# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 19:28:51 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (5R)-5-{4-[2-(5-ethylpyridin-2-yl)ethoxy]benzyl}-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc(CCOc2ccc(C[C@H]3SC(=O)NC3=O)cc2)nc1
#
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
 P1B  P1B  (5R)-5-{4-[2-(5-ethylpyridin-2-yl)ethoxy]benzyl}-1,3-thiazolidine-2,4-dione  ligand  45  25  .  2021-08-19  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P1B
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
 P1B  O4    O  O     0  -0.411    7.0645  -0.9974   0.8307
 P1B  C4    C  C     0   0.624    6.3717  -0.2510   0.1866
 P1B  N3    N  NH1   0  -0.659    6.7871   0.9464  -0.3242
 P1B  C5    C  CH1   0  -0.554    4.9183  -0.5251  -0.1492
 P1B  S1    S  S2    0   0.086    4.3173   0.9181  -1.0777
 P1B  C2    C  C     0   0.403    5.8876   1.7206  -1.0172
 P1B  O2    O  O     0  -0.401    6.1227   2.7899  -1.5091
 P1B  C6    C  CH2   0  -0.496    4.0827  -0.7913   1.1047
 P1B  C21   C  CR16  0  -0.189   -6.3952   1.0483  -1.0931
 P1B  C7    C  CR6   0   0.089    2.6427  -1.0499   0.7631
 P1B  C12   C  CR16  0  -0.279    2.2565  -2.2517   0.1670
 P1B  C11   C  CR16  0  -0.331    0.9418  -2.4885  -0.1830
 P1B  C10   C  CR6   0   0.375   -0.0346  -1.5177   0.0564
 P1B  C9    C  CR16  0  -0.369    0.3330  -0.3147   0.6509
 P1B  C8    C  CR16  0  -0.286    1.6636  -0.0946   0.9928
 P1B  O13   O  O2    0  -0.476   -1.2909  -1.8332  -0.3145
 P1B  C14   C  CH2   0  -0.169   -2.3250  -0.8885  -0.0999
 P1B  C15   C  CH2   0  -0.524   -3.6166  -1.4826  -0.6354
 P1B  C24   C  CH3   0  -0.654   -9.3407   1.3175   0.4135
 P1B  C20   C  CR6   0   0.035   -6.8426   1.1548   0.2185
 P1B  C19   C  CR16  0  -0.121   -6.1861   0.3715   1.1628
 P1B  N18   N  N     0  -0.416   -5.1865  -0.4540   0.8851
 P1B  C22   C  CR16  0  -0.333   -5.3490   0.1920  -1.3953
 P1B  C17   C  CR6   0   0.231   -4.7680  -0.5526  -0.3746
 P1B  H3    H  HNH1  0   0.440    7.7353   1.2761  -0.1841
 P1B  H5    H  HCH1  0   0.353    4.8864  -1.3954  -0.8096
 P1B  H61C  H  HCH2  0   0.282    4.5146  -1.6566   1.6125
 P1B  H62C  H  HCH2  0   0.278    4.1657   0.0595   1.7830
 P1B  H21   H  HCR6  0   0.262   -6.8597   1.6357  -1.8764
 P1B  H22   H  HCR6  0   0.264   -4.9861   0.1017  -2.4108
 P1B  H12   H  HCR6  0   0.254    2.9966  -3.0207  -0.0241
 P1B  H8    H  HCR6  0   0.255    1.9335   0.8474   1.4550
 P1B  H11   H  HCR6  0   0.262    0.6573  -3.4270  -0.6422
 P1B  H9    H  HCR6  0   0.279   -0.3917   0.4616   0.8544
 P1B  H141  H  HCH2  0   0.230   -2.4298  -0.6666   0.9679
 P1B  H142  H  HCH2  0   0.229   -2.0987   0.0512  -0.6164
 P1B  H151  H  HCH2  0   0.256   -3.5199  -1.6709  -1.7062
 P1B  H152  H  HCH2  0   0.259   -3.8074  -2.4403  -0.1452
 P1B  H241  H  HCH3  0   0.233  -10.1685   1.9728   0.6864
