# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 20:37:31 2021
#   Inital geometry file: a 163 line input string
#   Ligand name: (2R,4R,5R)-2-[(1R)-1-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}-2-oxoethyl]-5-methyl-1,3-thiazinane-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=O)[C@@H]2N[C@H]([C@@H](C)CS2)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
 59F  59F  '(2R,4R,5R)-2-[(1R)-1-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-(4-hydroxyphenyl)acetyl]amino}-2-oxoethyl]-5-methyl-1,3-thiazinane-4-carboxylic acid'  ligand  66  37  .  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_59F
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
 59F  C11  C  C     0   0.780   0.7553   8.3638  22.8509
 59F  C13  C  CH2   0  -0.314   4.2979   9.3550  22.9830
 59F  C14  C  CR16  0  -0.256  -2.4119   8.9512  24.3749
 59F  C15  C  CR16  0  -0.311  -3.2183   8.5459  22.1635
 59F  C17  C  C     0   0.483   3.6523   9.0610  25.2839
 59F  S01  S  S2    0   0.009  -4.7443   6.0427  25.4755
 59F  O02  O  O     0  -0.470  -1.4027   5.7281  24.9612
 59F  O05  O  O     0  -0.492   0.4439   8.8604  21.7854
 59F  O06  O  O     0  -0.437   1.7448   7.6971  25.4738
 59F  O07  O  O     0  -0.462   3.7827   9.0746  26.4925
 59F  O    O  OH1   0  -0.634  -5.2511  11.1376  23.6549
 59F  N01  N  NH1   0  -0.572  -5.7862   4.7962  23.2527
 59F  N02  N  NH1   0  -0.629  -2.7519   5.2121  23.2195
 59F  N03  N  NH1   0  -0.696   0.0029   7.4728  23.5036
 59F  N04  N  NT    0  -0.589   1.9950   8.7244  23.4465
 59F  N05  N  NT    0  -0.453   4.5388   9.5285  24.4024
 59F  C01  C  CH1   0  -0.243  -4.8862   4.5811  24.3617
 59F  C02  C  CH1   0  -0.186  -3.4853   4.1707  23.8763
 59F  C03  C  C1    0   0.194  -3.6668   2.9779  22.9667
 59F  C07  C  CH1   0  -0.228  -5.9109   6.1733  22.8214
 59F  C04  C  CH1   0  -0.209  -6.7533   7.0353  23.7958
 59F  C05  C  CH2   0  -0.576  -6.4497   6.6036  25.2374
 59F  C06  C  C     0   0.583  -1.8078   5.9429  23.8323
 59F  C08  C  CH3   0  -0.689  -8.2578   6.9375  23.5615
 59F  CA   C  CH1   0  -0.277  -1.3070   7.1337  23.0156
 59F  C09  C  C     0   0.544  -6.4298   6.3103  21.4084
 59F  C10  C  CR6   0   0.130  -2.3182   8.2498  23.1785
 59F  C12  C  CH2   0  -0.304   2.8508   9.6206  22.6662
 59F  C16  C  C     0   0.482   2.3625   8.4219  24.7232
 59F  C19  C  CH2   0  -0.320   5.8458   9.9942  24.8412
 59F  C20  C  CR16  0  -0.369  -3.3767   9.9272  24.5544
 59F  C21  C  CR16  0  -0.316  -4.1964   9.5130  22.3313
 59F  C22  C  CR6   0   0.348  -4.2818  10.2085  23.5333
 59F  C23  C  CH3   0  -0.664   6.8889   8.8876  24.8482
 59F  H1   H  HCH2  0   0.269   4.5925   8.3560  22.6477
 59F  H2   H  HCH2  0   0.282   4.9053  10.0774  22.4403
 59F  H3   H  HCR6  0   0.247  -1.7252   8.7422  25.1860
 59F  H4   H  HCR6  0   0.259  -3.1622   8.0171  21.2186
 59F  H5   H  HOH1  0   0.483  -7.3586   5.3824  20.0537
 59F  H6   H  HOH1  0   0.473  -5.2263  11.5373  24.5313
 59F  H9   H  HNH1  0   0.402  -2.9731   5.4141  22.2567
