# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 01:20:04 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 2-(4-chlorophenoxy)-N-{[(4R)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]1(CNC(=O)COc2ccc(Cl)cc2)NC(=O)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
 3PQ  3PQ  2-(4-chlorophenoxy)-N-{[(4R)-4-methyl-2,5-dioxoimidazolidin-4-yl]methyl}acetamide  ligand  35  21  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3PQ
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
 3PQ  C7   C   CR5   0   0.582  -5.2963   0.3282  -0.4184
 3PQ  C6   C   CH3   0  -0.639  -3.7577  -1.2250  -1.6448
 3PQ  N1   N   NR15  0  -0.697  -5.6544   0.0747   0.8658
 3PQ  C5   C   CR5   0  -0.044  -3.8539  -0.1496  -0.5687
 3PQ  C2   C   CR5   0   0.668  -4.6305  -0.5224   1.6031
 3PQ  C16  C   CR16  0  -0.379   3.5118   0.1457  -0.9012
 3PQ  C21  C   CR16  0  -0.347   3.6178  -0.1739   1.4825
 3PQ  C17  C   CR16  0  -0.196   4.8788  -0.0917  -0.9854
 3PQ  C20  C   CR16  0  -0.197   4.9764  -0.4107   1.3971
 3PQ  C13  C   CH2   0  -0.304   0.7577   0.5947  -0.5969
 3PQ  C9   C   CH2   0  -0.265  -2.9745   1.0730  -0.8924
 3PQ  C15  C   CR6   0   0.395   2.8738   0.1059   0.3350
 3PQ  C18  C   CR6   0  -0.064   5.6034  -0.3680   0.1585
 3PQ  C11  C   C     0   0.517  -0.6594   0.8277  -0.1006
 3PQ  N4   N   NR15  0  -0.651  -3.6003  -0.6790   0.7516
 3PQ  N10  N   NH1   0  -0.643  -1.5847   0.7412  -1.0740
 3PQ  O8   O   O     0  -0.429  -5.9706   0.8379  -1.2807
 3PQ  O3   O   O     0  -0.478  -4.7013  -0.8296   2.7723
 3PQ  O12  O   O     0  -0.466  -0.9091   1.0948   1.0587
 3PQ  O14  O   O2    0  -0.461   1.5563   0.3197   0.5222
 3PQ  CL1  CL  CL    0  -0.137   7.3097  -0.6635   0.0488
 3PQ  H1   H   HCH3  0   0.247  -4.0144  -0.8187  -2.6226
 3PQ  H2   H   HCH3  0   0.253  -2.7440  -1.6223  -1.6936
 3PQ  H3   H   HCH3  0   0.256  -4.4316  -2.0524  -1.4251
 3PQ  H4   H   HNR5  0   0.429  -6.5603   0.2880   1.2592
 3PQ  H6   H   HCR6  0   0.276   3.1250  -0.2050   2.4459
 3PQ  H7   H   HCR6  0   0.283   5.3648  -0.0592  -1.9511
 3PQ  H8   H   HCR6  0   0.282   5.5412  -0.6288   2.2933
 3PQ  H9   H   HCH2  0   0.261   0.7807  -0.2277  -1.3209
 3PQ  H10  H   HCH2  0   0.273   1.0910   1.5011  -1.1187
 3PQ  H11  H   HCH2  0   0.280  -3.3376   1.5254  -1.8154
 3PQ  H12  H   HCH2  0   0.276  -3.0713   1.8154  -0.0999
 3PQ  H13  H   HNR5  0   0.414  -2.7045  -1.0209   1.0592
 3PQ  H14  H   HNH1  0   0.415  -1.2820   0.5152  -2.0083
 3PQ  H5   H   HCR6  0   0.292   2.9729   0.3568  -1.8143

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
 3PQ  CL1  C18  single    1.735  0.020  1.735
 3PQ  C20  C18  aromatic  1.389  0.020  1.389
 3PQ  C20  C21  aromatic  1.382  0.020  1.382
 3PQ  C18  C17  aromatic  1.382  0.020  1.382
 3PQ  C21  C15  aromatic  1.396  0.020  1.396
 3PQ  C17  C16  aromatic  1.390  0.020  1.390
 3PQ  C15  C16  aromatic  1.392  0.020  1.392
