# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 15:40:35 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (2R,3R)-2,3-dihydroxy-4-oxo-4-[(2R)-2-phenylpyrrolidin-1-yl]-N-(thiophen-2-ylmethyl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]([C@@H](O)C(=O)N1CCC[C@@H]1c2ccccc2)C(=O)NCc3sccc3
#
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
 Z59  Z59  (2R,3R)-2,3-dihydroxy-4-oxo-4-[(2R)-2-phenylpyrrolidin-1-yl]-N-(thiophen-2-ylmethyl)butanamide  ligand  48  26  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z59
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
 Z59  C1    C  C     0   0.574  -1.2022   0.2687  -0.8178
 Z59  N2    N  NR5   0  -0.462  -1.7926   1.1684  -0.0225
 Z59  C3    C  CH1   0  -0.113   0.2172  -0.1935  -0.4756
 Z59  C4    C  CH1   0  -0.125   0.1908  -1.0233   0.8269
 Z59  C5    C  CR15  0  -0.138  -3.1625   1.6118  -0.2955
 Z59  C6    C  C     0   0.514   1.5763  -1.6384   1.0297
 Z59  C7    C  CR6   0   0.089  -4.1862   0.5084  -0.2463
 Z59  N8    N  NH1   0  -0.678   2.5216  -0.7723   1.4312
 Z59  S9    S  S2    0   0.117   4.2622  -0.0497  -1.0655
 Z59  C10   C  CR5   0  -0.264   4.7392  -0.2424   0.5807
 Z59  O11   O  O     0  -0.528  -1.7555  -0.2201  -1.7933
 Z59  C12   C  CR16  0  -0.242  -4.1054  -0.5161   0.6922
 Z59  C13   C  CR15  0  -0.394   5.6265   0.9322  -1.4070
 Z59  O14   O  O     0  -0.369   1.7727  -2.8192   0.8043
 Z59  C15   C  CR15  0  -0.089   5.8936   0.4330   0.8361
 Z59  C16   C  CR15  0  -0.229   6.4078   1.1056  -0.3077
 Z59  O17   O  OH1   0  -0.627   0.7091  -0.9600  -1.5282
 Z59  C18   C  CH2   0  -0.279   3.9301  -1.0806   1.5185
 Z59  O19   O  OH1   0  -0.561  -0.7848  -2.0142   0.7860
 Z59  C20   C  CH2   0  -0.305  -1.1353   1.9841   0.9965
 Z59  C21   C  CR16  0  -0.304  -5.0981  -1.4823   0.7659
 Z59  C23   C  CH2   0  -0.444  -3.3951   2.6774   0.7833
 Z59  C24   C  CR16  0  -0.276  -5.2772   0.5481  -1.1059
 Z59  C25   C  CH2   0  -0.470  -2.0038   3.2328   1.0496
 Z59  C26   C  CR16  0  -0.266  -6.2772  -0.4127  -1.0291
 Z59  C27   C  CR16  0  -0.180  -6.1897  -1.4329  -0.0927
 Z59  H3    H  HCH1  0   0.219   0.8706   0.6766  -0.3340
 Z59  H4    H  HCH1  0   0.259  -0.0347  -0.3662   1.6732
 Z59  H5    H  HCR5  0   0.246  -3.1954   2.0799  -1.2855
 Z59  HN8   H  HNH1  0   0.383   2.2521   0.1764   1.6400
 Z59  H12   H  HCR6  0   0.242  -3.2564  -0.5715   1.3618
 Z59  H13   H  HCR5  0   0.306   5.7712   1.3385  -2.3961
 Z59  H15   H  HCR5  0   0.276   6.3608   0.4555   1.8112
 Z59  H16   H  HCR5  0   0.197   7.3114   1.6980  -0.3050
 Z59  HO17  H  HOH1  0   0.448  -0.0526  -1.1756  -2.0890
 Z59  H18   H  HCH2  0   0.293   4.2903  -0.9184   2.5364
 Z59  H18A  H  HCH2  0   0.269   4.0535  -2.1417   1.3021
 Z59  HO19  H  HOH1  0   0.443  -0.4113  -2.7802   0.3314
 Z59  H20   H  HCH2  0   0.286  -1.1316   1.4769   1.9656
 Z59  H20A  H  HCH2  0   0.213  -0.1041   2.2092   0.7257
 Z59  H21   H  HCR6  0   0.261  -5.0181  -2.2777   1.4956
