# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 02:17:13 2021
#   Inital geometry file: a 165 line input string
#   Ligand name: (2R,5R)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}methyl]-5-methyl-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1CCN(C(=O)N[C@@H](C(=O)N[C@@H]([C@H]2SC[C@H](C)C(=N2)C(O)=O)C(O)=O)c3ccc(O)cc3)C(=O)C1=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
 59J  59J  '(2R,5R)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}methyl]-5-methyl-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  65  38  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_59J
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
 59J  C10  C  CR6   0   0.094  -41.7373   -9.5405  -38.6136
 59J  C12  C  CH2   0  -0.309  -42.1888   -5.3646  -41.9362
 59J  C13  C  CH2   0  -0.311  -42.9342   -4.1449  -42.4037
 59J  C14  C  CR16  0  -0.283  -42.0317  -10.3530  -39.7039
 59J  C15  C  CR16  0  -0.315  -40.6083   -9.8330  -37.8590
 59J  C16  C  C     0   0.484  -44.3691   -6.3213  -41.4723
 59J  C17  C  C     0   0.482  -44.8531   -5.5647  -42.7312
 59J  C20  C  CR16  0  -0.321  -41.2386  -11.4444  -40.0146
 59J  C21  C  CR16  0  -0.380  -39.8165  -10.9360  -38.1433
 59J  C22  C  CR6   0   0.354  -40.1357  -11.7569  -39.2209
 59J  C23  C  CH3   0  -0.664  -45.3337   -2.4602  -43.7155
 59J  S01  S  S2    0   0.001  -45.3596  -12.4262  -36.8513
 59J  O01  O  O     0  -0.418  -42.8207   -9.2012  -33.8007
 59J  O03  O  OH1   0  -0.570  -40.5656  -12.8229  -34.6797
 59J  O04  O  O     0  -0.416  -40.2966  -14.0744  -36.5077
 59J  O05  O  O     0  -0.488  -41.2429   -6.7863  -39.8688
 59J  O06  O  O     0  -0.437  -45.1965   -6.9881  -40.8886
 59J  O07  O  O     0  -0.462  -45.8943   -5.9403  -43.2339
 59J  O    O  OH1   0  -0.628  -39.4190  -12.8494  -39.5425
 59J  N01  N  N     0  -0.317  -43.0270  -12.3215  -35.2984
 59J  N02  N  NH1   0  -0.625  -43.4491   -9.7863  -36.3619
 59J  N03  N  NH1   0  -0.703  -43.2228   -7.6881  -39.2924
 59J  N04  N  NT    0  -0.591  -43.0621   -6.1993  -41.1088
 59J  N05  N  NT    0  -0.453  -44.1108   -4.5392  -43.1545
 59J  C01  C  CH1   0  -0.260  -44.3706  -11.8575  -35.4258
 59J  C02  C  CH1   0  -0.217  -44.3062  -10.3159  -35.3464
 59J  C03  C  C     0   0.569  -43.8026   -9.8708  -33.9767
 59J  C07  C  C     0   0.139  -42.4221  -13.0568  -36.1278
 59J  C04  C  CH1   0  -0.322  -42.9522  -13.6638  -37.3974
 59J  C05  C  CH2   0  -0.572  -44.0215  -12.7785  -38.0138
 59J  C06  C  C     0   0.568  -43.8325   -8.9552  -37.3446
 59J  C08  C  CH3   0  -0.643  -43.4318  -15.0948  -37.1461
 59J  CA   C  CH1   0  -0.255  -42.6628   -8.4213  -38.1921
 59J  C09  C  C     0   0.537  -40.9801  -13.3796  -35.7989
 59J  O08  O  OH1   0  -0.587  -44.5968  -10.3060  -33.0136
 59J  H2   H  HCH2  0   0.292  -41.3343   -5.0560  -41.3436
 59J  H3   H  HCH2  0   0.281  -42.2805   -3.5741  -43.0615
 59J  H4   H  HCH2  0   0.269  -43.1967   -3.5008  -41.5594
 59J  H5   H  HCR6  0   0.265  -42.8956  -10.1443  -40.3236
 59J  H6   H  HCR6  0   0.274  -40.3287   -9.1914  -37.0297
