# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 21:54:48 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N[C@@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1Cc4c[nH]c5ccccc45
#
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
 UYM  UYM  (3S,6S)-3,6-bis[(1H-indol-3-yl)methyl]piperazine-2,5-dione  ligand  48  28  .  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_UYM
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
 UYM  N    N  NR15  0  -0.688  -18.0882  39.5686  -20.8541
 UYM  C    C  C     0   0.536  -21.2692  34.5636  -21.2814
 UYM  O    O  O     0  -0.482  -20.7481  33.6483  -21.8999
 UYM  C1   C  CH1   0  -0.181  -20.7720  35.9794  -21.4784
 UYM  C10  C  CR16  0  -0.305  -17.6486  40.3335  -23.1994
 UYM  C11  C  CH1   0  -0.190  -22.8405  35.3421  -19.5123
 UYM  C12  C  CH2   0  -0.545  -22.4143  35.0102  -18.0681
 UYM  C15  C  C     0   0.535  -22.5005  36.7738  -19.8605
 UYM  C2   C  CH2   0  -0.551  -19.2878  36.0926  -21.0787
 UYM  C3   C  CR5   0  -0.009  -18.7588  37.4721  -21.2712
 UYM  C34  C  CR5   0   0.000  -20.9402  35.0424  -17.8462
 UYM  C35  C  CR15  0  -0.078  -20.0639  34.0124  -18.0553
 UYM  C37  C  CR56  0   0.340  -18.8056  35.7104  -17.3542
 UYM  C38  C  CR56  0   0.033  -20.1483  36.1500  -17.3952
 UYM  C39  C  CR16  0  -0.352  -20.4433  37.4610  -17.0008
 UYM  C4   C  CR15  0  -0.076  -18.5249  38.4013  -20.2957
 UYM  C40  C  CR16  0  -0.277  -19.4143  38.2832  -16.5853
 UYM  C41  C  CR16  0  -0.284  -18.0856  37.8255  -16.5573
 UYM  C42  C  CR16  0  -0.309  -17.7627  36.5387  -16.9414
 UYM  C5   C  CR56  0   0.353  -18.0318  39.4291  -22.2101
 UYM  C6   C  CR56  0   0.038  -18.4509  38.1149  -22.5153
 UYM  C7   C  CR16  0  -0.375  -18.4823  37.7028  -23.8527
 UYM  C8   C  CR16  0  -0.265  -18.1015  38.5954  -24.8356
 UYM  C9   C  CR16  0  -0.281  -17.6890  39.8984  -24.5102
 UYM  N1   N  NH1   0  -0.628  -21.5816  36.9699  -20.8100
 UYM  N2   N  NH1   0  -0.629  -22.3068  34.3879  -20.4536
 UYM  N36  N  NR15  0  -0.678  -18.7908  34.4095  -17.7645
 UYM  O1   O  O     0  -0.485  -23.0712  37.6889  -19.2851
 UYM  H1   H  HNR5  0   0.407  -17.8388  40.3965  -20.3391
 UYM  H2   H  HCH1  0   0.296  -20.8452  36.1668  -22.5549
 UYM  H3   H  HCR6  0   0.257  -17.3300  41.3381  -22.9508
 UYM  H4   H  HCH1  0   0.298  -23.9312  35.2765  -19.5546
 UYM  H5   H  HCH2  0   0.261  -22.9240  35.7016  -17.3946
 UYM  H6   H  HCH2  0   0.268  -22.8087  34.0176  -17.8381
 UYM  H7   H  HCH2  0   0.254  -18.7226  35.3781  -21.6805
 UYM  H8   H  HCH2  0   0.281  -19.1748  35.7956  -20.0353
 UYM  H9   H  HCR5  0   0.284  -20.2618  33.0047  -18.3867
 UYM  H10  H  HCR6  0   0.239  -21.4618  37.8270  -17.0282
