# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:14:40 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (2R)-3-{(5S)-3-[4-(cyclopropylethynyl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](C[C@H]1CN(C(=O)O1)c2ccc(cc2)C#CC3CC3)(C(=O)NO)[S](C)(=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
 JBA  JBA  (2R)-3-{(5S)-3-[4-(cyclopropylethynyl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)propanamide  ligand  50  28  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JBA
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
 JBA  O5   O  OS    0  -0.666    3.5271   2.6065  -1.3753
 JBA  S    S  S     0   1.222    4.2745   1.9322  -0.3147
 JBA  O4   O  OS    0  -0.667    5.7265   1.8177  -0.4509
 JBA  C18  C  CH3   0  -0.792    3.9173   2.7779   1.2100
 JBA  C1   C  CT    0  -0.424    3.6286   0.1986  -0.2124
 JBA  C    C  CH3   0  -0.709    3.7454  -0.3210  -1.6462
 JBA  C17  C  C     0   0.577    4.5216  -0.4976   0.8209
 JBA  N1   N  NH1   0  -0.361    5.3676  -1.4079   0.3315
 JBA  O3   O  OH1   0  -0.533    6.1224  -2.1500   1.1814
 JBA  O2   O  O     0  -0.459    4.4479  -0.2122   2.0029
 JBA  C2   C  CH2   0  -0.443    2.1863   0.2433   0.3041
 JBA  C3   C  CR15  0  -0.015    1.5261  -1.1088   0.5364
 JBA  O1   O  O     0  -0.463    1.2689  -1.7947  -0.6920
 JBA  C5   C  CR5   0   0.712   -0.0236  -1.6995  -1.0310
 JBA  O    O  O     0  -0.462   -0.4392  -2.1078  -2.0834
 JBA  N    N  NR5   0  -0.616   -0.7104  -1.1085  -0.0113
 JBA  C4   C  CH2   0  -0.326    0.1349  -0.9582   1.1564
 JBA  C6   C  CR6   0   0.376   -2.0873  -0.8714   0.0227
 JBA  C16  C  CR16  0  -0.294   -2.8368  -0.6694  -1.1392
 JBA  C15  C  CR16  0  -0.288   -4.1908  -0.4051  -1.0530
 JBA  C9   C  CR6   0  -0.122   -4.8397  -0.3223   0.1824
 JBA  C8   C  CR16  0  -0.283   -4.0803  -0.5150   1.3374
 JBA  C7   C  CR16  0  -0.327   -2.7265  -0.7872   1.2606
 JBA  C10  C  CSP   0   0.145   -6.2340  -0.0380   0.2612
 JBA  C11  C  CSP   0   0.089   -7.4136   0.2101   0.3284
 JBA  C12  C  CH1   0  -0.473   -8.8151   0.5038   0.4125
 JBA  C14  C  CH2   0  -0.478   -9.2679   1.8284   0.9782
 JBA  C13  C  CH2   0  -0.478   -9.4127   1.5639  -0.4798
 JBA  H19  H  HCH3  0   0.295    2.8439   2.8585   1.3559
 JBA  H21  H  HCH3  0   0.304    4.3864   2.2729   2.0471
 JBA  H20  H  HCH3  0   0.321    4.3401   3.7743   1.0838
 JBA  H1   H  HCH3  0   0.268    4.7418  -0.1670  -2.0612
 JBA  H3   H  HCH3  0   0.282    3.5193  -1.3836  -1.6972
 JBA  H2   H  HCH3  0   0.286    3.0330   0.1852  -2.2931
 JBA  H17  H  HNH1  0   0.437    5.3826  -1.7143  -0.6295
 JBA  H18  H  HOH1  0   0.483    6.9739  -1.6979   1.2558
 JBA  H5   H  HCH2  0   0.290    2.1678   0.7449   1.2725
 JBA  H4   H  HCH2  0   0.289    1.5717   0.8420  -0.3742
 JBA  H    H  HCR5  0   0.294    2.1559  -1.7546   1.1474
 JBA  H6   H  HCH2  0   0.287   -0.0609  -1.7352   1.8990
