# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 10:09:08 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (5R)-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
 RGZ  RGZ  (5R)-5-(4-{2-[methyl(pyridin-2-yl)amino]ethoxy}benzyl)-1,3-thiazolidine-2,4-dione  ligand  44  25  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RGZ
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
 RGZ  N16   N  NT    0  -0.481   4.8830   1.3780  -0.1753
 RGZ  C16   C  CH3   0  -0.554   5.0350   1.7968  -1.5484
 RGZ  C15   C  CH2   0  -0.355   4.0447   2.2046   0.6640
 RGZ  C14   C  CH2   0  -0.191   2.5831   2.1852   0.2559
 RGZ  O13   O  O2    0  -0.460   2.1257   0.8498   0.3283
 RGZ  C10   C  CR6   0   0.386   0.8817   0.5586  -0.0908
 RGZ  C9    C  CR16  0  -0.332   0.5351  -0.7955  -0.0993
 RGZ  C8    C  CR16  0  -0.279  -0.7241  -1.1880  -0.5082
 RGZ  C11   C  CR16  0  -0.372  -0.0548   1.5015  -0.5032
 RGZ  C12   C  CR16  0  -0.284  -1.3183   1.0858  -0.9141
 RGZ  C7    C  CR6   0   0.085  -1.6755  -0.2551  -0.9251
 RGZ  C6    C  CH2   0  -0.497  -3.0541  -0.6938  -1.3299
 RGZ  C5    C  CR15  0  -0.551  -3.9250  -1.0074  -0.1110
 RGZ  S1    S  S2    0   0.085  -4.1388   0.4374   0.9717
 RGZ  C2    C  CR5   0   0.403  -5.8988   0.3565   0.8788
 RGZ  O2    O  O     0  -0.401  -6.6438   1.1112   1.4409
 RGZ  N3    N  NR15  0  -0.658  -6.2812  -0.6877   0.0714
 RGZ  C4    C  CR5   0   0.622  -5.3166  -1.4607  -0.5095
 RGZ  O4    O  O     0  -0.411  -5.5357  -2.3846  -1.2513
 RGZ  C21   C  CR16  0  -0.149   6.0045  -2.1046  -0.3310
 RGZ  C20   C  CR16  0  -0.372   5.8164  -2.4604   1.0007
 RGZ  C19   C  CR16  0  -0.064   5.3058  -1.4869   1.8404
 RGZ  N18   N  N     0  -0.472   4.9966  -0.2575   1.4553
 RGZ  C22   C  CR16  0  -0.415   5.6863  -0.8324  -0.7582
 RGZ  C17   C  CR6   0   0.556   5.1754   0.0897   0.1795
 RGZ  H22   H  HCR6  0   0.268   5.8198  -0.5704  -1.7973
 RGZ  H19   H  HCR6  0   0.250   5.1367  -1.7086   2.8895
 RGZ  H20   H  HCR6  0   0.255   6.0529  -3.4482   1.3694
 RGZ  H161  H  HCH3  0   0.250   6.0482   1.6130  -1.9083
 RGZ  H162  H  HCH3  0   0.231   4.3373   1.3026  -2.2328
 RGZ  H163  H  HCH3  0   0.262   4.8605   2.8691  -1.6119
 RGZ  H151  H  HCH2  0   0.270   4.1510   1.8870   1.6980
 RGZ  H152  H  HCH2  0   0.255   4.3887   3.2401   0.6049
 RGZ  H141  H  HCH2  0   0.235   2.0139   2.8384   0.9276
 RGZ  H142  H  HCH2  0   0.225   2.4637   2.5749  -0.7619
 RGZ  H9    H  HCR6  0   0.260   1.2654  -1.5321   0.2126
 RGZ  H11   H  HCR6  0   0.277   0.1708   2.5593  -0.5091
 RGZ  H8    H  HCR6  0   0.254  -0.9696  -2.2442  -0.5107
 RGZ  H12   H  HCR6  0   0.255  -2.0346   1.8340  -1.2323
 RGZ  H61C  H  HCH2  0   0.278  -3.5380   0.0764  -1.9333
 RGZ  H62C  H  HCH2  0   0.282  -3.0008  -1.5986  -1.9394
 RGZ  H5    H  HCR5  0   0.353  -3.4676  -1.8096   0.4735
