# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 14:35:32 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 3-[4-(3-oxidanylidenepropyl)piperazin-1-yl]propanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=CCCN1CCN(CCC=O)CC1
#
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
 GEB  GEB  3-[4-(3-oxidanylidenepropyl)piperazin-1-yl]propanal  ligand  32  14  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GEB
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
 GEB  C32  C  C1    0   0.187  -4.3791   1.2949  -0.2714
 GEB  C33  C  CH2   0  -0.552  -3.5762   0.2623   0.4517
 GEB  C34  C  CH2   0  -0.290  -2.3334  -0.1483  -0.3434
 GEB  C35  C  CH2   0  -0.333  -0.6314  -0.4019   1.3801
 GEB  C36  C  CH2   0  -0.294   0.6038   0.2228   0.7412
 GEB  C37  C  CH2   0  -0.260   2.5495  -0.2390  -0.6149
 GEB  C38  C  CH2   0  -0.576   3.5909   0.2041   0.4111
 GEB  C39  C  C1    0   0.189   4.9254   0.4133  -0.2352
 GEB  C43  C  CH2   0  -0.290   0.4996  -1.3942  -1.0123
 GEB  C44  C  CH2   0  -0.332  -0.7352  -2.0026  -0.3629
 GEB  N16  N  NT    0  -0.410  -1.5079  -1.0614   0.4278
 GEB  N17  N  NT    0  -0.420   1.3490  -0.7740  -0.0088
 GEB  O6   O  O     0  -0.382  -5.5619   1.2245  -0.4999
 GEB  O7   O  O     0  -0.378   5.6252   1.3837  -0.0843
 GEB  H1   H  H     0   0.184  -3.7993   2.1801  -0.5921
 GEB  H2   H  HCH2  0   0.264  -3.2643   0.7256   1.3959
 GEB  H3   H  HCH2  0   0.254  -4.1893  -0.6071   0.6904
 GEB  H4   H  HCH2  0   0.248  -2.6503  -0.6574  -1.2559
 GEB  H5   H  HCH2  0   0.216  -1.7976   0.7546  -0.6708
 GEB  H6   H  HCH2  0   0.234  -0.3088  -1.1401   2.1214
 GEB  H7   H  HCH2  0   0.241  -1.1831   0.3645   1.9282
 GEB  H8   H  HCH2  0   0.194   0.3127   1.0751   0.1015
 GEB  H9   H  HCH2  0   0.244   1.2283   0.6307   1.5383
 GEB  H10  H  HCH2  0   0.206   2.3284   0.5984  -1.2981
 GEB  H11  H  HCH2  0   0.236   2.9881  -1.0306  -1.2305
 GEB  H12  H  HCH2  0   0.259   3.3010   1.1072   0.9479
 GEB  H13  H  HCH2  0   0.270   3.7152  -0.6029   1.1433
 GEB  H14  H  H     0   0.185   5.2555  -0.4227  -0.8799
 GEB  H15  H  HCH2  0   0.239   1.0637  -2.1851  -1.5137
 GEB  H16  H  HCH2  0   0.194   0.2002  -0.6755  -1.7960
 GEB  H17  H  HCH2  0   0.242  -1.3745  -2.4459  -1.1286
 GEB  H18  H  HCH2  0   0.231  -0.4165  -2.8175   0.2960

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
 GEB  C37  C38  single  1.528  0.020  1.528
 GEB  C37  N17  single  1.447  0.020  1.447
 GEB  C38  C39  single  1.497  0.020  1.497
 GEB  N17  C43  single  1.454  0.020  1.454
 GEB  N17  C36  single  1.453  0.020  1.453
 GEB  C39  O7   double  1.206  0.020  1.206
 GEB  C43  C44  single  1.522  0.020  1.522
 GEB  C36  C35  single  1.524  0.020  1.524
 GEB  C44  N16  single  1.452  0.020  1.452
 GEB  N16  C35  single  1.453  0.020  1.453
 GEB  N16  C34  single  1.453  0.020  1.453
 GEB  C33  C34  single  1.531  0.020  1.531
 GEB  C33  C32  single  1.495  0.020  1.495
 GEB  C32  O6   double  1.207  0.020  1.207
 GEB  C32  H1   single  0.930  0.020  1.080
 GEB  C33  H2   single  0.970  0.020  1.090
 GEB  C33  H3   single  0.970  0.020  1.090
 GEB  C34  H4   single  0.970  0.020  1.090
 GEB  C34  H5   single  0.970  0.020  1.090
 GEB  C35  H6   single  0.970  0.020  1.090
 GEB  C35  H7   single  0.970  0.020  1.090
 GEB  C36  H8   single  0.970  0.020  1.090
 GEB  C36  H9   single  0.970  0.020  1.090