 59F  H10  H  HNH1  0   0.426   0.2861   7.1362  24.4156
 59F  H11  H  HCH1  0   0.303  -5.2791   3.7438  24.9421
 59F  H12  H  HCH1  0   0.314  -2.9105   3.8276  24.7436
 59F  H13  H  H     0   0.212  -4.2802   2.1728  23.4043
 59F  H14  H  HCH1  0   0.306  -4.9130   6.6148  22.8078
 59F  H15  H  HCH1  0   0.264  -6.4361   8.0729  23.6650
 59F  H16  H  HCH2  0   0.295  -6.6089   7.4339  25.9251
 59F  H17  H  HCH2  0   0.266  -7.1227   5.8012  25.5506
 59F  H18  H  HCH3  0   0.250  -8.7975   7.4675  24.3473
 59F  H19  H  HCH3  0   0.244  -8.5577   7.3813  22.6119
 59F  H20  H  HCH3  0   0.225  -8.6019   5.9004  23.5770
 59F  H21  H  HCH1  0   0.305  -1.2511   6.8528  21.9593
 59F  H22  H  HCH2  0   0.274   2.5946  10.6617  22.8733
 59F  H23  H  HCH2  0   0.290   2.6823   9.4341  21.6108
 59F  H24  H  HCH2  0   0.264   5.7440  10.4308  25.8327
 59F  H25  H  HCH2  0   0.257   6.1486  10.7975  24.1682
 59F  H26  H  HCR6  0   0.269  -3.4281  10.4643  25.4950
 59F  H27  H  HCR6  0   0.261  -4.8990   9.7212  21.5351
 59F  H28  H  HCH3  0   0.242   7.8518   9.2889  25.1638
 59F  H29  H  HCH3  0   0.235   6.6136   8.0907  25.5387
 59F  H30  H  HCH3  0   0.235   7.0198   8.4521  23.8573
 59F  H7   H  HNH1  0   0.372  -6.6915   4.3933  23.4553
 59F  O01  O  O     0  -0.362  -3.1860   2.8826  21.8694
 59F  O03  O  OH1   0  -0.580  -7.0158   5.2180  20.9458
 59F  O04  O  O     0  -0.438  -6.3390   7.3352  20.7780

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
 59F  O04  C09  double    1.207  0.020  1.207
 59F  O01  C03  double    1.202  0.020  1.202
 59F  C09  O03  single    1.323  0.020  1.323
 59F  C09  C07  single    1.512  0.020  1.512
 59F  O05  C11  double    1.216  0.020  1.216
 59F  C03  C02  single    1.511  0.020  1.511
 59F  C07  N01  single    1.448  0.020  1.448
 59F  C07  C04  single    1.550  0.020  1.550
 59F  N01  C01  single    1.444  0.020  1.444
 59F  N02  C02  single    1.433  0.020  1.433
 59F  N02  C06  single    1.342  0.020  1.342
 59F  C12  C13  single    1.505  0.020  1.505
 59F  C12  N04  single    1.464  0.020  1.464
 59F  C11  N04  single    1.422  0.020  1.422
 59F  C11  N03  single    1.336  0.020  1.336
 59F  C15  C21  aromatic  1.386  0.020  1.386
 59F  C15  C10  aromatic  1.389  0.020  1.389
 59F  CA   C10  single    1.515  0.020  1.515
 59F  CA   C06  single    1.528  0.020  1.528
 59F  CA   N03  single    1.438  0.020  1.438
 59F  C21  C22  aromatic  1.391  0.020  1.391
 59F  C02  C01  single    1.538  0.020  1.538
 59F  C10  C14  aromatic  1.390  0.020  1.390
 59F  C13  N05  single    1.450  0.020  1.450
 59F  C08  C04  single    1.526  0.020  1.526
 59F  C04  C05  single    1.535  0.020  1.535
 59F  N04  C16  single    1.363  0.020  1.363
 59F  C06  O02  double    1.218  0.020  1.218
 59F  C22  O    single    1.348  0.020  1.348
 59F  C22  C20  aromatic  1.393  0.020  1.393
 59F  C01  S01  single    1.843  0.020  1.843
 59F  C14  C20  aromatic  1.384  0.020  1.384
 59F  C23  C19  single    1.521  0.020  1.521
 59F  S01  C05  single    1.811  0.020  1.811
 59F  N05  C19  single    1.455  0.020  1.455
