# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:50:54 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (1S)-2-(decyloxy)-1-[(2,2,2-trifluoroethoxy)methyl]ethyl methyl hydrogen (S)-phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCOC[C@@H](COCC(F)(F)F)O[P@](O)(=O)OC
#
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
 GLE  GLE  '(1S)-2-(decyloxy)-1-[(2,2,2-trifluoroethoxy)methyl]ethyl methyl hydrogen (S)-phosphate'  ligand  58  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GLE
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
 GLE  C1    C  CH2   0  -0.118   1.3688  -0.4964  -0.7985
 GLE  O1    O  O2    0  -0.483   0.5923  -0.1328   0.3059
 GLE  C2    C  CH1   0  -0.096   0.7167   0.0437  -2.0524
 GLE  O2    O  O2    0  -0.584  -0.5777  -0.5584  -2.1914
 GLE  C3    C  CH2   0  -0.121   1.5409  -0.2982  -3.2753
 GLE  O3    O  O2    0  -0.528   0.9540   0.3021  -4.4159
 GLE  C31   C  CH2   0  -0.310   1.5911  -0.0720  -5.6086
 GLE  C32   C  CT    0   0.964   0.9705   0.7177  -6.7353
 GLE  F31   F  F     0  -0.304   1.5332   0.3887  -7.9010
 GLE  F32   F  F     0  -0.309  -0.3455   0.4910  -6.8437
 GLE  F33   F  F     0  -0.305   1.1224   2.0358  -6.5689
 GLE  P2    P  P     0   1.446  -1.8927   0.2940  -2.4954
 GLE  O21   O  O     0  -0.699  -2.5554   0.9810  -1.3721
 GLE  O22   O  OH1   0  -0.763  -1.4938   1.3341  -3.6400
 GLE  C2P   C  CH3   0  -0.413  -4.1324  -0.7158  -3.4009
 GLE  O23   O  O2    0  -0.575  -2.7308  -0.8833  -3.1688
 GLE  C11   C  CH2   0  -0.126   1.2493  -0.3722   1.5313
 GLE  C12   C  CH2   0  -0.460   0.3236  -0.0475   2.6857
 GLE  C13   C  CH2   0  -0.424   1.0396  -0.1973   4.0231
 GLE  C14   C  CH2   0  -0.411   0.1380   0.0429   5.2270
 GLE  C15   C  CH2   0  -0.411   0.8828  -0.0804   6.5503
 GLE  C16   C  CH2   0  -0.411  -0.0029   0.1247   7.7725
 GLE  C17   C  CH2   0  -0.411   0.7598   0.0054   9.0861
 GLE  C18   C  CH2   0  -0.406  -0.1167   0.1949  10.3173
 GLE  C19   C  CH2   0  -0.418   0.6539   0.0843  11.6273
 GLE  C20   C  CH3   0  -0.662  -0.2308   0.2683  12.8523
 GLE  H11   H  HCH2  0   0.216   2.3806  -0.0734  -0.7342
 GLE  H12   H  HCH2  0   0.216   1.4810  -1.5880  -0.8691
 GLE  H2    H  HCH1  0   0.268   0.6348   1.1323  -1.9581
 GLE  H31   H  HCH2  0   0.244   2.5632   0.0709  -3.1393
 GLE  H32   H  HCH2  0   0.239   1.5891  -1.3861  -3.4021
 GLE  H311  H  HCH2  0   0.267   2.6642   0.1485  -5.5766
 GLE  H312  H  HCH2  0   0.268   1.4721  -1.1421  -5.8123
 GLE  HO2   H  HOH1  0   0.480  -0.7371   1.0449  -4.1833
 GLE  H2P1  H  HCH3  0   0.255  -4.5076  -1.6704  -3.7592
 GLE  H2P2  H  HCH3  0   0.240  -4.6594  -0.4456  -2.4863
 GLE  H2P3  H  HCH3  0   0.237  -4.3181   0.0439  -4.1609
 GLE  H111  H  HCH2  0   0.197   2.1598   0.2418   1.5951
 GLE  H112  H  HCH2  0   0.196   1.5697  -1.4216   1.5989
 GLE  H121  H  HCH2  0   0.222  -0.5465  -0.7104   2.6546
