# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 18:11:46 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (5S)-5-benzylimidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N[C@@H](Cc2ccccc2)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
 5FH  5FH  (5S)-5-benzylimidazolidine-2,4-dione  ligand  24  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5FH
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
 5FH  N1    N  NR15  0  -0.656   3.3953  12.6087  -27.1557
 5FH  C1    C  CR5   0   0.675   3.0237  11.5011  -27.8250
 5FH  O1    O  O     0  -0.478   2.0652  11.3373  -28.5468
 5FH  N2    N  NR15  0  -0.693   3.9900  10.5357  -27.5383
 5FH  C2    C  CR5   0   0.551   4.9568  10.9922  -26.6999
 5FH  O2    O  O     0  -0.432   5.9197  10.3853  -26.2962
 5FH  C3    C  CR15  0  -0.176   4.5730  12.4219  -26.3509
 5FH  C4    C  CH2   0  -0.525   4.3370  12.5922  -24.8431
 5FH  C5    C  CR6   0   0.113   3.2765  11.6739  -24.3043
 5FH  C6    C  CR16  0  -0.241   2.6315   9.5746  -23.2890
 5FH  C7    C  CR16  0  -0.298   1.9302  12.0284  -24.3668
 5FH  C8    C  CR16  0  -0.241   0.9450  11.1678  -23.9022
 5FH  C9    C  CR16  0  -0.268   1.2930   9.9358  -23.3639
 5FH  C10   C  CR16  0  -0.296   3.6137  10.4381  -23.7555
 5FH  H1    H  HNR5  0   0.416   2.8590  13.4606  -27.1834
 5FH  H3    H  HCR5  0   0.312   5.3786  13.0943  -26.6607
 5FH  H2    H  HNR5  0   0.427   3.9591   9.6024  -27.9234
 5FH  H41C  H  HCH2  0   0.271   5.2899  12.4210  -24.3394
 5FH  H42C  H  HCH2  0   0.278   4.0701  13.6356  -24.6637
 5FH  H7    H  HCR6  0   0.247   1.6477  12.9908  -24.7760
 5FH  H10   H  HCR6  0   0.250   4.6550  10.1479  -23.6857
 5FH  H6    H  HCR6  0   0.255   2.9146   8.6204  -22.8635
 5FH  H9    H  HCR6  0   0.255   0.5260   9.2643  -22.9994
 5FH  H8    H  HCR6  0   0.254  -0.0952  11.4622  -23.9569

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
 5FH  N1   C1    single    1.346  0.020  1.346
 5FH  N1   C3    single    1.439  0.020  1.439
 5FH  C1   O1    double    1.211  0.020  1.211
 5FH  C1   N2    single    1.396  0.020  1.396
 5FH  N2   C2    single    1.359  0.020  1.359
 5FH  C2   O2    double    1.208  0.020  1.208
 5FH  C2   C3    single    1.521  0.020  1.521
 5FH  C3   C4    single    1.536  0.020  1.536
 5FH  C4   C5    single    1.503  0.020  1.503
 5FH  C5   C7    aromatic  1.394  0.020  1.394
 5FH  C5   C10   aromatic  1.394  0.020  1.394
 5FH  C6   C9    aromatic  1.388  0.020  1.388
 5FH  C6   C10   aromatic  1.388  0.020  1.388
 5FH  C7   C8    aromatic  1.388  0.020  1.388
 5FH  C8   C9    aromatic  1.389  0.020  1.389
 5FH  N1   H1    single    0.860  0.020  1.020
 5FH  C3   H3    single    0.970  0.020  1.090
 5FH  N2   H2    single    0.860  0.020  1.020
 5FH  C4   H41C  single    0.970  0.020  1.090
 5FH  C4   H42C  single    0.970  0.020  1.090
 5FH  C7   H7    single    0.930  0.020  1.080
 5FH  C10  H10   single    0.930  0.020  1.080
 5FH  C6   H6    single    0.930  0.020  1.080
 5FH  C9   H9    single    0.930  0.020  1.080
 5FH  C8   H8    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
 5FH  H1    N1   C3    124.14  3.000
 5FH  H1    N1   C1    122.36  3.000
 5FH  C3    N1   C1    113.40  3.000
 5FH  N2    C1   O1    125.23  3.000
