# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 22:38:08 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (1R)-1-{[(2S)-3-hydroxy-2-{[(1R)-1-hydroxypentyl]oxy}propyl]oxy}hexan-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC[C@H](O)OC[C@H](CO)O[C@@H](O)CCCC
#
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
 2WD  2WD  (1R)-1-{[(2S)-3-hydroxy-2-{[(1R)-1-hydroxypentyl]oxy}propyl]oxy}hexan-1-ol  ligand  49  19  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2WD
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
 2WD  C1   C  CH2   0  -0.158   1.3320   2.6435  -1.5451
 2WD  C2   C  CH1   0  -0.034   1.2324   2.0692  -0.1422
 2WD  C3   C  CH2   0  -0.156  -0.1377   2.1570   0.5027
 2WD  O11  O  OH1   0  -0.659   0.5445   1.9201  -2.4557
 2WD  C21  C  CH1   0   0.299   3.0247   0.5407   0.1965
 2WD  O21  O  O2    0  -0.503   1.6698   0.7227  -0.1028
 2WD  C22  C  CH2   0  -0.500   3.3787  -0.8923  -0.1670
 2WD  O22  O  OH1   0  -0.660   3.3056   0.8535   1.5308
 2WD  C23  C  CH2   0  -0.411   4.8285  -1.2506   0.1336
 2WD  C24  C  CH2   0  -0.419   5.1860  -2.6666  -0.3034
 2WD  C25  C  CH3   0  -0.661   6.6233  -3.0408   0.0304
 2WD  C31  C  CH1   0   0.306  -2.2388   1.0830   0.5637
 2WD  O31  O  O2    0  -0.485  -1.0567   1.3110  -0.1439
 2WD  C32  C  CH2   0  -0.500  -2.9820  -0.0356  -0.1472
 2WD  O32  O  OH1   0  -0.665  -3.0067   2.2448   0.7021
 2WD  C33  C  CH2   0  -0.417  -4.2801  -0.4333   0.5445
 2WD  C34  C  CH2   0  -0.406  -4.9580  -1.6196  -0.1297
 2WD  C35  C  CH2   0  -0.419  -6.2527  -2.0407   0.5550
 2WD  C36  C  CH3   0  -0.662  -6.9291  -3.2199  -0.1303
 2WD  H1   H  HCH2  0   0.191   1.0355   3.7004  -1.4884
 2WD  H2   H  HCH2  0   0.203   2.3909   2.6383  -1.8391
 2WD  H3   H  HCH1  0   0.232   1.8740   2.7079   0.4799
 2WD  H4   H  HCH2  0   0.207  -0.0368   1.8758   1.5608
 2WD  H5   H  HCH2  0   0.203  -0.4609   3.2048   0.4805
 2WD  H6   H  HOH1  0   0.451   0.7498   2.2436  -3.3372
 2WD  H7   H  HCH1  0   0.195   3.6446   1.2354  -0.3871
 2WD  H8   H  HCH2  0   0.226   2.7075  -1.5742   0.3686
 2WD  H9   H  HCH2  0   0.232   3.1797  -1.0333  -1.2332
 2WD  H10  H  HOH1  0   0.445   2.8874   0.1958   2.0995
 2WD  H11  H  HCH2  0   0.212   5.4945  -0.5403  -0.3683
 2WD  H12  H  HCH2  0   0.214   5.0223  -1.1470   1.2047
 2WD  H13  H  HCH2  0   0.212   4.5041  -3.3761   0.1755
 2WD  H14  H  HCH2  0   0.213   5.0206  -2.7679  -1.3804
 2WD  H15  H  HCH3  0   0.227   6.8547  -4.0587  -0.2851
 2WD  H16  H  HCH3  0   0.216   7.3324  -2.3738  -0.4634
 2WD  H17  H  HCH3  0   0.216   6.8071  -2.9793   1.1047
 2WD  H18  H  HCH1  0   0.191  -2.0046   0.7809   1.5954
 2WD  H19  H  HCH2  0   0.227  -3.1865   0.2688  -1.1807
 2WD  H20  H  HCH2  0   0.231  -2.3205  -0.9045  -0.2035
 2WD  H21  H  HOH1  0   0.445  -3.3695   2.4817  -0.1601
 2WD  H22  H  HCH2  0   0.212  -4.0732  -0.6833   1.5910
 2WD  H23  H  HCH2  0   0.215  -4.9710   0.4140   0.5624
 2WD  H24  H  HCH2  0   0.208  -5.1663  -1.3722  -1.1765
 2WD  H25  H  HCH2  0   0.208  -4.2674  -2.4699  -0.1507
 2WD  H26  H  HCH2  0   0.211  -6.0438  -2.2943   1.5988