 GLE  H122  H  HCH2  0   0.222  -0.0504   0.9755   2.5810
 GLE  H131  H  HCH2  0   0.214   1.8837   0.4998   4.0595
 GLE  H132  H  HCH2  0   0.213   1.4729  -1.2010   4.0944
 GLE  H141  H  HCH2  0   0.209  -0.6930  -0.6708   5.2080
 GLE  H142  H  HCH2  0   0.209  -0.3142   1.0381   5.1548
 GLE  H151  H  HCH2  0   0.207   1.7023   0.6468   6.5709
 GLE  H152  H  HCH2  0   0.207   1.3549  -1.0677   6.6074
 GLE  H161  H  HCH2  0   0.206  -0.8186  -0.6069   7.7582
 GLE  H162  H  HCH2  0   0.206  -0.4794   1.1100   7.7177
 GLE  H171  H  HCH2  0   0.206   1.5704   0.7428   9.1010
 GLE  H172  H  HCH2  0   0.206   1.2448  -0.9762   9.1338
 GLE  H181  H  HCH2  0   0.205  -0.9229  -0.5476  10.3084
 GLE  H182  H  HCH2  0   0.205  -0.6078   1.1736  10.2688
 GLE  H191  H  HCH2  0   0.210   1.4551   0.8299  11.6391
 GLE  H192  H  HCH2  0   0.209   1.1487  -0.8911  11.6737
 GLE  H201  H  HCH3  0   0.225   0.3423   0.1969  13.7777
 GLE  H202  H  HCH3  0   0.215  -0.7186   1.2451  12.8424
 GLE  H203  H  HCH3  0   0.215  -1.0159  -0.4892  12.8907

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
 GLE  C1   O1    single  1.398  0.020  1.398
 GLE  C1   C2    single  1.513  0.020  1.513
 GLE  C1   H11   single  0.970  0.020  1.090
 GLE  C1   H12   single  0.970  0.020  1.090
 GLE  O1   C11   single  1.411  0.020  1.411
 GLE  C2   O2    single  1.434  0.020  1.434
 GLE  C2   C3    single  1.514  0.020  1.514
 GLE  C2   H2    single  0.970  0.020  1.090
 GLE  O2   P2    single  1.596  0.020  1.596
 GLE  C3   O3    single  1.416  0.020  1.416
 GLE  C3   H31   single  0.970  0.020  1.090
 GLE  C3   H32   single  0.970  0.020  1.090
 GLE  O3   C31   single  1.403  0.020  1.403
 GLE  C31  C32   single  1.509  0.020  1.509
 GLE  C31  H311  single  0.970  0.020  1.090
 GLE  C31  H312  single  0.970  0.020  1.090
 GLE  C32  F31   single  1.336  0.020  1.336
 GLE  C32  F32   single  1.340  0.020  1.340
 GLE  C32  F33   single  1.337  0.020  1.337
 GLE  P2   O21   double  1.474  0.020  1.474
 GLE  P2   O22   single  1.597  0.020  1.597
 GLE  P2   O23   single  1.594  0.020  1.594
 GLE  O22  HO2   single  0.850  0.020  0.980
 GLE  C2P  O23   single  1.431  0.020  1.431
 GLE  C2P  H2P1  single  0.970  0.020  1.090
 GLE  C2P  H2P2  single  0.970  0.020  1.090
 GLE  C2P  H2P3  single  0.970  0.020  1.090
 GLE  C11  C12   single  1.515  0.020  1.515
 GLE  C11  H111  single  0.970  0.020  1.090
 GLE  C11  H112  single  0.970  0.020  1.090
 GLE  C12  C13   single  1.524  0.020  1.524
 GLE  C12  H121  single  0.970  0.020  1.090
 GLE  C12  H122  single  0.970  0.020  1.090
 GLE  C13  C14   single  1.523  0.020  1.523
 GLE  C13  H131  single  0.970  0.020  1.090
 GLE  C13  H132  single  0.970  0.020  1.090
 GLE  C14  C15   single  1.524  0.020  1.524
 GLE  C14  H141  single  0.970  0.020  1.090
 GLE  C14  H142  single  0.970  0.020  1.090
 GLE  C15  C16   single  1.523  0.020  1.523
