# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:35:20 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: (2S)-4-{4-[4-(benzyloxy)phenyl]-2-oxopyridin-1(2H)-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@](CCN1C=CC(=CC1=O)c2ccc(OCc3ccccc3)cc2)(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
 J1M  J1M  (2S)-4-{4-[4-(benzyloxy)phenyl]-2-oxopyridin-1(2H)-yl}-N-hydroxy-2-methyl-2-(methylsulfonyl)butanamide  ligand  59  33  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J1M
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
 J1M  C12  C  CR6   0   0.068   -2.2328  -0.3052  -0.3492
 J1M  C14  C  CR16  0  -0.331   -4.4152  -0.5539  -1.3690
 J1M  C15  C  CR6   0   0.385   -5.0268  -0.0092  -0.2371
 J1M  O16  O  O2    0  -0.463   -6.3667   0.0874  -0.2731
 J1M  C17  C  CH2   0  -0.274   -7.0435   0.6352   0.8539
 J1M  C18  C  CR6   0   0.101   -8.5106   0.5964   0.5542
 J1M  C20  C  CR16  0  -0.242  -10.6426  -0.5296   0.6722
 J1M  C21  C  CR16  0  -0.261  -11.2299   0.4946  -0.0589
 J1M  C23  C  CR16  0  -0.288   -9.1069   1.6189  -0.1786
 J1M  C24  C  CR16  0  -0.368   -4.2331   0.3941   0.8353
 J1M  C25  C  CR16  0  -0.290   -2.8564   0.2399   0.7698
 J1M  C26  C  C     0   0.595    6.2029   1.5835   0.0465
 J1M  C01  C  CH3   0  -0.720    6.1383  -0.2347  -1.7925
 J1M  C02  C  CT    0  -0.419    5.6717   0.2147  -0.4089
 J1M  C03  C  CH2   0  -0.442    4.1408   0.2591  -0.3049
 J1M  C04  C  CH2   0  -0.336    3.4106  -1.0414  -0.6337
 J1M  C06  C  C1    0   0.068    1.2615  -0.5566  -1.6532
 J1M  C07  C  C1    0  -0.461   -0.0788  -0.3694  -1.6356
 J1M  C08  C  C     0   0.233   -0.7729  -0.4850  -0.4000
 J1M  C09  C  C1    0  -0.541   -0.0520  -0.7729   0.7258
 J1M  C10  C  C     0   0.593    1.3697  -0.9534   0.7158
 J1M  C13  C  CR16  0  -0.287   -3.0432  -0.6912  -1.4215
 J1M  C19  C  CR16  0  -0.294   -9.2882  -0.4783   0.9740
 J1M  C22  C  CR16  0  -0.242  -10.4598   1.5701  -0.4837
 J1M  N05  N  NT    0  -0.512    1.9692  -0.8523  -0.5350
 J1M  N28  N  NH1   0  -0.366    6.9829   2.2187  -0.8328
 J1M  O11  O  O     0  -0.519    2.0486  -1.1960   1.7143
 J1M  O27  O  O     0  -0.460    5.8877   2.0490   1.1263
 J1M  S30  S  S     0   1.218    6.4184  -0.9838   0.7793
 J1M  H1   H  HCR6  0   0.267   -5.0257  -0.8745  -2.2038
 J1M  H2   H  HCH2  0   0.246   -6.8195   0.0502   1.7516
 J1M  H3   H  HCH2  0   0.245   -6.7110   1.6634   1.0313
 J1M  H4   H  HCR6  0   0.259  -11.2386  -1.3677   1.0094
 J1M  H5   H  HCR6  0   0.259  -12.2856   0.4567  -0.2943
 J1M  H6   H  HCR6  0   0.255   -8.5121   2.4624  -0.5089
 J1M  H7   H  HCR6  0   0.287   -4.6613   0.8324   1.7258
 J1M  H8   H  HCR6  0   0.262   -2.2628   0.5767   1.6103
 J1M  H9   H  HOH1  0   0.483    6.9969   4.0944  -0.7640