 P1B  H242  H  HCH3  0   0.227   -9.4852   1.0099  -0.6229
 P1B  H243  H  HCH3  0   0.227   -9.3990   0.4258   1.0388
 P1B  H231  H  HCH2  0   0.244   -7.9861   2.9376  -0.0112
 P1B  H232  H  HCH2  0   0.243   -7.8980   2.3484   1.6362
 P1B  H19   H  HCR6  0   0.253   -6.4915   0.4195   2.2046
 P1B  C23   C  CH2   0  -0.506   -8.0017   2.0302   0.5965

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
 P1B  O4   C4    double    1.205  0.020  1.205
 P1B  C4   N3    single    1.367  0.020  1.367
 P1B  C4   C5    single    1.517  0.020  1.517
 P1B  N3   C2    single    1.374  0.020  1.374
 P1B  C5   S1    single    1.818  0.020  1.818
 P1B  C5   C6    single    1.530  0.020  1.530
 P1B  S1   C2    single    1.764  0.020  1.764
 P1B  C2   O2    double    1.200  0.020  1.200
 P1B  C6   C7    single    1.502  0.020  1.502
 P1B  C21  C20   aromatic  1.390  0.020  1.390
 P1B  C21  C22   aromatic  1.385  0.020  1.385
 P1B  C7   C12   aromatic  1.396  0.020  1.396
 P1B  C7   C8    aromatic  1.387  0.020  1.387
 P1B  C12  C11   aromatic  1.381  0.020  1.381
 P1B  C11  C10   aromatic  1.398  0.020  1.398
 P1B  C10  C9    aromatic  1.391  0.020  1.391
 P1B  C10  O13   single    1.347  0.020  1.347
 P1B  C9   C8    aromatic  1.391  0.020  1.391
 P1B  O13  C14   single    1.417  0.020  1.417
 P1B  C14  C15   single    1.519  0.020  1.519
 P1B  C15  C17   single    1.503  0.020  1.503
 P1B  C24  C23   single    1.528  0.020  1.528
 P1B  C23  C20   single    1.501  0.020  1.501
 P1B  C20  C19   aromatic  1.392  0.020  1.392
 P1B  C19  N18   aromatic  1.326  0.020  1.326
 P1B  N18  C17   aromatic  1.331  0.020  1.331
 P1B  C22  C17   aromatic  1.391  0.020  1.391
 P1B  N3   H3    single    0.860  0.020  1.020
 P1B  C5   H5    single    0.970  0.020  1.090
 P1B  C6   H61C  single    0.970  0.020  1.090
 P1B  C6   H62C  single    0.970  0.020  1.090
 P1B  C21  H21   single    0.930  0.020  1.080
 P1B  C22  H22   single    0.930  0.020  1.080
 P1B  C12  H12   single    0.930  0.020  1.080
 P1B  C8   H8    single    0.930  0.020  1.080
 P1B  C11  H11   single    0.930  0.020  1.080
 P1B  C9   H9    single    0.930  0.020  1.080
 P1B  C14  H141  single    0.970  0.020  1.090
 P1B  C14  H142  single    0.970  0.020  1.090
 P1B  C15  H151  single    0.970  0.020  1.090
 P1B  C15  H152  single    0.970  0.020  1.090
 P1B  C24  H241  single    0.970  0.020  1.090
 P1B  C24  H242  single    0.970  0.020  1.090
 P1B  C24  H243  single    0.970  0.020  1.090
 P1B  C23  H231  single    0.970  0.020  1.090
 P1B  C23  H232  single    0.970  0.020  1.090
 P1B  C19  H19   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
 P1B  C5    C4   N3    111.52  3.000
 P1B  C5    C4   O4    123.88  3.000
 P1B  N3    C4   O4    124.60  3.000
 P1B  H3    N3   C2    119.92  3.000
 P1B  H3    N3   C4    121.18  3.000
 P1B  C2    N3   C4    118.89  3.000
 P1B  H5    C5   C6    109.92  3.000