 UYM  H11  H  HCR5  0   0.296  -18.6372  38.3115  -19.2253
 UYM  H12  H  HCR6  0   0.245  -19.6301  39.2985  -16.2785
 UYM  H13  H  HCR6  0   0.248  -17.3008  38.4954  -16.2306
 UYM  H14  H  HCR6  0   0.258  -16.7392  36.1862  -16.9201
 UYM  H15  H  HCR6  0   0.241  -18.8004  36.7001  -24.1132
 UYM  H16  H  HCR6  0   0.243  -18.1204  38.2909  -25.8742
 UYM  H17  H  HCR6  0   0.247  -17.3975  40.5755  -25.3028
 UYM  H18  H  HNH1  0   0.404  -21.3581  37.9340  -21.0201
 UYM  H19  H  HNH1  0   0.402  -22.6222  33.4333  -20.3411
 UYM  H20  H  HNR5  0   0.406  -17.9735  33.8263  -17.8350

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
 UYM  C8   C9   aromatic  1.405  0.020  1.405
 UYM  C8   C7   aromatic  1.381  0.020  1.381
 UYM  C9   C10  aromatic  1.382  0.020  1.382
 UYM  C7   C6   aromatic  1.400  0.020  1.400
 UYM  C10  C5   aromatic  1.394  0.020  1.394
 UYM  C6   C5   aromatic  1.413  0.020  1.413
 UYM  C6   C3   aromatic  1.434  0.020  1.434
 UYM  C5   N    aromatic  1.364  0.020  1.364
 UYM  O    C    double    1.221  0.020  1.221
 UYM  C3   C2   single    1.490  0.020  1.490
 UYM  C3   C4   aromatic  1.367  0.020  1.367
 UYM  C1   C    single    1.513  0.020  1.513
 UYM  C1   C2   single    1.541  0.020  1.541
 UYM  C1   N1   single    1.443  0.020  1.443
 UYM  N    C4   aromatic  1.366  0.020  1.366
 UYM  C    N2   single    1.339  0.020  1.339
 UYM  N1   C15  single    1.336  0.020  1.336
 UYM  N2   C11  single    1.443  0.020  1.443
 UYM  C15  C11  single    1.512  0.020  1.512
 UYM  C15  O1   double    1.222  0.020  1.222
 UYM  C11  C12  single    1.542  0.020  1.542
 UYM  C35  C34  aromatic  1.368  0.020  1.368
 UYM  C35  N36  aromatic  1.365  0.020  1.365
 UYM  C12  C34  single    1.491  0.020  1.491
 UYM  C34  C38  aromatic  1.434  0.020  1.434
 UYM  N36  C37  aromatic  1.364  0.020  1.364
 UYM  C38  C37  aromatic  1.413  0.020  1.413
 UYM  C38  C39  aromatic  1.400  0.020  1.400
 UYM  C37  C42  aromatic  1.394  0.020  1.394
 UYM  C39  C40  aromatic  1.381  0.020  1.381
 UYM  C42  C41  aromatic  1.381  0.020  1.381
 UYM  C40  C41  aromatic  1.406  0.020  1.406
 UYM  N    H1   single    0.860  0.020  1.020
 UYM  C1   H2   single    0.970  0.020  1.090
 UYM  C10  H3   single    0.930  0.020  1.080
 UYM  C11  H4   single    0.970  0.020  1.090
 UYM  C12  H5   single    0.970  0.020  1.090
 UYM  C12  H6   single    0.970  0.020  1.090
 UYM  C2   H7   single    0.970  0.020  1.090
 UYM  C2   H8   single    0.970  0.020  1.090
 UYM  C35  H9   single    0.930  0.020  1.080
 UYM  C39  H10  single    0.930  0.020  1.080
 UYM  C4   H11  single    0.930  0.020  1.080