 J1M  H10  H  HCH3  0   0.274    7.2238  -0.2835  -1.8781
 J1M  H11  H  HCH3  0   0.292    5.7546  -1.2211  -2.0370
 J1M  H12  H  HCH3  0   0.282    5.7558   0.4531  -2.5472
 J1M  H13  H  HCH2  0   0.289    3.8498   0.6062   0.6861
 J1M  H14  H  HCH2  0   0.291    3.8086   1.0277  -1.0100
 J1M  H15  H  HCH2  0   0.281    3.6266  -1.3686  -1.6491
 J1M  H16  H  HCH2  0   0.277    3.6932  -1.8546   0.0300
 J1M  H17  H  H     0   0.310    1.8352  -0.4770  -2.5662
 J1M  H18  H  H     0   0.274   -0.5871  -0.1162  -2.5538
 J1M  H19  H  H     0   0.266   -0.5393  -0.8964   1.6843
 J1M  H20  H  HCR6  0   0.262   -2.6025  -1.1316  -2.3066
 J1M  H21  H  HCR6  0   0.255   -8.8331  -1.2798   1.5440
 J1M  H22  H  HCR6  0   0.259  -10.9142   2.3730  -1.0495
 J1M  H23  H  HCH3  0   0.316    6.0181  -1.5669   2.9882
 J1M  H24  H  HCH3  0   0.302    5.6545   0.1605   2.7215
 J1M  H25  H  HCH3  0   0.299    4.4973  -1.0950   2.1885
 J1M  H26  H  HNH1  0   0.436    7.3098   1.8200  -1.6994
 J1M  C31  C  CH3   0  -0.805    5.5470  -0.8429   2.3236
 J1M  O32  O  OS    0  -0.664    6.1838  -2.3335   0.2620
 J1M  O29  O  OH1   0  -0.533    7.5856   3.3830  -0.4775
 J1M  O33  O  OS    0  -0.668    7.8069  -0.5631   0.9706

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
 J1M  O29  N28  single    1.358  0.020  1.358
 J1M  N28  C26  single    1.336  0.020  1.336
 J1M  O27  C26  double    1.217  0.020  1.217
 J1M  C26  C02  single    1.537  0.020  1.537
 J1M  O32  S30  double    1.464  0.020  1.464
 J1M  O33  S30  double    1.463  0.020  1.463
 J1M  C04  N05  single    1.457  0.020  1.457
 J1M  C04  C03  single    1.527  0.020  1.527
 J1M  S30  C02  single    1.845  0.020  1.845
 J1M  S30  C31  single    1.779  0.020  1.779
 J1M  C02  C03  single    1.535  0.020  1.535
 J1M  C02  C01  single    1.528  0.020  1.528
 J1M  N05  C06  single    1.356  0.020  1.356
 J1M  N05  C10  single    1.391  0.020  1.391
 J1M  C06  C07  double    1.353  0.020  1.353
 J1M  O11  C10  double    1.232  0.020  1.232
 J1M  C10  C09  single    1.433  0.020  1.433
 J1M  C07  C08  single    1.422  0.020  1.422
 J1M  C09  C08  double    1.367  0.020  1.367
 J1M  C08  C12  single    1.472  0.020  1.472
 J1M  C13  C12  aromatic  1.398  0.020  1.398
 J1M  C13  C14  aromatic  1.380  0.020  1.380
 J1M  C12  C25  aromatic  1.392  0.020  1.392
 J1M  C14  C15  aromatic  1.397  0.020  1.397
 J1M  C25  C24  aromatic  1.387  0.020  1.387
 J1M  C15  C24  aromatic  1.394  0.020  1.394
 J1M  C15  O16  single    1.344  0.020  1.344
 J1M  C17  O16  single    1.424  0.020  1.424
 J1M  C17  C18  single    1.498  0.020  1.498
 J1M  C23  C18  aromatic  1.392  0.020  1.392
 J1M  C23  C22  aromatic  1.388  0.020  1.388
 J1M  C18  C19  aromatic  1.391  0.020  1.391
 J1M  C22  C21  aromatic  1.389  0.020  1.389
 J1M  C19  C20  aromatic  1.389  0.020  1.389
