# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 21:16:37 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  75  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 OK
;

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  -0.126   1.5627   0.3725   -4.0265
 MJI  O1    O  O2     0  -0.475   0.8091   0.1145   -2.8761
 MJI  C2    C  CH1    0  -0.034   0.7825  -0.0901   -5.2432
 MJI  O2    O  O2     0  -0.619  -0.4240   0.6351   -5.3532
 MJI  C3    C  CH2    0  -0.136   1.6032   0.1360   -6.4982
 MJI  O3    O  O2     0  -0.481   0.9041  -0.3974   -7.5961
 MJI  C31   C  CH2    0  -0.310   1.5199  -0.1176   -8.8132
 MJI  C32   C  CT     0   0.963   0.6572  -0.7035   -9.9041
 MJI  F31   F  F      0  -0.313   1.1934  -0.4618  -11.1082
 MJI  F32   F  F      0  -0.310   0.5248  -2.0305   -9.7870
 MJI  F33   F  F      0  -0.307  -0.5774  -0.1895   -9.9079
 MJI  P2    P  P      0   1.348  -1.8935  -0.0848   -5.3755
 MJI  O21   O  O      0  -0.804  -1.7773  -1.5623   -5.5910
 MJI  O22   O  OP    -1  -0.799  -2.7703   0.7569   -6.2493
 MJI  C2P   C  CH3    0  -0.402  -3.5467  -0.2450   -3.3638
 MJI  O23   O  O2     0  -0.604  -2.2805   0.1993   -3.8007
 MJI  C11   C  CH2    0  -0.122   1.5117   0.3660   -1.6838
 MJI  C12   C  CH2    0  -0.454   0.5782   0.1900   -0.5032
 MJI  C13   C  CH2    0  -0.425   1.3049   0.3469    0.8270
 MJI  C14   C  CH2    0  -0.411   0.3699   0.2592    2.0269
 MJI  C15   C  CH2    0  -0.412   1.0993   0.3214    3.3628
 MJI  C16   C  CH2    0  -0.412   0.1594   0.2722    4.5614
 MJI  C17   C  CH2    0  -0.412   0.8879   0.2476    5.8993
 MJI  C18   C  CH2    0  -0.412  -0.0547   0.2116    7.0961
 MJI  C19   C  CH2    0  -0.412   0.6708   0.1289    8.4333
 MJI  C20   C  CH2    0  -0.412  -0.2732   0.0963    9.6290
 MJI  C21   C  CH2    0  -0.412   0.4502  -0.0158   10.9652
 MJI  C22   C  CH2    0  -0.411  -0.4947  -0.0467   12.1602
 MJI  C23   C  CH2    0  -0.411   0.2271  -0.1673   13.4966
 MJI  C24   C  CH2    0  -0.406  -0.7191  -0.1962   14.6905
 MJI  C25   C  CH2    0  -0.419  -0.0004  -0.3123   16.0293
 MJI  C26   C  CH3    0  -0.662  -0.9589  -0.3382   17.2121
 MJI  H11   H  HCH2   0   0.196   1.8007   1.4440   -4.1112
 MJI  H12   H  HCH2   0   0.196   2.5214  -0.1659   -4.0027
 MJI  H21   H  HCH1   0   0.227   0.5833  -1.1623   -5.1429
 MJI  H31   H  HCH2   0   0.210   1.7826   1.2114   -6.6395
 MJI  H32   H  HCH2   0   0.211   2.5849  -0.3453   -6.3906
 MJI  H311  H  HCH2   0   0.245   1.6218   0.9616   -8.9910
 MJI  H312  H  HCH2   0   0.244   2.5238  -0.5568   -8.8903
 MJI  H2P1  H  HCH3   0   0.225  -3.6352  -0.0241   -2.3001
 MJI  H2P2  H  HCH3   0   0.204  -4.3658   0.2591   -3.8857
 MJI  H2P3  H  HCH3   0   0.204  -3.6745  -1.3236   -3.4964
 MJI  H111  H  HCH2   0   0.189   1.9243   1.3859   -1.6820
 MJI  H112  H  HCH2   0   0.189   2.3693  -0.3181   -1.5925
 MJI  H121  H  HCH2   0   0.219   0.1145  -0.8003   -0.5499
 MJI  H122  H  HCH2   0   0.219  -0.2340   0.9204   -0.5712
 MJI  H131  H  HCH2   0   0.212   1.8320   1.3072    0.8500
 MJI  H132  H  HCH2   0   0.212   2.0770  -0.4252    0.9120
