# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 12:30:21 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 4-(3-bromophenoxy)-N-[(3S)-2-oxothiolan-3-yl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1cccc(OCCCC(=O)N[C@H]2CCSC2=O)c1
#
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
 K5G  K5G  4-(3-bromophenoxy)-N-[(3S)-2-oxothiolan-3-yl]butanamide  ligand  36  20  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K5G
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
 K5G  BR1  BR  BR    0  -0.048  -6.6622   1.0299   0.0439
 K5G  C02  C   CR6   0  -0.092  -5.2050  -0.1478  -0.2069
 K5G  C03  C   CR16  0  -0.325  -3.9277   0.3089   0.0549
 K5G  C04  C   CR6   0   0.399  -2.8438  -0.5558  -0.1259
 K5G  C18  C   CR16  0  -0.378  -3.0634  -1.8590  -0.5661
 K5G  C19  C   CR16  0  -0.236  -4.3614  -2.2827  -0.8210
 K5G  C20  C   CR16  0  -0.260  -5.4492  -1.4422  -0.6477
 K5G  O05  O   O2    0  -0.474  -1.6361  -0.0383   0.1494
 K5G  C06  C   CH2   0  -0.175  -0.4836  -0.8550   0.0030
 K5G  C07  C   CH2   0  -0.456   0.7246  -0.0116   0.3518
 K5G  C08  C   CH2   0  -0.599   1.9975  -0.8361   0.2520
 K5G  C09  C   C     0   0.573   3.2398  -0.0522   0.6186
 K5G  O10  O   O     0  -0.486   3.2000   1.0168   1.2041
 K5G  N11  N   NH1   0  -0.638   4.3988  -0.6601   0.2833
 K5G  C12  C   CH1   0  -0.160   5.6840  -0.0858   0.5265
 K5G  C13  C   CH2   0  -0.456   6.7640  -1.0897   0.8946
 K5G  C14  C   CH2   0  -0.573   8.0889  -0.3465   0.7972
 K5G  S15  S   S2    0   0.031   7.9685   0.6862  -0.7022
 K5G  C16  C   C     0   0.254   6.2029   0.6870  -0.6886
 K5G  O17  O   O     0  -0.370   5.5225   1.2222  -1.5181
 K5G  H1   H   HCR6  0   0.285  -3.7464   1.3196   0.3978
 K5G  H2   H   HCR6  0   0.286  -2.2464  -2.5513  -0.7135
 K5G  H3   H   HCR6  0   0.272  -4.5269  -3.2956  -1.1637
 K5G  H4   H   HCR6  0   0.277  -6.4517  -1.7914  -0.8508
 K5G  H5   H   HCH2  0   0.227  -0.5494  -1.7249   0.6668
 K5G  H6   H   HCH2  0   0.228  -0.4082  -1.2263  -1.0254
 K5G  H7   H   HCH2  0   0.244   0.7768   0.8434  -0.3264
 K5G  H8   H   HCH2  0   0.281   1.9447  -1.6988   0.9252
 K5G  H9   H   HNH1  0   0.406   4.3609  -1.5058  -0.2653
 K5G  H10  H   HCH1  0   0.310   5.5895   0.6512   1.3317
 K5G  H11  H   HCH2  0   0.283   6.6161  -1.4851   1.8989
 K5G  H12  H   HCH2  0   0.263   6.7552  -1.9267   0.1919
 K5G  H13  H   HCH2  0   0.291   8.2508   0.2995   1.6593
 K5G  H14  H   HCH2  0   0.302   8.9395  -1.0158   0.6943
 K5G  H15  H   HCH2  0   0.244   0.6130   0.3810   1.3640
 K5G  H16  H   HCH2  0   0.268   2.1127  -1.2499  -0.7538

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
 K5G  BR1  C02  single    1.890  0.020  1.890
 K5G  C02  C03  aromatic  1.382  0.020  1.382
 K5G  C02  C20  aromatic  1.389  0.020  1.389
 K5G  C03  C04  aromatic  1.398  0.020  1.398
 K5G  C20  C19  aromatic  1.386  0.020  1.386