 2WD  H27  H  HCH2  0   0.211  -6.9411  -1.1904   0.5819
 2WD  H28  H  HCH3  0   0.216  -7.1993  -2.9767  -1.1595
 2WD  H29  H  HCH3  0   0.215  -6.2714  -4.0909  -0.1604
 2WD  H30  H  HCH3  0   0.226  -7.8422  -3.5144   0.3882

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
 2WD  C35  C36  single  1.522  0.020  1.522
 2WD  C35  C34  single  1.524  0.020  1.524
 2WD  C33  C34  single  1.524  0.020  1.524
 2WD  C33  C32  single  1.524  0.020  1.524
 2WD  O32  C31  single  1.399  0.020  1.399
 2WD  C31  C32  single  1.520  0.020  1.520
 2WD  C31  O31  single  1.396  0.020  1.396
 2WD  O31  C3   single  1.406  0.020  1.406
 2WD  C3   C2   single  1.517  0.020  1.517
 2WD  C2   C1   single  1.519  0.020  1.519
 2WD  C2   O21  single  1.416  0.020  1.416
 2WD  C1   O11  single  1.405  0.020  1.405
 2WD  C25  C24  single  1.522  0.020  1.522
 2WD  O21  C21  single  1.399  0.020  1.399
 2WD  C23  C24  single  1.524  0.020  1.524
 2WD  C23  C22  single  1.523  0.020  1.523
 2WD  C21  C22  single  1.520  0.020  1.520
 2WD  C21  O22  single  1.399  0.020  1.399
 2WD  C1   H1   single  0.970  0.020  1.090
 2WD  C1   H2   single  0.970  0.020  1.090
 2WD  C2   H3   single  0.970  0.020  1.090
 2WD  C3   H4   single  0.970  0.020  1.090
 2WD  C3   H5   single  0.970  0.020  1.090
 2WD  O11  H6   single  0.850  0.020  0.980
 2WD  C21  H7   single  0.970  0.020  1.090
 2WD  C22  H8   single  0.970  0.020  1.090
 2WD  C22  H9   single  0.970  0.020  1.090
 2WD  O22  H10  single  0.850  0.020  0.980
 2WD  C23  H11  single  0.970  0.020  1.090
 2WD  C23  H12  single  0.970  0.020  1.090
 2WD  C24  H13  single  0.970  0.020  1.090
 2WD  C24  H14  single  0.970  0.020  1.090
 2WD  C25  H15  single  0.970  0.020  1.090
 2WD  C25  H16  single  0.970  0.020  1.090
 2WD  C25  H17  single  0.970  0.020  1.090
 2WD  C31  H18  single  0.970  0.020  1.090
 2WD  C32  H19  single  0.970  0.020  1.090
 2WD  C32  H20  single  0.970  0.020  1.090
 2WD  O32  H21  single  0.850  0.020  0.980
 2WD  C33  H22  single  0.970  0.020  1.090
 2WD  C33  H23  single  0.970  0.020  1.090
 2WD  C34  H24  single  0.970  0.020  1.090
 2WD  C34  H25  single  0.970  0.020  1.090
 2WD  C35  H26  single  0.970  0.020  1.090
 2WD  C35  H27  single  0.970  0.020  1.090
 2WD  C36  H28  single  0.970  0.020  1.090
 2WD  C36  H29  single  0.970  0.020  1.090
 2WD  C36  H30  single  0.970  0.020  1.090

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
 2WD  H2   C1   H1   106.16  3.000
 2WD  H2   C1   O11  111.37  3.000
 2WD  H1   C1   O11  112.18  3.000
 2WD  H2   C1   C2   107.96  3.000
 2WD  H1   C1   C2   107.35  3.000
 2WD  O11  C1   C2   111.55  3.000
 2WD  H3   C2   O21  110.90  3.000
 2WD  H3   C2   C3   104.67  3.000
 2WD  O21  C2   C3   108.80  3.000
 2WD  H3   C2   C1   105.36  3.000
 2WD  O21  C2   C1   111.40  3.000
 2WD  C3   C2   C1   115.46  3.000
 2WD  H5   C3   H4   106.91  3.000
 2WD  H5   C3   O31  111.89  3.000
 2WD  H4   C3   O31  110.40  3.000
 2WD  H5   C3   C2   108.24  3.000
 2WD  H4   C3   C2   108.14  3.000
 2WD  O31  C3   C2   111.10  3.000