 GEB  C37  H10  single  0.970  0.020  1.090
 GEB  C37  H11  single  0.970  0.020  1.090
 GEB  C38  H12  single  0.970  0.020  1.090
 GEB  C38  H13  single  0.970  0.020  1.090
 GEB  C39  H14  single  0.930  0.020  1.080
 GEB  C43  H15  single  0.970  0.020  1.090
 GEB  C43  H16  single  0.970  0.020  1.090
 GEB  C44  H17  single  0.970  0.020  1.090
 GEB  C44  H18  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
 GEB  H1   C32  O6   120.38  3.000
 GEB  H1   C32  C33  114.31  3.000
 GEB  O6   C32  C33  125.30  3.000
 GEB  H3   C33  H2   107.95  3.000
 GEB  H3   C33  C34  110.87  3.000
 GEB  H2   C33  C34  109.23  3.000
 GEB  H3   C33  C32  110.78  3.000
 GEB  H2   C33  C32  106.11  3.000
 GEB  C34  C33  C32  111.71  3.000
 GEB  H5   C34  H4   105.99  3.000
 GEB  H5   C34  N16  113.41  3.000
 GEB  H4   C34  N16  108.39  3.000
 GEB  H5   C34  C33  109.25  3.000
 GEB  H4   C34  C33  108.87  3.000
 GEB  N16  C34  C33  110.74  3.000
 GEB  H7   C35  H6   106.39  3.000
 GEB  H7   C35  N16  110.05  3.000
 GEB  H6   C35  N16  108.39  3.000
 GEB  H7   C35  C36  109.40  3.000
 GEB  H6   C35  C36  108.74  3.000
 GEB  N16  C35  C36  113.59  3.000
 GEB  H9   C36  H8   106.57  3.000
 GEB  H9   C36  N17  109.87  3.000
 GEB  H8   C36  N17  111.44  3.000
 GEB  H9   C36  C35  108.10  3.000
 GEB  H8   C36  C35  110.20  3.000
 GEB  N17  C36  C35  110.53  3.000
 GEB  H11  C37  H10  106.32  3.000
 GEB  H11  C37  N17  107.49  3.000
 GEB  H10  C37  N17  111.95  3.000
 GEB  H11  C37  C38  108.33  3.000
 GEB  H10  C37  C38  109.41  3.000
 GEB  N17  C37  C38  113.04  3.000
 GEB  H13  C38  H12  108.13  3.000
 GEB  H13  C38  C39  106.85  3.000
 GEB  H12  C38  C39  109.51  3.000
 GEB  H13  C38  C37  108.19  3.000
 GEB  H12  C38  C37  112.94  3.000
 GEB  C39  C38  C37  110.99  3.000
 GEB  H14  C39  O7   120.52  3.000
 GEB  H14  C39  C38  114.33  3.000
 GEB  O7   C39  C38  125.14  3.000
 GEB  H16  C43  H15  106.56  3.000
 GEB  H16  C43  N17  111.75  3.000
 GEB  H15  C43  N17  108.89  3.000
 GEB  H16  C43  C44  110.06  3.000
 GEB  H15  C43  C44  108.97  3.000
 GEB  N17  C43  C44  110.49  3.000
 GEB  H18  C44  H17  106.87  3.000
 GEB  H18  C44  N16  108.03  3.000
 GEB  H17  C44  N16  109.48  3.000
 GEB  H18  C44  C43  108.54  3.000
 GEB  H17  C44  C43  109.77  3.000
 GEB  N16  C44  C43  113.89  3.000
 GEB  C44  N16  C35  109.28  3.000
 GEB  C35  N16  C34  113.93  3.000
 GEB  C44  N16  C34  114.88  3.000
 GEB  C43  N17  C37  110.69  3.000
 GEB  C43  N17  C36  110.44  3.000
 GEB  C37  N17  C36  112.83  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
 GEB  Var_01  C43  N17  C36  C35   56.72  30.0  1
 GEB  Var_02  C43  C44  N16  C35  -52.53  30.0  1
 GEB  Var_03  C44  C43  N17  C36  -56.51  30.0  1
 GEB  Var_04  C44  N16  C35  C36   52.55  30.0  1
 GEB  Var_05  N17  C43  C44  N16   55.65  30.0  1
 GEB  Var_06  N17  C36  C35  N16  -55.94  30.0  1
 GEB  Var_07  C38  C37  N17  C36   65.79  30.0  1
 GEB  Var_08  N16  C34  C33  C32  174.94  30.0  3
 GEB  Var_09  N17  C37  C38  C39  165.39  30.0  1
 GEB  Var_10  O6   C32  C33  C34  128.08  30.0  3
 GEB  Var_11  O7   C39  C38  C37  131.60  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
 GEB  plan-1  C38  0.020
 GEB  plan-1  C39  0.020
 GEB  plan-1  O7   0.020
 GEB  plan-1  H14  0.020
 GEB  plan-2  C32  0.020
 GEB  plan-2  C33  0.020
 GEB  plan-2  O6   0.020
 GEB  plan-2  H1   0.020