 59J  H7   H  HCH2  0   0.256  -43.7018   -3.3640  -44.8007
 59J  H8   H  HCH2  0   0.264  -45.2040   -4.2620  -44.8974
 59J  H9   H  HCR6  0   0.270  -41.4854  -12.0718  -40.8618
 59J  H10  H  HCR6  0   0.279  -38.9451  -11.1416  -37.5322
 59J  H11  H  HCH3  0   0.242  -45.6573   -1.8456  -44.5555
 59J  H12  H  HCH3  0   0.235  -46.2197   -2.7562  -43.1538
 59J  H13  H  HCH3  0   0.235  -44.7098   -1.8399  -43.0715
 59J  H14  H  HOH1  0   0.489  -39.6407  -13.0639  -34.5183
 59J  H15  H  HOH1  0   0.474  -38.7180  -12.9941  -38.8976
 59J  H16  H  HNH1  0   0.406  -42.4656   -9.9903  -36.2659
 59J  H17  H  HNH1  0   0.427  -44.2218   -7.7150  -39.4554
 59J  H18  H  HCH1  0   0.333  -44.9195  -12.2201  -34.5542
 59J  H19  H  HCH1  0   0.332  -45.3148   -9.9222  -35.4839
 59J  H20  H  HCH1  0   0.290  -42.1274  -13.7043  -38.1131
 59J  H21  H  HCH2  0   0.297  -44.4841  -13.2791  -38.8648
 59J  H22  H  HCH2  0   0.300  -43.5799  -11.8532  -38.3775
 59J  H23  H  HCH3  0   0.245  -42.6437  -15.7104  -36.7142
 59J  H24  H  HCH3  0   0.235  -44.2865  -15.1116  -36.4705
 59J  H25  H  HCH3  0   0.245  -43.7321  -15.5542  -38.0880
 59J  H26  H  HCH1  0   0.313  -42.1020   -7.7411  -37.5382
 59J  H27  H  HOH1  0   0.491  -44.2660  -10.0248  -32.1466
 59J  C11  C  C     0   0.784  -42.4391   -6.9095  -40.0462
 59J  O02  O  O     0  -0.458  -44.9841   -8.6225  -37.5506
 59J  H1   H  HCH2  0   0.275  -41.8207   -5.9394  -42.7884
 59J  C19  C  CH2   0  -0.319  -44.5773   -3.6755  -44.2289

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
 59J  C19  N05  single    1.455  0.020  1.455
 59J  C19  C23  single    1.521  0.020  1.521
 59J  O07  C17  double    1.216  0.020  1.216
 59J  N05  C17  single    1.335  0.020  1.335
 59J  N05  C13  single    1.450  0.020  1.450
 59J  C17  C16  single    1.546  0.020  1.546
 59J  C13  C12  single    1.504  0.020  1.504
 59J  C12  N04  single    1.464  0.020  1.464
 59J  O    C22  single    1.346  0.020  1.346
 59J  C20  C22  aromatic  1.394  0.020  1.394
 59J  C20  C14  aromatic  1.384  0.020  1.384
 59J  C16  N04  single    1.362  0.020  1.362
 59J  C16  O06  double    1.212  0.020  1.212
 59J  N04  C11  single    1.422  0.020  1.422
 59J  C22  C21  aromatic  1.392  0.020  1.392
 59J  C14  C10  aromatic  1.391  0.020  1.391
 59J  C11  O05  double    1.216  0.020  1.216
 59J  C11  N03  single    1.337  0.020  1.337
 59J  C21  C15  aromatic  1.387  0.020  1.387
 59J  N03  CA   single    1.436  0.020  1.436
 59J  C10  C15  aromatic  1.389  0.020  1.389
 59J  C10  CA   single    1.512  0.020  1.512
 59J  CA   C06  single    1.540  0.020  1.540
 59J  O02  C06  double    1.216  0.020  1.216
 59J  C06  N02  single    1.343  0.020  1.343
 59J  N02  C02  single    1.430  0.020  1.430
 59J  S01  C05  single    1.807  0.020  1.807
 59J  S01  C01  single    1.826  0.020  1.826
 59J  C05  C04  single    1.519  0.020  1.519
 59J  C02  C01  single    1.545  0.020  1.545
 59J  C02  C03  single    1.526  0.020  1.526
 59J  C01  N01  single    1.427  0.020  1.427
 59J  O01  C03  double    1.201  0.020  1.201
