# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 22:28:32 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (2R,3R)-4-[4-(2-chlorophenyl)piperazin-1-yl]-2,3-dihydroxy-4-oxo-N-(2-thiophen-2-ylethyl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]([C@@H](O)C(=O)N1CCN(CC1)c2ccccc2Cl)C(=O)NCCc3sccc3
#
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
 403  403  (2R,3R)-4-[4-(2-chlorophenyl)piperazin-1-yl]-2,3-dihydroxy-4-oxo-N-(2-thiophen-2-ylethyl)butanamide  ligand  53  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_403
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
 403  C1    C   CH1   0  -0.107   0.6164  -2.3642  -0.3339
 403  C2    C   C     0   0.532  -0.8556  -2.7911  -0.4103
 403  C3    C   CH1   0  -0.098   0.8737  -1.6730   1.0248
 403  N4    N   NT    0  -0.459  -1.7977  -1.8602  -0.6166
 403  N5    N   NT    0  -0.507  -3.7610   0.0827  -0.0513
 403  C6    C   C     0   0.528   2.3782  -1.4453   1.1806
 403  S8    S   S2    0   0.202   6.8641   2.0729   0.5929
 403  C9    C   CR5   0  -0.147   6.0793   1.2219  -0.6873
 403  O10   O   O     0  -0.496  -1.1089  -3.9792  -0.2475
 403  C11   C   CH2   0  -0.308  -3.2095  -2.2101  -0.6085
 403  C12   C   CH2   0  -0.326  -1.5696  -0.4625  -0.9424
 403  C13   C   CH2   0  -0.301  -2.3485   0.4297   0.0058
 403  C14   C   CH2   0  -0.312  -3.9709  -1.2975   0.3394
 403  C15   C   CR15  0  -0.470   8.3867   1.9943  -0.1929
 403  O17   O   O     0  -0.486   3.0230  -2.1283   1.9634
 403  C18   C   CR15  0  -0.237   6.9732   0.9016  -1.6651
 403  C19   C   CR15  0  -0.183   8.2959   1.3448  -1.3844
 403  N20   N   NH1   0  -0.642   2.9122  -0.5011   0.4044
 403  O21   O   OH1   0  -0.663   1.4214  -3.4942  -0.4663
 403  O22   O   OH1   0  -0.659   0.4019  -2.4500   2.0799
 403  C23   C   CH2   0  -0.555   4.6245   0.8940  -0.6253
 403  C25   C   CH2   0  -0.230   4.3304  -0.2010   0.3961
 403  H1    H   HCH1  0   0.267   0.8597  -1.6738  -1.1477
 403  H3    H   HCH1  0   0.266   0.3613  -0.7047   1.0463
 403  C151  C   CR6   0   0.391  -4.6487   1.0399   0.4528
 403  H11   H   HCH2  0   0.252  -3.6091  -2.1045  -1.6214
 403  H11A  H   HCH2  0   0.275  -3.3306  -3.2454  -0.3030
 403  H12   H   HCH2  0   0.261  -0.5154  -0.2050  -0.9037
 403  H12A  H   HCH2  0   0.268  -1.9095  -0.2791  -1.9661
 403  H13   H   HCH2  0   0.264  -2.1957   1.4671  -0.2854
 403  H13A  H   HCH2  0   0.230  -1.9590   0.3157   1.0289
 403  H14   H   HCH2  0   0.223  -3.6398  -1.4987   1.3692
 403  H14A  H   HCH2  0   0.265  -5.0331  -1.5377   0.2770
 403  H15   H   HCR5  0   0.294   9.2607   2.4323   0.2638
 403  H18   H   HCR5  0   0.262   6.6919   0.3649  -2.5611
 403  H19   H   HCR5  0   0.266   9.1388   1.1862  -2.0417
 403  HN20  H   HNH1  0   0.408   2.3016   0.0743  -0.1546
 403  HO21  H   HOH1  0   0.448   0.8699  -4.2547  -0.2281
 403  HO22  H   HOH1  0   0.449   1.1596  -2.9354   2.4363
 403  H23   H   HCH2  0   0.270   4.0398   1.7860  -0.3827
 403  H23A  H   HCH2  0   0.274   4.3065   0.5636  -1.6166
 403  H25   H   HCH2  0   0.243   4.6517   0.1166   1.3914
 403  H25A  H   HCH2  0   0.252   4.8974  -1.0994   0.1432
 403  C16   C   CR16  0  -0.278  -6.4357   2.9994   1.3968
 403  C17   C   CR16  0  -0.243  -6.2198   1.8384   2.1227
 403  C181  C   CR16  0  -0.329  -5.3312   0.8789   1.6597
 403  C191  C   CR6   0  -0.102  -4.9071   2.2099  -0.2740
