# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 10:02:45 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 2-[2-methyl-4-[[4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-selenazol-5-yl]methylsulfanyl]phenoxy]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(SCc2[se]c(nc2C)c3ccc(cc3)C(F)(F)F)ccc1OCC(O)=O
#
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
 8RR  8RR  '2-[2-methyl-4-[[4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-selenazol-5-yl]methylsulfanyl]phenoxy]ethanoic acid'  ligand  47  30  .  2022-07-24  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_8RR
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
 8RR  C13  C   CR5    0  -0.238    0.2767  -0.5188  -0.0707
 8RR  C17  C   CR16   0  -0.218   -4.3795  -0.8580   1.1573
 8RR  C21  C   CH2    0  -0.334   -8.4721  -0.8489   0.2151
 8RR  C22  C   C      0   0.441   -9.9218  -0.5757  -0.2190
 8RR  C26  C   CH3    0  -0.687   -6.2749   2.5935  -0.5629
 8RR  C05  C   CR6    0  -0.200    6.9897   0.2331   0.2558
 8RR  C06  C   CR16   0  -0.235    6.1543   1.2103  -0.2682
 8RR  C07  C   CR16   0  -0.281    4.7848   1.0068  -0.3002
 8RR  C08  C   CR6    0   0.116    4.2269  -0.1724   0.1901
 8RR  C09  C   CR5    0   0.009    2.7850  -0.4251   0.1699
 8RR  C11  C   CR5    0   0.312    0.8979  -1.5729   0.5352
 8RR  C12  C   CH3    0  -0.693    0.2073  -2.7734   1.0930
 8RR  C14  C   CH2    0  -0.609   -1.1823  -0.3249  -0.2715
 8RR  C16  C   CR6    0  -0.147   -3.6293   0.2788   0.8971
 8RR  C18  C   CR16   0  -0.351   -5.7356  -0.8902   0.8613
 8RR  C19  C   CR6    0   0.357   -6.3566   0.2255   0.3016
 8RR  C25  C   CR6    0   0.017   -5.6114   1.3896   0.0363
 8RR  C27  C   CR16   0  -0.239   -4.2607   1.3923   0.3409
 8RR  C29  C   CR16   0  -0.243    5.0779  -1.1469   0.7182
 8RR  C30  C   CR16   0  -0.228    6.4442  -0.9470   0.7521
 8RR  F01  F   F      0  -0.311    8.8344   0.8676   1.5612
 8RR  F03  F   F      0  -0.306    9.1558  -0.6672   0.0923
 8RR  F04  F   F      0  -0.306    8.8953   1.3772  -0.5274
 8RR  N10  N   N      0  -0.428    2.2564  -1.5035   0.6461
 8RR  O20  O   O2     0  -0.468   -7.6562   0.2844  -0.0147
 8RR  O23  O   O      0  -0.640  -10.2025   0.5425  -0.6718
 8RR  O24  O   OC    -1  -0.674  -10.6775  -1.5539  -0.0563
 8RR  S15  S   S2     0   0.003   -1.9049   0.3197   1.2895
 8RR  SE   SE  SE     0   0.289    1.5315   0.7599  -0.5508
 8RR  H1   H   HCR6   0   0.256   -3.9106  -1.7303   1.5943
 8RR  H2   H   HCH2   0   0.259   -8.4639  -1.1193   1.2780
 8RR  H3   H   HCH2   0   0.239   -8.0906  -1.7158  -0.3381
 8RR  H4   H   HCH3   0   0.240   -7.1094   2.9416   0.0475
 8RR  H5   H   HCH3   0   0.232   -5.5655   3.4141  -0.6596
 8RR  H6   H   HCH3   0   0.233   -6.6766   2.3811  -1.5552
 8RR  H7   H   HCR6   0   0.259    6.5510   2.1369  -0.6587
 8RR  H8   H   HCR6   0   0.225    4.1667   1.7924  -0.7177
 8RR  H9   H   HCH3   0   0.247    0.6189  -3.6877   0.6649
 8RR  H10  H   HCH3   0   0.251    0.3477  -2.8262   2.1737
 8RR  H11  H   HCH3   0   0.232   -0.8629  -2.7605   0.9006
 8RR  H12  H   HCH2   0   0.281   -1.3997   0.3732  -1.0790
