# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:00:55 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: S-[(1-hydroxy-2,2,5,5-tetramethyl-4-phenyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)N([O])C(C)(C)C(=C1CS[S](C)(=O)=O)c2ccccc2
#
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
 R1F  R1F  'S-[(1-hydroxy-2,2,5,5-tetramethyl-4-phenyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate'  ligand  44  22  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_R1F
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
 R1F  SD   S  S2    0   0.003  -1.8891  -0.9004   1.2441
 R1F  CE   C  CH2   0  -0.727  -0.1238  -1.1665   1.5762
 R1F  C3   C  CR5   0   0.163   0.8637  -0.4394   0.7236
 R1F  C2   C  CR5   0   0.029   2.2472  -1.0318   0.5996
 R1F  C9   C  CH3   0  -0.640   2.9305  -1.1887   1.9581
 R1F  C8   C  CH3   0  -0.633   2.2646  -2.3527  -0.1703
 R1F  N1   N  NR5   0  -0.029   2.9129   0.0127  -0.1837
 R1F  O1   O  O     0  -0.454   4.1189  -0.0638  -0.5217
 R1F  C4   C  CR5   0   0.073   0.7552   0.7230   0.0865
 R1F  C5   C  CR5   0   0.033   2.0447   1.1193  -0.5950
 R1F  C6   C  CH3   0  -0.636   2.5889   2.4462  -0.0694
 R1F  C7   C  CH3   0  -0.639   1.9229   1.1592  -2.1178
 R1F  C10  C  CR6   0   0.036  -0.4150   1.6203   0.0404
 R1F  C11  C  CR16  0  -0.282  -1.2674   1.6451  -1.0617
 R1F  C12  C  CR16  0  -0.237  -2.3638   2.4934  -1.0821
 R1F  C13  C  CR16  0  -0.266  -2.6199   3.3319  -0.0041
 R1F  C14  C  CR16  0  -0.240  -1.7704   3.3191   1.0936
 R1F  C15  C  CR16  0  -0.292  -0.6728   2.4694   1.1132
 R1F  H8   H  HCH2  0   0.336  -0.0216  -0.8569   2.6210
 R1F  H9   H  HCH2  0   0.299   0.0759  -2.2394   1.5787
 R1F  H10  H  HCH3  0   0.248   3.9689  -1.4959   1.8312
 R1F  H11  H  HCH3  0   0.241   2.9110  -0.2549   2.5217
 R1F  H12  H  HCH3  0   0.237   2.4323  -1.9547   2.5537
 R1F  H13  H  HCH3  0   0.247   1.7871  -2.2468  -1.1432
 R1F  H14  H  HCH3  0   0.244   3.2914  -2.6883  -0.3173
 R1F  H15  H  HCH3  0   0.228   1.7421  -3.1334   0.3827
 R1F  H17  H  HCH3  0   0.245   3.5752   2.6457  -0.4884
 R1F  H18  H  HCH3  0   0.237   1.9297   3.2643  -0.3598
 R1F  H19  H  HCH3  0   0.236   2.6681   2.4417   1.0185
 R1F  H20  H  HCH3  0   0.239   1.5374   0.2175  -2.5091
 R1F  H21  H  HCH3  0   0.236   1.2497   1.9596  -2.4242
 R1F  H22  H  HCH3  0   0.245   2.8957   1.3533  -2.5710
 R1F  H23  H  HCR6  0   0.248  -1.0896   0.9750  -1.8924
 R1F  H24  H  HCR6  0   0.254  -3.0265   2.4931  -1.9378
 R1F  H25  H  HCR6  0   0.255  -3.4782   3.9910  -0.0202
 R1F  H26  H  HCR6  0   0.254  -1.9622   3.9705   1.9366
 R1F  H27  H  HCR6  0   0.248  -0.0117   2.4596   1.9713
 R1F  S1   S  S     0   1.106  -2.1456  -1.9734  -0.5234
 R1F  C16  C  CH3   0  -0.786  -2.2392  -3.6720  -0.0046
 R1F  O2   O  OS    0  -0.650  -3.4553  -1.5487  -0.9949
 R1F  O3   O  OS    0  -0.618  -0.9821  -1.8274  -1.3845
 R1F  H1   H  HCH3  0   0.302  -3.0610  -3.7858   0.6968
 R1F  H2   H  HCH3  0   0.318  -2.4146  -4.2708  -0.8982
 R1F  H3   H  HCH3  0   0.292  -1.2992  -3.9664   0.4559

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
 R1F  O1   N1   single    1.255  0.020  1.255
 R1F  C6   C5   single    1.527  0.020  1.527
 R1F  C7   C5   single    1.528  0.020  1.528
 R1F  N1   C5   single    1.465  0.020  1.465
