# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 09:45:23 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (5S)-5-(4-{2-[methyl(pyridin-2-yl)amino]ethoxy}benzyl)-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCOc1ccc(C[C@@H]2SC(=O)NC2=O)cc1)c3ccccn3
#
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
 BRL  BRL  (5S)-5-(4-{2-[methyl(pyridin-2-yl)amino]ethoxy}benzyl)-1,3-thiazolidine-2,4-dione  ligand  44  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BRL
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
 BRL  S1    S  S2    0   0.086  -0.8880  -0.8182   3.8734
 BRL  O2    O  O     0  -0.401  -2.4800  -0.9242   5.9711
 BRL  O4    O  O     0  -0.410   1.5278   1.2280   6.0734
 BRL  O13   O  O2    0  -0.458   0.7052  -0.7099  -2.1617
 BRL  N3    N  NR15  0  -0.658  -0.4992   0.1986   6.2145
 BRL  N16   N  NT    0  -0.481   1.0619  -0.4532  -4.9788
 BRL  N18   N  N     0  -0.469  -1.1745  -1.0157  -4.8188
 BRL  C2    C  CR5   0   0.403  -1.4363  -0.5331   5.5256
 BRL  C4    C  CR5   0   0.621   0.6468   0.5760   5.5729
 BRL  C5    C  CR15  0  -0.552   0.6686   0.0833   4.1385
 BRL  C6    C  CH2   0  -0.498   0.8436   1.2350   3.1446
 BRL  C7    C  CR6   0   0.086   0.8379   0.7425   1.7250
 BRL  C8    C  CR16  0  -0.280  -0.2897   0.8771   0.9164
 BRL  C9    C  CR16  0  -0.335  -0.3072   0.3891  -0.3777
 BRL  C10   C  CR6   0   0.387   0.8129  -0.2598  -0.8996
 BRL  C11   C  CR16  0  -0.370   1.9478  -0.4036  -0.1038
 BRL  C12   C  CR16  0  -0.282   1.9469   0.0973   1.1917
 BRL  C14   C  CH2   0  -0.192   1.8248  -1.3063  -2.7843
 BRL  C15   C  CH2   0  -0.357   1.4455  -1.6225  -4.2201
 BRL  C16   C  CH3   0  -0.555   2.0990   0.5157  -5.2416
 BRL  C17   C  CR6   0   0.556  -0.2525  -0.0897  -5.0865
 BRL  C19   C  CR16  0  -0.062  -2.4561  -0.7077  -4.9501
 BRL  C20   C  CR16  0  -0.372  -2.9221   0.5293  -5.3579
 BRL  C21   C  CR16  0  -0.149  -1.9651   1.4990  -5.6385
 BRL  C22   C  CR16  0  -0.416  -0.6240   1.2052  -5.5051
 BRL  HN3   H  HNR5  0   0.440  -0.6687   0.4559   7.1802
 BRL  H5    H  HCR5  0   0.353   1.4970  -0.6223   4.0378
 BRL  H61   H  HCH2  0   0.282   1.7919   1.7257   3.3731
 BRL  H62   H  HCH2  0   0.277   0.0508   1.9695   3.2980
 BRL  H8    H  HCR6  0   0.252  -1.1707   1.3763   1.3020
 BRL  H9    H  HCR6  0   0.261  -1.1882   0.5058  -0.9966
 BRL  H11   H  HCR6  0   0.276   2.8363  -0.9001  -0.4694
 BRL  H12   H  HCR6  0   0.255   2.8400  -0.0227   1.7950
 BRL  H141  H  HCH2  0   0.235   2.1144  -2.2341  -2.2773
 BRL  H142  H  HCH2  0   0.225   2.6884  -0.6307  -2.7531
 BRL  H151  H  HCH2  0   0.272   0.6327  -2.3439  -4.2427
 BRL  H152  H  HCH2  0   0.255   2.3111  -2.0901  -4.6958
 BRL  H161  H  HCH3  0   0.262   3.0648   0.0153  -5.2094
 BRL  H162  H  HCH3  0   0.250   1.9947   0.9480  -6.2376
 BRL  H163  H  HCH3  0   0.231   2.1211   1.3369  -4.5174