 3PQ  C15  O14  single    1.348  0.020  1.348
 3PQ  O14  C13  single    1.402  0.020  1.402
 3PQ  O8   C7   double    1.208  0.020  1.208
 3PQ  C13  C11  single    1.520  0.020  1.520
 3PQ  N10  C9   single    1.440  0.020  1.440
 3PQ  N10  C11  single    1.346  0.020  1.346
 3PQ  C7   N1   single    1.357  0.020  1.357
 3PQ  C7   C5   single    1.527  0.020  1.527
 3PQ  C9   C5   single    1.540  0.020  1.540
 3PQ  C11  O12  double    1.216  0.020  1.216
 3PQ  N1   C2   single    1.396  0.020  1.396
 3PQ  C5   C6   single    1.524  0.020  1.524
 3PQ  C5   N4   single    1.445  0.020  1.445
 3PQ  C2   N4   single    1.346  0.020  1.346
 3PQ  C2   O3   double    1.211  0.020  1.211
 3PQ  C6   H1   single    0.970  0.020  1.090
 3PQ  C6   H2   single    0.970  0.020  1.090
 3PQ  C6   H3   single    0.970  0.020  1.090
 3PQ  N1   H4   single    0.860  0.020  1.020
 3PQ  C16  H5   single    0.930  0.020  1.080
 3PQ  C21  H6   single    0.930  0.020  1.080
 3PQ  C17  H7   single    0.930  0.020  1.080
 3PQ  C20  H8   single    0.930  0.020  1.080
 3PQ  C13  H9   single    0.970  0.020  1.090
 3PQ  C13  H10  single    0.970  0.020  1.090
 3PQ  C9   H11  single    0.970  0.020  1.090
 3PQ  C9   H12  single    0.970  0.020  1.090
 3PQ  N4   H13  single    0.860  0.020  1.020
 3PQ  N10  H14  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
 3PQ  O8   C7   C5   126.11  3.000
 3PQ  C5   C7   N1   106.50  3.000
 3PQ  O8   C7   N1   127.40  3.000
 3PQ  H3   C6   H2   107.91  3.000
 3PQ  H3   C6   H1   108.57  3.000
 3PQ  H2   C6   H1   108.35  3.000
 3PQ  H3   C6   C5   110.76  3.000
 3PQ  H2   C6   C5   110.33  3.000
 3PQ  H1   C6   C5   110.83  3.000
 3PQ  H4   N1   C2   122.84  3.000
 3PQ  H4   N1   C7   124.44  3.000
 3PQ  C2   N1   C7   112.72  3.000
 3PQ  N4   C5   C9   112.49  3.000
 3PQ  N4   C5   C6   112.06  3.000
 3PQ  C9   C5   C6   112.06  3.000
 3PQ  N4   C5   C7   100.98  3.000
 3PQ  C6   C5   C7   110.48  3.000
 3PQ  C9   C5   C7   108.16  3.000
 3PQ  O3   C2   N4   128.77  3.000
 3PQ  O3   C2   N1   125.15  3.000
 3PQ  N4   C2   N1   106.08  3.000
 3PQ  H5   C16  C15  121.82  3.000
 3PQ  H5   C16  C17  118.19  3.000
 3PQ  C15  C16  C17  119.98  3.000
 3PQ  H6   C21  C15  119.65  3.000
 3PQ  H6   C21  C20  119.84  3.000
 3PQ  C15  C21  C20  120.51  3.000
 3PQ  H7   C17  C18  120.63  3.000
 3PQ  H7   C17  C16  119.39  3.000
 3PQ  C18  C17  C16  119.98  3.000
 3PQ  H8   C20  C18  120.63  3.000
 3PQ  H8   C20  C21  119.79  3.000
 3PQ  C18  C20  C21  119.58  3.000
 3PQ  H10  C13  H9   107.41  3.000
 3PQ  H10  C13  O14  111.62  3.000
 3PQ  H9   C13  O14  111.60  3.000
 3PQ  H10  C13  C11  108.17  3.000
 3PQ  H9   C13  C11  110.51  3.000
 3PQ  O14  C13  C11  107.49  3.000
 3PQ  H12  C9   H11  107.66  3.000
 3PQ  H12  C9   N10  109.52  3.000
 3PQ  H11  C9   N10  108.07  3.000
 3PQ  H12  C9   C5   109.70  3.000
 3PQ  H11  C9   C5   108.49  3.000
 3PQ  N10  C9   C5   113.24  3.000
