# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 20:35:01 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[4-[(4S)-2,5-dioxoimidazolidin-4-yl]phenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1ccc(cc1)[C@@H]2NC(=O)NC2=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
 Z94  Z94  N-[4-[(4S)-2,5-dioxoimidazolidin-4-yl]phenyl]ethanamide  ligand  28  17  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Z94
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
 Z94  C1    C  CR15  0  -0.261   2.0414   0.3643  -0.7697
 Z94  C2    C  CR6   0   0.128   0.5844   0.1308  -0.4727
 Z94  C3    C  CR5   0   0.555   2.7239   1.1202   0.3708
 Z94  N4    N  NR15  0  -0.659   2.8468  -0.8234  -0.8525
 Z94  C5    C  CR16  0  -0.292  -0.3656   1.0290  -0.9357
 Z94  C6    C  CR16  0  -0.282   0.1598  -0.9402   0.3059
 Z94  N7    N  NR15  0  -0.694   3.7930   0.3636   0.7328
 Z94  O8    O  O     0  -0.418   2.3712   2.1696   0.8470
 Z94  C9    C  CR5   0   0.674   3.9080  -0.8057  -0.0181
 Z94  C10   C  CR16  0  -0.302  -1.7139   0.8821  -0.6424
 Z94  C11   C  CR16  0  -0.333  -1.1798  -1.1023   0.6037
 Z94  O12   O  O     0  -0.471   4.7949  -1.6215   0.0887
 Z94  C13   C  CR6   0   0.365  -2.1366  -0.1956   0.1368
 Z94  N14   N  NH1   0  -0.736  -3.4625  -0.4442   0.4967
 Z94  C15   C  C     0   0.516  -4.5958   0.2098   0.1293
 Z94  C16   C  CH3   0  -0.784  -5.8638  -0.3792   0.6928
 Z94  O17   O  O     0  -0.472  -4.6103   1.1824  -0.6043
 Z94  H1    H  HCR5  0   0.327   2.1353   0.9756  -1.6749
 Z94  HN4   H  HNR5  0   0.418   2.7773  -1.4859  -1.6082
 Z94  H5    H  HCR6  0   0.258  -0.0582   1.8688  -1.5474
 Z94  H6    H  HCR6  0   0.261   0.8726  -1.6642   0.6807
 Z94  HN7   H  HNR5  0   0.430   4.4406   0.6035   1.4703
 Z94  H10   H  HCR6  0   0.283  -2.4168   1.6023  -1.0256
 Z94  H11   H  HCR6  0   0.273  -1.4904  -1.9484   1.2055
 Z94  HN14  H  HNH1  0   0.416  -3.5907  -1.2433   1.0980
 Z94  H16   H  HCH3  0   0.255  -5.7001  -1.1502   1.4429
 Z94  H16A  H  HCH3  0   0.271  -6.4655   0.4138   1.1344
 Z94  H16B  H  HCH3  0   0.275  -6.4454  -0.8140  -0.1212

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
 Z94  C1   C2    single    1.505  0.020  1.505
 Z94  C1   C3    single    1.529  0.020  1.529
 Z94  C1   N4    single    1.437  0.020  1.437
 Z94  C2   C5    aromatic  1.387  0.020  1.387
 Z94  C2   C6    aromatic  1.390  0.020  1.390
 Z94  C3   N7    single    1.359  0.020  1.359
 Z94  C3   O8    double    1.205  0.020  1.205
 Z94  N4   C9    single    1.350  0.020  1.350
 Z94  C5   C10   aromatic  1.388  0.020  1.388
 Z94  C6   C11   aromatic  1.382  0.020  1.382
 Z94  N7   C9    single    1.394  0.020  1.394
 Z94  C9   O12   double    1.210  0.020  1.210
 Z94  C10  C13   aromatic  1.395  0.020  1.395
 Z94  C11  C13   aromatic  1.398  0.020  1.398
 Z94  C13  N14   single    1.396  0.020  1.396
 Z94  N14  C15   single    1.359  0.020  1.359
 Z94  C15  C16   single    1.507  0.020  1.507
 Z94  C15  O17   double    1.218  0.020  1.218
 Z94  C1   H1    single    0.970  0.020  1.090
 Z94  N4   HN4   single    0.860  0.020  1.020
 Z94  C5   H5    single    0.930  0.020  1.080
 Z94  C6   H6    single    0.930  0.020  1.080
 Z94  N7   HN7   single    0.860  0.020  1.020
 Z94  C10  H10   single    0.930  0.020  1.080
 Z94  C11  H11   single    0.930  0.020  1.080
 Z94  N14  HN14  single    0.860  0.020  1.020
 Z94  C16  H16   single    0.970  0.020  1.090
 Z94  C16  H16A  single    0.970  0.020  1.090
 Z94  C16  H16B  single    0.970  0.020  1.090

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
 Z94  H1    C1   N4    111.42  3.000
 Z94  H1    C1   C3    107.58  3.000
 Z94  N4    C1   C3    101.62  3.000
 Z94  H1    C1   C2    109.41  3.000
 Z94  N4    C1   C2    115.18  3.000
 Z94  C3    C1   C2    111.19  3.000
 Z94  C6    C2   C5    118.46  3.000
 Z94  C6    C2   C1    121.71  3.000