 Z59  H23   H  HCH2  0   0.281  -4.1122   3.4287   0.4553
 Z59  H23A  H  HCH2  0   0.214  -3.7925   2.2105   1.6879
 Z59  H24   H  HCR6  0   0.260  -5.3474   1.3355  -1.8477
 Z59  H25   H  HCH2  0   0.241  -1.9237   3.7492   2.0051
 Z59  H25A  H  HCH2  0   0.270  -1.7096   3.9297   0.2622
 Z59  H26   H  HCR6  0   0.203  -7.1204  -0.3672  -1.7062
 Z59  H27   H  HCR6  0   0.239  -6.9639  -2.1866  -0.0330

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
 Z59  N2   C1    single    1.338  0.020  1.338
 Z59  C1   O11   double    1.223  0.020  1.223
 Z59  C1   C3    single    1.531  0.020  1.531
 Z59  C5   N2    single    1.466  0.020  1.466
 Z59  C20  N2    single    1.461  0.020  1.461
 Z59  C3   C4    single    1.545  0.020  1.545
 Z59  C3   O17   single    1.392  0.020  1.392
 Z59  C3   H3    single    0.970  0.020  1.090
 Z59  C4   O19   single    1.391  0.020  1.391
 Z59  C4   C6    single    1.529  0.020  1.529
 Z59  C4   H4    single    0.970  0.020  1.090
 Z59  C23  C5    single    1.534  0.020  1.534
 Z59  C5   C7    single    1.506  0.020  1.506
 Z59  C5   H5    single    0.970  0.020  1.090
 Z59  O14  C6    double    1.218  0.020  1.218
 Z59  C6   N8    single    1.343  0.020  1.343
 Z59  C12  C7    aromatic  1.392  0.020  1.392
 Z59  C7   C24   aromatic  1.390  0.020  1.390
 Z59  N8   C18   single    1.444  0.020  1.444
 Z59  N8   HN8   single    0.860  0.020  1.020
 Z59  S9   C10   aromatic  1.725  0.020  1.725
 Z59  S9   C13   aromatic  1.715  0.020  1.715
 Z59  C18  C10   single    1.496  0.020  1.496
 Z59  C10  C15   aromatic  1.362  0.020  1.362
 Z59  C21  C12   aromatic  1.387  0.020  1.387
 Z59  C12  H12   single    0.930  0.020  1.080
 Z59  C13  C16   aromatic  1.360  0.020  1.360
 Z59  C13  H13   single    0.930  0.020  1.080
 Z59  C15  C16   aromatic  1.423  0.020  1.423
 Z59  C15  H15   single    0.930  0.020  1.080
 Z59  C16  H16   single    0.930  0.020  1.080
 Z59  O17  HO17  single    0.850  0.020  0.980
 Z59  C18  H18   single    0.970  0.020  1.090
 Z59  C18  H18A  single    0.970  0.020  1.090
 Z59  O19  HO19  single    0.850  0.020  0.980
 Z59  C25  C20   single    1.522  0.020  1.522
 Z59  C20  H20   single    0.970  0.020  1.090
 Z59  C20  H20A  single    0.970  0.020  1.090
 Z59  C21  C27   aromatic  1.390  0.020  1.390
 Z59  C21  H21   single    0.930  0.020  1.080
 Z59  C23  C25   single    1.522  0.020  1.522
 Z59  C23  H23   single    0.970  0.020  1.090
 Z59  C23  H23A  single    0.970  0.020  1.090
 Z59  C24  C26   aromatic  1.389  0.020  1.389
 Z59  C24  H24   single    0.930  0.020  1.080
 Z59  C25  H25   single    0.970  0.020  1.090
 Z59  C25  H25A  single    0.970  0.020  1.090
 Z59  C27  C26   aromatic  1.388  0.020  1.388
 Z59  C26  H26   single    0.930  0.020  1.080
 Z59  C27  H27   single    0.930  0.020  1.080

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
 Z59  O11   C1   C3   118.47  3.000
 Z59  C3    C1   N2   118.63  3.000
 Z59  O11   C1   N2   122.89  3.000
