# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 19:16:43 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (5S)-5-(1H-indol-3-ylmethyl)imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N[C@@H](Cc2c[nH]c3ccccc23)C(=O)N1
#
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
 I5H  I5H  (5S)-5-(1H-indol-3-ylmethyl)imidazolidine-2,4-dione  ligand  28  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I5H
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
 I5H  N1    N  NR15  0  -0.685   2.6519  -1.8171  -0.6410
 I5H  C2    C  CR15  0  -0.073   1.3902  -2.2192  -0.3106
 I5H  C3    C  CR5   0   0.005   0.7111  -1.1951   0.2888
 I5H  C4    C  CR56  0   0.015   1.6198  -0.0866   0.3311
 I5H  C5    C  CR16  0  -0.374   1.5366   1.2222   0.8234
 I5H  C6    C  CR16  0  -0.268   2.6363   2.0498   0.7130
 I5H  C7    C  CR16  0  -0.284   3.8267   1.5994   0.1172
 I5H  C8    C  CR16  0  -0.304   3.9405   0.3138  -0.3749
 I5H  C9    C  CR56  0   0.357   2.8281  -0.5194  -0.2605
 I5H  C10   C  CH2   0  -0.540  -0.7012  -1.2203   0.7704
 I5H  C11   C  CR15  0  -0.184  -1.6908  -0.7310  -0.2923
 I5H  C12   C  CR5   0   0.556  -3.1131  -0.6824   0.2410
 I5H  N13   N  NR15  0  -0.698  -3.5398   0.5967   0.0663
 I5H  C14   C  CR5   0   0.672  -2.5725   1.4130  -0.5212
 I5H  N15   N  NR15  0  -0.656  -1.4881   0.6346  -0.7027
 I5H  O16   O  O     0  -0.435  -3.7291  -1.5953   0.7370
 I5H  O17   O  O     0  -0.479  -2.7190   2.5835  -0.7951
 I5H  HN1   H  HNR5  0   0.410   3.3455  -2.4001  -1.0782
 I5H  H2    H  HCR5  0   0.284   1.0613  -3.2240  -0.5263
 I5H  H5    H  HCR6  0   0.242   0.6250   1.5829   1.2839
 I5H  H6    H  HCR6  0   0.246   2.5849   3.0629   1.0908
 I5H  H7    H  HCR6  0   0.250   4.6707   2.2731   0.0458
 I5H  H8    H  HCR6  0   0.259   4.8589  -0.0337  -0.8309
 I5H  H10   H  HCH2  0   0.270  -0.9886  -2.2363   1.0467
 I5H  H10A  H  HCH2  0   0.260  -0.8059  -0.6030   1.6665
 I5H  H11   H  HCR5  0   0.310  -1.6605  -1.4091  -1.1519
 I5H  HN13  H  HNR5  0   0.427  -4.4475   0.9400   0.3468
 I5H  HN15  H  HNR5  0   0.418  -0.6782   0.9541  -1.2086

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
 I5H  N1   C2    aromatic  1.365  0.020  1.365
 I5H  N1   C9    aromatic  1.364  0.020  1.364
 I5H  C2   C3    aromatic  1.367  0.020  1.367
 I5H  C3   C4    aromatic  1.434  0.020  1.434
 I5H  C3   C10   single    1.492  0.020  1.492
 I5H  C4   C5    aromatic  1.401  0.020  1.401
 I5H  C4   C9    aromatic  1.413  0.020  1.413
 I5H  C5   C6    aromatic  1.381  0.020  1.381
 I5H  C6   C7    aromatic  1.405  0.020  1.405
 I5H  C7   C8    aromatic  1.381  0.020  1.381
 I5H  C8   C9    aromatic  1.394  0.020  1.394
 I5H  C10  C11   single    1.532  0.020  1.532