 59J  C03  O08  single    1.322  0.020  1.322
 59J  C04  C07  single    1.504  0.020  1.504
 59J  C04  C08  single    1.530  0.020  1.530
 59J  N01  C07  double    1.263  0.020  1.263
 59J  C07  C09  single    1.514  0.020  1.514
 59J  C09  O04  double    1.205  0.020  1.205
 59J  C09  O03  single    1.317  0.020  1.317
 59J  C12  H1   single    0.970  0.020  1.090
 59J  C12  H2   single    0.970  0.020  1.090
 59J  C13  H3   single    0.970  0.020  1.090
 59J  C13  H4   single    0.970  0.020  1.090
 59J  C14  H5   single    0.930  0.020  1.080
 59J  C15  H6   single    0.930  0.020  1.080
 59J  C19  H7   single    0.970  0.020  1.090
 59J  C19  H8   single    0.970  0.020  1.090
 59J  C20  H9   single    0.930  0.020  1.080
 59J  C21  H10  single    0.930  0.020  1.080
 59J  C23  H11  single    0.970  0.020  1.090
 59J  C23  H12  single    0.970  0.020  1.090
 59J  C23  H13  single    0.970  0.020  1.090
 59J  O03  H14  single    0.850  0.020  0.980
 59J  O    H15  single    0.850  0.020  0.980
 59J  N02  H16  single    0.860  0.020  1.020
 59J  N03  H17  single    0.860  0.020  1.020
 59J  C01  H18  single    0.970  0.020  1.090
 59J  C02  H19  single    0.970  0.020  1.090
 59J  C04  H20  single    0.970  0.020  1.090
 59J  C05  H21  single    0.970  0.020  1.090
 59J  C05  H22  single    0.970  0.020  1.090
 59J  C08  H23  single    0.970  0.020  1.090
 59J  C08  H24  single    0.970  0.020  1.090
 59J  C08  H25  single    0.970  0.020  1.090
 59J  CA   H26  single    0.970  0.020  1.090
 59J  O08  H27  single    0.850  0.020  0.980

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
 59J  CA   C10  C15  120.12  3.000
 59J  CA   C10  C14  121.42  3.000
 59J  C15  C10  C14  118.34  3.000
 59J  H2   C12  H1   108.09  3.000
 59J  H2   C12  N04  108.86  3.000
 59J  H1   C12  N04  110.00  3.000
 59J  H2   C12  C13  109.24  3.000
 59J  H1   C12  C13  110.58  3.000
 59J  N04  C12  C13  110.03  3.000
 59J  H4   C13  H3   107.56  3.000
 59J  H4   C13  N05  111.40  3.000
 59J  H3   C13  N05  108.47  3.000
 59J  H4   C13  C12  110.89  3.000
 59J  H3   C13  C12  108.38  3.000
 59J  N05  C13  C12  110.03  3.000
 59J  H5   C14  C20  118.70  3.000
 59J  H5   C14  C10  120.29  3.000
 59J  C20  C14  C10  121.00  3.000
 59J  H6   C15  C21  118.67  3.000
 59J  H6   C15  C10  120.00  3.000
 59J  C21  C15  C10  121.33  3.000
 59J  N04  C16  O06  125.15  3.000
 59J  O06  C16  C17  116.58  3.000
 59J  N04  C16  C17  118.27  3.000
 59J  N05  C17  O07  125.63  3.000
 59J  N05  C17  C16  117.39  3.000
 59J  O07  C17  C16  116.97  3.000
 59J  H9   C20  C22  119.73  3.000
 59J  H9   C20  C14  120.12  3.000
 59J  C22  C20  C14  120.14  3.000
 59J  H10  C21  C22  120.60  3.000
 59J  H10  C21  C15  119.61  3.000
 59J  C22  C21  C15  119.79  3.000
 59J  O    C22  C21  122.81  3.000
 59J  C21  C22  C20  119.34  3.000
 59J  O    C22  C20  117.86  3.000
 59J  H13  C23  H12  108.37  3.000
 59J  H13  C23  H11  107.71  3.000
 59J  H12  C23  H11  107.99  3.000
 59J  H13  C23  C19  111.68  3.000
 59J  H12  C23  C19  111.18  3.000
 59J  H11  C23  C19  109.76  3.000
 59J  C05  S01  C01   99.31  3.000