 403  C20   C   CR16  0  -0.216  -5.7748   3.1839   0.1908
 403  CL1   CL  CL    0  -0.113  -4.1695   2.4353  -1.8279
 403  H21   H   HCR6  0   0.264  -7.1202   3.7562   1.7551
 403  H22   H   HCR6  0   0.263  -6.7319   1.6800   3.0625
 403  H231  H   HCR6  0   0.274  -5.1660  -0.0108   2.2535
 403  H24   H   HCR6  0   0.277  -5.9481   4.0751  -0.3975

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
 403  C1    C2    single    1.535  0.020  1.535
 403  C1    C3    single    1.546  0.020  1.546
 403  C1    O21   single    1.394  0.020  1.394
 403  C1    H1    single    0.970  0.020  1.090
 403  C2    N4    single    1.340  0.020  1.340
 403  C2    O10   double    1.226  0.020  1.226
 403  C3    C6    single    1.530  0.020  1.530
 403  C3    O22   single    1.393  0.020  1.393
 403  C3    H3    single    0.970  0.020  1.090
 403  N4    C11   single    1.455  0.020  1.455
 403  N4    C12   single    1.453  0.020  1.453
 403  N5    C13   single    1.456  0.020  1.456
 403  N5    C14   single    1.450  0.020  1.450
 403  N5    C151  single    1.399  0.020  1.399
 403  C6    O17   double    1.223  0.020  1.223
 403  C6    N20   single    1.334  0.020  1.334
 403  S8    C9    aromatic  1.726  0.020  1.726
 403  S8    C15   aromatic  1.715  0.020  1.715
 403  C9    C18   aromatic  1.363  0.020  1.363
 403  C9    C23   single    1.493  0.020  1.493
 403  C11   C14   single    1.520  0.020  1.520
 403  C11   H11   single    0.970  0.020  1.090
 403  C11   H11A  single    0.970  0.020  1.090
 403  C12   C13   single    1.517  0.020  1.517
 403  C12   H12   single    0.970  0.020  1.090
 403  C12   H12A  single    0.970  0.020  1.090
 403  C13   H13   single    0.970  0.020  1.090
 403  C13   H13A  single    0.970  0.020  1.090
 403  C14   H14   single    0.970  0.020  1.090
 403  C14   H14A  single    0.970  0.020  1.090
 403  C15   C19   aromatic  1.360  0.020  1.360
 403  C15   H15   single    0.930  0.020  1.080
 403  C18   C19   aromatic  1.423  0.020  1.423
 403  C18   H18   single    0.930  0.020  1.080
 403  C19   H19   single    0.930  0.020  1.080
 403  N20   C25   single    1.450  0.020  1.450
 403  N20   HN20  single    0.860  0.020  1.020
 403  O21   HO21  single    0.850  0.020  0.980
 403  O22   HO22  single    0.850  0.020  0.980
 403  C23   C25   single    1.526  0.020  1.526
 403  C23   H23   single    0.970  0.020  1.090
 403  C23   H23A  single    0.970  0.020  1.090
 403  C25   H25   single    0.970  0.020  1.090
 403  C25   H25A  single    0.970  0.020  1.090
 403  C181  C151  aromatic  1.396  0.020  1.396
 403  C151  C191  aromatic  1.401  0.020  1.401
 403  C16   C17   aromatic  1.386  0.020  1.386
 403  C17   C181  aromatic  1.387  0.020  1.387
 403  C191  C20   aromatic  1.385  0.020  1.385
 403  C16   C20   aromatic  1.388  0.020  1.388
 403  C191  CL1   single    1.735  0.020  1.735
 403  C16   H21   single    0.930  0.020  1.080
 403  C17   H22   single    0.930  0.020  1.080
 403  C181  H231  single    0.930  0.020  1.080
 403  C20   H24   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
 403  H1    C1    O21   108.20  3.000
 403  H1    C1    C3    109.54  3.000
 403  O21   C1    C3    110.48  3.000
 403  H1    C1    C2    110.59  3.000
 403  O21   C1    C2    108.89  3.000
 403  C3    C1    C2    109.13  3.000
 403  O10   C2    N4    123.26  3.000
 403  O10   C2    C1    117.47  3.000
 403  N4    C2    C1    119.24  3.000