 UYM  C40  H12  single    0.930  0.020  1.080
 UYM  C41  H13  single    0.930  0.020  1.080
 UYM  C42  H14  single    0.930  0.020  1.080
 UYM  C7   H15  single    0.930  0.020  1.080
 UYM  C8   H16  single    0.930  0.020  1.080
 UYM  C9   H17  single    0.930  0.020  1.080
 UYM  N1   H18  single    0.860  0.020  1.020
 UYM  N2   H19  single    0.860  0.020  1.020
 UYM  N36  H20  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
 UYM  H1   N    C5   125.63  3.000
 UYM  H1   N    C4   124.97  3.000
 UYM  C5   N    C4   109.40  3.000
 UYM  N2   C    C1   117.24  3.000
 UYM  N2   C    O    123.05  3.000
 UYM  C1   C    O    119.67  3.000
 UYM  H2   C1   N1   107.48  3.000
 UYM  H2   C1   C2   107.86  3.000
 UYM  N1   C1   C2   111.69  3.000
 UYM  H2   C1   C    105.43  3.000
 UYM  N1   C1   C    113.42  3.000
 UYM  C2   C1   C    110.57  3.000
 UYM  H3   C10  C9   121.23  3.000
 UYM  H3   C10  C5   121.33  3.000
 UYM  C9   C10  C5   117.44  3.000
 UYM  H4   C11  N2   107.71  3.000
 UYM  H4   C11  C15  105.79  3.000
 UYM  N2   C11  C15  113.13  3.000
 UYM  H4   C11  C12  107.40  3.000
 UYM  C15  C11  C12  110.93  3.000
 UYM  N2   C11  C12  111.50  3.000
 UYM  H6   C12  H5   106.08  3.000
 UYM  H6   C12  C34  110.19  3.000
 UYM  H5   C12  C34  110.86  3.000
 UYM  H6   C12  C11  107.04  3.000
 UYM  H5   C12  C11  108.21  3.000
 UYM  C34  C12  C11  114.08  3.000
 UYM  O1   C15  N1   123.08  3.000
 UYM  O1   C15  C11  119.70  3.000
 UYM  N1   C15  C11  117.22  3.000
 UYM  H8   C2   H7   107.19  3.000
 UYM  H8   C2   C3   109.81  3.000
 UYM  H7   C2   C3   110.54  3.000
 UYM  H8   C2   C1   109.14  3.000
 UYM  H7   C2   C1   107.91  3.000
 UYM  C3   C2   C1   112.11  3.000
 UYM  C6   C3   C4   106.12  3.000
 UYM  C4   C3   C2   126.71  3.000
 UYM  C6   C3   C2   127.11  3.000
 UYM  C38  C34  C35  106.01  3.000
 UYM  C38  C34  C12  127.54  3.000
 UYM  C35  C34  C12  126.45  3.000
 UYM  H9   C35  N36  120.54  3.000
 UYM  H9   C35  C34  129.23  3.000
 UYM  N36  C35  C34  110.23  3.000
 UYM  N36  C37  C42  130.35  3.000
 UYM  C42  C37  C38  122.30  3.000
 UYM  N36  C37  C38  107.35  3.000
 UYM  C39  C38  C37  118.89  3.000
 UYM  C39  C38  C34  134.04  3.000
 UYM  C37  C38  C34  107.06  3.000
 UYM  H10  C39  C40  120.48  3.000
 UYM  H10  C39  C38  120.50  3.000
 UYM  C40  C39  C38  119.01  3.000
 UYM  H11  C4   C3   129.26  3.000
 UYM  H11  C4   N    120.63  3.000
 UYM  C3   C4   N    110.11  3.000
 UYM  H12  C40  C41  119.23  3.000
 UYM  H12  C40  C39  119.68  3.000
 UYM  C41  C40  C39  121.10  3.000
 UYM  H13  C41  C42  119.41  3.000
 UYM  H13  C41  C40  119.33  3.000
 UYM  C42  C41  C40  121.25  3.000
 UYM  H14  C42  C41  121.26  3.000
