# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 19:56:52 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: (3S,6S)-3-[(1H-indol-3-yl)methyl]-6-(propan-2-yl)piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC1=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
 UYG  UYG  (3S,6S)-3-[(1H-indol-3-yl)methyl]-6-(propan-2-yl)piperazine-2,5-dione  ligand  40  21  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UYG
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
 UYG  C10  C  CR16  0  -0.302  11.9544  -13.3228   8.7046
 UYG  C11  C  CH1   0  -0.181  19.9203  -15.2280   9.1668
 UYG  C12  C  CH1   0  -0.236  20.8011  -14.3072   8.2975
 UYG  C13  C  CH3   0  -0.668  22.0330  -15.0492   7.7909
 UYG  N    N  NR15  0  -0.686  14.1518  -12.2484   8.1618
 UYG  C    C  C     0   0.527  18.1754  -16.6383   8.0578
 UYG  O    O  O     0  -0.483  17.8745  -17.6080   7.3785
 UYG  C1   C  CH1   0  -0.183  17.0989  -15.6735   8.5041
 UYG  C15  C  C     0   0.525  18.8158  -14.4300   9.8277
 UYG  C2   C  CH2   0  -0.543  16.4673  -14.9789   7.2801
 UYG  C3   C  CR5   0   0.000  15.3406  -14.0799   7.6572
 UYG  C4   C  CR15  0  -0.079  15.3720  -12.7172   7.7653
 UYG  C5   C  CR56  0   0.355  13.2954  -13.2980   8.3241
 UYG  C6   C  CR56  0   0.035  14.0115  -14.4763   8.0184
 UYG  C7   C  CR16  0  -0.374  13.3573  -15.7111   8.0983
 UYG  C8   C  CR16  0  -0.264  12.0290  -15.7402   8.4750
 UYG  C9   C  CR16  0  -0.282  11.3351  -14.5559   8.7751
 UYG  N1   N  NH1   0  -0.629  17.5556  -14.7224   9.4888
 UYG  N2   N  NH1   0  -0.634  19.4304  -16.3799   8.4429
 UYG  O1   O  O     0  -0.481  19.1009  -13.5585  10.6349
 UYG  H1   H  HCR6  0   0.257  11.4172  -12.4111   8.9339
 UYG  H2   H  HCH1  0   0.296  20.5450  -15.5980   9.9863
 UYG  H3   H  HCH1  0   0.244  21.1446  -13.5117   8.9640
 UYG  H4   H  HCH3  0   0.234  22.5839  -15.5198   8.6072
 UYG  H5   H  HCH3  0   0.222  21.7762  -15.8230   7.0642
 UYG  H6   H  HCH3  0   0.242  22.7102  -14.3555   7.2920
 UYG  H7   H  HNR5  0   0.408  13.9206  -11.2779   8.2946
 UYG  H8   H  HCH1  0   0.299  16.3273  -16.2912   8.9741
 UYG  H9   H  HCH3  0   0.236  19.1866  -13.0754   7.4872
 UYG  H10  H  HCH3  0   0.245  20.6859  -13.0135   6.5756
 UYG  H11  H  HCH3  0   0.226  19.6531  -14.4303   6.4542
 UYG  H12  H  HCH2  0   0.259  16.1165  -15.7573   6.5995
 UYG  H13  H  HCH2  0   0.267  17.2361  -14.4117   6.7517
 UYG  H14  H  HCR5  0   0.282  16.1901  -12.0379   7.5809
 UYG  H15  H  HCR6  0   0.240  13.8824  -16.6300   7.8655
 UYG  H16  H  HCR6  0   0.244  11.5098  -16.6877   8.5404
 UYG  H17  H  HCR6  0   0.247  10.2940  -14.6106   9.0660
 UYG  H18  H  HNH1  0   0.404  16.8360  -14.1654   9.9302
 UYG  H19  H  HNH1  0   0.406  20.1243  -17.0545   8.1508
 UYG  C14  C  CH3   0  -0.675  20.0321  -13.6747   7.1448

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
 UYG  O    C    double    1.222  0.020  1.222
 UYG  C2   C3   single    1.490  0.020  1.490
 UYG  C2   C1   single    1.543  0.020  1.543
 UYG  C4   C3   aromatic  1.367  0.020  1.367
 UYG  C4   N    aromatic  1.366  0.020  1.366
 UYG  C    C1   single    1.513  0.020  1.513
 UYG  C    N2   single    1.338  0.020  1.338
 UYG  C3   C6   aromatic  1.433  0.020  1.433
 UYG  N    C5   aromatic  1.364  0.020  1.364
 UYG  C1   N1   single    1.443  0.020  1.443
 UYG  N2   C11  single    1.446  0.020  1.446
 UYG  C14  C12  single    1.523  0.020  1.523