 J1M  C21  C20  aromatic  1.389  0.020  1.389
 J1M  C14  H1   single    0.930  0.020  1.080
 J1M  C17  H2   single    0.970  0.020  1.090
 J1M  C17  H3   single    0.970  0.020  1.090
 J1M  C20  H4   single    0.930  0.020  1.080
 J1M  C21  H5   single    0.930  0.020  1.080
 J1M  C23  H6   single    0.930  0.020  1.080
 J1M  C24  H7   single    0.930  0.020  1.080
 J1M  C25  H8   single    0.930  0.020  1.080
 J1M  O29  H9   single    0.850  0.020  0.980
 J1M  C01  H10  single    0.970  0.020  1.090
 J1M  C01  H11  single    0.970  0.020  1.090
 J1M  C01  H12  single    0.970  0.020  1.090
 J1M  C03  H13  single    0.970  0.020  1.090
 J1M  C03  H14  single    0.970  0.020  1.090
 J1M  C04  H15  single    0.970  0.020  1.090
 J1M  C04  H16  single    0.970  0.020  1.090
 J1M  C06  H17  single    0.930  0.020  1.080
 J1M  C07  H18  single    0.930  0.020  1.080
 J1M  C09  H19  single    0.930  0.020  1.080
 J1M  C13  H20  single    0.930  0.020  1.080
 J1M  C19  H21  single    0.930  0.020  1.080
 J1M  C22  H22  single    0.930  0.020  1.080
 J1M  C31  H23  single    0.970  0.020  1.090
 J1M  C31  H24  single    0.970  0.020  1.090
 J1M  C31  H25  single    0.970  0.020  1.090
 J1M  N28  H26  single    0.860  0.020  1.020

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
 J1M  C13  C12  C08  120.97  3.000
 J1M  C13  C12  C25  117.70  3.000
 J1M  C08  C12  C25  121.32  3.000
 J1M  H1   C14  C13  120.12  3.000
 J1M  H1   C14  C15  119.56  3.000
 J1M  C13  C14  C15  120.32  3.000
 J1M  C24  C15  O16  124.59  3.000
 J1M  O16  C15  C14  116.28  3.000
 J1M  C24  C15  C14  119.13  3.000
 J1M  C17  O16  C15  118.70  3.000
 J1M  H3   C17  H2   107.86  3.000
 J1M  H3   C17  C18  110.74  3.000
 J1M  H2   C17  C18  110.53  3.000
 J1M  H3   C17  O16  110.19  3.000
 J1M  H2   C17  O16  110.25  3.000
 J1M  C18  C17  O16  107.29  3.000
 J1M  C19  C18  C23  119.13  3.000
 J1M  C19  C18  C17  120.47  3.000
 J1M  C23  C18  C17  120.38  3.000
 J1M  H4   C20  C19  119.87  3.000
 J1M  H4   C20  C21  120.15  3.000
 J1M  C19  C20  C21  119.98  3.000
 J1M  H5   C21  C22  120.08  3.000
 J1M  H5   C21  C20  120.08  3.000
 J1M  C22  C21  C20  119.84  3.000
 J1M  H6   C23  C22  119.70  3.000
 J1M  H6   C23  C18  119.80  3.000
 J1M  C22  C23  C18  120.49  3.000
 J1M  H7   C24  C25  118.50  3.000
 J1M  H7   C24  C15  121.71  3.000
 J1M  C25  C24  C15  119.79  3.000
 J1M  H8   C25  C24  118.23  3.000
 J1M  H8   C25  C12  120.02  3.000
 J1M  C24  C25  C12  121.74  3.000
 J1M  O27  C26  N28  123.58  3.000
 J1M  O27  C26  C02  120.92  3.000
 J1M  N28  C26  C02  115.48  3.000
 J1M  H12  C01  H11  107.04  3.000
 J1M  H12  C01  H10  108.86  3.000
 J1M  H11  C01  H10  107.06  3.000
 J1M  H12  C01  C02  109.52  3.000
 J1M  H11  C01  C02  111.29  3.000
