# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 15:26:30 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (2S)-2,3-dihydroxypropyl octanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=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
 480  480  '(2S)-2,3-dihydroxypropyl octanoate'  ligand  37  15  .  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_480
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
 480  C8   C  CH3   0  -0.662  -7.9986   0.5714  -0.2063
 480  C24  C  CH2   0  -0.163   5.6274  -0.4287  -0.1994
 480  C7   C  CH2   0  -0.418  -6.7723  -0.3073  -0.0030
 480  C6   C  CH2   0  -0.406  -5.4634   0.4616  -0.1358
 480  C5   C  CH2   0  -0.411  -4.2314  -0.4112   0.0646
 480  C4   C  CH2   0  -0.415  -2.9205   0.3514  -0.0793
 480  C3   C  CH2   0  -0.417  -1.7009  -0.5345   0.1397
 480  C2   C  CH2   0  -0.583  -0.3973   0.2313  -0.0187
 480  C21  C  CH2   0  -0.187   3.1825  -0.6259   0.1344
 480  C1   C  C     0   0.608   0.8256  -0.6117   0.2215
 480  C22  C  CH1   0  -0.049   4.2967   0.2965  -0.3299
 480  O19  O  O     0  -0.454   0.8194  -1.7439   0.6370
 480  O23  O  OH1   0  -0.655   4.2835   1.5302   0.3443
 480  O20  O  O2    0  -0.459   1.9417   0.0485  -0.0709
 480  H1   H  HCH3  0   0.226  -8.9228  -0.0013  -0.1196
 480  H2   H  HCH3  0   0.216  -8.0372   1.3749   0.5318
 480  H3   H  HCH3  0   0.215  -7.9908   1.0353  -1.1947
 480  H4   H  HCH2  0   0.198   5.8078  -0.6625   0.8605
 480  H5   H  HCH2  0   0.203   5.5580  -1.3889  -0.7271
 480  H6   H  HCH2  0   0.210  -6.8163  -0.7779   0.9842
 480  H7   H  HCH2  0   0.210  -6.7851  -1.1264  -0.7288
 480  H8   H  HCH2  0   0.206  -5.4206   0.9332  -1.1241
 480  H9   H  HCH2  0   0.206  -5.4506   1.2818   0.5910
 480  H10  H  HCH2  0   0.208  -4.2726  -0.8756   1.0561
 480  H11  H  HCH2  0   0.208  -4.2499  -1.2360  -0.6565
 480  H12  H  HCH2  0   0.212  -2.8726   0.8063  -1.0747
 480  H13  H  HCH2  0   0.212  -2.9029   1.1817   0.6353
 480  H14  H  HCH2  0   0.224  -1.7500  -0.9770   1.1380
 480  H15  H  HCH2  0   0.224  -1.7257  -1.3677  -0.5683
 480  H16  H  HCH2  0   0.270  -0.3274   0.6776  -1.0150
 480  H17  H  HCH2  0   0.275  -0.3621   1.0731   0.6818
 480  H18  H  HCH2  0   0.240   3.2061  -1.5573  -0.4360
 480  H19  H  HCH2  0   0.236   3.3041  -0.8751   1.1939
 480  H20  H  HCH1  0   0.240   4.1344   0.5313  -1.3872
 480  H21  H  HOH1  0   0.457   7.4777  -0.0795  -0.6319
 480  H22  H  HOH1  0   0.445   4.4837   1.3769   1.2746
 480  O25  O  OH1   0  -0.667   6.6426   0.3863  -0.7302

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
 480  C6   C7   single  1.524  0.020  1.524
 480  C6   C5   single  1.523  0.020  1.523
 480  C7   C8   single  1.522  0.020  1.522
 480  C5   C4   single  1.523  0.020  1.523
 480  C4   C3   single  1.523  0.020  1.523
 480  C3   C2   single  1.520  0.020  1.520
 480  C2   C1   single  1.505  0.020  1.505
 480  O19  C1   double  1.206  0.020  1.206
 480  C1   O20  single  1.329  0.020  1.329
 480  O20  C21  single  1.427  0.020  1.427
 480  C21  C22  single  1.519  0.020  1.519
 480  C24  C22  single  1.521  0.020  1.521
 480  C24  O25  single  1.406  0.020  1.406
 480  C22  O23  single  1.406  0.020  1.406
 480  C8   H1   single  0.970  0.020  1.090
 480  C8   H2   single  0.970  0.020  1.090
 480  C8   H3   single  0.970  0.020  1.090
 480  C24  H4   single  0.970  0.020  1.090
 480  C24  H5   single  0.970  0.020  1.090
 480  C7   H6   single  0.970  0.020  1.090
 480  C7   H7   single  0.970  0.020  1.090
 480  C6   H8   single  0.970  0.020  1.090
 480  C6   H9   single  0.970  0.020  1.090
