# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 12:16:17 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: (1R)-2-(hexadecyloxy)-1-[(2,2,2-trifluoroethoxy)methyl]ethyl methyl hydrogen (R)-phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCCOC[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
 MJI  MJI  '(1R)-2-(hexadecyloxy)-1-[(2,2,2-trifluoroethoxy)methyl]ethyl methyl hydrogen (R)-phosphate'  ligand  76  32  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MJI
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
 MJI  C1    C  CH2   0  -0.118   1.5805   0.2986   -3.8629
 MJI  O1    O  O2    0  -0.482   0.9218  -0.2226   -2.7465
 MJI  C2    C  CH1   0  -0.095   0.8107  -0.0985   -5.1044
 MJI  O2    O  O2    0  -0.583  -0.5155   0.4387   -5.0098
 MJI  C3    C  CH2   0  -0.122   1.4650   0.4659   -6.3471
 MJI  O3    O  O2    0  -0.525   0.7734  -0.0015   -7.4910
 MJI  C31   C  CH2   0  -0.311   1.2282   0.5979   -8.6744
 MJI  C32   C  CT    0   0.965   0.5081  -0.0527   -9.8307
 MJI  F31   F  F     0  -0.304   0.8733   0.5095  -10.9857
 MJI  F32   F  F     0  -0.304   0.7667  -1.3614   -9.9171
 MJI  F33   F  F     0  -0.310  -0.8222   0.0726   -9.7236
 MJI  P2    P  P     0   1.447  -1.8182  -0.4511   -5.2454
 MJI  O21   O  O     0  -0.699  -2.2568  -1.3643   -4.1747
 MJI  O22   O  OH1   0  -0.761  -1.5629  -1.2605   -6.5992
 MJI  C2P   C  CH3   0  -0.412  -4.2238   0.5201   -5.5851
 MJI  O23   O  O2    0  -0.576  -2.8118   0.7513   -5.5740
 MJI  C11   C  CH2   0  -0.126   1.6165   0.0058   -1.5399
 MJI  C12   C  CH2   0  -0.458   0.7167  -0.3236   -0.3665
 MJI  C13   C  CH2   0  -0.425   1.4440  -0.1635    0.9636
 MJI  C14   C  CH2   0  -0.411   0.5266  -0.3364    2.1672
 MJI  C15   C  CH2   0  -0.412   1.2512  -0.1977    3.5002
 MJI  C16   C  CH2   0  -0.412   0.3142  -0.2787    4.6990
 MJI  C17   C  CH2   0  -0.412   1.0297  -0.1552    6.0385
 MJI  C18   C  CH2   0  -0.412   0.0781  -0.1889    7.2283
 MJI  C19   C  CH2   0  -0.412   0.7844  -0.0760    8.5735
 MJI  C20   C  CH2   0  -0.412  -0.1760  -0.0885    9.7566
 MJI  C21   C  CH2   0  -0.412   0.5246   0.0171   11.1054
 MJI  C22   C  CH2   0  -0.411  -0.4405   0.0123   12.2848
 MJI  C23   C  CH2   0  -0.411   0.2573   0.1037   13.6361
 MJI  C24   C  CH2   0  -0.406  -0.7101   0.1040   14.8132
 MJI  C25   C  CH2   0  -0.419  -0.0155   0.1905   16.1670
 MJI  C26   C  CH3   0  -0.662  -0.9946   0.1899   17.3331
 MJI  H11   H  HCH2  0   0.214   1.6609   1.3937   -3.8016
 MJI  H12   H  HCH2  0   0.216   2.6026  -0.0938   -3.9565
 MJI  H21   H  HCH1  0   0.269   0.7879  -1.1924   -5.1660
 MJI  H31   H  HCH2  0   0.238   1.4456   1.5618   -6.3120
 MJI  H32   H  HCH2  0   0.244   2.5135   0.1503   -6.3850
 MJI  H311  H  HCH2  0   0.267   1.0239   1.6748   -8.6878
 MJI  H312  H  HCH2  0   0.267   2.3069   0.4574   -8.8081
 MJI  HO21  H  HOH1  0   0.478  -0.9171  -0.8405   -7.1949
 MJI  H2P1  H  HCH3  0   0.255  -4.6919   1.4615   -5.8588
 MJI  H2P2  H  HCH3  0   0.237  -4.4999  -0.2360   -6.3211
