# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 18:26:54 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: (3S,6S)-3-ethyl-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[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
 WMA  WMA  (3S,6S)-3-ethyl-6-[(1H-indol-3-yl)methyl]piperazine-2,5-dione  ligand  37  20  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WMA
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
 WMA  N    N  NR15  0  -0.685  13.6976  -12.3483   7.7642
 WMA  C    C  C     0   0.566  18.1612  -16.2968   7.2584
 WMA  O    O  O     0  -0.478  17.9346  -17.0614   6.3350
 WMA  C1   C  CH1   0  -0.194  17.0717  -15.4138   7.8404
 WMA  C10  C  CR16  0  -0.302  11.9781  -13.4405   9.2208
 WMA  C11  C  CH1   0  -0.192  19.6747  -15.4233   9.0338
 WMA  C12  C  CH2   0  -0.457  21.1576  -15.0596   9.0441
 WMA  C13  C  CH3   0  -0.667  21.6042  -14.1986   7.8716
 WMA  C15  C  C     0   0.546  18.7857  -14.1979   9.1629
 WMA  C2   C  CH2   0  -0.540  16.0723  -14.9838   6.7598
 WMA  C3   C  CR5   0  -0.023  14.9747  -14.1312   7.3014
 WMA  C4   C  CR15  0  -0.078  14.8049  -12.7893   7.0988
 WMA  C5   C  CR56  0   0.355  13.1189  -13.3948   8.4208
 WMA  C6   C  CR56  0   0.041  13.8974  -14.5427   8.1546
 WMA  C7   C  CR16  0  -0.375  13.5098  -15.7699   8.7055
 WMA  C8   C  CR16  0  -0.264  12.3796  -15.8201   9.4976
 WMA  C9   C  CR16  0  -0.281  11.6222  -14.6647   9.7528
 WMA  N1   N  NH1   0  -0.642  17.6307  -14.2445   8.4842
 WMA  N2   N  NH1   0  -0.646  19.3624  -16.1853   7.8403
 WMA  H1   H  HNR5  0   0.408  13.3610  -11.3999   7.7603
 WMA  H2   H  HCH1  0   0.296  16.5401  -16.0298   8.5805
 WMA  H3   H  HCR6  0   0.257  11.3918  -12.5514   9.4159
 WMA  H4   H  HCH1  0   0.299  19.4746  -16.0353   9.9249
 WMA  H5   H  HCH2  0   0.246  21.7283  -15.9923   9.0572
 WMA  H6   H  HCH2  0   0.249  21.3776  -14.5613   9.9879
 WMA  H7   H  HCH3  0   0.238  22.6750  -14.0059   7.9331
 WMA  H8   H  HCH3  0   0.225  21.4160  -14.6853   6.9145
 WMA  H9   H  HCH3  0   0.228  21.0985  -13.2332   7.8625
 WMA  H10  H  HCH2  0   0.261  15.6629  -15.8857   6.3029
 WMA  H11  H  HCH2  0   0.261  16.6090  -14.4446   5.9756
 WMA  H12  H  HCR5  0   0.285  15.4005  -12.1092   6.5094
 WMA  H13  H  HCR6  0   0.241  14.0835  -16.6687   8.5128
 WMA  H14  H  HCR6  0   0.244  12.0684  -16.7623   9.9299
 WMA  H15  H  HCR6  0   0.247  10.7418  -14.7353  10.3786
 WMA  H16  H  HNH1  0   0.403  16.9922  -13.4715   8.6271
 WMA  H17  H  HNH1  0   0.402  20.0766  -16.8229   7.5145
 WMA  O1   O  O     0  -0.477  19.1119  -13.2504   9.8592

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
 WMA  O    C    double    1.220  0.020  1.220
 WMA  C2   C3   single    1.492  0.020  1.492
 WMA  C2   C1   single    1.534  0.020  1.534
 WMA  C4   C3   aromatic  1.368  0.020  1.368
 WMA  C4   N    aromatic  1.365  0.020  1.365
 WMA  C3   C6   aromatic  1.434  0.020  1.434
 WMA  C    C1   single    1.518  0.020  1.518
 WMA  C    N2   single    1.339  0.020  1.339
 WMA  C1   N1   single    1.447  0.020  1.447
 WMA  N    C5   aromatic  1.364  0.020  1.364
 WMA  N2   C11  single    1.450  0.020  1.450
 WMA  C6   C5   aromatic  1.412  0.020  1.412