 RGZ  H3    H  HNR5  0   0.440  -7.2652  -0.8602  -0.0993
 RGZ  H21   H  HCR6  0   0.263   6.3933  -2.8226  -1.0424

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
 RGZ  N16  C16   single    1.444  0.020  1.444
 RGZ  N16  C15   single    1.446  0.020  1.446
 RGZ  N16  C17   single    1.368  0.020  1.368
 RGZ  C15  C14   single    1.518  0.020  1.518
 RGZ  C14  O13   single    1.413  0.020  1.413
 RGZ  O13  C10   single    1.345  0.020  1.345
 RGZ  C10  C9    aromatic  1.398  0.020  1.398
 RGZ  C10  C11   aromatic  1.392  0.020  1.392
 RGZ  C9   C8    aromatic  1.381  0.020  1.381
 RGZ  C8   C7    aromatic  1.396  0.020  1.396
 RGZ  C11  C12   aromatic  1.392  0.020  1.392
 RGZ  C12  C7    aromatic  1.388  0.020  1.388
 RGZ  C7   C6    single    1.502  0.020  1.502
 RGZ  C6   C5    single    1.531  0.020  1.531
 RGZ  C5   S1    single    1.818  0.020  1.818
 RGZ  C5   C4    single    1.517  0.020  1.517
 RGZ  S1   C2    single    1.764  0.020  1.764
 RGZ  C2   O2    double    1.200  0.020  1.200
 RGZ  C2   N3    single    1.374  0.020  1.374
 RGZ  N3   C4    single    1.366  0.020  1.366
 RGZ  C4   O4    double    1.205  0.020  1.205
 RGZ  C21  C20   aromatic  1.391  0.020  1.391
 RGZ  C21  C22   aromatic  1.379  0.020  1.379
 RGZ  C20  C19   aromatic  1.383  0.020  1.383
 RGZ  C19  N18   aromatic  1.325  0.020  1.325
 RGZ  N18  C17   aromatic  1.334  0.020  1.334
 RGZ  C22  C17   aromatic  1.411  0.020  1.411
 RGZ  C16  H161  single    0.970  0.020  1.090
 RGZ  C16  H162  single    0.970  0.020  1.090
 RGZ  C16  H163  single    0.970  0.020  1.090
 RGZ  C15  H151  single    0.970  0.020  1.090
 RGZ  C15  H152  single    0.970  0.020  1.090
 RGZ  C14  H141  single    0.970  0.020  1.090
 RGZ  C14  H142  single    0.970  0.020  1.090
 RGZ  C9   H9    single    0.930  0.020  1.080
 RGZ  C11  H11   single    0.930  0.020  1.080
 RGZ  C8   H8    single    0.930  0.020  1.080
 RGZ  C12  H12   single    0.930  0.020  1.080
 RGZ  C6   H61C  single    0.970  0.020  1.090
 RGZ  C6   H62C  single    0.970  0.020  1.090
 RGZ  C5   H5    single    0.970  0.020  1.090
 RGZ  N3   H3    single    0.860  0.020  1.020
 RGZ  C21  H21   single    0.930  0.020  1.080
 RGZ  C22  H22   single    0.930  0.020  1.080
 RGZ  C19  H19   single    0.930  0.020  1.080
 RGZ  C20  H20   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
 RGZ  C17   N16  C15   120.78  3.000
 RGZ  C17   N16  C16   119.83  3.000
 RGZ  C15   N16  C16   116.58  3.000
 RGZ  H163  C16  H162  107.82  3.000
 RGZ  H163  C16  H161  107.20  3.000
 RGZ  H162  C16  H161  108.03  3.000
 RGZ  H163  C16  N16   108.93  3.000
 RGZ  H162  C16  N16   113.36  3.000
 RGZ  H161  C16  N16   111.27  3.000
 RGZ  H152  C15  H151  107.31  3.000
 RGZ  H152  C15  C14   107.50  3.000
 RGZ  H151  C15  C14   110.26  3.000
