.3381  -0.0987
 HY4  H10  H  HCH2   0   0.195  -0.7159   1.4601   1.4261
 HY4  H11  H  HCH1   0   0.216   0.6027   0.6466  -1.1954
 HY4  H12  H  HCH2   0   0.189   0.0478  -1.7138  -0.8903
 HY4  H13  H  HCH2   0   0.189   1.7847  -1.4347  -1.0268
 HY4  H14  H  HCH2   0   0.217   2.1589  -2.6800   1.0950
 HY4  H15  H  HCH2   0   0.217   0.4265  -2.9219   1.2685
 HY4  H16  H  HCH2   0   0.215   0.3898  -4.1805  -0.8942
 HY4  H17  H  HCH2   0   0.216   2.1169  -3.9574  -1.0557
 HY4  H18  H  HCH3   0   0.217   2.4934  -5.2553   1.0619
 HY4  H19  H  HCH3   0   0.217   0.7544  -5.4655   1.2418
 HY4  H20  H  HCH3   0   0.227   1.5966  -6.2128  -0.1125
 HY4  H21  H  HCH2   0   0.197   1.5293   2.7328  -0.1631
 HY4  H22  H  HCH2   0   0.196   1.8274   1.8377   1.3308
 HY4  H23  H  HCH2   0   0.190   4.0380   2.9796  -0.0653
 HY4  H24  H  HCH2   0   0.191   4.1537   1.8321   1.2679
 HY4  H25  H  HCH2   0   0.220   5.3536   0.2267  -0.2512
 HY4  H26  H  HCH2   0   0.220   5.2814   1.4132  -1.5447
 HY4  H27  H  HCH2   0   0.216   6.5783   3.0242  -0.1228
 HY4  H28  H  HCH2   0   0.216   6.6538   1.8318   1.1534
 HY4  H29  H  HCH3   0   0.228   8.7644   1.8242  -0.1633
 HY4  H30  H  HCH3   0   0.218   7.9340   0.2839  -0.3653
 HY4  H31  H  HCH3   0   0.218   7.8675   1.4933  -1.6425
 HY4  O14  O  OP    -1  -0.819  -3.6903   2.1057   0.1956

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
 HY4  C3   P13  single  1.825  0.020  1.825
 HY4  C3   C2   single  1.527  0.020  1.527
 HY4  P13  O11  deloc   1.508  0.020  1.508
 HY4  P13  O5   single  1.660  0.020  1.660
 HY4  C2   C1   single  1.522  0.020  1.522
 HY4  O5   C6   single  1.409  0.020  1.409
 HY4  C6   C7   single  1.518  0.020  1.518
 HY4  C7   C8   single  1.518  0.020  1.518
 HY4  C7   O50  single  1.410  0.020  1.410
 HY4  O9   C8   single  1.403  0.020  1.403
 HY4  O9   C26  single  1.407  0.020  1.407
 HY4  C29  C28  single  1.522  0.020  1.522
 HY4  O50  C33  single  1.407  0.020  1.407
 HY4  C26  C27  single  1.515  0.020  1.515
 HY4  C28  C27  single  1.524  0.020  1.524
 HY4  C33  C30  single  1.515  0.020  1.515
 HY4  C30  C31  single  1.524  0.020  1.524
 HY4  C31  C32  single  1.522  0.020  1.522
 HY4  C3   H2   single  0.970  0.020  1.090
 HY4  C3   H3   single  0.970  0.020  1.090
 HY4  C2   H4   single  0.970  0.020  1.090
 HY4  C2   H5   single  0.970  0.020  1.090
 HY4  C1   H6   single  0.970  0.020  1.090
 HY4  C1   H7   single  0.970  0.020  1.090
 HY4  C1   H8   single  0.970  0.020  1.090
 HY4  C6   H9   single  0.970  0.020  1.090
 HY4  C6   H10  single  0.970  0.020  1.090
 HY4  C7   H11  single  0.970  0.020  1.090
 HY4  C33  H12  single  0.970  0.020  1.090
 HY4  C33  H13  single  0.970  0.020  1.090
 HY4  C30  H14  single  0.970  0.020  1.090
 HY4  C30  H15  single  0.970  0.020  1.090
 HY4  C31  H16  single  0.970  0.020  1.090
 HY4  C31  H17  single  0.970  0.020  1.090
 HY4  C32  H18  single  0.970  0.020  1.090
 HY4  C32  H19  single  0.970  0.020  1.090
 HY4  C32  H20  single  0.970  0.020  1.090
 HY4  C8   H21  single  0.970  0.020  1.090
 HY4  C8   H22  single  0.970  0.020  1.090
 HY4  C26  H23  single  0.970  0.020  1.090
 HY4  C26  H24  single  0.970  0.020  1.090
 HY4  C27  H25  single  0.970  0.020  1.090
 HY4  C27  H26  single  0.970  0.020  1.090
 HY4  C28  H27  single  0.970  0.020  1.090
 HY4  C28  H28  single  0.970  0.020  1.090
 HY4  C29  H29  single  0.970  0.020  1.090
 HY4  C29  H30  single  0.970  0.020  1.090
 HY4  C29  H31  single  0.970  0.020  1.090
 HY4  P13  O14  deloc   1.509  0.020  1.509

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
 HY4  O14  P13  O5   108.64  3.000
 HY4  O14  P13  C3   110.47  3.000
 HY4  O5   P13  C3    97.88  3.000
 HY4  O14  P13  O11  118.64  3.000
 HY4  O5   P13  O11  109.04  3.000
 HY4  C3   P13  O11  110.14  3.000