 59J  H14  O03  C09  109.67  3.000
 59J  H15  O    C22  110.46  3.000
 59J  C07  N01  C01  125.57  3.000
 59J  H16  N02  C06  118.23  3.000
 59J  H16  N02  C02  116.20  3.000
 59J  C06  N02  C02  125.28  3.000
 59J  H17  N03  CA   119.65  3.000
 59J  H17  N03  C11  120.19  3.000
 59J  CA   N03  C11  120.04  3.000
 59J  C16  N04  C12  118.20  3.000
 59J  C16  N04  C11  125.11  3.000
 59J  C12  N04  C11  116.47  3.000
 59J  C19  N05  C17  120.78  3.000
 59J  C17  N05  C13  119.73  3.000
 59J  C19  N05  C13  118.74  3.000
 59J  H18  C01  C02  108.13  3.000
 59J  H18  C01  N01  107.10  3.000
 59J  C02  C01  N01  106.29  3.000
 59J  H18  C01  S01  104.33  3.000
 59J  N01  C01  S01  118.58  3.000
 59J  C02  C01  S01  111.93  3.000
 59J  H19  C02  C03  108.23  3.000
 59J  H19  C02  C01  108.36  3.000
 59J  C03  C02  C01  110.55  3.000
 59J  H19  C02  N02  109.31  3.000
 59J  C03  C02  N02  109.36  3.000
 59J  C01  C02  N02  110.97  3.000
 59J  O08  C03  C02  111.08  3.000
 59J  O08  C03  O01  124.60  3.000
 59J  C02  C03  O01  124.32  3.000
 59J  C09  C07  C04  115.67  3.000
 59J  C09  C07  N01  115.96  3.000
 59J  C04  C07  N01  128.37  3.000
 59J  H20  C04  C08  108.03  3.000
 59J  H20  C04  C05  106.68  3.000
 59J  C08  C04  C05  113.02  3.000
 59J  H20  C04  C07  107.57  3.000
 59J  C08  C04  C07  110.45  3.000
 59J  C05  C04  C07  110.83  3.000
 59J  H22  C05  H21  107.57  3.000
 59J  H22  C05  C04  110.22  3.000
 59J  H21  C05  C04  110.35  3.000
 59J  H22  C05  S01  110.48  3.000
 59J  H21  C05  S01  106.10  3.000
 59J  C04  C05  S01  111.95  3.000
 59J  CA   C06  N02  113.61  3.000
 59J  N02  C06  O02  124.30  3.000
 59J  CA   C06  O02  122.09  3.000
 59J  H25  C08  H24  108.25  3.000
 59J  H25  C08  H23  107.68  3.000
 59J  H24  C08  H23  108.24  3.000
 59J  H25  C08  C04  109.79  3.000
 59J  H24  C08  C04  111.24  3.000
 59J  H23  C08  C04  111.52  3.000
 59J  H26  CA   C06  105.97  3.000
 59J  H26  CA   N03  109.84  3.000
 59J  C06  CA   N03  107.60  3.000
 59J  H26  CA   C10  108.18  3.000
 59J  C06  CA   C10  111.20  3.000
 59J  N03  CA   C10  113.76  3.000
 59J  C07  C09  O04  122.37  3.000
 59J  O04  C09  O03  124.41  3.000
 59J  C07  C09  O03  113.22  3.000
 59J  H27  O08  C03  110.54  3.000
 59J  N04  C11  N03  117.09  3.000
 59J  N03  C11  O05  123.60  3.000
 59J  N04  C11  O05  119.31  3.000
 59J  H8   C19  H7   107.10  3.000
 59J  H8   C19  N05  108.56  3.000
 59J  H7   C19  N05  107.41  3.000
 59J  H8   C19  C23  110.59  3.000
 59J  H7   C19  C23  110.36  3.000
 59J  N05  C19  C23  112.61  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
 59J  CONST_01  C22  C20  C14  C10    0.00   0.0  0
 59J  CONST_02  C22  C21  C15  C10    0.00   0.0  0
 59J  CONST_03  C21  C22  C20  C14    0.00   0.0  0
 59J  CONST_04  C21  C15  C10  C14    0.00   0.0  0
 59J  CONST_05  C20  C22  C21  C15    0.00   0.0  0
 59J  CONST_06  C20  C14  C10  C15    0.00   0.0  0
 59J  CONST_07  C17  C16  N04  C12    0.00   0.0  0
 59J  CONST_08  C16  C17  N05  C13    0.00   0.0  0
 59J  CONST_09  O    C22  C20  C14  180.00   0.0  0