 WMA  C6   C7   aromatic  1.400  0.020  1.400
 WMA  C13  C12  single    1.522  0.020  1.522
 WMA  N1   C15  single    1.340  0.020  1.340
 WMA  C5   C10  aromatic  1.394  0.020  1.394
 WMA  C7   C8   aromatic  1.381  0.020  1.381
 WMA  C11  C15  single    1.519  0.020  1.519
 WMA  C11  C12  single    1.527  0.020  1.527
 WMA  C15  O1   double    1.220  0.020  1.220
 WMA  C10  C9   aromatic  1.381  0.020  1.381
 WMA  C8   C9   aromatic  1.405  0.020  1.405
 WMA  N    H1   single    0.860  0.020  1.020
 WMA  C1   H2   single    0.970  0.020  1.090
 WMA  C10  H3   single    0.930  0.020  1.080
 WMA  C11  H4   single    0.970  0.020  1.090
 WMA  C12  H5   single    0.970  0.020  1.090
 WMA  C12  H6   single    0.970  0.020  1.090
 WMA  C13  H7   single    0.970  0.020  1.090
 WMA  C13  H8   single    0.970  0.020  1.090
 WMA  C13  H9   single    0.970  0.020  1.090
 WMA  C2   H10  single    0.970  0.020  1.090
 WMA  C2   H11  single    0.970  0.020  1.090
 WMA  C4   H12  single    0.930  0.020  1.080
 WMA  C7   H13  single    0.930  0.020  1.080
 WMA  C8   H14  single    0.930  0.020  1.080
 WMA  C9   H15  single    0.930  0.020  1.080
 WMA  N1   H16  single    0.860  0.020  1.020
 WMA  N2   H17  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
 WMA  H1   N    C5   125.65  3.000
 WMA  H1   N    C4   125.02  3.000
 WMA  C5   N    C4   109.32  3.000
 WMA  N2   C    C1   115.38  3.000
 WMA  N2   C    O    123.20  3.000
 WMA  C1   C    O    121.42  3.000
 WMA  H2   C1   N1   109.87  3.000
 WMA  H2   C1   C2   108.43  3.000
 WMA  N1   C1   C2   109.79  3.000
 WMA  H2   C1   C    106.21  3.000
 WMA  N1   C1   C    111.30  3.000
 WMA  C2   C1   C    111.14  3.000
 WMA  H3   C10  C9   121.25  3.000
 WMA  H3   C10  C5   121.31  3.000
 WMA  C9   C10  C5   117.44  3.000
 WMA  H4   C11  N2   109.60  3.000
 WMA  H4   C11  C15  105.88  3.000
 WMA  N2   C11  C15  111.57  3.000
 WMA  H4   C11  C12  107.69  3.000
 WMA  C15  C11  C12  112.06  3.000
 WMA  N2   C11  C12  109.87  3.000
 WMA  H6   C12  H5   105.91  3.000
 WMA  H6   C12  C13  110.45  3.000
 WMA  H5   C12  C13  109.79  3.000
 WMA  H6   C12  C11  108.11  3.000
 WMA  H5   C12  C11  107.69  3.000
 WMA  C13  C12  C11  114.50  3.000
 WMA  H9   C13  H8   107.94  3.000
 WMA  H9   C13  H7   107.44  3.000
 WMA  H8   C13  H7   107.35  3.000
 WMA  H9   C13  C12  111.80  3.000
 WMA  H8   C13  C12  111.91  3.000
 WMA  H7   C13  C12  110.18  3.000
 WMA  O1   C15  N1   123.11  3.000
 WMA  O1   C15  C11  121.22  3.000
 WMA  N1   C15  C11  115.67  3.000
 WMA  H11  C2   H10  106.97  3.000
 WMA  H11  C2   C3   109.88  3.000
 WMA  H10  C2   C3   110.40  3.000
 WMA  H11  C2   C1   108.90  3.000
 WMA  H10  C2   C1   107.93  3.000
 WMA  C3   C2   C1   112.58  3.000
 WMA  C6   C3   C4   106.04  3.000
 WMA  C6   C3   C2   127.20  3.000
 WMA  C4   C3   C2   126.75  3.000
 WMA  H12  C4   C3   129.11  3.000
 WMA  H12  C4   N    120.68  3.000
 WMA  C3   C4   N    110.21  3.000
 WMA  C6   C5   C10  122.18  3.000
 WMA  C10  C5   N    130.43  3.000
 WMA  C6   C5   N    107.39  3.000
 WMA  C7   C6   C5   119.06  3.000
 WMA  C7   C6   C3   133.90  3.000
 WMA  C5   C6   C3   107.03  3.000
 WMA  H13  C7   C8   120.34  3.000