 8RR  H13  H   HCH2   0   0.288   -1.6639  -1.2725  -0.5135
 8RR  H14  H   HCR6   0   0.258   -6.2927  -1.7913   1.0781
 8RR  H15  H   HCR6   0   0.233   -3.6803   2.2848   0.1381
 8RR  H16  H   HCR6   0   0.244    4.6641  -2.0682   1.1030
 8RR  H17  H   HCR6   0   0.261    7.0751  -1.7226   1.1662
 8RR  C02  C   CT     0   1.054    8.4670   0.4539   0.3384

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
 8RR  O23  C22  deloc     1.239  0.020  1.239
 8RR  O24  C22  deloc     1.247  0.020  1.247
 8RR  C22  C21  single    1.538  0.020  1.538
 8RR  C17  C18  aromatic  1.388  0.020  1.388
 8RR  C17  C16  aromatic  1.387  0.020  1.387
 8RR  C18  C19  aromatic  1.394  0.020  1.394
 8RR  C14  S15  single    1.837  0.020  1.837
 8RR  C14  C13  single    1.485  0.020  1.485
 8RR  S15  C16  single    1.769  0.020  1.769
 8RR  C16  C27  aromatic  1.396  0.020  1.396
 8RR  C12  C11  single    1.493  0.020  1.493
 8RR  C21  O20  single    1.415  0.020  1.415
 8RR  C19  O20  single    1.339  0.020  1.339
 8RR  C19  C25  aromatic  1.407  0.020  1.407
 8RR  C27  C25  aromatic  1.385  0.020  1.385
 8RR  C25  C26  single    1.500  0.020  1.500
 8RR  C13  C11  aromatic  1.365  0.020  1.365
 8RR  C13  SE   aromatic  1.855  0.020  1.855
 8RR  C11  N10  aromatic  1.365  0.020  1.365
 8RR  SE   C09  aromatic  1.869  0.020  1.869
 8RR  N10  C09  aromatic  1.292  0.020  1.292
 8RR  C09  C08  single    1.464  0.020  1.464
 8RR  C08  C29  aromatic  1.397  0.020  1.397
 8RR  C08  C07  aromatic  1.394  0.020  1.394
 8RR  C29  C30  aromatic  1.381  0.020  1.381
 8RR  C07  C06  aromatic  1.385  0.020  1.385
 8RR  C30  C05  aromatic  1.392  0.020  1.392
 8RR  C06  C05  aromatic  1.388  0.020  1.388
 8RR  C05  C02  single    1.496  0.020  1.496
 8RR  C02  F01  single    1.342  0.020  1.342
 8RR  C02  F04  single    1.336  0.020  1.336
 8RR  C02  F03  single    1.339  0.020  1.339
 8RR  C17  H1   single    0.930  0.020  1.080
 8RR  C21  H2   single    0.970  0.020  1.090
 8RR  C21  H3   single    0.970  0.020  1.090
 8RR  C26  H4   single    0.970  0.020  1.090
 8RR  C26  H5   single    0.970  0.020  1.090
 8RR  C26  H6   single    0.970  0.020  1.090
 8RR  C06  H7   single    0.930  0.020  1.080
 8RR  C07  H8   single    0.930  0.020  1.080
 8RR  C12  H9   single    0.970  0.020  1.090
 8RR  C12  H10  single    0.970  0.020  1.090
 8RR  C12  H11  single    0.970  0.020  1.090
 8RR  C14  H12  single    0.970  0.020  1.090
 8RR  C14  H13  single    0.970  0.020  1.090
 8RR  C18  H14  single    0.930  0.020  1.080
 8RR  C27  H15  single    0.930  0.020  1.080
 8RR  C29  H16  single    0.930  0.020  1.080
 8RR  C30  H17  single    0.930  0.020  1.080

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
 8RR  SE   C13  C14  122.65  3.000
 8RR  SE   C13  C11  109.83  3.000
 8RR  C14  C13  C11  127.42  3.000
 8RR  H1   C17  C18  119.37  3.000
 8RR  H1   C17  C16  120.14  3.000
 8RR  C18  C17  C16  120.49  3.000
 8RR  H3   C21  H2   106.94  3.000
 8RR  H3   C21  O20  110.51  3.000
 8RR  H2   C21  O20  110.51  3.000
 8RR  H3   C21  C22  109.02  3.000
