# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 22:38:11 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 1,1'-(piperazine-1,4-diyl)di(ethan-1-one)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)C(C)=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
 T8Y  T8Y  1,1'-(piperazine-1,4-diyl)di(ethan-1-one)  ligand  26  12  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T8Y
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
 T8Y  N1   N  NT    0  -0.450  -1.3682  -0.0862   0.2878
 T8Y  C4   C  CH2   0  -0.312  -0.6377   1.1389   0.5516
 T8Y  C5   C  CH2   0  -0.303   0.5487   1.2625  -0.3960
 T8Y  C6   C  C     0   0.520  -2.6699  -0.1602  -0.0753
 T8Y  C7   C  CH3   0  -0.807  -3.4340   1.1390  -0.1820
 T8Y  N    N  NT    0  -0.448   1.3802   0.0770  -0.3117
 T8Y  C    C  CH3   0  -0.807   3.4200  -1.1561   0.2411
 T8Y  O    O  O     0  -0.505   3.2016   1.2128   0.3793
 T8Y  C1   C  C     0   0.520   2.6630   0.1454   0.1145
 T8Y  C2   C  CH2   0  -0.316   0.6483  -1.1451  -0.5830
 T8Y  C3   C  CH2   0  -0.300  -0.5381  -1.2737   0.3639
 T8Y  O1   O  O     0  -0.505  -3.2175  -1.2303  -0.3093
 T8Y  H7   H  HCH2  0   0.281  -1.2798   2.0081   0.4433
 T8Y  H8   H  HCH2  0   0.253  -0.2771   1.1273   1.5851
 T8Y  H9   H  HCH2  0   0.249   0.1867   1.3760  -1.4228
 T8Y  H10  H  HCH2  0   0.272   1.1334   2.1434  -0.1474
 T8Y  H13  H  HCH3  0   0.265  -3.0124   1.7901  -0.9489
 T8Y  H12  H  HCH3  0   0.270  -4.4647   0.9213  -0.4491
 T8Y  H11  H  HCH3  0   0.267  -3.4318   1.6936   0.7568
 T8Y  H2   H  HCH3  0   0.264   2.9590  -1.8219   0.9718
 T8Y  H    H  HCH3  0   0.267   3.4673  -1.6918  -0.7076
 T8Y  H1   H  HCH3  0   0.270   4.4350  -0.9443   0.5666
 T8Y  H3   H  HCH2  0   0.254   0.2866  -1.1227  -1.6157
 T8Y  H4   H  HCH2  0   0.282   1.2887  -2.0168  -0.4851
 T8Y  H5   H  HCH2  0   0.248  -0.1767  -1.3984   1.3900
 T8Y  H6   H  HCH2  0   0.272  -1.1254  -2.1504   0.1067

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
 T8Y  C1  C    single  1.511  0.020  1.511
 T8Y  C1  O    double  1.225  0.020  1.225
 T8Y  N   C1   single  1.354  0.020  1.354
 T8Y  C2  N    single  1.450  0.020  1.450
 T8Y  C3  C2   single  1.523  0.020  1.523
 T8Y  N1  C3   single  1.451  0.020  1.451
 T8Y  N1  C4   single  1.450  0.020  1.450
 T8Y  C4  C5   single  1.523  0.020  1.523
 T8Y  C5  N    single  1.450  0.020  1.450
 T8Y  C6  N1   single  1.353  0.020  1.353
 T8Y  C6  O1   double  1.225  0.020  1.225
 T8Y  C7  C6   single  1.511  0.020  1.511
 T8Y  C4  H7   single  0.970  0.020  1.090
 T8Y  C4  H8   single  0.970  0.020  1.090
 T8Y  C5  H9   single  0.970  0.020  1.090
 T8Y  C5  H10  single  0.970  0.020  1.090
 T8Y  C7  H13  single  0.970  0.020  1.090
 T8Y  C7  H12  single  0.970  0.020  1.090
 T8Y  C7  H11  single  0.970  0.020  1.090
 T8Y  C   H2   single  0.970  0.020  1.090
 T8Y  C   H    single  0.970  0.020  1.090
 T8Y  C   H1   single  0.970  0.020  1.090
 T8Y  C2  H3   single  0.970  0.020  1.090