 JBA  H7   H  HCH2  0   0.287   -0.0088   0.0150   1.6254
 JBA  H16  H  HCR6  0   0.280   -2.3753  -0.7045  -2.1133
 JBA  H15  H  HCR6  0   0.262   -4.7535  -0.2464  -1.9634
 JBA  H9   H  HCR6  0   0.263   -4.5525  -0.4524   2.3087
 JBA  H8   H  HCR6  0   0.286   -2.1759  -0.9374   2.1793
 JBA  H10  H  HCH1  0   0.291   -9.4490  -0.3496   0.6287
 JBA  H13  H  HCH2  0   0.265  -10.1541   1.8185   1.5986
 JBA  H14  H  HCH2  0   0.260   -8.4993   2.5200   1.2966
 JBA  H12  H  HCH2  0   0.261   -8.7451   2.0758  -1.1600
 JBA  H11  H  HCH2  0   0.265  -10.4006   1.3680  -0.8747

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
 JBA  O3   N1   single    1.358  0.020  1.358
 JBA  N1   C17  single    1.336  0.020  1.336
 JBA  O2   C17  double    1.218  0.020  1.218
 JBA  C17  C1   single    1.533  0.020  1.533
 JBA  O4   S    double    1.463  0.020  1.463
 JBA  C18  S    single    1.780  0.020  1.780
 JBA  C1   S    single    1.853  0.020  1.853
 JBA  C1   C    single    1.530  0.020  1.530
 JBA  C1   C2   single    1.533  0.020  1.533
 JBA  S    O5   double    1.462  0.020  1.462
 JBA  C2   C3   single    1.523  0.020  1.523
 JBA  C3   O1   single    1.430  0.020  1.430
 JBA  C3   C4   single    1.530  0.020  1.530
 JBA  O1   C5   single    1.340  0.020  1.340
 JBA  C4   N    single    1.449  0.020  1.449
 JBA  C5   N    single    1.364  0.020  1.364
 JBA  C5   O    double    1.203  0.020  1.203
 JBA  N    C6   single    1.398  0.020  1.398
 JBA  C16  C6   aromatic  1.397  0.020  1.397
 JBA  C16  C15  aromatic  1.382  0.020  1.382
 JBA  C6   C7   aromatic  1.396  0.020  1.396
 JBA  C15  C9   aromatic  1.398  0.020  1.398
 JBA  C7   C8   aromatic  1.383  0.020  1.383
 JBA  C9   C8   aromatic  1.396  0.020  1.396
 JBA  C9   C10  single    1.425  0.020  1.425
 JBA  C10  C11  triple    1.207  0.020  1.207
 JBA  C11  C12  single    1.434  0.020  1.434
 JBA  C13  C12  single    1.509  0.020  1.509
 JBA  C13  C14  single    1.489  0.020  1.489
 JBA  C12  C14  single    1.510  0.020  1.510
 JBA  C18  H19  single    0.970  0.020  1.090
 JBA  C18  H21  single    0.970  0.020  1.090
 JBA  C18  H20  single    0.970  0.020  1.090
 JBA  C    H1   single    0.970  0.020  1.090
 JBA  C    H3   single    0.970  0.020  1.090
 JBA  C    H2   single    0.970  0.020  1.090
 JBA  N1   H17  single    0.860  0.020  1.020
 JBA  O3   H18  single    0.850  0.020  0.980
 JBA  C2   H5   single    0.970  0.020  1.090
 JBA  C2   H4   single    0.970  0.020  1.090
 JBA  C3   H    single    0.970  0.020  1.090
 JBA  C4   H6   single    0.970  0.020  1.090
 JBA  C4   H7   single    0.970  0.020  1.090
 JBA  C16  H16  single    0.930  0.020  1.080
 JBA  C15  H15  single    0.930  0.020  1.080
 JBA  C8   H9   single    0.930  0.020  1.080
 JBA  C7   H8   single    0.930  0.020  1.080
 JBA  C12  H10  single    0.970  0.020  1.090
 JBA  C14  H13  single    0.970  0.020  1.090