 GLE  C15  H151  single  0.970  0.020  1.090
 GLE  C15  H152  single  0.970  0.020  1.090
 GLE  C16  C17   single  1.524  0.020  1.524
 GLE  C16  H161  single  0.970  0.020  1.090
 GLE  C16  H162  single  0.970  0.020  1.090
 GLE  C17  C18   single  1.523  0.020  1.523
 GLE  C17  H171  single  0.970  0.020  1.090
 GLE  C17  H172  single  0.970  0.020  1.090
 GLE  C18  C19   single  1.524  0.020  1.524
 GLE  C18  H181  single  0.970  0.020  1.090
 GLE  C18  H182  single  0.970  0.020  1.090
 GLE  C19  C20   single  1.522  0.020  1.522
 GLE  C19  H191  single  0.970  0.020  1.090
 GLE  C19  H192  single  0.970  0.020  1.090
 GLE  C20  H201  single  0.970  0.020  1.090
 GLE  C20  H202  single  0.970  0.020  1.090
 GLE  C20  H203  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
 GLE  H12   C1   H11   106.98  3.000
 GLE  H12   C1   C2    110.19  3.000
 GLE  H11   C1   C2    107.94  3.000
 GLE  H12   C1   O1    111.44  3.000
 GLE  H11   C1   O1    111.42  3.000
 GLE  C2    C1   O1    108.81  3.000
 GLE  C11   O1   C1    112.54  3.000
 GLE  H2    C2   C3    109.55  3.000
 GLE  H2    C2   O2    110.98  3.000
 GLE  C3    C2   O2    108.56  3.000
 GLE  H2    C2   C1    108.39  3.000
 GLE  C3    C2   C1    110.74  3.000
 GLE  O2    C2   C1    108.63  3.000
 GLE  P2    O2   C2    122.52  3.000
 GLE  H32   C3   H31   107.93  3.000
 GLE  H32   C3   O3    110.23  3.000
 GLE  H31   C3   O3    110.11  3.000
 GLE  H32   C3   C2    109.96  3.000
 GLE  H31   C3   C2    109.37  3.000
 GLE  O3    C3   C2    109.22  3.000
 GLE  C31   O3   C3    112.54  3.000
 GLE  H312  C31  H311  107.95  3.000
 GLE  H312  C31  C32   109.11  3.000
 GLE  H311  C31  C32   108.61  3.000
 GLE  H312  C31  O3    111.66  3.000
 GLE  H311  C31  O3    111.48  3.000
 GLE  C32   C31  O3    107.96  3.000
 GLE  F33   C32  F32   106.77  3.000
 GLE  F33   C32  F31   107.68  3.000
 GLE  F32   C32  F31   107.55  3.000
 GLE  F33   C32  C31   112.09  3.000
 GLE  F32   C32  C31   112.07  3.000
 GLE  F31   C32  C31   110.45  3.000
 GLE  O23   P2   O22   108.03  3.000
 GLE  O23   P2   O21   115.44  3.000
 GLE  O22   P2   O21   110.78  3.000
 GLE  O23   P2   O2     96.85  3.000
 GLE  O22   P2   O2    106.17  3.000
 GLE  O21   P2   O2    118.30  3.000
 GLE  HO2   O22  P2    113.57  3.000
 GLE  H2P3  C2P  H2P2  109.26  3.000
 GLE  H2P3  C2P  H2P1  108.87  3.000
 GLE  H2P2  C2P  H2P1  109.13  3.000
 GLE  H2P3  C2P  O23   111.19  3.000
 GLE  H2P2  C2P  O23   111.51  3.000
 GLE  H2P1  C2P  O23   106.80  3.000
 GLE  C2P   O23  P2    119.81  3.000
 GLE  H112  C11  H111  106.74  3.000
 GLE  H112  C11  C12   109.63  3.000
 GLE  H111  C11  C12   109.99  3.000
 GLE  H112  C11  O1    110.56  3.000
 GLE  H111  C11  O1    109.95  3.000
 GLE  C12   C11  O1    109.93  3.000
 GLE  H122  C12  H121  106.97  3.000
 GLE  H122  C12  C13   109.66  3.000
 GLE  H121  C12  C13   109.81  3.000