 UYM  H14  C42  C37  121.29  3.000
 UYM  C41  C42  C37  117.45  3.000
 UYM  C6   C5   C10  122.13  3.000
 UYM  C6   C5   N    107.31  3.000
 UYM  C10  C5   N    130.56  3.000
 UYM  C7   C6   C5   119.14  3.000
 UYM  C5   C6   C3   107.05  3.000
 UYM  C7   C6   C3   133.81  3.000
 UYM  H15  C7   C8   120.51  3.000
 UYM  H15  C7   C6   120.58  3.000
 UYM  C8   C7   C6   118.91  3.000
 UYM  H16  C8   C9   119.23  3.000
 UYM  H16  C8   C7   119.75  3.000
 UYM  C9   C8   C7   121.03  3.000
 UYM  H17  C9   C8   119.31  3.000
 UYM  H17  C9   C10  119.33  3.000
 UYM  C8   C9   C10  121.36  3.000
 UYM  H18  N1   C15  116.07  3.000
 UYM  H18  N1   C1   115.71  3.000
 UYM  C15  N1   C1   127.90  3.000
 UYM  H19  N2   C11  115.86  3.000
 UYM  H19  N2   C    115.73  3.000
 UYM  C11  N2   C    127.11  3.000
 UYM  H20  N36  C37  125.62  3.000
 UYM  H20  N36  C35  125.02  3.000
 UYM  C37  N36  C35  109.35  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
 UYM  CONST_01  C9   C10  C5   N    180.00   0.0  0
 UYM  CONST_02  C7   C6   C5   N    180.00   0.0  0
 UYM  CONST_03  C3   C6   C5   N      0.00   0.0  0
 UYM  CONST_04  C6   C3   C4   N      0.00   0.0  0
 UYM  CONST_05  C7   C8   C9   C10    0.00   0.0  0
 UYM  CONST_06  C7   C6   C5   C10    0.00   0.0  0
 UYM  CONST_07  C3   C6   C5   C10  180.00   0.0  0
 UYM  CONST_08  C4   N    C5   C10  180.00   0.0  0
 UYM  CONST_09  C8   C7   C6   C3   180.00   0.0  0
 UYM  CONST_10  C5   N    C4   C3     0.00   0.0  0
 UYM  CONST_11  C37  N36  C35  C34    0.00   0.0  0
 UYM  CONST_12  N36  C37  C38  C34    0.00   0.0  0
 UYM  CONST_13  C42  C37  C38  C34  180.00   0.0  0
 UYM  CONST_14  C40  C39  C38  C34  180.00   0.0  0
 UYM  CONST_15  C37  C38  C34  C35    0.00   0.0  0
 UYM  CONST_16  C39  C38  C34  C35  180.00   0.0  0
 UYM  CONST_17  C38  C37  N36  C35    0.00   0.0  0
 UYM  CONST_18  C42  C37  N36  C35  180.00   0.0  0
 UYM  CONST_19  C40  C39  C38  C37    0.00   0.0  0
 UYM  CONST_20  C40  C41  C42  C37    0.00   0.0  0
 UYM  CONST_21  N36  C35  C34  C38    0.00   0.0  0
 UYM  CONST_22  C41  C42  C37  C38    0.00   0.0  0
 UYM  CONST_23  C41  C40  C39  C38    0.00   0.0  0
 UYM  CONST_24  N36  C37  C38  C39  180.00   0.0  0
 UYM  CONST_25  C42  C37  C38  C39    0.00   0.0  0
 UYM  CONST_26  C42  C41  C40  C39    0.00   0.0  0
 UYM  CONST_27  C7   C6   C3   C4   180.00   0.0  0
 UYM  CONST_28  C5   C6   C3   C4     0.00   0.0  0
 UYM  CONST_29  C6   C5   N    C4     0.00   0.0  0
 UYM  CONST_30  N36  C37  C42  C41  180.00   0.0  0
 UYM  CONST_31  C8   C9   C10  C5     0.00   0.0  0
 UYM  CONST_32  C8   C7   C6   C5     0.00   0.0  0
 UYM  CONST_33  C9   C8   C7   C6     0.00   0.0  0