 3PQ  O14  C15  C21  116.02  3.000
 3PQ  O14  C15  C16  124.54  3.000
 3PQ  C21  C15  C16  119.44  3.000
 3PQ  CL1  C18  C20  119.67  3.000
 3PQ  C20  C18  C17  120.51  3.000
 3PQ  CL1  C18  C17  119.82  3.000
 3PQ  O12  C11  N10  124.25  3.000
 3PQ  O12  C11  C13  122.46  3.000
 3PQ  N10  C11  C13  113.28  3.000
 3PQ  H13  N4   C2   121.82  3.000
 3PQ  H13  N4   C5   124.03  3.000
 3PQ  C2   N4   C5   113.65  3.000
 3PQ  H14  N10  C11  118.59  3.000
 3PQ  H14  N10  C9   117.28  3.000
 3PQ  C11  N10  C9   123.87  3.000
 3PQ  C15  O14  C13  118.49  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
 3PQ  CONST_01  C20  C18  C17  C16     0.00   0.0  0
 3PQ  CONST_02  C20  C21  C15  C16     0.00   0.0  0
 3PQ  CONST_03  C17  C18  C20  C21     0.00   0.0  0
 3PQ  CONST_04  C17  C16  C15  C21     0.00   0.0  0
 3PQ  CONST_05  C18  C20  C21  C15     0.00   0.0  0
 3PQ  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 3PQ  CONST_07  N4   C2   N1   C7      0.00   0.0  0
 3PQ  CONST_08  C5   N4   C2   N1      0.00   0.0  0
 3PQ  CONST_09  C2   N1   C7   C5      0.00   0.0  0
 3PQ  CONST_10  CL1  C18  C17  C16   180.00   0.0  0
 3PQ  CONST_11  CL1  C18  C20  C21   180.00   0.0  0
 3PQ  CONST_12  O14  C15  C16  C17   180.00   0.0  0
 3PQ  CONST_13  O14  C15  C21  C20   180.00   0.0  0
 3PQ  CONST_14  O3   C2   N1   C7    180.00   0.0  0
 3PQ  CONST_15  O3   C2   N4   C5    180.00   0.0  0
 3PQ  CONST_16  O8   C7   N1   C2    180.00   0.0  0
 3PQ  CONST_17  H6   C21  C15  C16   180.00   0.0  0
 3PQ  CONST_18  H5   C16  C15  C21   180.00   0.0  0
 3PQ  CONST_19  H8   C20  C18  C17   180.00   0.0  0
 3PQ  CONST_20  H7   C17  C18  C20   180.00   0.0  0
 3PQ  CONST_21  H13  N4   C2   N1    180.00   0.0  0
 3PQ  CONST_22  H4   N1   C7   C5    180.00   0.0  0
 3PQ  CONST_23  C9   N10  C11  C13   180.00   0.0  0
 3PQ  CONST_24  O12  C11  N10  C9      0.00   0.0  0
 3PQ  CONST_25  H14  N10  C11  C13     0.00   0.0  0
 3PQ  Var_01    C11  N10  C9   C5    -95.39  30.0  2
 3PQ  Var_02    C11  C13  O14  C15  -178.54  30.0  3
 3PQ  Var_03    O14  C13  C11  N10  -162.93  30.0  1

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
 3PQ  chir_01  C5  C7  C6  N4  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
 3PQ  plan-1  C16  0.020
 3PQ  plan-1  C21  0.020
 3PQ  plan-1  C17  0.020
 3PQ  plan-1  C20  0.020
 3PQ  plan-1  C15  0.020
 3PQ  plan-1  C18  0.020
 3PQ  plan-1  O14  0.020
 3PQ  plan-1  CL1  0.020
 3PQ  plan-1  H6   0.020
 3PQ  plan-1  H7   0.020
 3PQ  plan-1  H8   0.020
 3PQ  plan-1  H5   0.020
 3PQ  plan-2  C13  0.020
 3PQ  plan-2  C9   0.020
 3PQ  plan-2  C11  0.020
 3PQ  plan-2  N10  0.020
 3PQ  plan-2  O12  0.020
 3PQ  plan-2  H14  0.020
 3PQ  plan-3  C7   0.020
 3PQ  plan-3  N1   0.020
 3PQ  plan-3  C5   0.020
 3PQ  plan-3  C2   0.020
 3PQ  plan-3  N4   0.020
 3PQ  plan-3  O8   0.020
 3PQ  plan-3  O3   0.020
 3PQ  plan-3  H4   0.020
 3PQ  plan-3  H13  0.020