 K5G  O10  C09  double    1.220  0.020  1.220
 K5G  C04  O05  single    1.342  0.020  1.342
 K5G  C04  C18  aromatic  1.393  0.020  1.393
 K5G  O05  C06  single    1.420  0.020  1.420
 K5G  C19  C18  aromatic  1.389  0.020  1.389
 K5G  C07  C06  single    1.514  0.020  1.514
 K5G  C07  C08  single    1.520  0.020  1.520
 K5G  C09  C08  single    1.514  0.020  1.514
 K5G  C09  N11  single    1.351  0.020  1.351
 K5G  C12  N11  single    1.429  0.020  1.429
 K5G  C12  C16  single    1.531  0.020  1.531
 K5G  C12  C13  single    1.520  0.020  1.520
 K5G  O17  C16  double    1.199  0.020  1.199
 K5G  C16  S15  single    1.766  0.020  1.766
 K5G  C13  C14  single    1.522  0.020  1.522
 K5G  S15  C14  single    1.825  0.020  1.825
 K5G  C03  H1   single    0.930  0.020  1.080
 K5G  C18  H2   single    0.930  0.020  1.080
 K5G  C19  H3   single    0.930  0.020  1.080
 K5G  C20  H4   single    0.930  0.020  1.080
 K5G  C06  H5   single    0.970  0.020  1.090
 K5G  C06  H6   single    0.970  0.020  1.090
 K5G  C07  H7   single    0.970  0.020  1.090
 K5G  C08  H8   single    0.970  0.020  1.090
 K5G  N11  H9   single    0.860  0.020  1.020
 K5G  C12  H10  single    0.970  0.020  1.090
 K5G  C13  H11  single    0.970  0.020  1.090
 K5G  C13  H12  single    0.970  0.020  1.090
 K5G  C14  H13  single    0.970  0.020  1.090
 K5G  C14  H14  single    0.970  0.020  1.090
 K5G  C07  H15  single    0.970  0.020  1.090
 K5G  C08  H16  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
 K5G  C20  C02  C03  122.06  3.000
 K5G  C20  C02  BR1  119.15  3.000
 K5G  C03  C02  BR1  118.79  3.000
 K5G  H1   C03  C04  119.24  3.000
 K5G  H1   C03  C02  121.56  3.000
 K5G  C04  C03  C02  119.19  3.000
 K5G  O05  C04  C18  124.56  3.000
 K5G  C18  C04  C03  119.82  3.000
 K5G  O05  C04  C03  115.62  3.000
 K5G  H2   C18  C19  119.07  3.000
 K5G  H2   C18  C04  121.55  3.000
 K5G  C19  C18  C04  119.38  3.000
 K5G  H3   C19  C20  119.17  3.000
 K5G  H3   C19  C18  119.12  3.000
 K5G  C20  C19  C18  121.71  3.000
 K5G  H4   C20  C19  120.58  3.000
 K5G  H4   C20  C02  121.59  3.000
 K5G  C19  C20  C02  117.83  3.000
 K5G  C06  O05  C04  119.16  3.000
 K5G  H6   C06  H5   107.67  3.000
 K5G  H6   C06  C07  110.49  3.000
 K5G  H5   C06  C07  110.51  3.000
 K5G  H6   C06  O05  110.33  3.000
 K5G  H5   C06  O05  110.19  3.000
 K5G  C07  C06  O05  107.67  3.000
 K5G  H15  C07  H7   107.41  3.000
 K5G  H15  C07  C08  109.98  3.000
 K5G  H7   C07  C08  110.11  3.000
 K5G  H15  C07  C06  109.41  3.000
 K5G  H7   C07  C06  109.33  3.000
 K5G  C08  C07  C06  110.54  3.000
 K5G  H16  C08  H8   105.80  3.000
 K5G  H16  C08  C09  109.40  3.000
 K5G  H8   C08  C09  107.37  3.000
 K5G  H16  C08  C07  110.73  3.000
 K5G  H8   C08  C07  110.27  3.000
 K5G  C09  C08  C07  112.98  3.000
 K5G  N11  C09  O10  122.79  3.000
 K5G  N11  C09  C08  114.26  3.000