 RGZ  H152  C15  N16   109.14  3.000
 RGZ  H151  C15  N16   109.17  3.000
 RGZ  C14   C15  N16   113.27  3.000
 RGZ  H142  C14  H141  107.48  3.000
 RGZ  H142  C14  O13   110.37  3.000
 RGZ  H141  C14  O13   111.31  3.000
 RGZ  H142  C14  C15   110.49  3.000
 RGZ  H141  C14  C15   109.13  3.000
 RGZ  O13   C14  C15   108.06  3.000
 RGZ  C10   O13  C14   119.22  3.000
 RGZ  C11   C10  C9    119.20  3.000
 RGZ  C11   C10  O13   124.63  3.000
 RGZ  C9    C10  O13   116.18  3.000
 RGZ  H9    C9   C8    120.45  3.000
 RGZ  H9    C9   C10   119.33  3.000
 RGZ  C8    C9   C10   120.22  3.000
 RGZ  H8    C8   C7    119.73  3.000
 RGZ  H8    C8   C9    118.95  3.000
 RGZ  C7    C8   C9    121.32  3.000
 RGZ  H11   C11  C12   118.67  3.000
 RGZ  H11   C11  C10   121.59  3.000
 RGZ  C12   C11  C10   119.73  3.000
 RGZ  H12   C12  C7    119.65  3.000
 RGZ  H12   C12  C11   118.71  3.000
 RGZ  C7    C12  C11   121.64  3.000
 RGZ  C6    C7   C12   121.37  3.000
 RGZ  C6    C7   C8    120.71  3.000
 RGZ  C12   C7   C8    117.90  3.000
 RGZ  H62C  C6   H61C  107.32  3.000
 RGZ  H62C  C6   C5    107.61  3.000
 RGZ  H61C  C6   C5    109.42  3.000
 RGZ  H62C  C6   C7    110.34  3.000
 RGZ  H61C  C6   C7    110.47  3.000
 RGZ  C5    C6   C7    111.55  3.000
 RGZ  H5    C5   C4    107.76  3.000
 RGZ  H5    C5   S1    108.30  3.000
 RGZ  C4    C5   S1    106.62  3.000
 RGZ  H5    C5   C6    109.77  3.000
 RGZ  C4    C5   C6    111.97  3.000
 RGZ  S1    C5   C6    112.24  3.000
 RGZ  C2    S1   C5     92.84  3.000
 RGZ  N3    C2   O2    125.47  3.000
 RGZ  N3    C2   S1    110.08  3.000
 RGZ  O2    C2   S1    124.45  3.000
 RGZ  H3    N3   C4    121.18  3.000
 RGZ  H3    N3   C2    119.90  3.000
 RGZ  C4    N3   C2    118.91  3.000
 RGZ  O4    C4   N3    124.57  3.000
 RGZ  O4    C4   C5    123.89  3.000
 RGZ  N3    C4   C5    111.54  3.000
 RGZ  H21   C21  C22   119.40  3.000
 RGZ  H21   C21  C20   120.52  3.000
 RGZ  C22   C21  C20   120.08  3.000
 RGZ  H20   C20  C19   121.13  3.000
 RGZ  H20   C20  C21   122.06  3.000
 RGZ  C19   C20  C21   116.81  3.000
 RGZ  H19   C19  N18   115.72  3.000
 RGZ  H19   C19  C20   120.03  3.000
 RGZ  N18   C19  C20   124.25  3.000
 RGZ  C17   N18  C19   119.21  3.000
 RGZ  H22   C22  C17   121.72  3.000
 RGZ  H22   C22  C21   119.55  3.000
 RGZ  C17   C22  C21   118.72  3.000
 RGZ  C22   C17  N18   120.93  3.000
 RGZ  C22   C17  N16   121.37  3.000
 RGZ  N18   C17  N16   117.67  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
 RGZ  CONST_01  C7    C8   C9   C10    0.00   0.0  0
 RGZ  CONST_02  C7    C12  C11  C10    0.00   0.0  0
 RGZ  CONST_03  C12   C11  C10  C9     0.00   0.0  0
 RGZ  CONST_04  C12   C7   C8   C9     0.00   0.0  0
 RGZ  CONST_05  C11   C10  C9   C8     0.00   0.0  0
 RGZ  CONST_06  C11   C12  C7   C8     0.00   0.0  0
