# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 22:03:26 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 1-[4-(pyridin-2-yl)piperazin-1-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCN(CC1)c2ccccn2
#
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
 8RA  8RA  1-[4-(pyridin-2-yl)piperazin-1-yl]ethan-1-one  ligand  30  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8RA
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
 8RA  N1   N  NT    0  -0.444  -2.3572   0.0759  -0.4217
 8RA  N3   N  N     0  -0.472   2.4237  -1.1803  -0.2445
 8RA  C4   C  CH2   0  -0.282  -0.3020  -1.1792  -0.0570
 8RA  C5   C  CH2   0  -0.296  -0.2659   1.2572   0.0604
 8RA  C6   C  CH2   0  -0.309  -1.5997   1.2828  -0.6707
 8RA  C7   C  CR6   0   0.539   1.8298  -0.0027  -0.0483
 8RA  C8   C  CR16  0  -0.414   2.5809   1.1325   0.3148
 8RA  C10  C  CR16  0  -0.364   4.5663  -0.2119   0.1955
 8RA  C1   C  CH3   0  -0.804  -4.2454  -1.2211   0.4361
 8RA  C2   C  C     0   0.515  -3.5575   0.1035   0.1995
 8RA  C3   C  CH2   0  -0.325  -1.6212  -1.1099  -0.8053
 8RA  N2   N  NT    0  -0.510   0.4666   0.0420  -0.2361
 8RA  C9   C  CR16  0  -0.149   3.9514   1.0141   0.4247
 8RA  C11  C  CR16  0  -0.062   3.7410  -1.2734  -0.1268
 8RA  O1   O  O     0  -0.506  -4.0824   1.1537   0.5488
 8RA  H1   H  HCH2  0   0.224  -0.5021  -1.3555   1.0093
 8RA  H2   H  HCH2  0   0.270   0.2717  -2.0229  -0.4290
 8RA  H3   H  HCH2  0   0.261   0.2969   2.1240  -0.2823
 8RA  H4   H  HCH2  0   0.231  -0.4304   1.3743   1.1405
 8RA  H5   H  HCH2  0   0.248  -1.4205   1.3716  -1.7469
 8RA  H6   H  HCH2  0   0.271  -2.1675   2.1526  -0.3539
 8RA  H7   H  HCR6  0   0.270   2.1154   2.0832   0.5261
 8RA  H8   H  HCR6  0   0.259   5.6359  -0.3413   0.2772
 8RA  H9   H  HCH3  0   0.264  -3.6578  -1.8789   1.0773
 8RA  H10  H  HCH3  0   0.269  -5.2011  -1.0390   0.9206
 8RA  H11  H  HCH3  0   0.266  -4.4290  -1.7518  -0.4987
 8RA  H12  H  HCH2  0   0.279  -2.1890  -2.0132  -0.6027
 8RA  H13  H  HCH2  0   0.250  -1.4331  -1.0774  -1.8830
 8RA  H14  H  HCR6  0   0.267   4.5379   1.8804   0.7031
 8RA  H15  H  HCR6  0   0.255   4.1613  -2.2588  -0.3004

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
 8RA  C9   C8   aromatic  1.380  0.020  1.380
 8RA  C9   C10  aromatic  1.391  0.020  1.391
 8RA  C8   C7   aromatic  1.409  0.020  1.409
 8RA  C10  C11  aromatic  1.383  0.020  1.383
 8RA  C4   N2   single    1.454  0.020  1.454
 8RA  C4   C3   single    1.518  0.020  1.518
 8RA  C7   N2   single    1.377  0.020  1.377
 8RA  C7   N3   aromatic  1.333  0.020  1.333
 8RA  C11  N3   aromatic  1.326  0.020  1.326
 8RA  N2   C5   single    1.450  0.020  1.450
 8RA  C3   N1   single    1.447  0.020  1.447
 8RA  C5   C6   single    1.521  0.020  1.521
 8RA  C1   C2   single    1.511  0.020  1.511
 8RA  N1   C2   single    1.352  0.020  1.352
 8RA  N1   C6   single    1.446  0.020  1.446
 8RA  C2   O1   double    1.225  0.020  1.225
 8RA  C4   H1   single    0.970  0.020  1.090
 8RA  C4   H2   single    0.970  0.020  1.090
 8RA  C5   H3   single    0.970  0.020  1.090
 8RA  C5   H4   single    0.970  0.020  1.090
 8RA  C6   H5   single    0.970  0.020  1.090
 8RA  C6   H6   single    0.970  0.020  1.090
 8RA  C8   H7   single    0.930  0.020  1.080
 8RA  C10  H8   single    0.930  0.020  1.080
 8RA  C1   H9   single    0.970  0.020  1.090
 8RA  C1   H10  single    0.970  0.020  1.090
 8RA  C1   H11  single    0.970  0.020  1.090
 8RA  C3   H12  single    0.970  0.020  1.090
 8RA  C3   H13  single    0.970  0.020  1.090
 8RA  C9   H14  single    0.930  0.020  1.080
 8RA  C11  H15  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