 GLE  H122  C12  C11   109.65  3.000
 GLE  H121  C12  C11   109.53  3.000
 GLE  C13   C12  C11   111.13  3.000
 GLE  H132  C13  H131  106.03  3.000
 GLE  H132  C13  C14   109.09  3.000
 GLE  H131  C13  C14   109.24  3.000
 GLE  H132  C13  C12   109.45  3.000
 GLE  H131  C13  C12   109.18  3.000
 GLE  C14   C13  C12   113.57  3.000
 GLE  H142  C14  H141  106.12  3.000
 GLE  H142  C14  C15   109.42  3.000
 GLE  H141  C14  C15   109.46  3.000
 GLE  H142  C14  C13   109.60  3.000
 GLE  H141  C14  C13   109.43  3.000
 GLE  C15   C14  C13   112.60  3.000
 GLE  H152  C15  H151  105.94  3.000
 GLE  H152  C15  C16   109.27  3.000
 GLE  H151  C15  C16   109.29  3.000
 GLE  H152  C15  C14   109.20  3.000
 GLE  H151  C15  C14   109.17  3.000
 GLE  C16   C15  C14   113.69  3.000
 GLE  H162  C16  H161  106.02  3.000
 GLE  H162  C16  C17   109.34  3.000
 GLE  H161  C16  C17   109.36  3.000
 GLE  H162  C16  C15   109.50  3.000
 GLE  H161  C16  C15   109.41  3.000
 GLE  C17   C16  C15   112.96  3.000
 GLE  H172  C17  H171  105.95  3.000
 GLE  H172  C17  C18   109.32  3.000
 GLE  H171  C17  C18   109.33  3.000
 GLE  H172  C17  C16   109.22  3.000
 GLE  H171  C17  C16   109.22  3.000
 GLE  C18   C17  C16   113.52  3.000
 GLE  H182  C18  H181  105.96  3.000
 GLE  H182  C18  C19   109.23  3.000
 GLE  H181  C18  C19   109.25  3.000
 GLE  H182  C18  C17   109.46  3.000
 GLE  H181  C18  C17   109.42  3.000
 GLE  C19   C18  C17   113.26  3.000
 GLE  H192  C19  H191  106.00  3.000
 GLE  H192  C19  C20   109.65  3.000
 GLE  H191  C19  C20   109.53  3.000
 GLE  H192  C19  C18   109.25  3.000
 GLE  H191  C19  C18   109.27  3.000
 GLE  C20   C19  C18   112.90  3.000
 GLE  H203  C20  H202  107.45  3.000
 GLE  H203  C20  H201  107.61  3.000
 GLE  H202  C20  H201  107.52  3.000
 GLE  H203  C20  C19   111.24  3.000
 GLE  H202  C20  C19   111.13  3.000
 GLE  H201  C20  C19   111.68  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
 GLE  Var_01  C12   C11  O1   C1   -176.16  30.0  3
 GLE  Var_02  C13   C12  C11  O1   -175.78  30.0  3
 GLE  Var_03  O21   P2   O2   C2    -80.80  30.0  3
 GLE  Var_04  C32   C31  O3   C3   -174.91  30.0  3
 GLE  Var_05  F31   C32  C31  O3   -179.36  30.0  3
 GLE  Var_06  C14   C13  C12  C11  -176.86  30.0  3
 GLE  Var_07  C15   C14  C13  C12  -178.66  30.0  3
 GLE  Var_08  C16   C15  C14  C13  -178.71  30.0  3
 GLE  Var_09  C17   C16  C15  C14  -179.69  30.0  3
 GLE  Var_10  C18   C17  C16  C15  -179.43  30.0  3
 GLE  Var_11  C19   C18  C17  C16  -179.59  30.0  3
 GLE  Var_12  C20   C19  C18  C17  -179.73  30.0  3
 GLE  Var_13  H31   C3   O3   C31    65.46  30.0  1
 GLE  Var_14  H2P1  C2P  O23  P2   -173.91  30.0  3
 GLE  Var_15  H11   C1   O1   C11   -49.85  30.0  1
 GLE  Var_16  H201  C20  C19  C18  -179.34  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
 GLE  chir_01  C2  C1   O2   C3   positiv
 GLE  chir_02  P2  O21  O22  O23  both