 R1F  N1   C2   single    1.465  0.020  1.465
 R1F  C5   C4   single    1.511  0.020  1.511
 R1F  C9   C2   single    1.529  0.020  1.529
 R1F  C2   C8   single    1.529  0.020  1.529
 R1F  C2   C3   single    1.510  0.020  1.510
 R1F  C4   C10  single    1.475  0.020  1.475
 R1F  C4   C3   double    1.330  0.020  1.330
 R1F  C11  C10  aromatic  1.394  0.020  1.394
 R1F  C11  C12  aromatic  1.386  0.020  1.386
 R1F  C10  C15  aromatic  1.392  0.020  1.392
 R1F  C3   CE   single    1.494  0.020  1.494
 R1F  C12  C13  aromatic  1.389  0.020  1.389
 R1F  C15  C14  aromatic  1.388  0.020  1.388
 R1F  C13  C14  aromatic  1.388  0.020  1.388
 R1F  CE   SD   single    1.816  0.020  1.816
 R1F  CE   H8   single    0.970  0.020  1.090
 R1F  CE   H9   single    0.970  0.020  1.090
 R1F  C9   H10  single    0.970  0.020  1.090
 R1F  C9   H11  single    0.970  0.020  1.090
 R1F  C9   H12  single    0.970  0.020  1.090
 R1F  C8   H13  single    0.970  0.020  1.090
 R1F  C8   H14  single    0.970  0.020  1.090
 R1F  C8   H15  single    0.970  0.020  1.090
 R1F  C6   H17  single    0.970  0.020  1.090
 R1F  C6   H18  single    0.970  0.020  1.090
 R1F  C6   H19  single    0.970  0.020  1.090
 R1F  C7   H20  single    0.970  0.020  1.090
 R1F  C7   H21  single    0.970  0.020  1.090
 R1F  C7   H22  single    0.970  0.020  1.090
 R1F  C11  H23  single    0.930  0.020  1.080
 R1F  C12  H24  single    0.930  0.020  1.080
 R1F  C13  H25  single    0.930  0.020  1.080
 R1F  C14  H26  single    0.930  0.020  1.080
 R1F  C15  H27  single    0.930  0.020  1.080
 R1F  SD   S1   single    2.084  0.020  2.084
 R1F  S1   C16  single    1.779  0.020  1.779
 R1F  S1   O2   double    1.455  0.020  1.455
 R1F  S1   O3   double    1.455  0.020  1.455
 R1F  C16  H1   single    0.970  0.020  1.090
 R1F  C16  H2   single    0.970  0.020  1.090
 R1F  C16  H3   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
 R1F  S1   SD   CE   101.50  3.000
 R1F  H9   CE   H8   105.00  3.000
 R1F  H9   CE   C3   111.04  3.000
 R1F  H8   CE   C3   110.21  3.000
 R1F  H9   CE   SD   108.81  3.000
 R1F  H8   CE   SD   102.94  3.000
 R1F  C3   CE   SD   117.84  3.000
 R1F  C4   C3   C2   112.23  3.000
 R1F  C4   C3   CE   130.17  3.000
 R1F  C2   C3   CE   117.49  3.000
 R1F  N1   C2   C8   109.96  3.000
 R1F  C8   C2   C9   110.71  3.000
 R1F  N1   C2   C9   110.19  3.000
 R1F  C8   C2   C3   113.00  3.000
 R1F  C9   C2   C3   112.13  3.000
 R1F  N1   C2   C3   100.40  3.000
 R1F  H12  C9   H11  108.12  3.000
 R1F  H12  C9   H10  107.50  3.000
 R1F  H11  C9   H10  108.56  3.000
 R1F  H12  C9   C2   110.68  3.000
 R1F  H11  C9   C2   111.30  3.000
 R1F  H10  C9   C2   110.56  3.000
 R1F  H15  C8   H14  107.42  3.000
 R1F  H15  C8   H13  108.22  3.000
 R1F  H14  C8   H13  108.81  3.000
 R1F  H15  C8   C2   110.97  3.000
 R1F  H14  C8   C2   110.16  3.000
 R1F  H13  C8   C2   111.15  3.000
 R1F  C5   N1   O1   122.67  3.000
 R1F  C5   N1   C2   114.78  3.000
 R1F  O1   N1   C2   122.49  3.000
 R1F  C10  C4   C5   120.21  3.000
 R1F  C10  C4   C3   127.68  3.000
 R1F  C5   C4   C3   112.06  3.000
 R1F  C7   C5   C6   110.40  3.000
 R1F  C7   C5   C4   112.84  3.000
 R1F  C6   C5   C4   112.12  3.000
 R1F  C4   C5   N1   100.42  3.000
 R1F  C7   C5   N1   110.28  3.000