 Z59  C20   N2   C5   112.42  3.000
 Z59  C20   N2   C1   126.25  3.000
 Z59  C5    N2   C1   120.34  3.000
 Z59  H3    C3   O17  108.89  3.000
 Z59  H3    C3   C4   109.11  3.000
 Z59  O17   C3   C4   110.36  3.000
 Z59  H3    C3   C1   109.97  3.000
 Z59  O17   C3   C1   108.95  3.000
 Z59  C4    C3   C1   109.56  3.000
 Z59  H4    C4   O19  107.80  3.000
 Z59  H4    C4   C6   108.99  3.000
 Z59  O19   C4   C6   110.66  3.000
 Z59  H4    C4   C3   109.44  3.000
 Z59  C6    C4   C3   108.21  3.000
 Z59  O19   C4   C3   111.71  3.000
 Z59  H5    C5   C23  109.52  3.000
 Z59  H5    C5   C7   108.79  3.000
 Z59  C23   C5   C7   112.51  3.000
 Z59  H5    C5   N2   109.01  3.000
 Z59  C7    C5   N2   114.05  3.000
 Z59  C23   C5   N2   102.76  3.000
 Z59  O14   C6   N8   124.53  3.000
 Z59  N8    C6   C4   114.70  3.000
 Z59  O14   C6   C4   120.75  3.000
 Z59  C24   C7   C12  118.93  3.000
 Z59  C24   C7   C5   119.51  3.000
 Z59  C12   C7   C5   121.46  3.000
 Z59  HN8   N8   C18  116.68  3.000
 Z59  HN8   N8   C6   118.72  3.000
 Z59  C18   N8   C6   124.51  3.000
 Z59  C13   S9   C10   91.95  3.000
 Z59  C18   C10  C15  128.25  3.000
 Z59  C15   C10  S9   110.98  3.000
 Z59  C18   C10  S9   120.76  3.000
 Z59  H12   C12  C21  119.52  3.000
 Z59  H12   C12  C7   120.01  3.000
 Z59  C21   C12  C7   120.47  3.000
 Z59  H13   C13  C16  128.03  3.000
 Z59  H13   C13  S9   120.31  3.000
 Z59  C16   C13  S9   111.65  3.000
 Z59  H15   C15  C16  123.97  3.000
 Z59  H15   C15  C10  123.07  3.000
 Z59  C16   C15  C10  112.96  3.000
 Z59  H16   C16  C15  124.01  3.000
 Z59  H16   C16  C13  123.53  3.000
 Z59  C15   C16  C13  112.45  3.000
 Z59  HO17  O17  C3   106.39  3.000
 Z59  H18A  C18  H18  107.00  3.000
 Z59  H18A  C18  C10  111.09  3.000
 Z59  H18   C18  C10  108.83  3.000
 Z59  H18A  C18  N8   107.83  3.000
 Z59  H18   C18  N8   110.26  3.000
 Z59  C10   C18  N8   111.72  3.000
 Z59  HO19  O19  C4   107.91  3.000
 Z59  H20A  C20  H20  108.22  3.000
 Z59  H20A  C20  C25  112.29  3.000
 Z59  H20   C20  C25  110.58  3.000
 Z59  H20A  C20  N2   111.57  3.000
 Z59  H20   C20  N2   111.13  3.000
 Z59  C25   C20  N2   103.04  3.000
 Z59  H21   C21  C27  120.04  3.000
 Z59  H21   C21  C12  119.66  3.000
 Z59  C27   C21  C12  120.30  3.000
 Z59  H23A  C23  H23  107.73  3.000
 Z59  H23A  C23  C25  110.10  3.000
 Z59  H23   C23  C25  113.77  3.000
 Z59  H23A  C23  C5   109.90  3.000
 Z59  H23   C23  C5   111.54  3.000
 Z59  C25   C23  C5   103.77  3.000
 Z59  H24   C24  C26  119.58  3.000
 Z59  H24   C24  C7   119.67  3.000
 Z59  C26   C24  C7   120.75  3.000
 Z59  H25A  C25  H25  108.07  3.000
 Z59  H25A  C25  C23  110.68  3.000
 Z59  H25   C25  C23  113.20  3.000
 Z59  H25A  C25  C20  110.17  3.000
 Z59  H25   C25  C20  112.19  3.000
 Z59  C23   C25  C20  102.49  3.000
 Z59  H26   C26  C27  120.15  3.000
 Z59  H26   C26  C24  119.81  3.000
 Z59  C27   C26  C24  120.03  3.000
 Z59  H27   C27  C26  120.28  3.000