 UYG  C6   C5   aromatic  1.412  0.020  1.412
 UYG  C6   C7   aromatic  1.400  0.020  1.400
 UYG  C5   C10  aromatic  1.394  0.020  1.394
 UYG  C13  C12  single    1.525  0.020  1.525
 UYG  C7   C8   aromatic  1.381  0.020  1.381
 UYG  N1   C15  single    1.337  0.020  1.337
 UYG  C12  C11  single    1.543  0.020  1.543
 UYG  C11  C15  single    1.514  0.020  1.514
 UYG  C10  C9   aromatic  1.382  0.020  1.382
 UYG  C15  O1   double    1.222  0.020  1.222
 UYG  C8   C9   aromatic  1.405  0.020  1.405
 UYG  C10  H1   single    0.930  0.020  1.080
 UYG  C11  H2   single    0.970  0.020  1.090
 UYG  C12  H3   single    0.970  0.020  1.090
 UYG  C13  H4   single    0.970  0.020  1.090
 UYG  C13  H5   single    0.970  0.020  1.090
 UYG  C13  H6   single    0.970  0.020  1.090
 UYG  N    H7   single    0.860  0.020  1.020
 UYG  C1   H8   single    0.970  0.020  1.090
 UYG  C14  H9   single    0.970  0.020  1.090
 UYG  C14  H10  single    0.970  0.020  1.090
 UYG  C14  H11  single    0.970  0.020  1.090
 UYG  C2   H12  single    0.970  0.020  1.090
 UYG  C2   H13  single    0.970  0.020  1.090
 UYG  C4   H14  single    0.930  0.020  1.080
 UYG  C7   H15  single    0.930  0.020  1.080
 UYG  C8   H16  single    0.930  0.020  1.080
 UYG  C9   H17  single    0.930  0.020  1.080
 UYG  N1   H18  single    0.860  0.020  1.020
 UYG  N2   H19  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
 UYG  H1   C10  C9   121.22  3.000
 UYG  H1   C10  C5   121.33  3.000
 UYG  C9   C10  C5   117.45  3.000
 UYG  H2   C11  N2   107.39  3.000
 UYG  H2   C11  C15  105.52  3.000
 UYG  N2   C11  C15  113.02  3.000
 UYG  H2   C11  C12  107.33  3.000
 UYG  C15  C11  C12  110.35  3.000
 UYG  N2   C11  C12  112.76  3.000
 UYG  H3   C12  C14  108.54  3.000
 UYG  H3   C12  C13  107.63  3.000
 UYG  C14  C12  C13  111.01  3.000
 UYG  H3   C12  C11  105.68  3.000
 UYG  C13  C12  C11  110.98  3.000
 UYG  C14  C12  C11  112.71  3.000
 UYG  H6   C13  H5   107.00  3.000
 UYG  H6   C13  H4   107.64  3.000
 UYG  H5   C13  H4   108.11  3.000
 UYG  H6   C13  C12  110.13  3.000
 UYG  H5   C13  C12  112.08  3.000
 UYG  H4   C13  C12  111.66  3.000
 UYG  H7   N    C5   125.58  3.000
 UYG  H7   N    C4   125.06  3.000
 UYG  C5   N    C4   109.35  3.000
 UYG  N2   C    C1   117.34  3.000
 UYG  N2   C    O    122.98  3.000
 UYG  C1   C    O    119.67  3.000
 UYG  H8   C1   N1   107.58  3.000
 UYG  H8   C1   C2   107.83  3.000
 UYG  N1   C1   C2   111.98  3.000
 UYG  H8   C1   C    105.57  3.000
 UYG  N1   C1   C    113.35  3.000
 UYG  C2   C1   C    110.15  3.000
 UYG  O1   C15  N1   122.91  3.000
 UYG  O1   C15  C11  119.61  3.000
 UYG  N1   C15  C11  117.48  3.000
 UYG  H13  C2   H12  107.15  3.000
 UYG  H13  C2   C3   109.98  3.000
 UYG  H12  C2   C3   110.18  3.000
 UYG  H13  C2   C1   109.24  3.000
 UYG  H12  C2   C1   107.76  3.000
 UYG  C3   C2   C1   112.37  3.000
 UYG  C6   C3   C4   106.08  3.000
 UYG  C6   C3   C2   126.74  3.000
 UYG  C4   C3   C2   127.15  3.000
 UYG  H14  C4   C3   129.14  3.000
 UYG  H14  C4   N    120.71  3.000
 UYG  C3   C4   N    110.15  3.000
 UYG  C6   C5   N    107.33  3.000
 UYG  C6   C5   C10  122.13  3.000
 UYG  N    C5   C10  130.54  3.000
 UYG  C7   C6   C5   119.13  3.000
 UYG  C7   C6   C3   133.77  3.000
 UYG  C5   C6   C3   107.10  3.000
 UYG  H15  C7   C8   120.45  3.000
 UYG  H15  C7   C6   120.62  3.000