 403  H3    C3    O22   108.65  3.000
 403  H3    C3    C6    109.05  3.000
 403  O22   C3    C6    109.82  3.000
 403  H3    C3    C1    109.54  3.000
 403  O22   C3    C1    111.10  3.000
 403  C6    C3    C1    108.65  3.000
 403  C12   N4    C11   112.64  3.000
 403  C12   N4    C2    126.32  3.000
 403  C11   N4    C2    120.94  3.000
 403  C151  N5    C14   117.53  3.000
 403  C151  N5    C13   116.00  3.000
 403  C14   N5    C13   110.91  3.000
 403  N20   C6    O17   123.84  3.000
 403  N20   C6    C3    116.10  3.000
 403  O17   C6    C3    120.05  3.000
 403  C15   S8    C9     92.37  3.000
 403  C23   C9    C18   128.13  3.000
 403  C23   C9    S8    121.38  3.000
 403  C18   C9    S8    110.47  3.000
 403  H11A  C11   H11   108.16  3.000
 403  H11A  C11   C14   109.94  3.000
 403  H11   C11   C14   109.66  3.000
 403  H11A  C11   N4    109.82  3.000
 403  H11   C11   N4    109.03  3.000
 403  C14   C11   N4    110.19  3.000
 403  H12A  C12   H12   107.17  3.000
 403  H12A  C12   C13   109.07  3.000
 403  H12   C12   C13   109.67  3.000
 403  H12A  C12   N4    108.80  3.000
 403  H12   C12   N4    111.87  3.000
 403  C13   C12   N4    110.18  3.000
 403  H13A  C13   H13   107.33  3.000
 403  H13A  C13   C12   109.78  3.000
 403  H13   C13   C12   108.74  3.000
 403  H13A  C13   N5    110.80  3.000
 403  H13   C13   N5    110.67  3.000
 403  C12   C13   N5    109.48  3.000
 403  H14A  C14   H14   107.84  3.000
 403  H14A  C14   C11   108.65  3.000
 403  H14   C14   C11   108.85  3.000
 403  H14A  C14   N5    109.58  3.000
 403  H14   C14   N5    112.50  3.000
 403  C11   C14   N5    109.33  3.000
 403  H15   C15   C19   128.22  3.000
 403  H15   C15   S8    120.43  3.000
 403  C19   C15   S8    111.34  3.000
 403  H18   C18   C19   124.04  3.000
 403  H18   C18   C9    122.70  3.000
 403  C19   C18   C9    113.26  3.000
 403  H19   C19   C18   124.02  3.000
 403  H19   C19   C15   123.43  3.000
 403  C18   C19   C15   112.55  3.000
 403  HN20  N20   C25   118.11  3.000
 403  HN20  N20   C6    118.96  3.000
 403  C25   N20   C6    122.79  3.000
 403  HO21  O21   C1    106.51  3.000
 403  HO22  O22   C3    107.08  3.000
 403  H23A  C23   H23   107.00  3.000
 403  H23A  C23   C25   109.53  3.000
 403  H23   C23   C25   109.50  3.000
 403  H23A  C23   C9    108.21  3.000
 403  H23   C23   C9    110.55  3.000
 403  C25   C23   C9    111.92  3.000
 403  H25A  C25   H25   107.29  3.000
 403  H25A  C25   C23   109.59  3.000
 403  H25   C25   C23   110.14  3.000
 403  H25A  C25   N20   109.81  3.000
 403  H25   C25   N20   110.03  3.000
 403  C23   C25   N20   109.93  3.000
 403  C191  C151  C181  117.04  3.000
 403  C191  C151  N5    120.08  3.000
 403  C181  C151  N5    122.87  3.000
 403  H21   C16   C20   119.76  3.000
 403  H21   C16   C17   120.74  3.000
 403  C20   C16   C17   119.50  3.000
 403  H22   C17   C181  119.46  3.000
 403  H22   C17   C16   120.25  3.000
 403  C181  C17   C16   120.28  3.000
 403  H231  C181  C17   118.89  3.000
 403  H231  C181  C151  119.64  3.000
 403  C17   C181  C151  121.46  3.000
 403  CL1   C191  C20   118.40  3.000
 403  CL1   C191  C151  119.65  3.000
 403  C20   C191  C151  121.91  3.000
 403  H24   C20   C191  119.82  3.000
 403  H24   C20   C16   120.39  3.000
 403  C191  C20   C16   119.78  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
 403  CONST_01  C19   C18   C9    S8       0.00   0.0  0