 I5H  C11  C12   single    1.520  0.020  1.520
 I5H  C11  N15   single    1.440  0.020  1.440
 I5H  C12  N13   single    1.360  0.020  1.360
 I5H  C12  O16   double    1.208  0.020  1.208
 I5H  N13  C14   single    1.395  0.020  1.395
 I5H  C14  N15   single    1.347  0.020  1.347
 I5H  C14  O17   double    1.211  0.020  1.211
 I5H  N1   HN1   single    0.860  0.020  1.020
 I5H  C2   H2    single    0.930  0.020  1.080
 I5H  C5   H5    single    0.930  0.020  1.080
 I5H  C6   H6    single    0.930  0.020  1.080
 I5H  C7   H7    single    0.930  0.020  1.080
 I5H  C8   H8    single    0.930  0.020  1.080
 I5H  C10  H10   single    0.970  0.020  1.090
 I5H  C10  H10A  single    0.970  0.020  1.090
 I5H  C11  H11   single    0.970  0.020  1.090
 I5H  N13  HN13  single    0.860  0.020  1.020
 I5H  N15  HN15  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
 I5H  HN1   N1   C9   125.70  3.000
 I5H  HN1   N1   C2   124.87  3.000
 I5H  C9    N1   C2   109.41  3.000
 I5H  H2    C2   C3   129.33  3.000
 I5H  H2    C2   N1   120.52  3.000
 I5H  C3    C2   N1   110.16  3.000
 I5H  C10   C3   C4   127.10  3.000
 I5H  C10   C3   C2   126.79  3.000
 I5H  C4    C3   C2   106.09  3.000
 I5H  C9    C4   C5   118.95  3.000
 I5H  C9    C4   C3   107.02  3.000
 I5H  C5    C4   C3   134.02  3.000
 I5H  H5    C5   C6   120.31  3.000
 I5H  H5    C5   C4   120.70  3.000
 I5H  C6    C5   C4   118.99  3.000
 I5H  H6    C6   C7   119.22  3.000
 I5H  H6    C6   C5   119.69  3.000
 I5H  C7    C6   C5   121.09  3.000
 I5H  H7    C7   C8   119.45  3.000
 I5H  H7    C7   C6   119.28  3.000
 I5H  C8    C7   C6   121.27  3.000
 I5H  H8    C8   C9   121.30  3.000
 I5H  H8    C8   C7   121.24  3.000
 I5H  C9    C8   C7   117.46  3.000
 I5H  C8    C9   C4   122.24  3.000
 I5H  C8    C9   N1   130.44  3.000
 I5H  C4    C9   N1   107.32  3.000
 I5H  H10A  C10  H10  107.03  3.000
 I5H  H10A  C10  C11  109.05  3.000
 I5H  H10   C10  C11  107.62  3.000
 I5H  H10A  C10  C3   110.22  3.000
 I5H  H10   C10  C3   110.28  3.000
 I5H  C11   C10  C3   112.46  3.000
 I5H  H11   C11  N15  111.07  3.000
 I5H  H11   C11  C12  108.73  3.000
 I5H  N15   C11  C12  101.62  3.000
 I5H  H11   C11  C10  109.19  3.000
 I5H  N15   C11  C10  114.17  3.000
 I5H  C12   C11  C10  111.80  3.000
 I5H  O16   C12  N13  127.14  3.000
 I5H  O16   C12  C11  126.67  3.000
 I5H  N13   C12  C11  106.19  3.000
 I5H  HN13  N13  C14  122.75  3.000
 I5H  HN13  N13  C12  124.47  3.000
 I5H  C14   N13  C12  112.76  3.000
 I5H  O17   C14  N15  128.71  3.000
 I5H  O17   C14  N13  125.22  3.000
 I5H  N15   C14  N13  106.07  3.000
 I5H  HN15  N15  C14  122.14  3.000
 I5H  HN15  N15  C11  123.86  3.000