 2WD  H6   O11  C1   107.54  3.000
 2WD  H7   C21  O22  104.59  3.000
 2WD  H7   C21  C22  109.73  3.000
 2WD  O22  C21  C22  113.09  3.000
 2WD  H7   C21  O21  110.51  3.000
 2WD  O22  C21  O21  111.67  3.000
 2WD  C22  C21  O21  107.27  3.000
 2WD  C21  O21  C2   115.38  3.000
 2WD  H9   C22  H8   106.53  3.000
 2WD  H9   C22  C23  109.59  3.000
 2WD  H8   C22  C23  109.87  3.000
 2WD  H9   C22  C21  108.20  3.000
 2WD  H8   C22  C21  109.08  3.000
 2WD  C23  C22  C21  113.34  3.000
 2WD  H10  O22  C21  108.82  3.000
 2WD  H12  C23  H11  106.24  3.000
 2WD  H12  C23  C24  109.11  3.000
 2WD  H11  C23  C24  109.18  3.000
 2WD  H12  C23  C22  109.86  3.000
 2WD  H11  C23  C22  109.61  3.000
 2WD  C24  C23  C22  112.65  3.000
 2WD  H14  C24  H13  106.05  3.000
 2WD  H14  C24  C25  109.62  3.000
 2WD  H13  C24  C25  109.45  3.000
 2WD  H14  C24  C23  109.43  3.000
 2WD  H13  C24  C23  109.31  3.000
 2WD  C25  C24  C23  112.76  3.000
 2WD  H17  C25  H16  107.54  3.000
 2WD  H17  C25  H15  107.55  3.000
 2WD  H16  C25  H15  107.56  3.000
 2WD  H17  C25  C24  111.16  3.000
 2WD  H16  C25  C24  111.34  3.000
 2WD  H15  C25  C24  111.49  3.000
 2WD  H18  C31  O32  104.60  3.000
 2WD  H18  C31  C32  109.92  3.000
 2WD  O32  C31  C32  112.89  3.000
 2WD  H18  C31  O31  109.86  3.000
 2WD  C32  C31  O31  107.29  3.000
 2WD  O32  C31  O31  112.27  3.000
 2WD  C31  O31  C3   114.73  3.000
 2WD  H20  C32  H19  106.55  3.000
 2WD  H20  C32  C33  109.34  3.000
 2WD  H19  C32  C33  109.97  3.000
 2WD  H20  C32  C31  108.25  3.000
 2WD  H19  C32  C31  109.13  3.000
 2WD  C33  C32  C31  113.35  3.000
 2WD  H21  O32  C31  108.77  3.000
 2WD  H23  C33  H22  106.29  3.000
 2WD  H23  C33  C34  109.23  3.000
 2WD  H22  C33  C34  109.20  3.000
 2WD  H23  C33  C32  110.09  3.000
 2WD  H22  C33  C32  109.41  3.000
 2WD  C34  C33  C32  112.42  3.000
 2WD  H25  C34  H24  106.06  3.000
 2WD  H25  C34  C35  109.25  3.000
 2WD  H24  C34  C35  109.28  3.000
 2WD  H25  C34  C33  109.41  3.000
 2WD  H24  C34  C33  109.36  3.000
 2WD  C35  C34  C33  113.23  3.000
 2WD  H27  C35  H26  106.06  3.000
 2WD  H27  C35  C36  109.48  3.000
 2WD  H26  C35  C36  109.55  3.000
 2WD  H27  C35  C34  109.32  3.000
 2WD  H26  C35  C34  109.29  3.000
 2WD  C36  C35  C34  112.91  3.000
 2WD  H30  C36  H29  107.58  3.000
 2WD  H30  C36  H28  107.52  3.000
 2WD  H29  C36  H28  107.51  3.000
 2WD  H30  C36  C35  111.54  3.000
 2WD  H29  C36  C35  111.27  3.000
 2WD  H28  C36  C35  111.21  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
 2WD  Var_01  C24  C23  C22  C21  -177.01  30.0  1
 2WD  Var_02  C25  C24  C23  C22  -178.42  30.0  3
 2WD  Var_03  C34  C33  C32  C31  -176.00  30.0  1
 2WD  Var_04  C35  C34  C33  C32   179.51  30.0  3
 2WD  Var_05  C36  C35  C34  C33   179.59  30.0  1
 2WD  Var_06  H15  C25  C24  C23   179.64  30.0  3
 2WD  Var_07  H4   C3   O31  C31    45.42  30.0  3
 2WD  Var_08  H28  C36  C35  C34   -61.06  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
 2WD  chir_01  C2   C3   C1   O21  positiv
 2WD  chir_02  C21  O21  O22  C22  negativ
 2WD  chir_03  C31  O32  O31  C32  positiv