 8RR  H2   C21  C22  108.94  3.000
 8RR  O20  C21  C22  110.82  3.000
 8RR  O24  C22  O23  128.22  3.000
 8RR  O24  C22  C21  113.28  3.000
 8RR  O23  C22  C21  118.50  3.000
 8RR  H6   C26  H5   107.80  3.000
 8RR  H6   C26  H4   106.81  3.000
 8RR  H5   C26  H4   107.91  3.000
 8RR  H6   C26  C25  111.71  3.000
 8RR  H5   C26  C25  110.62  3.000
 8RR  H4   C26  C25  111.78  3.000
 8RR  C30  C05  C06  119.71  3.000
 8RR  C06  C05  C02  120.74  3.000
 8RR  C30  C05  C02  119.51  3.000
 8RR  H7   C06  C07  118.72  3.000
 8RR  H7   C06  C05  121.26  3.000
 8RR  C07  C06  C05  120.02  3.000
 8RR  H8   C07  C08  121.38  3.000
 8RR  H8   C07  C06  117.82  3.000
 8RR  C08  C07  C06  120.80  3.000
 8RR  C29  C08  C09  118.99  3.000
 8RR  C29  C08  C07  118.63  3.000
 8RR  C09  C08  C07  122.38  3.000
 8RR  SE   C09  N10  113.38  3.000
 8RR  N10  C09  C08  122.82  3.000
 8RR  SE   C09  C08  123.80  3.000
 8RR  N10  C11  C12  118.09  3.000
 8RR  N10  C11  C13  116.72  3.000
 8RR  C12  C11  C13  125.18  3.000
 8RR  H11  C12  H10  107.61  3.000
 8RR  H11  C12  H9   108.18  3.000
 8RR  H10  C12  H9   107.44  3.000
 8RR  H11  C12  C11  112.30  3.000
 8RR  H10  C12  C11  110.45  3.000
 8RR  H9   C12  C11  110.67  3.000
 8RR  H13  C14  H12  107.72  3.000
 8RR  H13  C14  S15  108.65  3.000
 8RR  H12  C14  S15  109.06  3.000
 8RR  H13  C14  C13  110.52  3.000
 8RR  H12  C14  C13  112.32  3.000
 8RR  S15  C14  C13  108.50  3.000
 8RR  S15  C16  C27  120.73  3.000
 8RR  C27  C16  C17  118.96  3.000
 8RR  S15  C16  C17  120.31  3.000
 8RR  H14  C18  C19  121.19  3.000
 8RR  H14  C18  C17  118.67  3.000
 8RR  C19  C18  C17  120.14  3.000
 8RR  O20  C19  C25  115.66  3.000
 8RR  C25  C19  C18  120.12  3.000
 8RR  O20  C19  C18  124.23  3.000
 8RR  C27  C25  C19  118.46  3.000
 8RR  C27  C25  C26  121.20  3.000
 8RR  C19  C25  C26  120.34  3.000
 8RR  H15  C27  C25  118.87  3.000
 8RR  H15  C27  C16  119.30  3.000
 8RR  C25  C27  C16  121.83  3.000
 8RR  H16  C29  C30  119.56  3.000
 8RR  H16  C29  C08  119.72  3.000
 8RR  C30  C29  C08  120.72  3.000
 8RR  H17  C30  C29  118.84  3.000
 8RR  H17  C30  C05  121.05  3.000
 8RR  C29  C30  C05  120.11  3.000
 8RR  C11  N10  C09  114.82  3.000
 8RR  C19  O20  C21  119.08  3.000
 8RR  C16  S15  C14  100.77  3.000
 8RR  C09  SE   C13   85.23  3.000
 8RR  F04  C02  F03  107.14  3.000
 8RR  F03  C02  F01  106.55  3.000
 8RR  F04  C02  F01  106.83  3.000
 8RR  F03  C02  C05  111.99  3.000
 8RR  F04  C02  C05  112.50  3.000
 8RR  F01  C02  C05  111.48  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
 8RR  CONST_01  C09  N10  C11  C13    0.00   0.0  0
 8RR  CONST_02  N10  C09  SE   C13    0.00   0.0  0
 8RR  CONST_03  C08  C09  SE   C13  180.00   0.0  0
 8RR  CONST_04  C25  C19  C18  C17    0.00   0.0  0
 8RR  CONST_05  C25  C27  C16  C17    0.00   0.0  0
 8RR  CONST_06  C08  C29  C30  C05    0.00   0.0  0
 8RR  CONST_07  C08  C07  C06  C05    0.00   0.0  0
 8RR  CONST_08  C09  C08  C07  C06  180.00   0.0  0
 8RR  CONST_09  C29  C08  C07  C06    0.00   0.0  0
 8RR  CONST_10  C29  C30  C05  C06    0.00   0.0  0
 8RR  CONST_11  SE   C09  C08  C07    0.00   0.0  0
