# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:55:17 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: ethyl 1-pyrazin-2-ylpiperidine-4-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C1CCN(CC1)c2cnccn2
#
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
 HGE  HGE  'ethyl 1-pyrazin-2-ylpiperidine-4-carboxylate'  ligand  34  17  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HGE
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
 HGE  N1   N  N     0  -0.343  -4.1739  -1.0934  -1.1439
 HGE  C4   C  CH2   0  -0.433   0.6482   1.9139   0.8579
 HGE  C5   C  CH2   0  -0.311  -0.4230   0.8787   1.1686
 HGE  C6   C  CH2   0  -0.309  -0.0385  -0.2113  -0.9863
 HGE  C7   C  CH2   0  -0.436   1.0259   0.8187  -1.3357
 HGE  C8   C  CR6   0   0.500  -2.3188  -0.0297  -0.0757
 HGE  C10  C  CR16  0  -0.157  -4.9457  -0.6534  -0.1504
 HGE  C2   C  C     0   0.616   2.6381   0.3899   0.5916
 HGE  O    O  O2    0  -0.452   3.3632  -0.2974  -0.2768
 HGE  C1   C  CH2   0  -0.182   4.3196  -1.2420   0.2291
 HGE  C    C  CH3   0  -0.688   4.9949  -1.8915  -0.9537
 HGE  C3   C  CH1   0  -0.418   1.7143   1.3806  -0.0923
 HGE  N    N  NT    0  -0.503  -1.0055   0.3282  -0.0472
 HGE  N2   N  N     0  -0.438  -3.1020   0.3823   0.9210
 HGE  C11  C  CR16  0  -0.098  -4.3912   0.0797   0.8788
 HGE  C9   C  CR16  0  -0.177  -2.8935  -0.8019  -1.1202
 HGE  H1   H  HCH2  0   0.245   0.1794   2.7835   0.3912
 HGE  H2   H  HCH2  0   0.250   1.0875   2.2572   1.7946
 HGE  H3   H  HCH2  0   0.231  -0.0020   0.0664   1.7743
 HGE  H4   H  HCH2  0   0.272  -1.2095   1.3376   1.7592
 HGE  H5   H  HCH2  0   0.268  -0.5274  -0.5052  -1.9105
 HGE  H6   H  HCH2  0   0.232   0.4252  -1.1182  -0.5737
 HGE  H7   H  HCH2  0   0.258   1.7388   0.3696  -2.0260
 HGE  H8   H  HCH2  0   0.248   0.5524   1.6473  -1.8673
 HGE  H9   H  HCR6  0   0.262  -5.9999  -0.8974  -0.1746
 HGE  H10  H  HCH2  0   0.235   5.0461  -0.7263   0.8600
 HGE  H11  H  HCH2  0   0.235   3.8097  -1.9860   0.8441
 HGE  H12  H  HCH3  0   0.236   5.5224  -1.1612  -1.5671
 HGE  H13  H  HCH3  0   0.239   5.7256  -2.6150  -0.5935
 HGE  H14  H  HCH3  0   0.236   4.2798  -2.4223  -1.5820
 HGE  H15  H  HCH1  0   0.302   2.3590   2.2118  -0.4026
 HGE  H16  H  HCR6  0   0.264  -5.0037   0.4331   1.7009
 HGE  H17  H  HCR6  0   0.266  -2.3045  -1.1902  -1.9400
 HGE  O1   O  O     0  -0.451   2.7428   0.2609   1.7873

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
 HGE  C    C1   single    1.509  0.020  1.509
 HGE  C1   O    single    1.436  0.020  1.436
 HGE  O    C2   single    1.324  0.020  1.324
 HGE  O1   C2   double    1.207  0.020  1.207
 HGE  C2   C3   single    1.517  0.020  1.517
 HGE  C4   C3   single    1.524  0.020  1.524
 HGE  C4   C5   single    1.522  0.020  1.522
 HGE  C3   C7   single    1.528  0.020  1.528
 HGE  C5   N    single    1.456  0.020  1.456
 HGE  C7   C6   single    1.522  0.020  1.522
 HGE  C6   N    single    1.452  0.020  1.452
 HGE  N2   C11  aromatic  1.325  0.020  1.325
 HGE  N2   C8   aromatic  1.333  0.020  1.333
 HGE  N    C8   single    1.361  0.020  1.361
 HGE  C11  C10  aromatic  1.380  0.020  1.380
 HGE  C8   C9   aromatic  1.420  0.020  1.420
 HGE  C10  N1   aromatic  1.333  0.020  1.333
 HGE  C9   N1   aromatic  1.313  0.020  1.313
 HGE  C4   H1   single    0.970  0.020  1.090
 HGE  C4   H2   single    0.970  0.020  1.090
 HGE  C5   H3   single    0.970  0.020  1.090
 HGE  C5   H4   single    0.970  0.020  1.090
 HGE  C6   H5   single    0.970  0.020  1.090
 HGE  C6   H6   single    0.970  0.020  1.090
 HGE  C7   H7   single    0.970  0.020  1.090
 HGE  C7   H8   single    0.970  0.020  1.090
 HGE  C10  H9   single    0.930  0.020  1.080
 HGE  C1   H10  single    0.970  0.020  1.090
 HGE  C1   H11  single    0.970  0.020  1.090
 HGE  C    H12  single    0.970  0.020  1.090
 HGE  C    H13  single    0.970  0.020  1.090
 HGE  C    H14  single    0.970  0.020  1.090