 HY4  H3   C3   H2   106.73  3.000
 HY4  H3   C3   C2   109.82  3.000
 HY4  H2   C3   C2   109.58  3.000
 HY4  H3   C3   P13  109.47  3.000
 HY4  H2   C3   P13  109.61  3.000
 HY4  C2   C3   P13  111.51  3.000
 HY4  H5   C2   H4   106.26  3.000
 HY4  H5   C2   C1   109.51  3.000
 HY4  H4   C2   C1   109.46  3.000
 HY4  H5   C2   C3   109.23  3.000
 HY4  H4   C2   C3   109.45  3.000
 HY4  C1   C2   C3   112.72  3.000
 HY4  H8   C1   H7   107.52  3.000
 HY4  H8   C1   H6   107.62  3.000
 HY4  H7   C1   H6   107.64  3.000
 HY4  H8   C1   C2   111.18  3.000
 HY4  H7   C1   C2   111.24  3.000
 HY4  H6   C1   C2   111.45  3.000
 HY4  C6   O5   P13  117.80  3.000
 HY4  H10  C6   H9   107.03  3.000
 HY4  H10  C6   C7   109.22  3.000
 HY4  H9   C6   C7   109.39  3.000
 HY4  H10  C6   O5   111.49  3.000
 HY4  H9   C6   O5   111.12  3.000
 HY4  C7   C6   O5   108.55  3.000
 HY4  H11  C7   C8   108.33  3.000
 HY4  H11  C7   O50  110.73  3.000
 HY4  C8   C7   O50  109.15  3.000
 HY4  H11  C7   C6   108.24  3.000
 HY4  O50  C7   C6   109.45  3.000
 HY4  C8   C7   C6   110.94  3.000
 HY4  C33  O50  C7   115.53  3.000
 HY4  H13  C33  H12  106.87  3.000
 HY4  H13  C33  C30  109.65  3.000
 HY4  H12  C33  C30  109.49  3.000
 HY4  H13  C33  O50  110.91  3.000
 HY4  H12  C33  O50  110.76  3.000
 HY4  C30  C33  O50  109.13  3.000
 HY4  H15  C30  H14  106.81  3.000
 HY4  H15  C30  C31  109.32  3.000
 HY4  H14  C30  C31  109.60  3.000
 HY4  H15  C30  C33  109.33  3.000
 HY4  H14  C30  C33  109.66  3.000
 HY4  C31  C30  C33  111.98  3.000
 HY4  H17  C31  H16  106.11  3.000
 HY4  H17  C31  C32  109.61  3.000
 HY4  H16  C31  C32  109.52  3.000
 HY4  H17  C31  C30  109.52  3.000
 HY4  H16  C31  C30  109.32  3.000
 HY4  C32  C31  C30  112.55  3.000
 HY4  H20  C32  H19  107.62  3.000
 HY4  H20  C32  H18  107.60  3.000
 HY4  H19  C32  H18  107.51  3.000
 HY4  H20  C32  C31  111.54  3.000
 HY4  H19  C32  C31  111.15  3.000
 HY4  H18  C32  C31  111.22  3.000
 HY4  H22  C8   H21  106.87  3.000
 HY4  H22  C8   O9   110.87  3.000
 HY4  H21  C8   O9   110.98  3.000
 HY4  H22  C8   C7   109.49  3.000
 HY4  H21  C8   C7   109.80  3.000
 HY4  O9   C8   C7   108.81  3.000
 HY4  C26  O9   C8   113.20  3.000
 HY4  H24  C26  H23  106.45  3.000
 HY4  H24  C26  C27  109.90  3.000
 HY4  H23  C26  C27  109.88  3.000
 HY4  H24  C26  O9   110.25  3.000
 HY4  H23  C26  O9   110.77  3.000
 HY4  C27  C26  O9   109.54  3.000
 HY4  H26  C27  H25  106.73  3.000
 HY4  H26  C27  C28  109.61  3.000
 HY4  H25  C27  C28  109.51  3.000
 HY4  H26  C27  C26  109.55  3.000
 HY4  H25  C27  C26  109.34  3.000
 HY4  C28  C27  C26  111.96  3.000
 HY4  H28  C28  H27  106.05  3.000
 HY4  H28  C28  C29  109.48  3.000
 HY4  H27  C28  C29  109.52  3.000
 HY4  H28  C28  C27  109.35  3.000
 HY4  H27  C28  C27  109.56  3.000
 HY4  C29  C28  C27  112.68  3.000
 HY4  H31  C29  H30  107.47  3.000
 HY4  H31  C29  H29  107.66  3.000
 HY4  H30  C29  H29  107.67  3.000
 HY4  H31  C29  C28  111.23  3.000
 HY4  H30  C29  C28  111.20  3.000
 HY4  H29  C29  C28  111.41  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
 HY4  Var_01  C2   C3   P13  O11    69.66  30.0  1
 HY4  Var_02  C1   C2   C3   P13  -178.84  30.0  3
 HY4  Var_03  C7   C6   O5   P13   168.57  30.0  3
 HY4  Var_04  C30  C33  O50  C7    179.10  30.0  3
 HY4  Var_05  C31  C30  C33  O50   177.94  30.0  3
 HY4  Var_06  C32  C31  C30  C33  -179.00  30.0  3
 HY4  Var_07  C27  C26  O9   C8    179.96  30.0  3
 HY4  Var_08  C28  C27  C26  O9   -177.28  30.0  3
 HY4  Var_09  C29  C28  C27  C26  -179.73  30.0  1
 HY4  Var_10  H6   C1   C2   C3   -178.78  30.0  3
 HY4  Var_11  H18  C32  C31  C30   -60.73  30.0  3
 HY4  Var_12  H21  C8   O9   C26    70.38  30.0  3
 HY4  Var_13  H29  C29  C28  C27  -179.37  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
 HY4  chir_02  C7  C6  C8  O50  negativ