 BRL  H19   H  HCR6  0   0.249  -3.1585  -1.5020  -4.7168
 BRL  H20   H  HCR6  0   0.254  -3.9810   0.7251  -5.4475
 BRL  H21   H  HCR6  0   0.262  -2.2635   2.4900  -5.9565
 BRL  H22   H  HCR6  0   0.267   0.1126   1.9687  -5.7070

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
 BRL  S1   C2    single    1.764  0.020  1.764
 BRL  S1   C5    single    1.818  0.020  1.818
 BRL  O2   C2    double    1.200  0.020  1.200
 BRL  O4   C4    double    1.205  0.020  1.205
 BRL  O13  C10   single    1.344  0.020  1.344
 BRL  O13  C14   single    1.413  0.020  1.413
 BRL  N3   C2    single    1.374  0.020  1.374
 BRL  N3   C4    single    1.366  0.020  1.366
 BRL  N3   HN3   single    0.860  0.020  1.020
 BRL  N16  C15   single    1.446  0.020  1.446
 BRL  N16  C16   single    1.443  0.020  1.443
 BRL  N16  C17   single    1.368  0.020  1.368
 BRL  N18  C17   aromatic  1.334  0.020  1.334
 BRL  N18  C19   aromatic  1.325  0.020  1.325
 BRL  C4   C5    single    1.517  0.020  1.517
 BRL  C5   C6    single    1.531  0.020  1.531
 BRL  C5   H5    single    0.970  0.020  1.090
 BRL  C6   C7    single    1.503  0.020  1.503
 BRL  C6   H61   single    0.970  0.020  1.090
 BRL  C6   H62   single    0.970  0.020  1.090
 BRL  C7   C8    aromatic  1.394  0.020  1.394
 BRL  C7   C12   aromatic  1.389  0.020  1.389
 BRL  C8   C9    aromatic  1.383  0.020  1.383
 BRL  C8   H8    single    0.930  0.020  1.080
 BRL  C9   C10   aromatic  1.396  0.020  1.396
 BRL  C9   H9    single    0.930  0.020  1.080
 BRL  C10  C11   aromatic  1.394  0.020  1.394
 BRL  C11  C12   aromatic  1.389  0.020  1.389
 BRL  C11  H11   single    0.930  0.020  1.080
 BRL  C12  H12   single    0.930  0.020  1.080
 BRL  C14  C15   single    1.518  0.020  1.518
 BRL  C14  H141  single    0.970  0.020  1.090
 BRL  C14  H142  single    0.970  0.020  1.090
 BRL  C15  H151  single    0.970  0.020  1.090
 BRL  C15  H152  single    0.970  0.020  1.090
 BRL  C16  H161  single    0.970  0.020  1.090
 BRL  C16  H162  single    0.970  0.020  1.090
 BRL  C16  H163  single    0.970  0.020  1.090
 BRL  C17  C22   aromatic  1.411  0.020  1.411
 BRL  C19  C20   aromatic  1.383  0.020  1.383
 BRL  C19  H19   single    0.930  0.020  1.080
 BRL  C20  C21   aromatic  1.391  0.020  1.391
 BRL  C20  H20   single    0.930  0.020  1.080
 BRL  C21  C22   aromatic  1.379  0.020  1.379
 BRL  C21  H21   single    0.930  0.020  1.080
 BRL  C22  H22   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
 BRL  C5    S1   C2     92.83  3.000
 BRL  C14   O13  C10   119.44  3.000
 BRL  HN3   N3   C4    121.16  3.000
 BRL  HN3   N3   C2    119.92  3.000
 BRL  C4    N3   C2    118.91  3.000
 BRL  C17   N16  C16   119.85  3.000
 BRL  C17   N16  C15   120.74  3.000
 BRL  C16   N16  C15   116.60  3.000
 BRL  C19   N18  C17   119.17  3.000