 MJI  H2P3  H  HCH3  0   0.241  -4.5832   0.2144   -4.6032
 MJI  H111  H  HCH2  0   0.196   1.9338   1.0560   -1.4726
 MJI  H112  H  HCH2  0   0.198   2.5307  -0.6046   -1.5058
 MJI  H121  H  HCH2  0   0.223   0.3430  -1.3476   -0.4613
 MJI  H122  H  HCH2  0   0.220  -0.1559   0.3366   -0.3891
 MJI  H131  H  HCH2  0   0.212   1.9091   0.8275    1.0088
 MJI  H132  H  HCH2  0   0.215   2.2646  -0.8864    1.0204
 MJI  H141  H  HCH2  0   0.210   0.0382  -1.3161    2.1199
 MJI  H142  H  HCH2  0   0.208  -0.2779   0.4055    2.1144
 MJI  H151  H  HCH2  0   0.206   1.7865   0.7583    3.5246
 MJI  H152  H  HCH2  0   0.208   2.0176  -0.9762    3.5812
 MJI  H161  H  HCH2  0   0.207  -0.2362  -1.2261    4.6688
 MJI  H162  H  HCH2  0   0.206  -0.4407   0.5114    4.6179
 MJI  H171  H  HCH2  0   0.206   1.6035   0.7783    6.0599
 MJI  H172  H  HCH2  0   0.207   1.7628  -0.9635    6.1357
 MJI  H181  H  HCH2  0   0.206  -0.5036  -1.1175    7.2016
 MJI  H182  H  HCH2  0   0.206  -0.6488   0.6252    7.1308
 MJI  H191  H  HCH2  0   0.206   1.3775   0.8454    8.5972
 MJI  H192  H  HCH2  0   0.206   1.5001  -0.8989    8.6787
 MJI  H201  H  HCH2  0   0.206  -0.7730  -1.0072    9.7290
 MJI  H202  H  HCH2  0   0.206  -0.8884   0.7374    9.6518
 MJI  H211  H  HCH2  0   0.206   1.1262   0.9328   11.1325
 MJI  H212  H  HCH2  0   0.206   1.2322  -0.8125   11.2132
 MJI  H221  H  HCH2  0   0.206  -1.0492  -0.8986   12.2515
 MJI  H222  H  HCH2  0   0.206  -1.1420   0.8476   12.1812
 MJI  H231  H  HCH2  0   0.206   0.8688   1.0127   13.6688
 MJI  H232  H  HCH2  0   0.206   0.9559  -0.7338   13.7415
 MJI  H241  H  HCH2  0   0.205  -1.3242  -0.8034   14.7789
 MJI  H242  H  HCH2  0   0.205  -1.4070   0.9433   14.7095
 MJI  H251  H  HCH2  0   0.210   0.5977   1.0966   16.2017
 MJI  H252  H  HCH2  0   0.210   0.6799  -0.6485   16.2704
 MJI  H261  H  HCH3  0   0.225  -0.4793   0.2486   18.2925
 MJI  H262  H  HCH3  0   0.216  -1.6780   1.0386   17.2718
 MJI  H263  H  HCH3  0   0.215  -1.5984  -0.7195   17.3380

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
 MJI  C1   O1    single  1.397  0.020  1.397
 MJI  C1   C2    single  1.514  0.020  1.514
 MJI  C1   H11   single  0.970  0.020  1.090
 MJI  C1   H12   single  0.970  0.020  1.090
 MJI  O1   C11   single  1.411  0.020  1.411
 MJI  C2   O2    single  1.434  0.020  1.434
 MJI  C2   C3    single  1.514  0.020  1.514
 MJI  C2   H21   single  0.970  0.020  1.090
 MJI  O2   P2    single  1.595  0.020  1.595
 MJI  C3   O3    single  1.416  0.020  1.416
 MJI  C3   H31   single  0.970  0.020  1.090
 MJI  C3   H32   single  0.970  0.020  1.090
 MJI  O3   C31   single  1.402  0.020  1.402
 MJI  C31  C32   single  1.510  0.020  1.510
 MJI  C31  H311  single  0.970  0.020  1.090
 MJI  C31  H312  single  0.970  0.020  1.090
 MJI  C32  F31   single  1.335  0.020  1.335
 MJI  C32  F32   single  1.337  0.020  1.337
 MJI  C32  F33   single  1.340  0.020  1.340
 MJI  P2   O21   double  1.474  0.020  1.474
 MJI  P2   O22   single  1.598  0.020  1.598