 Z94  C5    C2   C1    119.78  3.000
 Z94  O8    C3   N7    127.58  3.000
 Z94  O8    C3   C1    126.48  3.000
 Z94  N7    C3   C1    105.94  3.000
 Z94  HN4   N4   C9    121.77  3.000
 Z94  HN4   N4   C1    123.23  3.000
 Z94  C9    N4   C1    113.20  3.000
 Z94  H5    C5   C10   118.50  3.000
 Z94  H5    C5   C2    119.74  3.000
 Z94  C10   C5   C2    121.76  3.000
 Z94  H6    C6   C11   119.02  3.000
 Z94  H6    C6   C2    120.51  3.000
 Z94  C11   C6   C2    120.47  3.000
 Z94  HN7   N7   C9    122.63  3.000
 Z94  HN7   N7   C3    124.51  3.000
 Z94  C9    N7   C3    112.85  3.000
 Z94  O12   C9   N7    125.34  3.000
 Z94  O12   C9   N4    128.46  3.000
 Z94  N7    C9   N4    106.20  3.000
 Z94  H10   C10  C13   121.16  3.000
 Z94  H10   C10  C5    119.22  3.000
 Z94  C13   C10  C5    119.61  3.000
 Z94  H11   C11  C13   119.71  3.000
 Z94  H11   C11  C6    119.28  3.000
 Z94  C13   C11  C6    121.01  3.000
 Z94  N14   C13  C11   116.63  3.000
 Z94  N14   C13  C10   124.69  3.000
 Z94  C11   C13  C10   118.68  3.000
 Z94  HN14  N14  C15   115.89  3.000
 Z94  HN14  N14  C13   114.56  3.000
 Z94  C15   N14  C13   129.53  3.000
 Z94  O17   C15  C16   121.80  3.000
 Z94  O17   C15  N14   123.84  3.000
 Z94  C16   C15  N14   114.35  3.000
 Z94  H16B  C16  H16A  107.35  3.000
 Z94  H16B  C16  H16   108.19  3.000
 Z94  H16A  C16  H16   108.64  3.000
 Z94  H16B  C16  C15   108.98  3.000
 Z94  H16A  C16  C15   109.38  3.000
 Z94  H16   C16  C15   114.08  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
 Z94  CONST_01  C13   C10  C5   C2     0.00   0.0  0
 Z94  CONST_02  C13   C11  C6   C2     0.00   0.0  0
 Z94  CONST_03  C11   C6   C2   C5     0.00   0.0  0
 Z94  CONST_04  C11   C13  C10  C5     0.00   0.0  0
 Z94  CONST_05  C10   C5   C2   C6     0.00   0.0  0
 Z94  CONST_06  C10   C13  C11  C6     0.00   0.0  0
 Z94  CONST_07  C10   C5   C2   C1   180.00   0.0  0
 Z94  CONST_08  C11   C6   C2   C1   180.00   0.0  0
 Z94  CONST_09  C9    N7   C3   C1     0.00   0.0  0
 Z94  CONST_10  N7    C9   N4   C1     0.00   0.0  0
 Z94  CONST_11  N4    C9   N7   C3     0.00   0.0  0
 Z94  CONST_12  N14   C13  C10  C5   180.00   0.0  0
 Z94  CONST_13  N14   C13  C11  C6   180.00   0.0  0
 Z94  CONST_14  O12   C9   N4   C1   180.00   0.0  0
 Z94  CONST_15  O12   C9   N7   C3   180.00   0.0  0
 Z94  CONST_16  C9    N7   C3   O8   180.00   0.0  0
 Z94  CONST_17  H5    C5   C2   C1     0.00   0.0  0
 Z94  CONST_18  H6    C6   C2   C1     0.00   0.0  0
 Z94  CONST_19  H10   C10  C5   C2   180.00   0.0  0
 Z94  CONST_20  H11   C11  C6   C2   180.00   0.0  0
 Z94  CONST_21  HN7   N7   C3   C1   180.00   0.0  0
 Z94  CONST_22  HN4   N4   C9   N7   180.00   0.0  0
 Z94  CONST_23  C15   N14  C13  C10    0.00   0.0  0
 Z94  CONST_24  C15   N14  C13  C11  180.00   0.0  0
 Z94  CONST_25  HN14  N14  C13  C10  180.00   0.0  0
 Z94  CONST_26  C16   C15  N14  C13  180.00   0.0  0
 Z94  CONST_27  O17   C15  N14  C13    0.00   0.0  0
 Z94  Var_01    H16   C16  C15  N14    9.19  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
 Z94  chir_01  C1  C2  C3  N4  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
 Z94  plan-1  C1    0.020
 Z94  plan-1  C2    0.020
 Z94  plan-1  C5    0.020
 Z94  plan-1  C6    0.020
 Z94  plan-1  C10   0.020
 Z94  plan-1  C11   0.020
 Z94  plan-1  C13   0.020
 Z94  plan-1  N14   0.020
 Z94  plan-1  H5    0.020
 Z94  plan-1  H6    0.020
 Z94  plan-1  H10   0.020
 Z94  plan-1  H11   0.020
 Z94  plan-2  C13   0.020
 Z94  plan-2  N14   0.020
 Z94  plan-2  C15   0.020
 Z94  plan-2  C16   0.020
 Z94  plan-2  O17   0.020
 Z94  plan-2  HN14  0.020
 Z94  plan-3  C1    0.020
 Z94  plan-3  C3    0.020
 Z94  plan-3  N4    0.020
 Z94  plan-3  N7    0.020
 Z94  plan-3  O8    0.020
 Z94  plan-3  C9    0.020
 Z94  plan-3  O12   0.020
 Z94  plan-3  HN4   0.020
 Z94  plan-3  HN7   0.020