 BRL  N3    C2   O2    125.48  3.000
 BRL  N3    C2   S1    110.10  3.000
 BRL  O2    C2   S1    124.42  3.000
 BRL  C5    C4   N3    111.50  3.000
 BRL  C5    C4   O4    123.92  3.000
 BRL  N3    C4   O4    124.58  3.000
 BRL  H5    C5   C6    109.83  3.000
 BRL  H5    C5   C4    107.93  3.000
 BRL  C6    C5   C4    111.78  3.000
 BRL  H5    C5   S1    108.39  3.000
 BRL  C6    C5   S1    112.09  3.000
 BRL  C4    C5   S1    106.65  3.000
 BRL  H62   C6   H61   107.40  3.000
 BRL  H62   C6   C7    110.52  3.000
 BRL  H61   C6   C7    110.38  3.000
 BRL  H62   C6   C5    109.38  3.000
 BRL  H61   C6   C5    107.55  3.000
 BRL  C7    C6   C5    111.48  3.000
 BRL  C12   C7   C8    117.89  3.000
 BRL  C12   C7   C6    120.78  3.000
 BRL  C8    C7   C6    121.29  3.000
 BRL  H8    C8   C9    119.02  3.000
 BRL  H8    C8   C7    119.72  3.000
 BRL  C9    C8   C7    121.26  3.000
 BRL  H9    C9   C10   119.29  3.000
 BRL  H9    C9   C8    120.46  3.000
 BRL  C10   C9   C8    120.25  3.000
 BRL  C11   C10  C9    119.21  3.000
 BRL  C11   C10  O13   124.53  3.000
 BRL  C9    C10  O13   116.26  3.000
 BRL  H11   C11  C12   118.78  3.000
 BRL  H11   C11  C10   121.56  3.000
 BRL  C12   C11  C10   119.66  3.000
 BRL  H12   C12  C11   118.58  3.000
 BRL  H12   C12  C7    119.68  3.000
 BRL  C11   C12  C7    121.74  3.000
 BRL  H142  C14  H141  107.46  3.000
 BRL  H142  C14  C15   110.60  3.000
 BRL  H141  C14  C15   109.09  3.000
 BRL  H142  C14  O13   110.58  3.000
 BRL  H141  C14  O13   111.27  3.000
 BRL  C15   C14  O13   107.86  3.000
 BRL  H152  C15  H151  107.41  3.000
 BRL  H152  C15  C14   107.63  3.000
 BRL  H151  C15  C14   110.17  3.000
 BRL  H152  C15  N16   109.13  3.000
 BRL  H151  C15  N16   109.11  3.000
 BRL  C14   C15  N16   113.21  3.000
 BRL  H163  C16  H162  107.97  3.000
 BRL  H163  C16  H161  107.90  3.000
 BRL  H162  C16  H161  107.11  3.000
 BRL  H163  C16  N16   113.42  3.000
 BRL  H162  C16  N16   111.32  3.000
 BRL  H161  C16  N16   108.89  3.000
 BRL  C22   C17  N18   120.98  3.000
 BRL  C22   C17  N16   121.36  3.000
 BRL  N18   C17  N16   117.64  3.000
 BRL  H19   C19  C20   119.98  3.000
 BRL  H19   C19  N18   115.76  3.000
 BRL  C20   C19  N18   124.27  3.000
 BRL  H20   C20  C21   122.08  3.000
 BRL  H20   C20  C19   121.10  3.000
 BRL  C21   C20  C19   116.82  3.000
 BRL  H21   C21  C22   119.43  3.000
 BRL  H21   C21  C20   120.52  3.000
 BRL  C22   C21  C20   120.06  3.000
 BRL  H22   C22  C21   119.64  3.000
 BRL  H22   C22  C17   121.65  3.000
 BRL  C21   C22  C17   118.70  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
 BRL  CONST_01  C21   C22  C17  N18     0.00   0.0  0
 BRL  CONST_02  C21   C20  C19  N18     0.00   0.0  0
 BRL  CONST_03  C10   C9   C8   C7      0.00   0.0  0
 BRL  CONST_04  C10   C11  C12  C7      0.00   0.0  0