 I5H  C14   N15  C11  113.33  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
 I5H  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 I5H  CONST_02  C3    C4   C9   N1     0.00   0.0  0
 I5H  CONST_03  C5    C4   C9   N1   180.00   0.0  0
 I5H  CONST_04  C7    C8   C9   N1   180.00   0.0  0
 I5H  CONST_05  C4    C9   N1   C2     0.00   0.0  0
 I5H  CONST_06  C8    C9   N1   C2   180.00   0.0  0
 I5H  CONST_07  C5    C4   C3   C2   180.00   0.0  0
 I5H  CONST_08  C9    C4   C3   C2     0.00   0.0  0
 I5H  CONST_09  C9    N1   C2   C3     0.00   0.0  0
 I5H  CONST_10  C6    C5   C4   C3   180.00   0.0  0
 I5H  CONST_11  C8    C9   C4   C3   180.00   0.0  0
 I5H  CONST_12  C7    C6   C5   C4     0.00   0.0  0
 I5H  CONST_13  C7    C8   C9   C4     0.00   0.0  0
 I5H  CONST_14  C8    C9   C4   C5     0.00   0.0  0
 I5H  CONST_15  C8    C7   C6   C5     0.00   0.0  0
 I5H  CONST_16  C9    C4   C5   C6     0.00   0.0  0
 I5H  CONST_17  C9    C8   C7   C6     0.00   0.0  0
 I5H  CONST_18  C14   N13  C12  C11    0.00   0.0  0
 I5H  CONST_19  N13   C14  N15  C11    0.00   0.0  0
 I5H  CONST_20  N15   C14  N13  C12    0.00   0.0  0
 I5H  CONST_21  C10   C3   C2   N1   180.00   0.0  0
 I5H  CONST_22  C10   C3   C4   C5     0.00   0.0  0
 I5H  CONST_23  C10   C3   C4   C9   180.00   0.0  0
 I5H  CONST_24  O17   C14  N15  C11  180.00   0.0  0
 I5H  CONST_25  O17   C14  N13  C12  180.00   0.0  0
 I5H  CONST_26  O16   C12  N13  C14  180.00   0.0  0
 I5H  CONST_27  H8    C8   C9   N1     0.00   0.0  0
 I5H  CONST_28  HN1   N1   C2   C3   180.00   0.0  0
 I5H  CONST_29  H5    C5   C4   C3     0.00   0.0  0
 I5H  CONST_30  H2    C2   C3   C4   180.00   0.0  0
 I5H  CONST_31  H6    C6   C5   C4   180.00   0.0  0
 I5H  CONST_32  H7    C7   C6   C5   180.00   0.0  0
 I5H  CONST_33  HN13  N13  C12  C11  180.00   0.0  0
 I5H  CONST_34  HN15  N15  C14  N13  180.00   0.0  0
 I5H  Var_01    C11   C10  C3   C2   -92.10  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
 I5H  chir_01  C11  C10  C12  N15  negativ

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
 I5H  plan-1  N1    0.020
 I5H  plan-1  C2    0.020
 I5H  plan-1  C3    0.020
 I5H  plan-1  C4    0.020
 I5H  plan-1  C5    0.020
 I5H  plan-1  C6    0.020
 I5H  plan-1  C7    0.020
 I5H  plan-1  C8    0.020
 I5H  plan-1  C9    0.020
 I5H  plan-1  C10   0.020
 I5H  plan-1  HN1   0.020
 I5H  plan-1  H2    0.020
 I5H  plan-1  H5    0.020
 I5H  plan-1  H6    0.020
 I5H  plan-1  H7    0.020
 I5H  plan-1  H8    0.020
 I5H  plan-2  C11   0.020
 I5H  plan-2  C12   0.020
 I5H  plan-2  N13   0.020
 I5H  plan-2  C14   0.020
 I5H  plan-2  N15   0.020
 I5H  plan-2  O16   0.020
 I5H  plan-2  O17   0.020
 I5H  plan-2  HN13  0.020
 I5H  plan-2  HN15  0.020