 MJI  P2   O23   single  1.594  0.020  1.594
 MJI  O22  HO21  single  0.850  0.020  0.980
 MJI  C2P  O23   single  1.431  0.020  1.431
 MJI  C2P  H2P1  single  0.970  0.020  1.090
 MJI  C2P  H2P2  single  0.970  0.020  1.090
 MJI  C2P  H2P3  single  0.970  0.020  1.090
 MJI  C11  C12   single  1.515  0.020  1.515
 MJI  C11  H111  single  0.970  0.020  1.090
 MJI  C11  H112  single  0.970  0.020  1.090
 MJI  C12  C13   single  1.524  0.020  1.524
 MJI  C12  H121  single  0.970  0.020  1.090
 MJI  C12  H122  single  0.970  0.020  1.090
 MJI  C13  C14   single  1.523  0.020  1.523
 MJI  C13  H131  single  0.970  0.020  1.090
 MJI  C13  H132  single  0.970  0.020  1.090
 MJI  C14  C15   single  1.524  0.020  1.524
 MJI  C14  H141  single  0.970  0.020  1.090
 MJI  C14  H142  single  0.970  0.020  1.090
 MJI  C15  C16   single  1.524  0.020  1.524
 MJI  C15  H151  single  0.970  0.020  1.090
 MJI  C15  H152  single  0.970  0.020  1.090
 MJI  C16  C17   single  1.524  0.020  1.524
 MJI  C16  H161  single  0.970  0.020  1.090
 MJI  C16  H162  single  0.970  0.020  1.090
 MJI  C17  C18   single  1.524  0.020  1.524
 MJI  C17  H171  single  0.970  0.020  1.090
 MJI  C17  H172  single  0.970  0.020  1.090
 MJI  C18  C19   single  1.524  0.020  1.524
 MJI  C18  H181  single  0.970  0.020  1.090
 MJI  C18  H182  single  0.970  0.020  1.090
 MJI  C19  C20   single  1.524  0.020  1.524
 MJI  C19  H191  single  0.970  0.020  1.090
 MJI  C19  H192  single  0.970  0.020  1.090
 MJI  C20  C21   single  1.524  0.020  1.524
 MJI  C20  H201  single  0.970  0.020  1.090
 MJI  C20  H202  single  0.970  0.020  1.090
 MJI  C21  C22   single  1.524  0.020  1.524
 MJI  C21  H211  single  0.970  0.020  1.090
 MJI  C21  H212  single  0.970  0.020  1.090
 MJI  C22  C23   single  1.524  0.020  1.524
 MJI  C22  H221  single  0.970  0.020  1.090
 MJI  C22  H222  single  0.970  0.020  1.090
 MJI  C23  C24   single  1.524  0.020  1.524
 MJI  C23  H231  single  0.970  0.020  1.090
 MJI  C23  H232  single  0.970  0.020  1.090
 MJI  C24  C25   single  1.524  0.020  1.524
 MJI  C24  H241  single  0.970  0.020  1.090
 MJI  C24  H242  single  0.970  0.020  1.090
 MJI  C25  C26   single  1.523  0.020  1.523
 MJI  C25  H251  single  0.970  0.020  1.090
 MJI  C25  H252  single  0.970  0.020  1.090
 MJI  C26  H261  single  0.970  0.020  1.090
 MJI  C26  H262  single  0.970  0.020  1.090
 MJI  C26  H263  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
 MJI  H12   C1   H11   107.00  3.000
 MJI  H12   C1   C2    108.03  3.000
 MJI  H11   C1   C2    110.13  3.000
 MJI  H12   C1   O1    111.92  3.000
 MJI  H11   C1   O1    111.19  3.000
 MJI  C2    C1   O1    108.52  3.000
 MJI  C11   O1   C1    113.01  3.000
 MJI  H21   C2   C3    109.57  3.000
 MJI  H21   C2   O2    111.01  3.000
 MJI  C3    C2   O2    108.31  3.000
 MJI  H21   C2   C1    108.58  3.000
 MJI  C3    C2   C1    110.83  3.000
 MJI  O2    C2   C1    108.54  3.000
 MJI  P2    O2   C2    122.45  3.000
 MJI  H32   C3   H31   107.82  3.000