 JBA  C14  H14  single    0.970  0.020  1.090
 JBA  C13  H12  single    0.970  0.020  1.090
 JBA  C13  H11  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
 JBA  C1   S    C18  109.11  3.000
 JBA  C1   S    O4   106.14  3.000
 JBA  C18  S    O4   108.43  3.000
 JBA  C1   S    O5   107.06  3.000
 JBA  C18  S    O5   107.44  3.000
 JBA  O4   S    O5   118.42  3.000
 JBA  H20  C18  H21  110.32  3.000
 JBA  H20  C18  H19  109.34  3.000
 JBA  H21  C18  H19  111.00  3.000
 JBA  H20  C18  S    104.91  3.000
 JBA  H21  C18  S    110.69  3.000
 JBA  H19  C18  S    110.41  3.000
 JBA  C2   C1   C17  109.53  3.000
 JBA  C2   C1   C    113.44  3.000
 JBA  C17  C1   C    115.67  3.000
 JBA  C2   C1   S    108.62  3.000
 JBA  C    C1   S    103.86  3.000
 JBA  C17  C1   S    105.01  3.000
 JBA  H2   C    H3   106.90  3.000
 JBA  H2   C    H1   107.85  3.000
 JBA  H3   C    H1   108.07  3.000
 JBA  H2   C    C1   110.45  3.000
 JBA  H3   C    C1   111.10  3.000
 JBA  H1   C    C1   112.25  3.000
 JBA  O2   C17  N1   123.61  3.000
 JBA  O2   C17  C1   120.83  3.000
 JBA  N1   C17  C1   115.56  3.000
 JBA  H17  N1   O3   114.97  3.000
 JBA  H17  N1   C17  124.44  3.000
 JBA  O3   N1   C17  119.69  3.000
 JBA  H18  O3   N1   106.39  3.000
 JBA  H4   C2   H5   106.82  3.000
 JBA  H4   C2   C3   109.70  3.000
 JBA  H5   C2   C3   105.40  3.000
 JBA  H4   C2   C1   109.62  3.000
 JBA  H5   C2   C1   109.18  3.000
 JBA  C3   C2   C1   115.70  3.000
 JBA  H    C3   C4   110.89  3.000
 JBA  H    C3   O1   107.54  3.000
 JBA  C4   C3   O1   103.40  3.000
 JBA  H    C3   C2   111.18  3.000
 JBA  C4   C3   C2   111.63  3.000
 JBA  O1   C3   C2   111.89  3.000
 JBA  C5   O1   C3   110.91  3.000
 JBA  N    C5   O    128.83  3.000
 JBA  O    C5   O1   122.05  3.000
 JBA  N    C5   O1   109.11  3.000
 JBA  C6   N    C4   122.51  3.000
 JBA  C6   N    C5   126.00  3.000
 JBA  C4   N    C5   110.70  3.000
 JBA  H7   C4   H6   108.60  3.000
 JBA  H7   C4   N    111.25  3.000
 JBA  H6   C4   N    111.67  3.000
 JBA  H7   C4   C3   112.46  3.000
 JBA  H6   C4   C3   111.61  3.000
 JBA  N    C4   C3   101.16  3.000
 JBA  C7   C6   C16  118.89  3.000
 JBA  C7   C6   N    118.88  3.000
 JBA  C16  C6   N    122.19  3.000
 JBA  H16  C16  C15  118.80  3.000
 JBA  H16  C16  C6   121.12  3.000
 JBA  C15  C16  C6   120.08  3.000
 JBA  H15  C15  C9   119.57  3.000
 JBA  H15  C15  C16  119.01  3.000
 JBA  C9   C15  C16  121.41  3.000
 JBA  C10  C9   C8   120.94  3.000
 JBA  C10  C9   C15  120.99  3.000
 JBA  C8   C9   C15  118.07  3.000
 JBA  H9   C8   C7   119.25  3.000
 JBA  H9   C8   C9   119.84  3.000
 JBA  C7   C8   C9   120.92  3.000
 JBA  H8   C7   C8   118.59  3.000
 JBA  H8   C7   C6   120.79  3.000
 JBA  C8   C7   C6   120.63  3.000
 JBA  C11  C10  C9   180.00  3.000
 JBA  C12  C11  C10  180.00  3.000
 JBA  H10  C12  C13  116.05  3.000