 480  C5   H10  single  0.970  0.020  1.090
 480  C5   H11  single  0.970  0.020  1.090
 480  C4   H12  single  0.970  0.020  1.090
 480  C4   H13  single  0.970  0.020  1.090
 480  C3   H14  single  0.970  0.020  1.090
 480  C3   H15  single  0.970  0.020  1.090
 480  C2   H16  single  0.970  0.020  1.090
 480  C2   H17  single  0.970  0.020  1.090
 480  C21  H18  single  0.970  0.020  1.090
 480  C21  H19  single  0.970  0.020  1.090
 480  C22  H20  single  0.970  0.020  1.090
 480  O25  H21  single  0.850  0.020  0.980
 480  O23  H22  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
 480  H3   C8   H2   107.44  3.000
 480  H3   C8   H1   107.52  3.000
 480  H2   C8   H1   107.62  3.000
 480  H3   C8   C7   111.13  3.000
 480  H2   C8   C7   111.28  3.000
 480  H1   C8   C7   111.65  3.000
 480  H5   C24  H4   106.71  3.000
 480  H5   C24  O25  111.79  3.000
 480  H4   C24  O25  111.62  3.000
 480  H5   C24  C22  108.69  3.000
 480  H4   C24  C22  109.11  3.000
 480  O25  C24  C22  108.84  3.000
 480  H7   C7   H6   106.01  3.000
 480  H7   C7   C6   109.26  3.000
 480  H6   C7   C6   109.27  3.000
 480  H7   C7   C8   109.51  3.000
 480  H6   C7   C8   109.65  3.000
 480  C6   C7   C8   112.90  3.000
 480  H9   C6   H8   105.99  3.000
 480  H9   C6   C5   109.40  3.000
 480  H8   C6   C5   109.49  3.000
 480  H9   C6   C7   109.26  3.000
 480  H8   C6   C7   109.22  3.000
 480  C5   C6   C7   113.22  3.000
 480  H11  C5   H10  106.01  3.000
 480  H11  C5   C4   109.22  3.000
 480  H10  C5   C4   109.27  3.000
 480  H11  C5   C6   109.34  3.000
 480  H10  C5   C6   109.36  3.000
 480  C4   C5   C6   113.38  3.000
 480  H13  C4   H12  106.10  3.000
 480  H13  C4   C3   109.52  3.000
 480  H12  C4   C3   109.71  3.000
 480  H13  C4   C5   109.36  3.000
 480  H12  C4   C5   109.35  3.000
 480  C3   C4   C5   112.60  3.000
 480  H15  C3   H14  106.37  3.000
 480  H15  C3   C2   109.62  3.000
 480  H14  C3   C2   109.73  3.000
 480  H15  C3   C4   109.38  3.000
 480  H14  C3   C4   109.32  3.000
 480  C2   C3   C4   112.25  3.000
 480  H17  C2   H16  105.47  3.000
 480  H17  C2   C1   107.60  3.000
 480  H16  C2   C1   108.78  3.000
 480  H17  C2   C3   110.36  3.000
 480  H16  C2   C3   110.81  3.000
 480  C1   C2   C3   113.46  3.000
 480  H19  C21  H18  107.98  3.000
 480  H19  C21  O20  110.07  3.000
 480  H18  C21  O20  110.28  3.000
 480  H19  C21  C22  110.63  3.000
 480  H18  C21  C22  110.01  3.000
 480  O20  C21  C22  107.87  3.000
 480  O20  C1   O19  123.12  3.000
 480  O20  C1   C2   111.65  3.000
 480  O19  C1   C2   125.22  3.000
 480  H20  C22  O23  105.87  3.000
 480  H20  C22  C21  108.45  3.000
 480  O23  C22  C21  112.30  3.000
 480  H20  C22  C24  108.34  3.000
 480  O23  C22  C24  112.67  3.000
 480  C21  C22  C24  109.02  3.000
 480  H22  O23  C22  108.74  3.000
 480  C1   O20  C21  117.62  3.000
 480  H21  O25  C24  107.93  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
 480  Var_01  C5   C6   C7   C8  -179.92  30.0  1
 480  Var_02  C4   C5   C6   C7   179.50  30.0  3
 480  Var_03  C3   C4   C5   C6   179.36  30.0  3
 480  Var_04  C2   C3   C4   C5   179.46  30.0  3
 480  Var_05  C1   C2   C3   C4   178.75  30.0  3
 480  Var_06  O19  C1   C2   C3    -7.57  30.0  3
 480  Var_07  C22  C21  O20  C1   177.29  30.0  3
 480  Var_08  H1   C8   C7   C6   179.27  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
 480  chir_01  C22  C21  C24  O23  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 480  plan-1  C2   0.020
 480  plan-1  C1   0.020
 480  plan-1  O19  0.020
 480  plan-1  O20  0.020