 R1F  C6   C5   N1   110.39  3.000
 R1F  H19  C6   H18  108.23  3.000
 R1F  H19  C6   H17  108.57  3.000
 R1F  H18  C6   H17  107.91  3.000
 R1F  H19  C6   C5   111.43  3.000
 R1F  H18  C6   C5   110.17  3.000
 R1F  H17  C6   C5   110.43  3.000
 R1F  H22  C7   H21  107.66  3.000
 R1F  H22  C7   H20  108.66  3.000
 R1F  H21  C7   H20  108.37  3.000
 R1F  H22  C7   C5   110.34  3.000
 R1F  H21  C7   C5   110.41  3.000
 R1F  H20  C7   C5   111.30  3.000
 R1F  C15  C10  C11  119.03  3.000
 R1F  C15  C10  C4   119.59  3.000
 R1F  C11  C10  C4   121.38  3.000
 R1F  H23  C11  C12  119.84  3.000
 R1F  H23  C11  C10  119.71  3.000
 R1F  C12  C11  C10  120.41  3.000
 R1F  H24  C12  C13  120.05  3.000
 R1F  H24  C12  C11  119.71  3.000
 R1F  C13  C12  C11  120.24  3.000
 R1F  H25  C13  C14  120.18  3.000
 R1F  H25  C13  C12  120.14  3.000
 R1F  C14  C13  C12  119.68  3.000
 R1F  H26  C14  C15  119.83  3.000
 R1F  H26  C14  C13  120.12  3.000
 R1F  C15  C14  C13  120.05  3.000
 R1F  H27  C15  C14  119.95  3.000
 R1F  H27  C15  C10  119.46  3.000
 R1F  C14  C15  C10  120.59  3.000
 R1F  O3   S1   O2   119.92  3.000
 R1F  O3   S1   C16  108.09  3.000
 R1F  O2   S1   C16  109.02  3.000
 R1F  O3   S1   SD   110.61  3.000
 R1F  O2   S1   SD   103.61  3.000
 R1F  C16  S1   SD   104.53  3.000
 R1F  H3   C16  H2   109.73  3.000
 R1F  H3   C16  H1   110.62  3.000
 R1F  H2   C16  H1   110.49  3.000
 R1F  H3   C16  S1   109.67  3.000
 R1F  H2   C16  S1   107.10  3.000
 R1F  H1   C16  S1   109.16  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
 R1F  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 R1F  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 R1F  CONST_03  C14  C15  C10  C11     0.00   0.0  0
 R1F  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 R1F  CONST_05  C15  C10  C11  C12     0.00   0.0  0
 R1F  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 R1F  CONST_07  C12  C11  C10  C4    180.00   0.0  0
 R1F  CONST_08  C14  C15  C10  C4    180.00   0.0  0
 R1F  CONST_09  H23  C11  C10  C4      0.00   0.0  0
 R1F  CONST_10  H27  C15  C10  C4      0.00   0.0  0
 R1F  CONST_11  H24  C12  C11  C10   180.00   0.0  0
 R1F  CONST_12  H26  C14  C15  C10   180.00   0.0  0
 R1F  CONST_13  H25  C13  C12  C11   180.00   0.0  0
 R1F  Var_01    C5   N1   C2   C3     -3.25  30.0  1
 R1F  Var_02    N1   C5   C4   C3     -2.38  30.0  1
 R1F  Var_03    C11  C10  C4   C3   -100.75  30.0  2
 R1F  Var_04    C4   C5   N1   C2      3.52  30.0  1
 R1F  Var_05    C5   C4   C3   C2      0.54  30.0  1
 R1F  Var_06    C4   C3   C2   N1      1.55  30.0  1
 R1F  Var_07    C2   C3   CE   SD   -156.17  30.0  1
 R1F  Var_08    H10  C9   C2   C3   -172.73  30.0  3
 R1F  Var_09    H13  C8   C2   C3     53.76  30.0  3
 R1F  Var_10    H17  C6   C5   N1     62.06  30.0  3
 R1F  Var_11    H20  C7   C5   N1     57.62  30.0  3
 R1F  Var_12    C16  S1   SD   CE     78.31  30.0  3
 R1F  Var_13    H1   C16  S1   SD     58.12  30.0  3

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
 R1F  plan-1  C4   0.020
 R1F  plan-1  C10  0.020
 R1F  plan-1  C11  0.020
 R1F  plan-1  C12  0.020
 R1F  plan-1  C13  0.020
 R1F  plan-1  C14  0.020
 R1F  plan-1  C15  0.020
 R1F  plan-1  H23  0.020
 R1F  plan-1  H24  0.020
 R1F  plan-1  H25  0.020
 R1F  plan-1  H26  0.020
 R1F  plan-1  H27  0.020