 JBA  H10  C12  C14  116.12  3.000
 JBA  C13  C12  C14   59.10  3.000
 JBA  H10  C12  C11  114.93  3.000
 JBA  C14  C12  C11  119.65  3.000
 JBA  C13  C12  C11  119.74  3.000
 JBA  H14  C14  H13  114.78  3.000
 JBA  H14  C14  C13  118.09  3.000
 JBA  H13  C14  C13  118.70  3.000
 JBA  H14  C14  C12  117.26  3.000
 JBA  H13  C14  C12  116.90  3.000
 JBA  C13  C14  C12   60.42  3.000
 JBA  H11  C13  H12  114.81  3.000
 JBA  H11  C13  C14  118.59  3.000
 JBA  H12  C13  C14  118.14  3.000
 JBA  H11  C13  C12  116.76  3.000
 JBA  H12  C13  C12  117.38  3.000
 JBA  C14  C13  C12   60.48  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
 JBA  CONST_01  C9   C15  C16  C6      0.00   0.0  0
 JBA  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 JBA  CONST_03  C8   C7   C6   C16     0.00   0.0  0
 JBA  CONST_04  C8   C9   C15  C16     0.00   0.0  0
 JBA  CONST_05  C7   C6   C16  C15     0.00   0.0  0
 JBA  CONST_06  C7   C8   C9   C15     0.00   0.0  0
 JBA  CONST_07  C15  C16  C6   N     180.00   0.0  0
 JBA  CONST_08  C8   C7   C6   N     180.00   0.0  0
 JBA  CONST_09  C10  C9   C15  C16   180.00   0.0  0
 JBA  CONST_10  C10  C9   C8   C7    180.00   0.0  0
 JBA  CONST_11  H16  C16  C6   N       0.00   0.0  0
 JBA  CONST_12  H8   C7   C6   N       0.00   0.0  0
 JBA  CONST_13  H15  C15  C16  C6    180.00   0.0  0
 JBA  CONST_14  H9   C8   C7   C6    180.00   0.0  0
 JBA  CONST_15  O3   N1   C17  C1    180.00   0.0  0
 JBA  CONST_16  O2   C17  N1   O3      0.00   0.0  0
 JBA  CONST_17  H17  N1   C17  C1      0.00   0.0  0
 JBA  Var_01    N    C5   O1   C3     -7.03  30.0  1
 JBA  Var_02    C5   N    C4   C3     18.26  30.0  1
 JBA  Var_03    C4   N    C5   O1     -8.13  30.0  1
 JBA  Var_04    C16  C6   N    C5    -28.44  30.0  2
 JBA  Var_05    C14  C13  C12  C11  -108.78  30.0  1
 JBA  Var_06    H13  C14  C13  C12  -106.40  30.0  1
 JBA  Var_07    C13  C12  C11  C10   148.53  30.0  3
 JBA  Var_08    H19  C18  S    O5     52.34  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
 JBA  chir_01  C1   S    C    C2   positiv
 JBA  chir_02  C3   O1   C4   C2   positiv
 JBA  chir_03  C12  C11  C13  C14  both

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
 JBA  plan-1  C1   0.020
 JBA  plan-1  C17  0.020
 JBA  plan-1  N1   0.020
 JBA  plan-1  O3   0.020
 JBA  plan-1  O2   0.020
 JBA  plan-1  H17  0.020
 JBA  plan-2  N    0.020
 JBA  plan-2  C6   0.020
 JBA  plan-2  C16  0.020
 JBA  plan-2  C15  0.020
 JBA  plan-2  C9   0.020
 JBA  plan-2  C8   0.020
 JBA  plan-2  C7   0.020
 JBA  plan-2  C10  0.020
 JBA  plan-2  C11  0.020
 JBA  plan-2  H16  0.020
 JBA  plan-2  H15  0.020
 JBA  plan-2  H9   0.020
 JBA  plan-2  H8   0.020
 JBA  plan-3  C5   0.020
 JBA  plan-3  N    0.020
 JBA  plan-3  C4   0.020
 JBA  plan-3  C6   0.020
 JBA  plan-4  O1   0.020
 JBA  plan-4  C5   0.020
 JBA  plan-4  O    0.020
 JBA  plan-4  N    0.020