 403  CONST_02  C18   C19   C15   S8       0.00   0.0  0
 403  CONST_03  C19   C15   S8    C9       0.00   0.0  0
 403  CONST_04  C15   C19   C18   C9       0.00   0.0  0
 403  CONST_05  C18   C9    S8    C15      0.00   0.0  0
 403  CONST_06  C16   C17   C181  C151     0.00   0.0  0
 403  CONST_07  C16   C20   C191  C151     0.00   0.0  0
 403  CONST_08  C191  C20   C16   C17      0.00   0.0  0
 403  CONST_09  C191  C151  C181  C17      0.00   0.0  0
 403  CONST_10  C20   C191  C151  C181     0.00   0.0  0
 403  CONST_11  C20   C16   C17   C181     0.00   0.0  0
 403  CONST_12  C17   C181  C151  N5     180.00   0.0  0
 403  CONST_13  C20   C191  C151  N5     180.00   0.0  0
 403  CONST_14  CL1   C191  C151  N5       0.00   0.0  0
 403  CONST_15  C23   C9    S8    C15    180.00   0.0  0
 403  CONST_16  C23   C9    C18   C19    180.00   0.0  0
 403  CONST_17  CL1   C191  C20   C16    180.00   0.0  0
 403  CONST_18  CL1   C191  C151  C181   180.00   0.0  0
 403  CONST_19  H231  C181  C151  N5       0.00   0.0  0
 403  CONST_20  H18   C18   C9    S8     180.00   0.0  0
 403  CONST_21  H19   C19   C15   S8     180.00   0.0  0
 403  CONST_22  H15   C15   S8    C9     180.00   0.0  0
 403  CONST_23  H22   C17   C181  C151   180.00   0.0  0
 403  CONST_24  H24   C20   C191  C151   180.00   0.0  0
 403  CONST_25  H21   C16   C17   C181   180.00   0.0  0
 403  CONST_26  C11   N4    C2    C1     180.00   0.0  0
 403  CONST_27  C12   N4    C2    C1       0.00   0.0  0
 403  CONST_28  C11   N4    C2    O10      0.00   0.0  0
 403  CONST_29  C12   N4    C2    O10    180.00   0.0  0
 403  CONST_30  C25   N20   C6    C3     180.00   0.0  0
 403  CONST_31  C25   N20   C6    O17      0.00   0.0  0
 403  CONST_32  HN20  N20   C6    C3       0.00   0.0  0
 403  Var_01    N5    C14   C11   N4      56.77  30.0  1
 403  Var_02    N5    C13   C12   N4     -56.55  30.0  1
 403  Var_03    C13   C12   N4    C11     55.31  30.0  1
 403  Var_04    C13   N5    C14   C11    -60.32  30.0  1
 403  Var_05    C14   C11   N4    C12    -55.40  30.0  1
 403  Var_06    C14   N5    C13   C12     60.32  30.0  1
 403  Var_07    C181  C151  N5    C13   -107.75  30.0  2
 403  Var_08    C25   C23   C9    S8     -71.65  30.0  2
 403  Var_09    N20   C25   C23   C9    -179.02  30.0  3
 403  Var_10    C23   C25   N20   C6     178.28  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
 403  chir_01  C1  C2   C3  O21  negativ
 403  chir_02  C3  O22  C1  C6   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
 403  plan-1  S8    0.020
 403  plan-1  C9    0.020
 403  plan-1  C15   0.020
 403  plan-1  C18   0.020
 403  plan-1  C19   0.020
 403  plan-1  C23   0.020
 403  plan-1  H15   0.020
 403  plan-1  H18   0.020
 403  plan-1  H19   0.020
 403  plan-2  N5    0.020
 403  plan-2  C151  0.020
 403  plan-2  C16   0.020
 403  plan-2  C17   0.020
 403  plan-2  C181  0.020
 403  plan-2  C191  0.020
 403  plan-2  C20   0.020
 403  plan-2  CL1   0.020
 403  plan-2  H21   0.020
 403  plan-2  H22   0.020
 403  plan-2  H231  0.020
 403  plan-2  H24   0.020
 403  plan-3  C3    0.020
 403  plan-3  C6    0.020
 403  plan-3  O17   0.020
 403  plan-3  N20   0.020
 403  plan-3  C25   0.020
 403  plan-3  HN20  0.020
 403  plan-4  C1    0.020
 403  plan-4  C2    0.020
 403  plan-4  N4    0.020
 403  plan-4  O10   0.020
 403  plan-4  C11   0.020
 403  plan-4  C12   0.020