 P1B  H5    C5   S1    108.29  3.000
 P1B  C6    C5   S1    112.09  3.000
 P1B  H5    C5   C4    107.80  3.000
 P1B  C6    C5   C4    111.92  3.000
 P1B  S1    C5   C4    106.64  3.000
 P1B  C2    S1   C5     92.83  3.000
 P1B  O2    C2   S1    124.43  3.000
 P1B  O2    C2   N3    125.47  3.000
 P1B  S1    C2   N3    110.10  3.000
 P1B  H62C  C6   H61C  107.37  3.000
 P1B  H62C  C6   C7    110.40  3.000
 P1B  H61C  C6   C7    110.38  3.000
 P1B  H62C  C6   C5    109.40  3.000
 P1B  H61C  C6   C5    107.63  3.000
 P1B  C7    C6   C5    111.53  3.000
 P1B  H21   C21  C22   120.07  3.000
 P1B  H21   C21  C20   120.17  3.000
 P1B  C22   C21  C20   119.76  3.000
 P1B  C8    C7   C12   117.93  3.000
 P1B  C8    C7   C6    121.35  3.000
 P1B  C12   C7   C6    120.70  3.000
 P1B  H12   C12  C11   118.93  3.000
 P1B  H12   C12  C7    119.80  3.000
 P1B  C11   C12  C7    121.28  3.000
 P1B  H11   C11  C10   119.41  3.000
 P1B  H11   C11  C12   120.41  3.000
 P1B  C10   C11  C12   120.18  3.000
 P1B  O13   C10  C9    124.51  3.000
 P1B  O13   C10  C11   116.21  3.000
 P1B  C9    C10  C11   119.29  3.000
 P1B  H9    C9   C8    118.76  3.000
 P1B  H9    C9   C10   121.60  3.000
 P1B  C8    C9   C10   119.64  3.000
 P1B  H8    C8   C9    118.73  3.000
 P1B  H8    C8   C7    119.58  3.000
 P1B  C9    C8   C7    121.69  3.000
 P1B  C14   O13  C10   118.86  3.000
 P1B  H142  C14  H141  107.78  3.000
 P1B  H142  C14  C15   110.17  3.000
 P1B  H141  C14  C15   109.96  3.000
 P1B  H142  C14  O13   110.46  3.000
 P1B  H141  C14  O13   110.63  3.000
 P1B  C15   C14  O13   107.84  3.000
 P1B  H152  C15  H151  107.72  3.000
 P1B  H152  C15  C17   109.31  3.000
 P1B  H151  C15  C17   110.18  3.000
 P1B  H152  C15  C14   109.45  3.000
 P1B  H151  C15  C14   109.75  3.000
 P1B  C17   C15  C14   110.38  3.000
 P1B  H243  C24  H242  107.88  3.000
 P1B  H243  C24  H241  107.90  3.000
 P1B  H242  C24  H241  107.87  3.000
 P1B  H243  C24  C23   111.07  3.000
 P1B  H242  C24  C23   111.19  3.000
 P1B  H241  C24  C23   110.79  3.000
 P1B  C19   C20  C23   121.45  3.000
 P1B  C19   C20  C21   116.45  3.000
 P1B  C23   C20  C21   122.07  3.000
 P1B  H19   C19  N18   116.11  3.000
 P1B  H19   C19  C20   119.54  3.000
 P1B  N18   C19  C20   124.34  3.000
 P1B  C17   N18  C19   118.77  3.000
 P1B  H22   C22  C17   120.27  3.000
 P1B  H22   C22  C21   120.63  3.000
 P1B  C17   C22  C21   119.11  3.000
 P1B  C22   C17  N18   121.58  3.000
 P1B  C22   C17  C15   121.60  3.000
 P1B  N18   C17  C15   116.80  3.000
 P1B  H232  C23  H231  106.63  3.000
 P1B  H232  C23  C20   109.65  3.000
 P1B  H231  C23  C20   109.48  3.000
 P1B  H232  C23  C24   109.46  3.000
 P1B  H231  C23  C24   109.48  3.000
 P1B  C20   C23  C24   112.00  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
 P1B  CONST_01  N18   C19  C20  C21     0.00   0.0  0
 P1B  CONST_02  N18   C17  C22  C21     0.00   0.0  0