 59F  N05  C17  single    1.335  0.020  1.335
 59F  C16  O06  double    1.213  0.020  1.213
 59F  C16  C17  single    1.545  0.020  1.545
 59F  C17  O07  double    1.216  0.020  1.216
 59F  C13  H1   single    0.970  0.020  1.090
 59F  C13  H2   single    0.970  0.020  1.090
 59F  C14  H3   single    0.930  0.020  1.080
 59F  C15  H4   single    0.930  0.020  1.080
 59F  O03  H5   single    0.850  0.020  0.980
 59F  O    H6   single    0.850  0.020  0.980
 59F  N01  H7   single    0.890  0.020  1.040
 59F  N02  H9   single    0.860  0.020  1.020
 59F  N03  H10  single    0.860  0.020  1.020
 59F  C01  H11  single    0.970  0.020  1.090
 59F  C02  H12  single    0.970  0.020  1.090
 59F  C03  H13  single    0.930  0.020  1.080
 59F  C07  H14  single    0.970  0.020  1.090
 59F  C04  H15  single    0.970  0.020  1.090
 59F  C05  H16  single    0.970  0.020  1.090
 59F  C05  H17  single    0.970  0.020  1.090
 59F  C08  H18  single    0.970  0.020  1.090
 59F  C08  H19  single    0.970  0.020  1.090
 59F  C08  H20  single    0.970  0.020  1.090
 59F  CA   H21  single    0.970  0.020  1.090
 59F  C12  H22  single    0.970  0.020  1.090
 59F  C12  H23  single    0.970  0.020  1.090
 59F  C19  H24  single    0.970  0.020  1.090
 59F  C19  H25  single    0.970  0.020  1.090
 59F  C20  H26  single    0.930  0.020  1.080
 59F  C21  H27  single    0.930  0.020  1.080
 59F  C23  H28  single    0.970  0.020  1.090
 59F  C23  H29  single    0.970  0.020  1.090
 59F  C23  H30  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
 59F  N04  C11  N03  117.09  3.000
 59F  N03  C11  O05  123.78  3.000
 59F  N04  C11  O05  119.13  3.000
 59F  H2   C13  H1   107.63  3.000
 59F  H2   C13  C12  108.33  3.000
 59F  H1   C13  C12  110.83  3.000
 59F  H2   C13  N05  108.41  3.000
 59F  H1   C13  N05  111.38  3.000
 59F  C12  C13  N05  110.16  3.000
 59F  H3   C14  C20  118.74  3.000
 59F  H3   C14  C10  120.29  3.000
 59F  C20  C14  C10  120.96  3.000
 59F  H4   C15  C21  118.84  3.000
 59F  H4   C15  C10  119.97  3.000
 59F  C21  C15  C10  121.19  3.000
 59F  C16  C17  N05  117.37  3.000
 59F  C16  C17  O07  117.07  3.000
 59F  N05  C17  O07  125.55  3.000
 59F  C05  S01  C01   95.38  3.000
 59F  H6   O    C22  110.45  3.000
 59F  H7   N01  C07  111.18  3.000
 59F  H7   N01  C01  110.16  3.000
 59F  C07  N01  C01  115.08  3.000
 59F  H9   N02  C06  118.77  3.000
 59F  H9   N02  C02  118.09  3.000
 59F  C06  N02  C02  123.13  3.000
 59F  H10  N03  CA   118.81  3.000
 59F  H10  N03  C11  120.27  3.000
 59F  CA   N03  C11  120.28  3.000
 59F  C16  N04  C12  118.52  3.000
 59F  C16  N04  C11  124.84  3.000
 59F  C12  N04  C11  116.21  3.000
 59F  C19  N05  C17  120.62  3.000
 59F  C17  N05  C13  119.62  3.000
 59F  C19  N05  C13  118.86  3.000
 59F  H11  C01  C02  106.90  3.000
 59F  H11  C01  N01  107.35  3.000
 59F  C02  C01  N01  111.40  3.000
 59F  H11  C01  S01  108.33  3.000
 59F  C02  C01  S01  109.40  3.000
 59F  N01  C01  S01  113.20  3.000
 59F  H12  C02  C03  107.00  3.000