 MJI  H141  H  HCH2   0   0.208  -0.2038  -0.6730    1.9737
 MJI  H142  H  HCH2   0   0.209  -0.3652   1.0698    1.9719
 MJI  H151  H  HCH2   0   0.207   1.7015   1.2358    3.4100
 MJI  H152  H  HCH2   0   0.207   1.8088  -0.5113    3.4249
 MJI  H161  H  HCH2   0   0.206  -0.4798  -0.6147    4.4837
 MJI  H162  H  HCH2   0   0.207  -0.5161   1.1343    4.5279
 MJI  H171  H  HCH2   0   0.206   1.5411   1.1241    5.9772
 MJI  H172  H  HCH2   0   0.206   1.5494  -0.6255    5.9338
 MJI  H181  H  HCH2   0   0.206  -0.7301  -0.6460    6.9982
 MJI  H182  H  HCH2   0   0.206  -0.6939   1.1017    7.0816
 MJI  H191  H  HCH2   0   0.206   1.3524   0.9812    8.5323
 MJI  H192  H  HCH2   0   0.206   1.3032  -0.7662    8.4470
 MJI  H201  H  HCH2   0   0.206  -0.9654  -0.7463    9.5201
 MJI  H202  H  HCH2   0   0.206  -0.8943   0.9993    9.6255
 MJI  H211  H  HCH2   0   0.206   1.1452   0.8243   11.0745
 MJI  H212  H  HCH2   0   0.206   1.0681  -0.9210   10.9684
 MJI  H221  H  HCH2   0   0.206  -1.1928  -0.8839   12.0480
 MJI  H222  H  HCH2   0   0.206  -1.1094   0.8607   12.1596
 MJI  H231  H  HCH2   0   0.206   0.9261   0.6692   13.6086
 MJI  H232  H  HCH2   0   0.206   0.8406  -1.0755   13.4978
 MJI  H241  H  HCH2   0   0.205  -1.4167  -1.0342   14.5800
 MJI  H242  H  HCH2   0   0.205  -1.3347   0.7107   14.6877
 MJI  H251  H  HCH2   0   0.210   0.6963   0.5248   16.1389
 MJI  H252  H  HCH2   0   0.210   0.6137  -1.2185   16.0337
 MJI  H261  H  HCH3   0   0.225  -0.4270  -0.4146   18.1612
 MJI  H262  H  HCH3   0   0.215  -1.5652   0.5691   17.2457
 MJI  H263  H  HCH3   0   0.216  -1.6411  -1.1876   17.1457

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  1.399  0.020  1.399
 MJI  C1   C2    single  1.518  0.020  1.518
 MJI  C1   H11   single  0.970  0.020  1.090
 MJI  C1   H12   single  0.970  0.020  1.090
 MJI  O1   C11   single  1.407  0.020  1.407
 MJI  C2   O2    single  1.412  0.020  1.412
 MJI  C2   C3    single  1.516  0.020  1.516
 MJI  C2   H21   single  0.970  0.020  1.090
 MJI  O2   P2    single  1.637  0.020  1.637
 MJI  C3   O3    single  1.407  0.020  1.407
 MJI  C3   H31   single  0.970  0.020  1.090
 MJI  C3   H32   single  0.970  0.020  1.090
 MJI  O3   C31   single  1.392  0.020  1.392
 MJI  C31  C32   single  1.509  0.020  1.509
 MJI  C31  H311  single  0.970  0.020  1.090
 MJI  C31  H312  single  0.970  0.020  1.090
 MJI  C32  F31   single  1.340  0.020  1.340
 MJI  C32  F32   single  1.339  0.020  1.339
 MJI  C32  F33   single  1.337  0.020  1.337
 MJI  P2   O21   deloc   1.498  0.020  1.498
 MJI  P2   O22   deloc   1.497  0.020  1.497
 MJI  P2   O23   single  1.646  0.020  1.646
 MJI  C2P  O23   single  1.411  0.020  1.411
 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  1.524  0.020  1.524
 MJI  C13  H131  single  0.970  0.020  1.090
 MJI  C13  H132  single  0.970  0.020  1.090
 MJI  C14  C15   single  1.523  0.020  1.523
 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   106.84  3.000
 MJI  H12   C1   C2    108.44  3.000
 MJI  H11   C1   C2    110.25  3.000
 MJI  H12   C1   O1    111.19  3.000
 MJI  H11   C1   O1    111.04  3.000
 MJI  C2    C1   O1    109.03  3.000