 K5G  O10  C09  C08  122.91  3.000
 K5G  H9   N11  C12  117.60  3.000
 K5G  H9   N11  C09  118.68  3.000
 K5G  C12  N11  C09  123.28  3.000
 K5G  H10  C12  C16  105.84  3.000
 K5G  H10  C12  C13  109.13  3.000
 K5G  C16  C12  C13  106.55  3.000
 K5G  H10  C12  N11  108.53  3.000
 K5G  C13  C12  N11  114.52  3.000
 K5G  C16  C12  N11  111.89  3.000
 K5G  H12  C13  H11  108.28  3.000
 K5G  H12  C13  C14  109.86  3.000
 K5G  H11  C13  C14  110.75  3.000
 K5G  H12  C13  C12  110.15  3.000
 K5G  H11  C13  C12  111.50  3.000
 K5G  C14  C13  C12  106.29  3.000
 K5G  H14  C14  H13  108.89  3.000
 K5G  H14  C14  S15  108.80  3.000
 K5G  H13  C14  S15  108.93  3.000
 K5G  H14  C14  C13  112.73  3.000
 K5G  H13  C14  C13  111.61  3.000
 K5G  S15  C14  C13  105.75  3.000
 K5G  C16  S15  C14   93.43  3.000
 K5G  O17  C16  S15  124.22  3.000
 K5G  S15  C16  C12  110.18  3.000
 K5G  O17  C16  C12  125.60  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
 K5G  CONST_01  C18  C04  C03  C02     0.00   0.0  0
 K5G  CONST_02  C18  C19  C20  C02     0.00   0.0  0
 K5G  CONST_03  C19  C20  C02  C03     0.00   0.0  0
 K5G  CONST_04  C19  C18  C04  C03     0.00   0.0  0
 K5G  CONST_05  C20  C02  C03  C04     0.00   0.0  0
 K5G  CONST_06  C20  C19  C18  C04     0.00   0.0  0
 K5G  CONST_07  C04  C03  C02  BR1   180.00   0.0  0
 K5G  CONST_08  C19  C20  C02  BR1   180.00   0.0  0
 K5G  CONST_09  O05  C04  C03  C02   180.00   0.0  0
 K5G  CONST_10  O05  C04  C18  C19   180.00   0.0  0
 K5G  CONST_11  H3   C19  C20  C02   180.00   0.0  0
 K5G  CONST_12  H4   C20  C02  C03   180.00   0.0  0
 K5G  CONST_13  H2   C18  C04  C03   180.00   0.0  0
 K5G  CONST_14  H1   C03  C04  C18   180.00   0.0  0
 K5G  CONST_15  C12  N11  C09  C08   180.00   0.0  0
 K5G  CONST_16  C12  N11  C09  O10     0.00   0.0  0
 K5G  CONST_17  H9   N11  C09  C08     0.00   0.0  0
 K5G  Var_01    S15  C14  C13  C12   -41.12  30.0  1
 K5G  Var_02    O17  C16  S15  C14  -178.11  30.0  1
 K5G  Var_03    C07  C06  O05  C04   178.94  30.0  3
 K5G  Var_04    C08  C07  C06  O05   178.50  30.0  1
 K5G  Var_05    C09  C08  C07  C06  -178.79  30.0  3
 K5G  Var_06    O10  C09  C08  C07    15.00  30.0  2

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
 K5G  chir_01  C12  N11  C16  C13  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
 K5G  plan-1  BR1  0.020
 K5G  plan-1  C02  0.020
 K5G  plan-1  C03  0.020
 K5G  plan-1  C04  0.020
 K5G  plan-1  C18  0.020
 K5G  plan-1  C19  0.020
 K5G  plan-1  C20  0.020
 K5G  plan-1  O05  0.020
 K5G  plan-1  H1   0.020
 K5G  plan-1  H2   0.020
 K5G  plan-1  H3   0.020
 K5G  plan-1  H4   0.020
 K5G  plan-2  C08  0.020
 K5G  plan-2  C09  0.020
 K5G  plan-2  O10  0.020
 K5G  plan-2  N11  0.020
 K5G  plan-2  C12  0.020
 K5G  plan-2  H9   0.020
 K5G  plan-3  C12  0.020
 K5G  plan-3  S15  0.020
 K5G  plan-3  C16  0.020
 K5G  plan-3  O17  0.020