 T8Y  C2  H4   single  0.970  0.020  1.090
 T8Y  C3  H5   single  0.970  0.020  1.090
 T8Y  C3  H6   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
 T8Y  C3   N1  C6   121.30  3.000
 T8Y  C6   N1  C4   125.41  3.000
 T8Y  C3   N1  C4   113.18  3.000
 T8Y  H8   C4  H7   107.30  3.000
 T8Y  H8   C4  C5   109.37  3.000
 T8Y  H7   C4  C5   109.48  3.000
 T8Y  H8   C4  N1   109.19  3.000
 T8Y  H7   C4  N1   111.11  3.000
 T8Y  C5   C4  N1   110.35  3.000
 T8Y  H10  C5  H9   107.98  3.000
 T8Y  H10  C5  N    109.93  3.000
 T8Y  H9   C5  N    109.20  3.000
 T8Y  H10  C5  C4   110.05  3.000
 T8Y  H9   C5  C4   109.53  3.000
 T8Y  N    C5  C4   110.12  3.000
 T8Y  O1   C6  C7   120.77  3.000
 T8Y  C7   C6  N1   117.28  3.000
 T8Y  O1   C6  N1   121.95  3.000
 T8Y  H11  C7  H12  108.39  3.000
 T8Y  H11  C7  H13  107.51  3.000
 T8Y  H12  C7  H13  108.26  3.000
 T8Y  H11  C7  C6   112.06  3.000
 T8Y  H12  C7  C6   108.95  3.000
 T8Y  H13  C7  C6   111.56  3.000
 T8Y  C2   N   C1   125.44  3.000
 T8Y  C2   N   C5   112.87  3.000
 T8Y  C1   N   C5   121.35  3.000
 T8Y  H1   C   H    108.41  3.000
 T8Y  H1   C   H2   108.25  3.000
 T8Y  H    C   H2   107.54  3.000
 T8Y  H1   C   C1   108.97  3.000
 T8Y  H    C   C1   111.84  3.000
 T8Y  H2   C   C1   111.73  3.000
 T8Y  O    C1  C    120.82  3.000
 T8Y  O    C1  N    121.94  3.000
 T8Y  C    C1  N    117.24  3.000
 T8Y  H4   C2  H3   107.24  3.000
 T8Y  H4   C2  C3   109.60  3.000
 T8Y  H3   C2  C3   109.32  3.000
 T8Y  H4   C2  N    111.22  3.000
 T8Y  H3   C2  N    109.03  3.000
 T8Y  C3   C2  N    110.36  3.000
 T8Y  H6   C3  H5   107.96  3.000
 T8Y  H6   C3  C2   110.00  3.000
 T8Y  H5   C3  C2   109.58  3.000
 T8Y  H6   C3  N1   109.81  3.000
 T8Y  H5   C3  N1   109.34  3.000
 T8Y  C2   C3  N1   110.12  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
 T8Y  CONST_01  O1   C6  N1  C4  180.00   0.0  0
 T8Y  CONST_02  C7   C6  N1  C4    0.00   0.0  0
 T8Y  CONST_03  C    C1  N   C5  180.00   0.0  0
 T8Y  CONST_04  O    C1  N   C5    0.00   0.0  0
 T8Y  CONST_05  C3   N1  C6  C7  180.00   0.0  0
 T8Y  CONST_06  C2   N   C1  C     0.00   0.0  0
 T8Y  CONST_07  C2   N   C1  O   180.00   0.0  0
 T8Y  CONST_08  O1   C6  N1  C3    0.00   0.0  0
 T8Y  Var_01    N    C2  C3  N1   54.53  30.0  1
 T8Y  Var_02    N    C5  C4  N1  -54.55  30.0  1
 T8Y  Var_03    C2   C3  N1  C4  -55.75  30.0  1
 T8Y  Var_04    C2   N   C5  C4   56.40  30.0  1
 T8Y  Var_05    C3   N1  C4  C5   55.89  30.0  1
 T8Y  Var_06    C3   C2  N   C5  -56.52  30.0  1
 T8Y  Var_07    H13  C7  C6  N1   62.31  30.0  3
 T8Y  Var_08    H2   C   C1  N   -61.83  30.0  3

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
 T8Y  plan-1  N1  0.020
 T8Y  plan-1  C4  0.020
 T8Y  plan-1  C6  0.020
 T8Y  plan-1  C7  0.020
 T8Y  plan-1  C3  0.020
 T8Y  plan-1  O1  0.020
 T8Y  plan-2  C5  0.020
 T8Y  plan-2  N   0.020
 T8Y  plan-2  C   0.020
 T8Y  plan-2  O   0.020
 T8Y  plan-2  C1  0.020
 T8Y  plan-2  C2  0.020