 MJI  C11   O1   C1    113.27  3.000
 MJI  H21   C2   C3    108.68  3.000
 MJI  H21   C2   O2    110.77  3.000
 MJI  C3    C2   O2    108.75  3.000
 MJI  H21   C2   C1    108.57  3.000
 MJI  C3    C2   C1    109.87  3.000
 MJI  O2    C2   C1    110.19  3.000
 MJI  P2    O2   C2    122.84  3.000
 MJI  H32   C3   H31   107.18  3.000
 MJI  H32   C3   O3    110.76  3.000
 MJI  H31   C3   O3    110.59  3.000
 MJI  H32   C3   C2    109.71  3.000
 MJI  H31   C3   C2    109.91  3.000
 MJI  O3    C3   C2    108.68  3.000
 MJI  C31   O3   C3    112.72  3.000
 MJI  H312  C31  H311  107.26  3.000
 MJI  H312  C31  C32   108.45  3.000
 MJI  H311  C31  C32   108.51  3.000
 MJI  H312  C31  O3    112.65  3.000
 MJI  H311  C31  O3    112.33  3.000
 MJI  C32   C31  O3    107.52  3.000
 MJI  F33   C32  F32   106.85  3.000
 MJI  F33   C32  F31   107.30  3.000
 MJI  F32   C32  F31   107.27  3.000
 MJI  F33   C32  C31   112.37  3.000
 MJI  F32   C32  C31   112.22  3.000
 MJI  F31   C32  C31   110.53  3.000
 MJI  O23   P2   O22   108.88  3.000
 MJI  O23   P2   O21   109.04  3.000
 MJI  O22   P2   O21   121.08  3.000
 MJI  O23   P2   O2     97.01  3.000
 MJI  O22   P2   O2    106.65  3.000
 MJI  O21   P2   O2    111.49  3.000
 MJI  H2P3  C2P  H2P2  107.99  3.000
 MJI  H2P3  C2P  H2P1  107.97  3.000
 MJI  H2P2  C2P  H2P1  108.14  3.000
 MJI  H2P3  C2P  O23   112.19  3.000
 MJI  H2P2  C2P  O23   112.27  3.000
 MJI  H2P1  C2P  O23   108.13  3.000
 MJI  C2P   O23  P2    116.92  3.000
 MJI  H112  C11  H111  106.48  3.000
 MJI  H112  C11  C12   110.07  3.000
 MJI  H111  C11  C12   109.72  3.000
 MJI  H112  C11  O1    110.38  3.000
 MJI  H111  C11  O1    110.76  3.000
 MJI  C12   C11  O1    109.39  3.000
 MJI  H122  C12  H121  106.67  3.000
 MJI  H122  C12  C13   109.84  3.000
 MJI  H121  C12  C13   109.42  3.000
 MJI  H122  C12  C11   109.34  3.000
 MJI  H121  C12  C11   109.44  3.000
 MJI  C13   C12  C11   111.98  3.000
 MJI  H132  C13  H131  106.09  3.000
 MJI  H132  C13  C14   109.32  3.000
 MJI  H131  C13  C14   109.21  3.000
 MJI  H132  C13  C12   109.35  3.000
 MJI  H131  C13  C12   109.76  3.000
 MJI  C14   C13  C12   112.88  3.000
 MJI  H142  C14  H141  106.01  3.000
 MJI  H142  C14  C15   109.58  3.000
 MJI  H141  C14  C15   109.14  3.000
 MJI  H142  C14  C13   109.25  3.000
 MJI  H141  C14  C13   109.39  3.000
 MJI  C15   C14  C13   113.23  3.000
 MJI  H152  C15  H151  106.01  3.000
 MJI  H152  C15  C16   109.28  3.000
 MJI  H151  C15  C16   109.39  3.000
 MJI  H152  C15  C14   109.19  3.000
 MJI  H151  C15  C14   109.57  3.000
 MJI  C16   C15  C14   113.15  3.000
 MJI  H162  C16  H161  105.95  3.000
 MJI  H162  C16  C17   109.53  3.000
 MJI  H161  C16  C17   109.15  3.000
 MJI  H162  C16  C15   109.32  3.000
 MJI  H161  C16  C15   109.27  3.000
 MJI  C17   C16  C15   113.35  3.000
 MJI  H172  C17  H171  105.97  3.000
 MJI  H172  C17  C18   109.26  3.000
 MJI  H171  C17  C18   109.38  3.000
 MJI  H172  C17  C16   109.21  3.000
 MJI  H171  C17  C16   109.54  3.000
 MJI  C18   C17  C16   113.22  3.000
 MJI  H182  C18  H181  105.96  3.000
 MJI  H182  C18  C19   109.48  3.000