 J1M  H10  C01  C02  112.86  3.000
 J1M  S30  C02  C03  112.25  3.000
 J1M  C03  C02  C01  111.99  3.000
 J1M  S30  C02  C01  105.57  3.000
 J1M  C01  C02  C26  115.13  3.000
 J1M  C03  C02  C26  107.39  3.000
 J1M  S30  C02  C26  104.34  3.000
 J1M  H14  C03  H13  106.32  3.000
 J1M  H14  C03  C04  108.31  3.000
 J1M  H13  C03  C04  109.84  3.000
 J1M  H14  C03  C02  106.22  3.000
 J1M  H13  C03  C02  109.70  3.000
 J1M  C04  C03  C02  115.95  3.000
 J1M  H16  C04  H15  107.05  3.000
 J1M  H16  C04  N05  108.23  3.000
 J1M  H15  C04  N05  107.37  3.000
 J1M  H16  C04  C03  112.41  3.000
 J1M  H15  C04  C03  111.22  3.000
 J1M  N05  C04  C03  110.36  3.000
 J1M  H17  C06  N05  115.82  3.000
 J1M  H17  C06  C07  121.75  3.000
 J1M  N05  C06  C07  122.43  3.000
 J1M  H18  C07  C08  121.89  3.000
 J1M  H18  C07  C06  119.18  3.000
 J1M  C08  C07  C06  118.91  3.000
 J1M  C09  C08  C07  118.38  3.000
 J1M  C09  C08  C12  121.34  3.000
 J1M  C07  C08  C12  120.28  3.000
 J1M  H19  C09  C10  116.01  3.000
 J1M  H19  C09  C08  121.05  3.000
 J1M  C10  C09  C08  122.93  3.000
 J1M  O11  C10  N05  120.39  3.000
 J1M  O11  C10  C09  124.47  3.000
 J1M  N05  C10  C09  115.13  3.000
 J1M  H20  C13  C14  118.45  3.000
 J1M  H20  C13  C12  120.23  3.000
 J1M  C14  C13  C12  121.30  3.000
 J1M  H21  C19  C20  119.78  3.000
 J1M  H21  C19  C18  119.69  3.000
 J1M  C20  C19  C18  120.54  3.000
 J1M  H22  C22  C23  119.88  3.000
 J1M  H22  C22  C21  120.10  3.000
 J1M  C23  C22  C21  120.02  3.000
 J1M  C10  N05  C06  122.18  3.000
 J1M  C10  N05  C04  118.55  3.000
 J1M  C06  N05  C04  119.25  3.000
 J1M  H26  N28  O29  114.82  3.000
 J1M  H26  N28  C26  124.53  3.000
 J1M  O29  N28  C26  119.63  3.000
 J1M  O33  S30  O32  117.59  3.000
 J1M  O33  S30  C31  109.18  3.000
 J1M  O32  S30  C31  107.53  3.000
 J1M  C31  S30  C02  108.02  3.000
 J1M  O33  S30  C02  106.34  3.000
 J1M  O32  S30  C02  107.84  3.000
 J1M  H25  C31  H24  110.83  3.000
 J1M  H25  C31  H23  109.80  3.000
 J1M  H24  C31  H23  110.36  3.000
 J1M  H25  C31  S30  110.27  3.000
 J1M  H24  C31  S30  110.07  3.000
 J1M  H23  C31  S30  105.37  3.000
 J1M  H9   O29  N28  106.44  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
 J1M  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 J1M  CONST_02  C15  C24  C25  C12     0.00   0.0  0
 J1M  CONST_03  C25  C12  C13  C14     0.00   0.0  0
 J1M  CONST_04  C25  C24  C15  C14     0.00   0.0  0
 J1M  CONST_05  C21  C22  C23  C18     0.00   0.0  0
 J1M  CONST_06  C21  C20  C19  C18     0.00   0.0  0
 J1M  CONST_07  C23  C18  C19  C20     0.00   0.0  0
 J1M  CONST_08  C23  C22  C21  C20     0.00   0.0  0
 J1M  CONST_09  C13  C12  C25  C24     0.00   0.0  0
 J1M  CONST_10  C13  C14  C15  C24     0.00   0.0  0
 J1M  CONST_11  C22  C23  C18  C19     0.00   0.0  0