 8RA  C3   N1   C2   126.15  3.000
 8RA  C2   N1   C6   121.81  3.000
 8RA  C3   N1   C6   111.82  3.000
 8RA  C11  N3   C7   119.43  3.000
 8RA  H2   C4   H1   107.69  3.000
 8RA  H2   C4   N2   109.33  3.000
 8RA  H1   C4   N2   110.51  3.000
 8RA  H2   C4   C3   109.00  3.000
 8RA  H1   C4   C3   109.11  3.000
 8RA  N2   C4   C3   111.12  3.000
 8RA  H4   C5   H3   107.58  3.000
 8RA  H4   C5   N2   111.47  3.000
 8RA  H3   C5   N2   109.98  3.000
 8RA  H4   C5   C6   109.84  3.000
 8RA  H3   C5   C6   106.77  3.000
 8RA  N2   C5   C6   111.03  3.000
 8RA  H6   C6   H5   107.91  3.000
 8RA  H6   C6   C5   109.37  3.000
 8RA  H5   C6   C5   109.29  3.000
 8RA  H6   C6   N1   110.13  3.000
 8RA  H5   C6   N1   108.83  3.000
 8RA  C5   C6   N1   111.25  3.000
 8RA  N2   C7   C8   122.47  3.000
 8RA  N2   C7   N3   116.71  3.000
 8RA  C8   C7   N3   120.81  3.000
 8RA  H7   C8   C9   119.22  3.000
 8RA  H7   C8   C7   122.03  3.000
 8RA  C9   C8   C7   118.74  3.000
 8RA  H8   C10  C11  121.10  3.000
 8RA  H8   C10  C9   122.06  3.000
 8RA  C11  C10  C9   116.83  3.000
 8RA  H11  C1   H10  108.40  3.000
 8RA  H11  C1   H9   107.54  3.000
 8RA  H10  C1   H9   108.23  3.000
 8RA  H11  C1   C2   111.65  3.000
 8RA  H10  C1   C2   108.85  3.000
 8RA  H9   C1   C2   112.05  3.000
 8RA  O1   C2   C1   120.78  3.000
 8RA  O1   C2   N1   121.93  3.000
 8RA  C1   C2   N1   117.28  3.000
 8RA  H13  C3   H12  107.36  3.000
 8RA  H13  C3   C4   109.72  3.000
 8RA  H12  C3   C4   108.93  3.000
 8RA  H13  C3   N1   108.90  3.000
 8RA  H12  C3   N1   111.48  3.000
 8RA  C4   C3   N1   110.40  3.000
 8RA  C7   N2   C5   119.98  3.000
 8RA  C5   N2   C4   114.31  3.000
 8RA  C7   N2   C4   118.64  3.000
 8RA  H14  C9   C10  120.56  3.000
 8RA  H14  C9   C8   119.33  3.000
 8RA  C10  C9   C8   120.11  3.000
 8RA  H15  C11  C10  120.21  3.000
 8RA  H15  C11  N3   115.74  3.000
 8RA  C10  C11  N3   124.05  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
 8RA  CONST_01  C9   C8   C7   N3    0.00   0.0  0
 8RA  CONST_02  C9   C10  C11  N3    0.00   0.0  0
 8RA  CONST_03  C10  C9   C8   C7    0.00   0.0  0
 8RA  CONST_04  C10  C11  N3   C7    0.00   0.0  0
 8RA  CONST_05  C11  C10  C9   C8    0.00   0.0  0
 8RA  CONST_06  C11  N3   C7   C8    0.00   0.0  0
 8RA  CONST_07  C9   C8   C7   N2  180.00   0.0  0
 8RA  CONST_08  C11  N3   C7   N2  180.00   0.0  0
 8RA  CONST_09  H7   C8   C7   N3  180.00   0.0  0
 8RA  CONST_10  H8   C10  C11  N3  180.00   0.0  0
 8RA  CONST_11  H14  C9   C8   C7  180.00   0.0  0
 8RA  CONST_12  H15  C11  N3   C7  180.00   0.0  0
 8RA  CONST_13  C1   C2   N1   C6  180.00   0.0  0
 8RA  CONST_14  O1   C2   N1   C6    0.00   0.0  0
 8RA  CONST_15  C3   N1   C2   C1    0.00   0.0  0
 8RA  CONST_16  O1   C2   N1   C3  180.00   0.0  0
 8RA  Var_01    N2   C4   C3   N1  -54.14  30.0  1
 8RA  Var_02    N2   C5   C6   N1   52.50  30.0  1
 8RA  Var_03    C4   N2   C7   N3   26.15  30.0  2
 8RA  Var_04    C6   C5   N2   C4  -50.77  30.0  1
 8RA  Var_05    C6   N1   C3   C4   57.96  30.0  1
 8RA  Var_06    C3   C4   N2   C5   51.87  30.0  1
 8RA  Var_07    C3   N1   C6   C5  -57.35  30.0  1
 8RA  Var_08    H9   C1   C2   N1   61.53  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
 8RA  plan-1  N3   0.020
 8RA  plan-1  C7   0.020
 8RA  plan-1  C8   0.020
 8RA  plan-1  C10  0.020
 8RA  plan-1  N2   0.020
 8RA  plan-1  C9   0.020
 8RA  plan-1  C11  0.020
 8RA  plan-1  H7   0.020
 8RA  plan-1  H8   0.020
 8RA  plan-1  H14  0.020
 8RA  plan-1  H15  0.020
 8RA  plan-2  N1   0.020
 8RA  plan-2  C6   0.020
 8RA  plan-2  C1   0.020
 8RA  plan-2  C2   0.020
 8RA  plan-2  C3   0.020
 8RA  plan-2  O1   0.020