 UYM  CONST_34  C9   C10  C5   C6     0.00   0.0  0
 UYM  CONST_35  C11  N2   C    C1     0.00   0.0  0
 UYM  CONST_36  C11  C15  N1   C1     0.00   0.0  0
 UYM  CONST_37  C2   C3   C4   N    180.00   0.0  0
 UYM  CONST_38  N36  C35  C34  C12  180.00   0.0  0
 UYM  CONST_39  C37  C38  C34  C12  180.00   0.0  0
 UYM  CONST_40  C39  C38  C34  C12    0.00   0.0  0
 UYM  CONST_41  C7   C6   C3   C2     0.00   0.0  0
 UYM  CONST_42  C5   C6   C3   C2   180.00   0.0  0
 UYM  CONST_43  C11  N2   C    O    180.00   0.0  0
 UYM  CONST_44  O1   C15  N1   C1   180.00   0.0  0
 UYM  CONST_45  H3   C10  C5   N      0.00   0.0  0
 UYM  CONST_46  H16  C8   C9   C10  180.00   0.0  0
 UYM  CONST_47  H1   N    C5   C10    0.00   0.0  0
 UYM  CONST_48  H15  C7   C6   C3     0.00   0.0  0
 UYM  CONST_49  H20  N36  C35  C34  180.00   0.0  0
 UYM  CONST_50  H10  C39  C38  C34    0.00   0.0  0
 UYM  CONST_51  H9   C35  N36  C37  180.00   0.0  0
 UYM  CONST_52  H13  C41  C42  C37  180.00   0.0  0
 UYM  CONST_53  H14  C42  C37  C38  180.00   0.0  0
 UYM  CONST_54  H12  C40  C39  C38  180.00   0.0  0
 UYM  CONST_55  H17  C9   C10  C5   180.00   0.0  0
 UYM  CONST_56  H11  C4   N    C5   180.00   0.0  0
 UYM  CONST_57  H19  N2   C    C1   180.00   0.0  0
 UYM  CONST_58  H18  N1   C15  C11  180.00   0.0  0
 UYM  Var_01    C6   C3   C2   C1   -73.29  30.0  2
 UYM  Var_02    C35  C34  C12  C11  -86.37  30.0  2

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
 UYM  chir_01  C1   C   C2   N1   positiv
 UYM  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
 UYM  plan-1  C12  0.020
 UYM  plan-1  C34  0.020
 UYM  plan-1  C35  0.020
 UYM  plan-1  C37  0.020
 UYM  plan-1  C38  0.020
 UYM  plan-1  C39  0.020
 UYM  plan-1  C40  0.020
 UYM  plan-1  C41  0.020
 UYM  plan-1  C42  0.020
 UYM  plan-1  N36  0.020
 UYM  plan-1  H9   0.020
 UYM  plan-1  H10  0.020
 UYM  plan-1  H12  0.020
 UYM  plan-1  H13  0.020
 UYM  plan-1  H14  0.020
 UYM  plan-1  H20  0.020
 UYM  plan-2  N    0.020
 UYM  plan-2  C10  0.020
 UYM  plan-2  C2   0.020
 UYM  plan-2  C3   0.020
 UYM  plan-2  C4   0.020
 UYM  plan-2  C5   0.020
 UYM  plan-2  C6   0.020
 UYM  plan-2  C7   0.020
 UYM  plan-2  C8   0.020
 UYM  plan-2  C9   0.020
 UYM  plan-2  H1   0.020
 UYM  plan-2  H3   0.020
 UYM  plan-2  H11  0.020
 UYM  plan-2  H15  0.020
 UYM  plan-2  H16  0.020
 UYM  plan-2  H17  0.020
 UYM  plan-3  C    0.020
 UYM  plan-3  O    0.020
 UYM  plan-3  C1   0.020
 UYM  plan-3  C11  0.020
 UYM  plan-3  N2   0.020
 UYM  plan-3  H19  0.020
 UYM  plan-4  C1   0.020
 UYM  plan-4  C11  0.020
 UYM  plan-4  C15  0.020
 UYM  plan-4  N1   0.020
 UYM  plan-4  O1   0.020
 UYM  plan-4  H18  0.020