 59F  H12  C02  C01  108.15  3.000
 59F  C03  C02  C01  106.93  3.000
 59F  H12  C02  N02  108.77  3.000
 59F  C01  C02  N02  114.63  3.000
 59F  C03  C02  N02  111.05  3.000
 59F  H13  C03  C02  113.85  3.000
 59F  H13  C03  O01  121.80  3.000
 59F  C02  C03  O01  124.35  3.000
 59F  H14  C07  C09  105.41  3.000
 59F  H14  C07  C04  106.25  3.000
 59F  C09  C07  C04  110.53  3.000
 59F  H14  C07  N01  108.03  3.000
 59F  C04  C07  N01  112.85  3.000
 59F  C09  C07  N01  113.21  3.000
 59F  H15  C04  C08  109.19  3.000
 59F  H15  C04  C05  108.78  3.000
 59F  C08  C04  C05  108.73  3.000
 59F  H15  C04  C07  107.16  3.000
 59F  C05  C04  C07  109.05  3.000
 59F  C08  C04  C07  113.82  3.000
 59F  H17  C05  H16  106.77  3.000
 59F  H17  C05  C04  110.72  3.000
 59F  H16  C05  C04  110.45  3.000
 59F  H17  C05  S01  108.35  3.000
 59F  H16  C05  S01  106.89  3.000
 59F  C04  C05  S01  113.38  3.000
 59F  CA   C06  N02  114.25  3.000
 59F  CA   C06  O02  121.57  3.000
 59F  N02  C06  O02  124.12  3.000
 59F  H20  C08  H19  108.18  3.000
 59F  H20  C08  H18  107.17  3.000
 59F  H19  C08  H18  107.07  3.000
 59F  H20  C08  C04  111.67  3.000
 59F  H19  C08  C04  112.26  3.000
 59F  H18  C08  C04  110.25  3.000
 59F  H21  CA   C10  109.09  3.000
 59F  H21  CA   C06  109.42  3.000
 59F  C10  CA   C06  107.32  3.000
 59F  H21  CA   N03  109.97  3.000
 59F  C06  CA   N03  107.50  3.000
 59F  C10  CA   N03  113.43  3.000
 59F  C07  C09  O04  122.65  3.000
 59F  C07  C09  O03  113.84  3.000
 59F  O04  C09  O03  123.50  3.000
 59F  CA   C10  C15  120.74  3.000
 59F  CA   C10  C14  120.62  3.000
 59F  C15  C10  C14  118.55  3.000
 59F  H23  C12  H22  108.17  3.000
 59F  H23  C12  N04  108.80  3.000
 59F  H22  C12  N04  110.21  3.000
 59F  H23  C12  C13  108.89  3.000
 59F  H22  C12  C13  110.73  3.000
 59F  N04  C12  C13  109.98  3.000
 59F  N04  C16  O06  125.12  3.000
 59F  O06  C16  C17  116.61  3.000
 59F  N04  C16  C17  118.26  3.000
 59F  H25  C19  H24  107.02  3.000
 59F  H25  C19  C23  110.38  3.000
 59F  H24  C19  C23  110.60  3.000
 59F  H25  C19  N05  107.39  3.000
 59F  H24  C19  N05  108.61  3.000
 59F  C23  C19  N05  112.62  3.000
 59F  H26  C20  C22  120.33  3.000
 59F  H26  C20  C14  119.66  3.000
 59F  C22  C20  C14  120.01  3.000
 59F  H27  C21  C22  119.97  3.000
 59F  H27  C21  C15  120.23  3.000
 59F  C22  C21  C15  119.79  3.000
 59F  C21  C22  C20  119.50  3.000
 59F  C20  C22  O    122.69  3.000
 59F  C21  C22  O    117.81  3.000
 59F  H30  C23  H29  108.30  3.000
 59F  H30  C23  H28  107.71  3.000
 59F  H29  C23  H28  108.00  3.000
 59F  H30  C23  C19  111.64  3.000
 59F  H29  C23  C19  111.21  3.000
 59F  H28  C23  C19  109.84  3.000
 59F  H5   O03  C09  109.77  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
 59F  CONST_01  C21  C15  C10  C14    0.00   0.0  0
 59F  CONST_02  C21  C22  C20  C14    0.00   0.0  0
 59F  CONST_03  C20  C22  C21  C15    0.00   0.0  0
 59F  CONST_04  C20  C14  C10  C15    0.00   0.0  0
 59F  CONST_05  C22  C21  C15  C10    0.00   0.0  0
 59F  CONST_06  C22  C20  C14  C10    0.00   0.0  0