 MJI  H32   C3   O3    110.14  3.000
 MJI  H31   C3   O3    110.31  3.000
 MJI  H32   C3   C2    109.55  3.000
 MJI  H31   C3   C2    109.80  3.000
 MJI  O3    C3   C2    109.21  3.000
 MJI  C31   O3   C3    112.47  3.000
 MJI  H312  C31  H311  107.93  3.000
 MJI  H312  C31  C32   108.71  3.000
 MJI  H311  C31  C32   108.97  3.000
 MJI  H312  C31  O3    111.55  3.000
 MJI  H311  C31  O3    111.70  3.000
 MJI  C32   C31  O3    107.91  3.000
 MJI  F33   C32  F32   106.78  3.000
 MJI  F33   C32  F31   107.53  3.000
 MJI  F32   C32  F31   107.66  3.000
 MJI  F33   C32  C31   111.84  3.000
 MJI  F32   C32  C31   112.28  3.000
 MJI  F31   C32  C31   110.52  3.000
 MJI  O23   P2   O22   107.88  3.000
 MJI  O23   P2   O21   115.57  3.000
 MJI  O22   P2   O21   110.44  3.000
 MJI  O23   P2   O2     96.82  3.000
 MJI  O22   P2   O2    106.10  3.000
 MJI  O21   P2   O2    118.77  3.000
 MJI  HO21  O22  P2    113.94  3.000
 MJI  H2P3  C2P  H2P2  109.28  3.000
 MJI  H2P3  C2P  H2P1  109.15  3.000
 MJI  H2P2  C2P  H2P1  108.76  3.000
 MJI  H2P3  C2P  O23   111.34  3.000
 MJI  H2P2  C2P  O23   111.53  3.000
 MJI  H2P1  C2P  O23   106.69  3.000
 MJI  C2P   O23  P2    119.66  3.000
 MJI  H112  C11  H111  106.77  3.000
 MJI  H112  C11  C12   110.43  3.000
 MJI  H111  C11  C12   109.38  3.000
 MJI  H112  C11  O1    110.24  3.000
 MJI  H111  C11  O1    110.43  3.000
 MJI  C12   C11  O1    109.56  3.000
 MJI  H122  C12  H121  106.88  3.000
 MJI  H122  C12  C13   109.58  3.000
 MJI  H121  C12  C13   109.69  3.000
 MJI  H122  C12  C11   109.05  3.000
 MJI  H121  C12  C11   109.83  3.000
 MJI  C13   C12  C11   111.69  3.000
 MJI  H132  C13  H131  106.07  3.000
 MJI  H132  C13  C14   109.60  3.000
 MJI  H131  C13  C14   109.02  3.000
 MJI  H132  C13  C12   109.47  3.000
 MJI  H131  C13  C12   109.48  3.000
 MJI  C14   C13  C12   112.96  3.000
 MJI  H142  C14  H141  106.02  3.000
 MJI  H142  C14  C15   109.25  3.000
 MJI  H141  C14  C15   109.34  3.000
 MJI  H142  C14  C13   109.10  3.000
 MJI  H141  C14  C13   109.63  3.000
 MJI  C15   C14  C13   113.24  3.000
 MJI  H152  C15  H151  106.05  3.000
 MJI  H152  C15  C16   109.53  3.000
 MJI  H151  C15  C16   109.22  3.000
 MJI  H152  C15  C14   109.43  3.000
 MJI  H151  C15  C14   109.34  3.000
 MJI  C16   C15  C14   113.02  3.000
 MJI  H162  C16  H161  105.98  3.000
 MJI  H162  C16  C17   109.28  3.000
 MJI  H161  C16  C17   109.28  3.000
 MJI  H162  C16  C15   109.09  3.000
 MJI  H161  C16  C15   109.46  3.000
 MJI  C17   C16  C15   113.49  3.000
 MJI  H172  C17  H171  106.04  3.000
 MJI  H172  C17  C18   109.40  3.000
 MJI  H171  C17  C18   109.30  3.000
 MJI  H172  C17  C16   109.42  3.000
 MJI  H171  C17  C16   109.40  3.000
 MJI  C18   C17  C16   113.04  3.000
 MJI  H182  C18  H181  105.97  3.000
 MJI  H182  C18  C19   109.33  3.000
 MJI  H181  C18  C19   109.29  3.000
 MJI  H182  C18  C17   109.17  3.000
 MJI  H181  C18  C17   109.33  3.000
 MJI  C19   C18  C17   113.47  3.000
 MJI  H192  C19  H191  106.02  3.000
 MJI  H192  C19  C20   109.33  3.000