 P1B  CONST_03  C10   C11  C12  C7      0.00   0.0  0
 P1B  CONST_04  C10   C9   C8   C7      0.00   0.0  0
 P1B  CONST_05  C9    C8   C7   C12     0.00   0.0  0
 P1B  CONST_06  C9    C10  C11  C12     0.00   0.0  0
 P1B  CONST_07  C8    C7   C12  C11     0.00   0.0  0
 P1B  CONST_08  C8    C9   C10  C11     0.00   0.0  0
 P1B  CONST_09  C17   C22  C21  C20     0.00   0.0  0
 P1B  CONST_10  C17   N18  C19  C20     0.00   0.0  0
 P1B  CONST_11  C22   C21  C20  C19     0.00   0.0  0
 P1B  CONST_12  C22   C17  N18  C19     0.00   0.0  0
 P1B  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 P1B  CONST_14  C11   C12  C7   C6    180.00   0.0  0
 P1B  CONST_15  C9    C8   C7   C6    180.00   0.0  0
 P1B  CONST_16  C15   C17  C22  C21   180.00   0.0  0
 P1B  CONST_17  O13   C10  C11  C12   180.00   0.0  0
 P1B  CONST_18  O13   C10  C9   C8    180.00   0.0  0
 P1B  CONST_19  C19   N18  C17  C15   180.00   0.0  0
 P1B  CONST_20  C22   C21  C20  C23   180.00   0.0  0
 P1B  CONST_21  N18   C19  C20  C23   180.00   0.0  0
 P1B  CONST_22  C2    N3   C4   O4    180.00   0.0  0
 P1B  CONST_23  H19   C19  C20  C21   180.00   0.0  0
 P1B  CONST_24  H11   C11  C12  C7    180.00   0.0  0
 P1B  CONST_25  H9    C9   C8   C7    180.00   0.0  0
 P1B  CONST_26  H8    C8   C7   C12   180.00   0.0  0
 P1B  CONST_27  H12   C12  C11  C10   180.00   0.0  0
 P1B  CONST_28  H22   C22  C21  C20   180.00   0.0  0
 P1B  CONST_29  H21   C21  C20  C19   180.00   0.0  0
 P1B  CONST_30  H3    N3   C4   C5    180.00   0.0  0
 P1B  Var_01    S1    C2   N3   C4     -0.05  30.0  1
 P1B  Var_02    C12   C7   C6   C5     72.81  30.0  2
 P1B  Var_03    C24   C23  C20  C21    85.21  30.0  2
 P1B  Var_04    N18   C17  C15  C14   -72.45  30.0  2
 P1B  Var_05    C15   C14  O13  C10   178.64  30.0  3
 P1B  Var_06    C17   C15  C14  O13   177.19  30.0  3
 P1B  Var_07    H241  C24  C23  C20  -179.58  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
 P1B  chir_01  C5  C4  S1  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
 P1B  plan-1  C21  0.020
 P1B  plan-1  C15  0.020
 P1B  plan-1  C20  0.020
 P1B  plan-1  C19  0.020
 P1B  plan-1  N18  0.020
 P1B  plan-1  C22  0.020
 P1B  plan-1  C17  0.020
 P1B  plan-1  H21  0.020
 P1B  plan-1  H22  0.020
 P1B  plan-1  H19  0.020
 P1B  plan-1  C23  0.020
 P1B  plan-2  C6   0.020
 P1B  plan-2  C7   0.020
 P1B  plan-2  C12  0.020
 P1B  plan-2  C11  0.020
 P1B  plan-2  C10  0.020
 P1B  plan-2  C9   0.020
 P1B  plan-2  C8   0.020
 P1B  plan-2  O13  0.020
 P1B  plan-2  H12  0.020
 P1B  plan-2  H8   0.020
 P1B  plan-2  H11  0.020
 P1B  plan-2  H9   0.020
 P1B  plan-3  O4   0.020
 P1B  plan-3  C4   0.020
 P1B  plan-3  N3   0.020
 P1B  plan-3  C5   0.020
 P1B  plan-3  C2   0.020
 P1B  plan-3  H3   0.020
 P1B  plan-4  N3   0.020
 P1B  plan-4  S1   0.020
 P1B  plan-4  C2   0.020
 P1B  plan-4  O2   0.020