 MJI  H181  C18  C19   109.23  3.000
 MJI  H182  C18  C17   109.34  3.000
 MJI  H181  C18  C17   109.24  3.000
 MJI  C19   C18  C17   113.32  3.000
 MJI  H192  C19  H191  105.98  3.000
 MJI  H192  C19  C20   109.28  3.000
 MJI  H191  C19  C20   109.33  3.000
 MJI  H192  C19  C18   109.27  3.000
 MJI  H191  C19  C18   109.47  3.000
 MJI  C20   C19  C18   113.25  3.000
 MJI  H202  C20  H201  105.97  3.000
 MJI  H202  C20  C21   109.42  3.000
 MJI  H201  C20  C21   109.29  3.000
 MJI  H202  C20  C19   109.33  3.000
 MJI  H201  C20  C19   109.26  3.000
 MJI  C21   C20  C19   113.30  3.000
 MJI  H212  C21  H211  105.98  3.000
 MJI  H212  C21  C22   109.30  3.000
 MJI  H211  C21  C22   109.30  3.000
 MJI  H212  C21  C20   109.33  3.000
 MJI  H211  C21  C20   109.40  3.000
 MJI  C22   C21  C20   113.26  3.000
 MJI  H222  C22  H221  105.98  3.000
 MJI  H222  C22  C23   109.37  3.000
 MJI  H221  C22  C23   109.34  3.000
 MJI  H222  C22  C21   109.31  3.000
 MJI  H221  C22  C21   109.28  3.000
 MJI  C23   C22  C21   113.31  3.000
 MJI  H232  C23  H231  105.98  3.000
 MJI  H232  C23  C24   109.33  3.000
 MJI  H231  C23  C24   109.30  3.000
 MJI  H232  C23  C22   109.38  3.000
 MJI  H231  C23  C22   109.35  3.000
 MJI  C24   C23  C22   113.24  3.000
 MJI  H242  C24  H241  105.95  3.000
 MJI  H242  C24  C25   109.28  3.000
 MJI  H241  C24  C25   109.30  3.000
 MJI  H242  C24  C23   109.33  3.000
 MJI  H241  C24  C23   109.32  3.000
 MJI  C25   C24  C23   113.39  3.000
 MJI  H252  C25  H251  106.00  3.000
 MJI  H252  C25  C26   109.63  3.000
 MJI  H251  C25  C26   109.63  3.000
 MJI  H252  C25  C24   109.34  3.000
 MJI  H251  C25  C24   109.26  3.000
 MJI  C26   C25  C24   112.76  3.000
 MJI  H263  C26  H262  107.54  3.000
 MJI  H263  C26  H261  107.66  3.000
 MJI  H262  C26  H261  107.59  3.000
 MJI  H263  C26  C25   111.06  3.000
 MJI  H262  C26  C25   111.06  3.000
 MJI  H261  C26  C25   111.73  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    174.52  30.0  3
 MJI  Var_02  C13   C12  C11  O1    175.74  30.0  3
 MJI  Var_03  O21   P2   O2   C2    -13.40  30.0  3
 MJI  Var_04  C32   C31  O3   C3   -178.34  30.0  3
 MJI  Var_05  F31   C32  C31  O3    179.68  30.0  3
 MJI  Var_06  C14   C13  C12  C11   176.46  30.0  3
 MJI  Var_07  C15   C14  C13  C12   176.14  30.0  3
 MJI  Var_08  C16   C15  C14  C13   178.42  30.0  3
 MJI  Var_09  C17   C16  C15  C14   176.45  30.0  3
 MJI  Var_10  C18   C17  C16  C15   179.46  30.0  3
 MJI  Var_11  C19   C18  C17  C16   177.62  30.0  3
 MJI  Var_12  C20   C19  C18  C17   179.86  30.0  3
 MJI  Var_13  C21   C20  C19  C18   178.79  30.0  3
 MJI  Var_14  C22   C21  C20  C19   179.93  30.0  3
 MJI  Var_15  C23   C22  C21  C20   179.65  30.0  3
 MJI  Var_16  C24   C23  C22  C21   179.93  30.0  3
 MJI  Var_17  C25   C24  C23  C22  -179.82  30.0  3
 MJI  Var_18  C26   C25  C24  C23   179.93  30.0  3
 MJI  Var_19  H31   C3   O3   C31    53.22  30.0  1
 MJI  Var_20  H2P1  C2P  O23  P2    177.61  30.0  3
 MJI  Var_21  H11   C1   O1   C11   -65.27  30.0  2
 MJI  Var_22  H261  C26  C25  C24  -179.60  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