 8RR  CONST_12  N10  C09  C08  C07  180.00   0.0  0
 8RR  CONST_13  C30  C29  C08  C07    0.00   0.0  0
 8RR  CONST_14  C30  C05  C06  C07    0.00   0.0  0
 8RR  CONST_15  C11  N10  C09  C08  180.00   0.0  0
 8RR  CONST_16  C11  C13  SE   C09    0.00   0.0  0
 8RR  CONST_17  C30  C29  C08  C09  180.00   0.0  0
 8RR  CONST_18  SE   C09  N10  C11    0.00   0.0  0
 8RR  CONST_19  C19  C18  C17  C16    0.00   0.0  0
 8RR  CONST_20  C19  C25  C27  C16    0.00   0.0  0
 8RR  CONST_21  C27  C16  C17  C18    0.00   0.0  0
 8RR  CONST_22  C27  C25  C19  C18    0.00   0.0  0
 8RR  CONST_23  SE   C09  C08  C29  180.00   0.0  0
 8RR  CONST_24  N10  C09  C08  C29    0.00   0.0  0
 8RR  CONST_25  SE   C13  C11  N10    0.00   0.0  0
 8RR  CONST_26  O20  C19  C18  C17  180.00   0.0  0
 8RR  CONST_27  C18  C19  C25  C26  180.00   0.0  0
 8RR  CONST_28  C16  C27  C25  C26  180.00   0.0  0
 8RR  CONST_29  C29  C30  C05  C02  180.00   0.0  0
 8RR  CONST_30  C07  C06  C05  C02  180.00   0.0  0
 8RR  CONST_31  C14  C13  SE   C09  180.00   0.0  0
 8RR  CONST_32  C12  C11  N10  C09  180.00   0.0  0
 8RR  CONST_33  SE   C13  C11  C12  180.00   0.0  0
 8RR  CONST_34  N10  C11  C13  C14  180.00   0.0  0
 8RR  CONST_35  S15  C16  C17  C18  180.00   0.0  0
 8RR  CONST_36  S15  C16  C27  C25  180.00   0.0  0
 8RR  CONST_37  O20  C19  C25  C27  180.00   0.0  0
 8RR  CONST_38  H15  C27  C16  C17  180.00   0.0  0
 8RR  CONST_39  H16  C29  C30  C05  180.00   0.0  0
 8RR  CONST_40  H8   C07  C06  C05  180.00   0.0  0
 8RR  CONST_41  H17  C30  C05  C06  180.00   0.0  0
 8RR  CONST_42  H7   C06  C07  C08  180.00   0.0  0
 8RR  CONST_43  H14  C18  C17  C16  180.00   0.0  0
 8RR  CONST_44  H1   C17  C18  C19  180.00   0.0  0
 8RR  Var_01    C18  C19  O20  C21   -0.47  30.0  2
 8RR  Var_02    F01  C02  C05  C06   97.50  30.0  2
 8RR  Var_03    S15  C14  C13  C11   80.84  30.0  2
 8RR  Var_04    C27  C16  S15  C14  -91.62  30.0  2
 8RR  Var_05    H9   C12  C11  C13  125.28  30.0  2
 8RR  Var_06    H4   C26  C25  C19   57.21  30.0  2
 8RR  Var_07    H2   C21  O20  C19   59.33  30.0  1
 8RR  Var_08    O23  C22  C21  O20   -1.15  30.0  2

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
 8RR  plan-1  C13  0.020
 8RR  plan-1  C08  0.020
 8RR  plan-1  C09  0.020
 8RR  plan-1  C11  0.020
 8RR  plan-1  C12  0.020
 8RR  plan-1  C14  0.020
 8RR  plan-1  N10  0.020
 8RR  plan-1  SE   0.020
 8RR  plan-2  C17  0.020
 8RR  plan-2  C26  0.020
 8RR  plan-2  C16  0.020
 8RR  plan-2  C18  0.020
 8RR  plan-2  C19  0.020
 8RR  plan-2  C25  0.020
 8RR  plan-2  C27  0.020
 8RR  plan-2  O20  0.020
 8RR  plan-2  S15  0.020
 8RR  plan-2  H1   0.020
 8RR  plan-2  H14  0.020
 8RR  plan-2  H15  0.020
 8RR  plan-3  C05  0.020
 8RR  plan-3  C06  0.020
 8RR  plan-3  C07  0.020
 8RR  plan-3  C08  0.020
 8RR  plan-3  C09  0.020
 8RR  plan-3  C29  0.020
 8RR  plan-3  C30  0.020
 8RR  plan-3  H7   0.020
 8RR  plan-3  H8   0.020
 8RR  plan-3  H16  0.020
 8RR  plan-3  H17  0.020
 8RR  plan-3  C02  0.020
 8RR  plan-4  C21  0.020
 8RR  plan-4  C22  0.020
 8RR  plan-4  O23  0.020
 8RR  plan-4  O24  0.020