 MJI  H191  C19  C20   109.33  3.000
 MJI  H192  C19  C18   109.39  3.000
 MJI  H191  C19  C18   109.41  3.000
 MJI  C20   C19  C18   113.12  3.000
 MJI  H202  C20  H201  105.97  3.000
 MJI  H202  C20  C21   109.36  3.000
 MJI  H201  C20  C21   109.32  3.000
 MJI  H202  C20  C19   109.23  3.000
 MJI  H201  C20  C19   109.31  3.000
 MJI  C21   C20  C19   113.39  3.000
 MJI  H212  C21  H211  106.00  3.000
 MJI  H212  C21  C22   109.30  3.000
 MJI  H211  C21  C22   109.34  3.000
 MJI  H212  C21  C20   109.36  3.000
 MJI  H211  C21  C20   109.41  3.000
 MJI  C22   C21  C20   113.19  3.000
 MJI  H222  C22  H221  105.97  3.000
 MJI  H222  C22  C23   109.35  3.000
 MJI  H221  C22  C23   109.34  3.000
 MJI  H222  C22  C21   109.26  3.000
 MJI  H221  C22  C21   109.32  3.000
 MJI  C23   C22  C21   113.34  3.000
 MJI  H232  C23  H231  105.98  3.000
 MJI  H232  C23  C24   109.31  3.000
 MJI  H231  C23  C24   109.34  3.000
 MJI  H232  C23  C22   109.36  3.000
 MJI  H231  C23  C22   109.38  3.000
 MJI  C24   C23  C22   113.23  3.000
 MJI  H242  C24  H241  105.94  3.000
 MJI  H242  C24  C25   109.30  3.000
 MJI  H241  C24  C25   109.28  3.000
 MJI  H242  C24  C23   109.31  3.000
 MJI  H241  C24  C23   109.35  3.000
 MJI  C25   C24  C23   113.38  3.000
 MJI  H252  C25  H251  106.00  3.000
 MJI  H252  C25  C26   109.62  3.000
 MJI  H251  C25  C26   109.65  3.000
 MJI  H252  C25  C24   109.27  3.000
 MJI  H251  C25  C24   109.30  3.000
 MJI  C26   C25  C24   112.78  3.000
 MJI  H263  C26  H262  107.56  3.000
 MJI  H263  C26  H261  107.58  3.000
 MJI  H262  C26  H261  107.67  3.000
 MJI  H263  C26  C25   111.07  3.000
 MJI  H262  C26  C25   111.06  3.000
 MJI  H261  C26  C25   111.71  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
 MJI  Var_01  C12   C11  O1   C1    168.27  30.0  3
 MJI  Var_02  C13   C12  C11  O1    177.01  30.0  3
 MJI  Var_03  O21   P2   O2   C2     76.93  30.0  3
 MJI  Var_04  C32   C31  O3   C3    175.38  30.0  3
 MJI  Var_05  F31   C32  C31  O3    178.10  30.0  3
 MJI  Var_06  C14   C13  C12  C11   173.62  30.0  3
 MJI  Var_07  C15   C14  C13  C12   179.16  30.0  3
 MJI  Var_08  C16   C15  C14  C13   176.16  30.0  3
 MJI  Var_09  C17   C16  C15  C14   179.42  30.0  3
 MJI  Var_10  C18   C17  C16  C15   178.00  30.0  3
 MJI  Var_11  C19   C18  C17  C16   179.59  30.0  3
 MJI  Var_12  C20   C19  C18  C17   179.10  30.0  3
 MJI  Var_13  C21   C20  C19  C18   179.71  30.0  3
 MJI  Var_14  C22   C21  C20  C19   179.67  30.0  3
 MJI  Var_15  C23   C22  C21  C20   179.43  30.0  3
 MJI  Var_16  C24   C23  C22  C21   179.78  30.0  3
 MJI  Var_17  C25   C24  C23  C22   179.80  30.0  3
 MJI  Var_18  C26   C25  C24  C23   179.99  30.0  3
 MJI  Var_19  H31   C3   O3   C31    52.55  30.0  1
 MJI  Var_20  H2P1  C2P  O23  P2   -178.35  30.0  3
 MJI  Var_21  H11   C1   O1   C11   -63.26  30.0  1
 MJI  Var_22  H261  C26  C25  C24   179.78  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
 MJI  chir_01  C2  C1   O2   C3   negativ
 MJI  chir_02  P2  O21  O22  O23  both