 RGZ  CONST_07  N18   C19  C20  C21    0.00   0.0  0
 RGZ  CONST_08  N18   C17  C22  C21    0.00   0.0  0
 RGZ  CONST_09  C17   C22  C21  C20    0.00   0.0  0
 RGZ  CONST_10  C17   N18  C19  C20    0.00   0.0  0
 RGZ  CONST_11  C22   C21  C20  C19    0.00   0.0  0
 RGZ  CONST_12  C22   C17  N18  C19    0.00   0.0  0
 RGZ  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 RGZ  CONST_14  C19   N18  C17  N16  180.00   0.0  0
 RGZ  CONST_15  C21   C22  C17  N16  180.00   0.0  0
 RGZ  CONST_16  C8    C9   C10  O13  180.00   0.0  0
 RGZ  CONST_17  C12   C11  C10  O13  180.00   0.0  0
 RGZ  CONST_18  C6    C7   C8   C9   180.00   0.0  0
 RGZ  CONST_19  C6    C7   C12  C11  180.00   0.0  0
 RGZ  CONST_20  O4    C4   N3   C2   180.00   0.0  0
 RGZ  CONST_21  H8    C8   C9   C10  180.00   0.0  0
 RGZ  CONST_22  H12   C12  C11  C10  180.00   0.0  0
 RGZ  CONST_23  H11   C11  C10  C9   180.00   0.0  0
 RGZ  CONST_24  H9    C9   C10  C11  180.00   0.0  0
 RGZ  CONST_25  H19   C19  C20  C21  180.00   0.0  0
 RGZ  CONST_26  H22   C22  C21  C20  180.00   0.0  0
 RGZ  CONST_27  H21   C21  C20  C19  180.00   0.0  0
 RGZ  CONST_28  H20   C20  C19  N18  180.00   0.0  0
 RGZ  CONST_29  H3    N3   C4   C5   180.00   0.0  0
 RGZ  CONST_30  N18   C17  N16  C16  180.00   0.0  0
 RGZ  CONST_31  C22   C17  N16  C16    0.00   0.0  0
 RGZ  Var_01    N3    C2   S1   C5    -0.53  30.0  1
 RGZ  Var_02    C4    N3   C2   S1    -0.20  30.0  1
 RGZ  Var_03    C5    C6   C7   C8    77.40  30.0  2
 RGZ  Var_04    C9    C10  O13  C14  174.67  30.0  2
 RGZ  Var_05    C17   N16  C15  C14  -94.46  30.0  2
 RGZ  Var_06    H141  C14  O13  C10   65.45  30.0  1
 RGZ  Var_07    H161  C16  N16  C17  -56.00  30.0  3
 RGZ  Var_08    O13   C14  C15  N16   59.36  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
 RGZ  chir_01  C5  C6  S1  C4  negativ

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
 RGZ  plan-1  O13  0.020
 RGZ  plan-1  C10  0.020
 RGZ  plan-1  C9   0.020
 RGZ  plan-1  C8   0.020
 RGZ  plan-1  C11  0.020
 RGZ  plan-1  C12  0.020
 RGZ  plan-1  C7   0.020
 RGZ  plan-1  C6   0.020
 RGZ  plan-1  H9   0.020
 RGZ  plan-1  H11  0.020
 RGZ  plan-1  H8   0.020
 RGZ  plan-1  H12  0.020
 RGZ  plan-2  N16  0.020
 RGZ  plan-2  C21  0.020
 RGZ  plan-2  C20  0.020
 RGZ  plan-2  C19  0.020
 RGZ  plan-2  N18  0.020
 RGZ  plan-2  C22  0.020
 RGZ  plan-2  C17  0.020
 RGZ  plan-2  H22  0.020
 RGZ  plan-2  H19  0.020
 RGZ  plan-2  H20  0.020
 RGZ  plan-2  H21  0.020
 RGZ  plan-3  N16  0.020
 RGZ  plan-3  C16  0.020
 RGZ  plan-3  C15  0.020
 RGZ  plan-3  C17  0.020
 RGZ  plan-4  C5   0.020
 RGZ  plan-4  C2   0.020
 RGZ  plan-4  N3   0.020
 RGZ  plan-4  C4   0.020
 RGZ  plan-4  O4   0.020
 RGZ  plan-4  H3   0.020
 RGZ  plan-5  S1   0.020
 RGZ  plan-5  C2   0.020
 RGZ  plan-5  O2   0.020
 RGZ  plan-5  N3   0.020