 HGE  C3   H15  single    0.970  0.020  1.090
 HGE  C11  H16  single    0.930  0.020  1.080
 HGE  C9   H17  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
 HGE  C9   N1   C10  118.54  3.000
 HGE  H2   C4   H1   106.82  3.000
 HGE  H2   C4   C3   111.34  3.000
 HGE  H1   C4   C3   108.19  3.000
 HGE  H2   C4   C5   108.82  3.000
 HGE  H1   C4   C5   109.06  3.000
 HGE  C3   C4   C5   112.43  3.000
 HGE  H4   C5   H3   106.89  3.000
 HGE  H4   C5   N    108.92  3.000
 HGE  H3   C5   N    109.54  3.000
 HGE  H4   C5   C4   109.48  3.000
 HGE  H3   C5   C4   110.26  3.000
 HGE  N    C5   C4   111.61  3.000
 HGE  H6   C6   H5   106.62  3.000
 HGE  H6   C6   N    110.18  3.000
 HGE  H5   C6   N    110.56  3.000
 HGE  H6   C6   C7   110.46  3.000
 HGE  H5   C6   C7   107.61  3.000
 HGE  N    C6   C7   111.27  3.000
 HGE  H8   C7   H7   106.74  3.000
 HGE  H8   C7   C3   108.20  3.000
 HGE  H7   C7   C3   111.86  3.000
 HGE  H8   C7   C6   108.78  3.000
 HGE  H7   C7   C6   108.92  3.000
 HGE  C3   C7   C6   112.16  3.000
 HGE  C9   C8   N2   118.69  3.000
 HGE  C9   C8   N    123.27  3.000
 HGE  N2   C8   N    118.03  3.000
 HGE  H9   C10  C11  121.86  3.000
 HGE  H9   C10  N1   118.22  3.000
 HGE  C11  C10  N1   119.91  3.000
 HGE  C3   C2   O    112.13  3.000
 HGE  C3   C2   O1   124.69  3.000
 HGE  O    C2   O1   123.14  3.000
 HGE  C1   O    C2   118.37  3.000
 HGE  H11  C1   H10  107.89  3.000
 HGE  H11  C1   C    110.93  3.000
 HGE  H10  C1   C    111.01  3.000
 HGE  H11  C1   O    109.61  3.000
 HGE  H10  C1   O    109.63  3.000
 HGE  C    C1   O    107.76  3.000
 HGE  H14  C    H13  107.89  3.000
 HGE  H14  C    H12  108.63  3.000
 HGE  H13  C    H12  107.84  3.000
 HGE  H14  C    C1   111.58  3.000
 HGE  H13  C    C1   109.08  3.000
 HGE  H12  C    C1   111.67  3.000
 HGE  H15  C3   C2   105.34  3.000
 HGE  H15  C3   C7   108.25  3.000
 HGE  C2   C3   C7   113.64  3.000
 HGE  H15  C3   C4   108.80  3.000
 HGE  C7   C3   C4   108.71  3.000
 HGE  C2   C3   C4   111.91  3.000
 HGE  C8   N    C6   122.09  3.000
 HGE  C8   N    C5   120.18  3.000
 HGE  C6   N    C5   114.46  3.000
 HGE  C11  N2   C8   118.51  3.000
 HGE  H16  C11  N2   116.81  3.000
 HGE  H16  C11  C10  120.77  3.000
 HGE  N2   C11  C10  122.42  3.000
 HGE  H17  C9   C8   122.15  3.000
 HGE  H17  C9   N1   115.95  3.000
 HGE  C8   C9   N1   121.90  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
 HGE  CONST_01  N2   C11  C10  N1     0.00   0.0  0
 HGE  CONST_02  N2   C8   C9   N1     0.00   0.0  0
 HGE  CONST_03  C10  C11  N2   C8     0.00   0.0  0
 HGE  CONST_04  C10  N1   C9   C8     0.00   0.0  0
 HGE  CONST_05  C9   C8   N2   C11    0.00   0.0  0
 HGE  CONST_06  C9   N1   C10  C11    0.00   0.0  0
 HGE  CONST_07  N    C8   C9   N1   180.00   0.0  0
 HGE  CONST_08  C11  N2   C8   N    180.00   0.0  0
 HGE  CONST_09  H16  C11  C10  N1   180.00   0.0  0
 HGE  CONST_10  H17  C9   N1   C10  180.00   0.0  0
 HGE  CONST_11  H9   C10  C11  N2   180.00   0.0  0
 HGE  Var_01    C6   N    C5   C4    53.73  30.0  1
 HGE  Var_02    C7   C6   N    C5   -54.37  30.0  1
 HGE  Var_03    N2   C8   N    C5    13.39  30.0  2
 HGE  Var_04    N    C5   C4   C3   -53.31  30.0  1
 HGE  Var_05    N    C6   C7   C3    54.63  30.0  1
 HGE  Var_06    C3   C2   O    C1   177.85  30.0  3
 HGE  Var_07    C    C1   O    C2   179.48  30.0  1
 HGE  Var_08    H12  C    C1   O     60.98  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
 HGE  chir_01  C3  C2  C4  C7  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
 HGE  plan-1  N1   0.020
 HGE  plan-1  C8   0.020
 HGE  plan-1  C10  0.020
 HGE  plan-1  N    0.020
 HGE  plan-1  N2   0.020
 HGE  plan-1  C11  0.020
 HGE  plan-1  C9   0.020
 HGE  plan-1  H9   0.020
 HGE  plan-1  H16  0.020
 HGE  plan-1  H17  0.020
 HGE  plan-2  C2   0.020
 HGE  plan-2  O    0.020
 HGE  plan-2  C3   0.020
 HGE  plan-2  O1   0.020