 59F  CONST_07  C16  C17  N05  C13    0.00   0.0  0
 59F  CONST_08  O    C22  C20  C14  180.00   0.0  0
 59F  CONST_09  O    C22  C21  C15  180.00   0.0  0
 59F  CONST_10  C21  C15  C10  CA   180.00   0.0  0
 59F  CONST_11  C20  C14  C10  CA   180.00   0.0  0
 59F  CONST_12  O07  C17  N05  C13  180.00   0.0  0
 59F  CONST_13  C19  N05  C17  C16  180.00   0.0  0
 59F  CONST_14  H4   C15  C10  C14  180.00   0.0  0
 59F  CONST_15  H3   C14  C10  C15  180.00   0.0  0
 59F  CONST_16  H27  C21  C15  C10  180.00   0.0  0
 59F  CONST_17  H26  C20  C14  C10  180.00   0.0  0
 59F  CONST_18  C12  N04  C11  O05    0.00   0.0  0
 59F  CONST_19  C16  N04  C11  O05  180.00   0.0  0
 59F  CONST_20  C19  N05  C17  O07    0.00   0.0  0
 59F  CONST_21  C12  N04  C11  N03  180.00   0.0  0
 59F  CONST_22  C16  N04  C11  N03    0.00   0.0  0
 59F  CONST_23  CA   N03  C11  N04  180.00   0.0  0
 59F  CONST_24  H10  N03  C11  N04    0.00   0.0  0
 59F  CONST_25  H5   O03  C09  C07  180.00   0.0  0
 59F  CONST_26  C02  N02  C06  O02    0.00   0.0  0
 59F  CONST_27  CA   N03  C11  O05    0.00   0.0  0
 59F  CONST_28  CA   C06  N02  C02  180.00   0.0  0
 59F  CONST_29  H9   N02  C06  O02  180.00   0.0  0
 59F  Var_01    C16  N04  C12  C13   37.06  30.0  1
 59F  Var_02    C12  C13  N05  C17   41.83  30.0  1
 59F  Var_03    C12  N04  C16  C17    0.96  30.0  1
 59F  Var_04    N05  C13  C12  N04  -57.89  30.0  1
 59F  Var_05    N05  C17  C16  N04  -19.99  30.0  1
 59F  Var_06    C04  C05  S01  C01  -64.26  30.0  1
 59F  Var_07    C23  C19  N05  C13  -79.00  30.0  3
 59F  Var_08    H28  C23  C19  N05  178.88  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
 59F  chir_01  C01  N01  C02  S01  negativ
 59F  chir_02  C02  N02  C01  C03  negativ
 59F  chir_03  C07  N01  C09  C04  negativ
 59F  chir_04  C04  C07  C08  C05  negativ
 59F  chir_05  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
 59F  plan-1  C14  0.020
 59F  plan-1  C15  0.020
 59F  plan-1  O    0.020
 59F  plan-1  CA   0.020
 59F  plan-1  C10  0.020
 59F  plan-1  C20  0.020
 59F  plan-1  C21  0.020
 59F  plan-1  C22  0.020
 59F  plan-1  H3   0.020
 59F  plan-1  H4   0.020
 59F  plan-1  H26  0.020
 59F  plan-1  H27  0.020
 59F  plan-2  C07  0.020
 59F  plan-2  C09  0.020
 59F  plan-2  H5   0.020
 59F  plan-2  O03  0.020
 59F  plan-2  O04  0.020
 59F  plan-3  C02  0.020
 59F  plan-3  C03  0.020
 59F  plan-3  H13  0.020
 59F  plan-3  O01  0.020
 59F  plan-4  C11  0.020
 59F  plan-4  O05  0.020
 59F  plan-4  N03  0.020
 59F  plan-4  N04  0.020
 59F  plan-4  CA   0.020
 59F  plan-4  C12  0.020
 59F  plan-4  C16  0.020
 59F  plan-4  H10  0.020
 59F  plan-5  O02  0.020
 59F  plan-5  N02  0.020
 59F  plan-5  C02  0.020
 59F  plan-5  C06  0.020
 59F  plan-5  CA   0.020
 59F  plan-5  H9   0.020
 59F  plan-6  C17  0.020
 59F  plan-6  O06  0.020
 59F  plan-6  N04  0.020
 59F  plan-6  C16  0.020
 59F  plan-7  C13  0.020
 59F  plan-7  C17  0.020
 59F  plan-7  O07  0.020
 59F  plan-7  N05  0.020
 59F  plan-7  C16  0.020
 59F  plan-7  C19  0.020