 59J  CONST_10  O    C22  C21  C15  180.00   0.0  0
 59J  CONST_11  CA   C10  C14  C20  180.00   0.0  0
 59J  CONST_12  CA   C10  C15  C21  180.00   0.0  0
 59J  CONST_13  C17  C16  N04  C11  180.00   0.0  0
 59J  CONST_14  O06  C16  N04  C12  180.00   0.0  0
 59J  CONST_15  O07  C17  N05  C13  180.00   0.0  0
 59J  CONST_16  C19  N05  C17  C16  180.00   0.0  0
 59J  CONST_17  H9   C20  C14  C10  180.00   0.0  0
 59J  CONST_18  H10  C21  C15  C10  180.00   0.0  0
 59J  CONST_19  H6   C15  C10  C14  180.00   0.0  0
 59J  CONST_20  H5   C14  C10  C15  180.00   0.0  0
 59J  CONST_21  O05  C11  N04  C12    0.00   0.0  0
 59J  CONST_22  O05  C11  N04  C16  180.00   0.0  0
 59J  CONST_23  O06  C16  N04  C11    0.00   0.0  0
 59J  CONST_24  N03  C11  N04  C12  180.00   0.0  0
 59J  CONST_25  N03  C11  N04  C16    0.00   0.0  0
 59J  CONST_26  O07  C17  N05  C19    0.00   0.0  0
 59J  CONST_27  CA   N03  C11  N04  180.00   0.0  0
 59J  CONST_28  H17  N03  C11  N04    0.00   0.0  0
 59J  CONST_29  H14  O03  C09  C07  180.00   0.0  0
 59J  CONST_30  C02  N02  C06  O02    0.00   0.0  0
 59J  CONST_31  CA   N03  C11  O05    0.00   0.0  0
 59J  CONST_32  CA   C06  N02  C02  180.00   0.0  0
 59J  CONST_33  H16  N02  C06  O02  180.00   0.0  0
 59J  CONST_34  H27  O08  C03  O01    0.00   0.0  0
 59J  Var_01    C17  N05  C13  C12   40.99  30.0  1
 59J  Var_02    C16  N04  C12  C13   38.54  30.0  1
 59J  Var_03    N05  C13  C12  N04  -58.32  30.0  1
 59J  Var_04    N05  C17  C16  N04  -19.81  30.0  1
 59J  Var_05    C04  C05  S01  C01   50.91  30.0  1
 59J  Var_06    C04  C07  N01  C01   -2.62  30.0  1
 59J  Var_07    C23  C19  N05  C13  -77.63  30.0  3
 59J  Var_08    H11  C23  C19  N05  179.78  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
 59J  chir_01  C01  S01  C02  N01  positiv
 59J  chir_02  C02  N02  C01  C03  negativ
 59J  chir_03  C04  C08  C07  C05  positiv
 59J  chir_04  CA   N03  C10  C06  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
 59J  plan-1  C10  0.020
 59J  plan-1  C14  0.020
 59J  plan-1  C15  0.020
 59J  plan-1  C20  0.020
 59J  plan-1  C21  0.020
 59J  plan-1  C22  0.020
 59J  plan-1  O    0.020
 59J  plan-1  CA   0.020
 59J  plan-1  H5   0.020
 59J  plan-1  H6   0.020
 59J  plan-1  H9   0.020
 59J  plan-1  H10  0.020
 59J  plan-2  O01  0.020
 59J  plan-2  C02  0.020
 59J  plan-2  C03  0.020
 59J  plan-2  O08  0.020
 59J  plan-2  H27  0.020
 59J  plan-3  O03  0.020
 59J  plan-3  O04  0.020
 59J  plan-3  C07  0.020
 59J  plan-3  C09  0.020
 59J  plan-3  H14  0.020
 59J  plan-4  N02  0.020
 59J  plan-4  C02  0.020
 59J  plan-4  C06  0.020
 59J  plan-4  CA   0.020
 59J  plan-4  H16  0.020
 59J  plan-4  O02  0.020
 59J  plan-5  C12  0.020
 59J  plan-5  C16  0.020
 59J  plan-5  C17  0.020
 59J  plan-5  O05  0.020
 59J  plan-5  O06  0.020
 59J  plan-5  N03  0.020
 59J  plan-5  N04  0.020
 59J  plan-5  CA   0.020
 59J  plan-5  H17  0.020
 59J  plan-5  C11  0.020
 59J  plan-6  C13  0.020
 59J  plan-6  C16  0.020
 59J  plan-6  C17  0.020
 59J  plan-6  O07  0.020
 59J  plan-6  N05  0.020
 59J  plan-6  C19  0.020