 5FH  N2    C1   N1    106.01  3.000
 5FH  O1    C1   N1    128.76  3.000
 5FH  H2    N2   C2    124.57  3.000
 5FH  H2    N2   C1    122.66  3.000
 5FH  C2    N2   C1    112.77  3.000
 5FH  C3    C2   O2    126.65  3.000
 5FH  C3    C2   N2    106.13  3.000
 5FH  O2    C2   N2    127.21  3.000
 5FH  H3    C3   C4    108.84  3.000
 5FH  H3    C3   C2    109.08  3.000
 5FH  C4    C3   C2    111.61  3.000
 5FH  H3    C3   N1    111.38  3.000
 5FH  C4    C3   N1    114.15  3.000
 5FH  C2    C3   N1    101.56  3.000
 5FH  H42C  C4   H41C  106.71  3.000
 5FH  H42C  C4   C5    110.64  3.000
 5FH  H41C  C4   C5    110.78  3.000
 5FH  H42C  C4   C3    107.75  3.000
 5FH  H41C  C4   C3    107.56  3.000
 5FH  C5    C4   C3    113.13  3.000
 5FH  C10   C5   C7    118.49  3.000
 5FH  C10   C5   C4    120.82  3.000
 5FH  C7    C5   C4    120.68  3.000
 5FH  H6    C6   C10   119.69  3.000
 5FH  H6    C6   C9    120.18  3.000
 5FH  C10   C6   C9    120.14  3.000
 5FH  H7    C7   C8    119.48  3.000
 5FH  H7    C7   C5    119.66  3.000
 5FH  C8    C7   C5    120.86  3.000
 5FH  H8    C8   C9    120.11  3.000
 5FH  H8    C8   C7    119.76  3.000
 5FH  C9    C8   C7    120.13  3.000
 5FH  H9    C9   C8    120.21  3.000
 5FH  H9    C9   C6    120.23  3.000
 5FH  C8    C9   C6    119.55  3.000
 5FH  H10   C10  C6    119.46  3.000
 5FH  H10   C10  C5    119.70  3.000
 5FH  C6    C10  C5    120.84  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
 5FH  CONST_01  C9   C8   C7   C5    0.00   0.0  0
 5FH  CONST_02  C9   C6   C10  C5    0.00   0.0  0
 5FH  CONST_03  C7   C8   C9   C6    0.00   0.0  0
 5FH  CONST_04  C7   C5   C10  C6    0.00   0.0  0
 5FH  CONST_05  C10  C5   C7   C8    0.00   0.0  0
 5FH  CONST_06  C10  C6   C9   C8    0.00   0.0  0
 5FH  CONST_07  C2   N2   C1   N1    0.00   0.0  0
 5FH  CONST_08  C3   C2   N2   C1    0.00   0.0  0
 5FH  CONST_09  C3   N1   C1   N2    0.00   0.0  0
 5FH  CONST_10  C8   C7   C5   C4  180.00   0.0  0
 5FH  CONST_11  C6   C10  C5   C4  180.00   0.0  0
 5FH  CONST_12  O2   C2   N2   C1  180.00   0.0  0
 5FH  CONST_13  C3   N1   C1   O1  180.00   0.0  0
 5FH  CONST_14  C2   N2   C1   O1  180.00   0.0  0
 5FH  CONST_15  H8   C8   C7   C5  180.00   0.0  0
 5FH  CONST_16  H6   C6   C10  C5  180.00   0.0  0
 5FH  CONST_17  H10  C10  C5   C7  180.00   0.0  0
 5FH  CONST_18  H9   C9   C8   C7  180.00   0.0  0
 5FH  CONST_19  H7   C7   C8   C9  180.00   0.0  0
 5FH  CONST_20  H2   N2   C1   N1  180.00   0.0  0
 5FH  CONST_21  H1   N1   C1   N2  180.00   0.0  0
 5FH  Var_01    C7   C5   C4   C3  -85.08  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
 5FH  chir_01  C3  N1  C2  C4  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
 5FH  plan-1  C4   0.020
 5FH  plan-1  C5   0.020
 5FH  plan-1  C6   0.020
 5FH  plan-1  C7   0.020
 5FH  plan-1  C8   0.020
 5FH  plan-1  C9   0.020
 5FH  plan-1  C10  0.020
 5FH  plan-1  H7   0.020
 5FH  plan-1  H10  0.020
 5FH  plan-1  H6   0.020
 5FH  plan-1  H9   0.020
 5FH  plan-1  H8   0.020
 5FH  plan-2  N1   0.020
 5FH  plan-2  C1   0.020
 5FH  plan-2  O1   0.020
 5FH  plan-2  N2   0.020
 5FH  plan-2  C2   0.020
 5FH  plan-2  O2   0.020
 5FH  plan-2  C3   0.020
 5FH  plan-2  H1   0.020
 5FH  plan-2  H2   0.020