 J1M  CONST_12  C22  C21  C20  C19     0.00   0.0  0
 J1M  CONST_13  C08  C12  C13  C14   180.00   0.0  0
 J1M  CONST_14  C08  C12  C25  C24   180.00   0.0  0
 J1M  CONST_15  C09  C10  N05  C06     0.00   0.0  0
 J1M  CONST_16  C13  C14  C15  O16   180.00   0.0  0
 J1M  CONST_17  C25  C24  C15  O16   180.00   0.0  0
 J1M  CONST_18  C22  C23  C18  C17   180.00   0.0  0
 J1M  CONST_19  C20  C19  C18  C17   180.00   0.0  0
 J1M  CONST_20  C09  C10  N05  C04   180.00   0.0  0
 J1M  CONST_21  O11  C10  N05  C06   180.00   0.0  0
 J1M  CONST_22  H1   C14  C13  C12   180.00   0.0  0
 J1M  CONST_23  H7   C24  C25  C12   180.00   0.0  0
 J1M  CONST_24  H20  C13  C14  C15   180.00   0.0  0
 J1M  CONST_25  H8   C25  C24  C15   180.00   0.0  0
 J1M  CONST_26  H22  C22  C23  C18   180.00   0.0  0
 J1M  CONST_27  H4   C20  C19  C18   180.00   0.0  0
 J1M  CONST_28  H6   C23  C22  C21   180.00   0.0  0
 J1M  CONST_29  H21  C19  C20  C21   180.00   0.0  0
 J1M  CONST_30  H5   C21  C22  C23   180.00   0.0  0
 J1M  CONST_31  O11  C10  N05  C04     0.00   0.0  0
 J1M  CONST_32  O27  C26  N28  O29     0.00   0.0  0
 J1M  CONST_33  C02  C26  N28  O29   180.00   0.0  0
 J1M  CONST_34  H26  N28  C26  C02     0.00   0.0  0
 J1M  Var_01    C07  C08  C12  C25  -147.65  30.0  3
 J1M  Var_02    C18  C17  O16  C15  -178.86  30.0  2
 J1M  Var_03    C23  C18  C17  O16   -84.37  30.0  2
 J1M  Var_04    C24  C15  O16  C17    -0.11  30.0  1
 J1M  Var_05    C06  N05  C04  C03    95.01  30.0  3
 J1M  Var_06    N05  C04  C03  C02  -178.34  30.0  2
 J1M  Var_07    H23  C31  S30  C02   179.83  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
 J1M  chir_01  C02  S30  C03  C01  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
 J1M  plan-1  C17  0.020
 J1M  plan-1  C18  0.020
 J1M  plan-1  C20  0.020
 J1M  plan-1  C21  0.020
 J1M  plan-1  C23  0.020
 J1M  plan-1  C19  0.020
 J1M  plan-1  C22  0.020
 J1M  plan-1  H4   0.020
 J1M  plan-1  H5   0.020
 J1M  plan-1  H6   0.020
 J1M  plan-1  H21  0.020
 J1M  plan-1  H22  0.020
 J1M  plan-2  C12  0.020
 J1M  plan-2  C14  0.020
 J1M  plan-2  C15  0.020
 J1M  plan-2  O16  0.020
 J1M  plan-2  C24  0.020
 J1M  plan-2  C25  0.020
 J1M  plan-2  C08  0.020
 J1M  plan-2  C13  0.020
 J1M  plan-2  H1   0.020
 J1M  plan-2  H7   0.020
 J1M  plan-2  H8   0.020
 J1M  plan-2  H20  0.020
 J1M  plan-3  C12  0.020
 J1M  plan-3  C04  0.020
 J1M  plan-3  C06  0.020
 J1M  plan-3  C07  0.020
 J1M  plan-3  C08  0.020
 J1M  plan-3  C09  0.020
 J1M  plan-3  C10  0.020
 J1M  plan-3  N05  0.020
 J1M  plan-3  O11  0.020
 J1M  plan-3  H17  0.020
 J1M  plan-3  H18  0.020
 J1M  plan-3  H19  0.020
 J1M  plan-4  C26  0.020
 J1M  plan-4  C02  0.020
 J1M  plan-4  N28  0.020
 J1M  plan-4  O27  0.020
 J1M  plan-4  H26  0.020
 J1M  plan-4  O29  0.020