 Z59  H27   C27  C21  120.21  3.000
 Z59  C26   C27  C21  119.52  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
 Z59  CONST_01  C27  C21  C12  C7     0.00   0.0  0
 Z59  CONST_02  C27  C26  C24  C7     0.00   0.0  0
 Z59  CONST_03  C16  C15  C10  S9     0.00   0.0  0
 Z59  CONST_04  C15  C16  C13  S9     0.00   0.0  0
 Z59  CONST_05  C16  C13  S9   C10    0.00   0.0  0
 Z59  CONST_06  C13  C16  C15  C10    0.00   0.0  0
 Z59  CONST_07  C26  C24  C7   C12    0.00   0.0  0
 Z59  CONST_08  C26  C27  C21  C12    0.00   0.0  0
 Z59  CONST_09  C15  C10  S9   C13    0.00   0.0  0
 Z59  CONST_10  C24  C7   C12  C21    0.00   0.0  0
 Z59  CONST_11  C24  C26  C27  C21    0.00   0.0  0
 Z59  CONST_12  C21  C12  C7   C5   180.00   0.0  0
 Z59  CONST_13  C26  C24  C7   C5   180.00   0.0  0
 Z59  CONST_14  C18  C10  S9   C13  180.00   0.0  0
 Z59  CONST_15  C18  C10  C15  C16  180.00   0.0  0
 Z59  CONST_16  H12  C12  C7   C5     0.00   0.0  0
 Z59  CONST_17  H24  C24  C7   C5     0.00   0.0  0
 Z59  CONST_18  H21  C21  C12  C7   180.00   0.0  0
 Z59  CONST_19  H26  C26  C24  C7   180.00   0.0  0
 Z59  CONST_20  H15  C15  C10  S9   180.00   0.0  0
 Z59  CONST_21  H16  C16  C13  S9   180.00   0.0  0
 Z59  CONST_22  H13  C13  S9   C10  180.00   0.0  0
 Z59  CONST_23  H27  C27  C21  C12  180.00   0.0  0
 Z59  CONST_24  C5   N2   C1   C3   180.00   0.0  0
 Z59  CONST_25  C20  N2   C1   C3     0.00   0.0  0
 Z59  CONST_26  O11  C1   N2   C5     0.00   0.0  0
 Z59  CONST_27  C20  N2   C1   O11  180.00   0.0  0
 Z59  CONST_28  C18  N8   C6   C4   180.00   0.0  0
 Z59  CONST_29  C18  N8   C6   O14    0.00   0.0  0
 Z59  CONST_30  HN8  N8   C6   C4     0.00   0.0  0
 Z59  Var_01    C23  C25  C20  N2    34.29  30.0  1
 Z59  Var_02    C25  C20  N2   C5   -17.00  30.0  1
 Z59  Var_03    C20  C25  C23  C5   -39.44  30.0  1
 Z59  Var_04    S9   C10  C18  N8   -47.39  30.0  2
 Z59  Var_05    C10  C18  N8   C6   116.78  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
 Z59  chir_01  C3  C1   C4   O17  negativ
 Z59  chir_02  C4  O19  C3   C6   positiv
 Z59  chir_03  C5  N2   C23  C7   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
 Z59  plan-1  S9   0.020
 Z59  plan-1  C10  0.020
 Z59  plan-1  C13  0.020
 Z59  plan-1  C15  0.020
 Z59  plan-1  C16  0.020
 Z59  plan-1  C18  0.020
 Z59  plan-1  H13  0.020
 Z59  plan-1  H15  0.020
 Z59  plan-1  H16  0.020
 Z59  plan-2  C5   0.020
 Z59  plan-2  C7   0.020
 Z59  plan-2  C12  0.020
 Z59  plan-2  C21  0.020
 Z59  plan-2  C24  0.020
 Z59  plan-2  C26  0.020
 Z59  plan-2  C27  0.020
 Z59  plan-2  H12  0.020
 Z59  plan-2  H21  0.020
 Z59  plan-2  H24  0.020
 Z59  plan-2  H26  0.020
 Z59  plan-2  H27  0.020
 Z59  plan-3  C4   0.020
 Z59  plan-3  C6   0.020
 Z59  plan-3  N8   0.020
 Z59  plan-3  O14  0.020
 Z59  plan-3  C18  0.020
 Z59  plan-3  HN8  0.020
 Z59  plan-4  C1   0.020
 Z59  plan-4  N2   0.020
 Z59  plan-4  C3   0.020
 Z59  plan-4  C5   0.020
 Z59  plan-4  O11  0.020
 Z59  plan-4  C20  0.020