 BRL  CONST_05  C11   C12  C7   C8      0.00   0.0  0
 BRL  CONST_06  C11   C10  C9   C8      0.00   0.0  0
 BRL  CONST_07  C12   C7   C8   C9      0.00   0.0  0
 BRL  CONST_08  C12   C11  C10  C9      0.00   0.0  0
 BRL  CONST_09  C20   C19  N18  C17     0.00   0.0  0
 BRL  CONST_10  C20   C21  C22  C17     0.00   0.0  0
 BRL  CONST_11  C22   C17  N18  C19     0.00   0.0  0
 BRL  CONST_12  C22   C21  C20  C19     0.00   0.0  0
 BRL  CONST_13  C5    C4   N3   C2      0.00   0.0  0
 BRL  CONST_14  C8    C9   C10  O13   180.00   0.0  0
 BRL  CONST_15  C12   C11  C10  O13   180.00   0.0  0
 BRL  CONST_16  C19   N18  C17  N16   180.00   0.0  0
 BRL  CONST_17  C21   C22  C17  N16   180.00   0.0  0
 BRL  CONST_18  C9    C8   C7   C6    180.00   0.0  0
 BRL  CONST_19  C11   C12  C7   C6    180.00   0.0  0
 BRL  CONST_20  C2    N3   C4   O4    180.00   0.0  0
 BRL  CONST_21  H22   C22  C17  N18   180.00   0.0  0
 BRL  CONST_22  H20   C20  C19  N18   180.00   0.0  0
 BRL  CONST_23  H9    C9   C8   C7    180.00   0.0  0
 BRL  CONST_24  H11   C11  C12  C7    180.00   0.0  0
 BRL  CONST_25  H12   C12  C7   C8    180.00   0.0  0
 BRL  CONST_26  H8    C8   C9   C10   180.00   0.0  0
 BRL  CONST_27  H19   C19  N18  C17   180.00   0.0  0
 BRL  CONST_28  H21   C21  C22  C17   180.00   0.0  0
 BRL  CONST_29  HN3   N3   C4   C5    180.00   0.0  0
 BRL  CONST_31  C16   N16  C17  N18   180.00   0.0  0
 BRL  CONST_33  C22   C17  N16  C16     0.00   0.0  0
 BRL  Var_01    C4    N3   C2   S1     -0.10  30.0  1
 BRL  Var_02    C8    C7   C6   C5    102.08  30.0  2
 BRL  Var_03    C15   C14  O13  C10  -175.95  30.0  3
 BRL  Var_04    C17   N16  C15  C14   -94.19  30.0  2
 BRL  Var_05    H161  C16  N16  C17  -174.00  30.0  3
 BRL  Var_06    N16   C15  C14  O13    59.72  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
 BRL  chir_01  C5  S1  C4  C6  positiv

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
 BRL  plan-1  N16  0.020
 BRL  plan-1  N18  0.020
 BRL  plan-1  C17  0.020
 BRL  plan-1  C19  0.020
 BRL  plan-1  C20  0.020
 BRL  plan-1  C21  0.020
 BRL  plan-1  C22  0.020
 BRL  plan-1  H19  0.020
 BRL  plan-1  H20  0.020
 BRL  plan-1  H21  0.020
 BRL  plan-1  H22  0.020
 BRL  plan-2  O13  0.020
 BRL  plan-2  C6   0.020
 BRL  plan-2  C7   0.020
 BRL  plan-2  C8   0.020
 BRL  plan-2  C9   0.020
 BRL  plan-2  C10  0.020
 BRL  plan-2  C11  0.020
 BRL  plan-2  C12  0.020
 BRL  plan-2  H8   0.020
 BRL  plan-2  H9   0.020
 BRL  plan-2  H11  0.020
 BRL  plan-2  H12  0.020
 BRL  plan-3  N16  0.020
 BRL  plan-3  C15  0.020
 BRL  plan-3  C16  0.020
 BRL  plan-3  C17  0.020
 BRL  plan-4  O4   0.020
 BRL  plan-4  N3   0.020
 BRL  plan-4  C2   0.020
 BRL  plan-4  C4   0.020
 BRL  plan-4  C5   0.020
 BRL  plan-4  HN3  0.020
 BRL  plan-5  S1   0.020
 BRL  plan-5  O2   0.020
 BRL  plan-5  N3   0.020
 BRL  plan-5  C2   0.020