 WMA  H13  C7   C6   120.70  3.000
 WMA  C8   C7   C6   118.96  3.000
 WMA  H14  C8   C9   119.23  3.000
 WMA  H14  C8   C7   119.74  3.000
 WMA  C9   C8   C7   121.03  3.000
 WMA  H15  C9   C8   119.33  3.000
 WMA  H15  C9   C10  119.34  3.000
 WMA  C8   C9   C10  121.33  3.000
 WMA  H16  N1   C15  116.45  3.000
 WMA  H16  N1   C1   115.84  3.000
 WMA  C15  N1   C1   125.88  3.000
 WMA  H17  N2   C11  116.38  3.000
 WMA  H17  N2   C    116.16  3.000
 WMA  C11  N2   C    126.48  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
 WMA  CONST_01  C6   C3   C4   N       0.00   0.0  0
 WMA  CONST_02  C3   C6   C5   N       0.00   0.0  0
 WMA  CONST_03  C7   C6   C5   N     180.00   0.0  0
 WMA  CONST_04  C9   C10  C5   N     180.00   0.0  0
 WMA  CONST_05  C4   N    C5   C10   180.00   0.0  0
 WMA  CONST_06  C3   C6   C5   C10   180.00   0.0  0
 WMA  CONST_07  C7   C6   C5   C10     0.00   0.0  0
 WMA  CONST_08  C7   C8   C9   C10     0.00   0.0  0
 WMA  CONST_09  C5   N    C4   C3      0.00   0.0  0
 WMA  CONST_10  C8   C7   C6   C3    180.00   0.0  0
 WMA  CONST_11  C5   C6   C3   C4      0.00   0.0  0
 WMA  CONST_12  C7   C6   C3   C4    180.00   0.0  0
 WMA  CONST_13  C6   C5   N    C4      0.00   0.0  0
 WMA  CONST_14  C8   C7   C6   C5      0.00   0.0  0
 WMA  CONST_15  C8   C9   C10  C5      0.00   0.0  0
 WMA  CONST_16  C9   C10  C5   C6      0.00   0.0  0
 WMA  CONST_17  C9   C8   C7   C6      0.00   0.0  0
 WMA  CONST_18  C11  N2   C    C1      0.00   0.0  0
 WMA  CONST_19  C11  C15  N1   C1      0.00   0.0  0
 WMA  CONST_20  C2   C3   C4   N     180.00   0.0  0
 WMA  CONST_21  C5   C6   C3   C2    180.00   0.0  0
 WMA  CONST_22  C7   C6   C3   C2      0.00   0.0  0
 WMA  CONST_23  C11  N2   C    O     180.00   0.0  0
 WMA  CONST_24  O1   C15  N1   C1    180.00   0.0  0
 WMA  CONST_25  H3   C10  C5   N       0.00   0.0  0
 WMA  CONST_26  H1   N    C5   C10     0.00   0.0  0
 WMA  CONST_27  H14  C8   C9   C10   180.00   0.0  0
 WMA  CONST_28  H13  C7   C6   C3      0.00   0.0  0
 WMA  CONST_29  H12  C4   N    C5    180.00   0.0  0
 WMA  CONST_30  H15  C9   C10  C5    180.00   0.0  0
 WMA  CONST_31  H17  N2   C    C1    180.00   0.0  0
 WMA  CONST_32  H16  N1   C15  C11   180.00   0.0  0
 WMA  Var_01    C4   C3   C2   C1    108.17  30.0  2
 WMA  Var_02    H7   C13  C12  C11  -178.37  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
 WMA  chir_01  C1   C2  C    N1   negativ
 WMA  chir_02  C11  N2  C15  C12  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
 WMA  plan-1  N    0.020
 WMA  plan-1  C10  0.020
 WMA  plan-1  C2   0.020
 WMA  plan-1  C3   0.020
 WMA  plan-1  C4   0.020
 WMA  plan-1  C5   0.020
 WMA  plan-1  C6   0.020
 WMA  plan-1  C7   0.020
 WMA  plan-1  C8   0.020
 WMA  plan-1  C9   0.020
 WMA  plan-1  H1   0.020
 WMA  plan-1  H3   0.020
 WMA  plan-1  H12  0.020
 WMA  plan-1  H13  0.020
 WMA  plan-1  H14  0.020
 WMA  plan-1  H15  0.020
 WMA  plan-2  C    0.020
 WMA  plan-2  O    0.020
 WMA  plan-2  C1   0.020
 WMA  plan-2  C11  0.020
 WMA  plan-2  N2   0.020
 WMA  plan-2  H17  0.020
 WMA  plan-3  C1   0.020
 WMA  plan-3  C11  0.020
 WMA  plan-3  C15  0.020
 WMA  plan-3  N1   0.020
 WMA  plan-3  H16  0.020
 WMA  plan-3  O1   0.020