 UYG  C8   C7   C6   118.93  3.000
 UYG  H16  C8   C9   119.21  3.000
 UYG  H16  C8   C7   119.75  3.000
 UYG  C9   C8   C7   121.03  3.000
 UYG  H17  C9   C8   119.33  3.000
 UYG  H17  C9   C10  119.33  3.000
 UYG  C8   C9   C10  121.33  3.000
 UYG  H18  N1   C15  116.07  3.000
 UYG  H18  N1   C1   115.82  3.000
 UYG  C15  N1   C1   127.97  3.000
 UYG  H19  N2   C    115.58  3.000
 UYG  H19  N2   C11  116.34  3.000
 UYG  C    N2   C11  128.01  3.000
 UYG  H11  C14  H10  107.32  3.000
 UYG  H11  C14  H9   108.03  3.000
 UYG  H10  C14  H9   107.18  3.000
 UYG  H11  C14  C12  111.51  3.000
 UYG  H10  C14  C12  110.13  3.000
 UYG  H9   C14  C12  112.44  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
 UYG  CONST_01  C4   N    C5   C10  180.00   0.0  0
 UYG  CONST_02  C3   C6   C5   C10  180.00   0.0  0
 UYG  CONST_03  C7   C6   C5   C10    0.00   0.0  0
 UYG  CONST_04  C7   C8   C9   C10    0.00   0.0  0
 UYG  CONST_05  C6   C3   C4   N      0.00   0.0  0
 UYG  CONST_06  C3   C6   C5   N      0.00   0.0  0
 UYG  CONST_07  C7   C6   C5   N    180.00   0.0  0
 UYG  CONST_08  C9   C10  C5   N    180.00   0.0  0
 UYG  CONST_09  C5   N    C4   C3     0.00   0.0  0
 UYG  CONST_10  C8   C7   C6   C3   180.00   0.0  0
 UYG  CONST_11  C5   C6   C3   C4     0.00   0.0  0
 UYG  CONST_12  C7   C6   C3   C4   180.00   0.0  0
 UYG  CONST_13  C6   C5   N    C4     0.00   0.0  0
 UYG  CONST_14  C8   C7   C6   C5     0.00   0.0  0
 UYG  CONST_15  C8   C9   C10  C5     0.00   0.0  0
 UYG  CONST_16  C9   C10  C5   C6     0.00   0.0  0
 UYG  CONST_17  C9   C8   C7   C6     0.00   0.0  0
 UYG  CONST_18  C1   C    N2   C11    0.00   0.0  0
 UYG  CONST_19  C1   N1   C15  C11    0.00   0.0  0
 UYG  CONST_20  C2   C3   C4   N    180.00   0.0  0
 UYG  CONST_21  C5   C6   C3   C2   180.00   0.0  0
 UYG  CONST_22  C7   C6   C3   C2     0.00   0.0  0
 UYG  CONST_23  O    C    N2   C11  180.00   0.0  0
 UYG  CONST_24  O1   C15  N1   C1   180.00   0.0  0
 UYG  CONST_25  H7   N    C5   C10    0.00   0.0  0
 UYG  CONST_26  H16  C8   C9   C10  180.00   0.0  0
 UYG  CONST_27  H1   C10  C5   N      0.00   0.0  0
 UYG  CONST_28  H15  C7   C6   C3     0.00   0.0  0
 UYG  CONST_29  H14  C4   N    C5   180.00   0.0  0
 UYG  CONST_30  H17  C9   C10  C5   180.00   0.0  0
 UYG  CONST_31  H18  N1   C15  C11  180.00   0.0  0
 UYG  CONST_32  H19  N2   C    C1   180.00   0.0  0
 UYG  Var_01    C4   C3   C2   C1   101.49  30.0  2
 UYG  Var_02    H9   C14  C12  C11   59.04  30.0  3
 UYG  Var_03    H4   C13  C12  C11  -52.95  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
 UYG  chir_01  C11  N2  C12  C15  negativ
 UYG  chir_02  C1   N1  C    C2   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
 UYG  plan-1  C10  0.020
 UYG  plan-1  N    0.020
 UYG  plan-1  C2   0.020
 UYG  plan-1  C3   0.020
 UYG  plan-1  C4   0.020
 UYG  plan-1  C5   0.020
 UYG  plan-1  C6   0.020
 UYG  plan-1  C7   0.020
 UYG  plan-1  C8   0.020
 UYG  plan-1  C9   0.020
 UYG  plan-1  H1   0.020
 UYG  plan-1  H7   0.020
 UYG  plan-1  H14  0.020
 UYG  plan-1  H15  0.020
 UYG  plan-1  H16  0.020
 UYG  plan-1  H17  0.020
 UYG  plan-2  C11  0.020
 UYG  plan-2  C    0.020
 UYG  plan-2  O    0.020
 UYG  plan-2  C1   0.020
 UYG  plan-2  N2   0.020
 UYG  plan-2  H19  0.020
 UYG  plan-3  C11  0.020
 UYG  plan-3  C1   0.020
 UYG  plan-3  C15  0.020
 UYG  plan-3  N1   0.020
 UYG  plan-3  O1   0.020
 UYG  plan-3  H18  0.020

