# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 23:12:06 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: piperidine-1-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)N1CCCCC1
#
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
 MRZ  MRZ  piperidine-1-carboximidamide  ligand  22  9  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MRZ
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
 MRZ  C1   C  CH2   0  -0.441  -2.5681   0.0660  -0.0006
 MRZ  C6   C  CH2   0  -0.436  -1.7934  -1.1933   0.3635
 MRZ  C5   C  CH2   0  -0.273  -0.4320  -1.2306  -0.3172
 MRZ  N4   N  NT    0  -0.469   0.3248  -0.0259  -0.0260
 MRZ  C3   C  CH2   0  -0.294  -0.3677   1.1970  -0.4121
 MRZ  C2   C  CH2   0  -0.432  -1.7192   1.2987   0.2780
 MRZ  C7   C  C     0   0.554   1.6993  -0.1052  -0.0593
 MRZ  N8   N  NH2   0  -0.840   2.3570   1.0799   0.2100
 MRZ  N9   N  N     0  -0.715   2.2827  -1.2122  -0.3446
 MRZ  H1   H  HCH2  0   0.212  -2.8314   0.0389  -1.0634
 MRZ  H2   H  HCH2  0   0.233  -3.5075   0.1130   0.5544
 MRZ  H3   H  HCH2  0   0.216  -1.6528  -1.2400   1.4477
 MRZ  H4   H  HCH2  0   0.232  -2.3520  -2.0871   0.0771
 MRZ  H5   H  HCH2  0   0.249   0.1362  -2.0916   0.0252
 MRZ  H6   H  HCH2  0   0.204  -0.5661  -1.3486  -1.4025
 MRZ  H7   H  HCH2  0   0.250   0.2317   2.0700  -0.1688
 MRZ  H8   H  HCH2  0   0.214  -0.5153   1.2144  -1.5021
 MRZ  H9   H  HCH2  0   0.233  -2.2226   2.2039  -0.0684
 MRZ  H10  H  HCH2  0   0.219  -1.5650   1.4102   1.3554
 MRZ  H11  H  HNH2  0   0.385   1.9419   1.6784   0.9074
 MRZ  H12  H  HNH2  0   0.384   3.3475   0.9768   0.3629
 MRZ  H13  H  H     0   0.315   3.2836  -1.1297  -0.2082

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
 MRZ  N9  C7   double  1.283  0.020  1.283
 MRZ  C3  C2   single  1.521  0.020  1.521
 MRZ  C3  N4   single  1.457  0.020  1.457
 MRZ  C2  C1   single  1.522  0.020  1.522
 MRZ  C7  N4   single  1.377  0.020  1.377
 MRZ  C7  N8   single  1.382  0.020  1.382
 MRZ  N4  C5   single  1.452  0.020  1.452
 MRZ  C1  C6   single  1.523  0.020  1.523
 MRZ  C5  C6   single  1.523  0.020  1.523
 MRZ  C1  H1   single  0.970  0.020  1.090
 MRZ  C1  H2   single  0.970  0.020  1.090
 MRZ  C6  H3   single  0.970  0.020  1.090
 MRZ  C6  H4   single  0.970  0.020  1.090
 MRZ  C5  H5   single  0.970  0.020  1.090
 MRZ  C5  H6   single  0.970  0.020  1.090
 MRZ  C3  H7   single  0.970  0.020  1.090
 MRZ  C3  H8   single  0.970  0.020  1.090
 MRZ  C2  H9   single  0.970  0.020  1.090
 MRZ  C2  H10  single  0.970  0.020  1.090
 MRZ  N8  H11  single  0.890  0.020  1.040
 MRZ  N8  H12  single  0.890  0.020  1.040
 MRZ  N9  H13  single  0.890  0.020  1.040

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
 MRZ  H2   C1  H1   106.70  3.000
 MRZ  H2   C1  C2   110.60  3.000
 MRZ  H1   C1  C2   109.37  3.000
 MRZ  H2   C1  C6   110.59  3.000
 MRZ  H1   C1  C6   109.51  3.000
 MRZ  C2   C1  C6   110.01  3.000
 MRZ  H4   C6  H3   106.89  3.000
 MRZ  H4   C6  C5   108.67  3.000
 MRZ  H3   C6  C5   109.09  3.000
 MRZ  H4   C6  C1   110.72  3.000
 MRZ  H3   C6  C1   109.73  3.000
 MRZ  C5   C6  C1   111.61  3.000
 MRZ  H6   C5  H5   106.83  3.000
 MRZ  H6   C5  N4   110.51  3.000
 MRZ  H5   C5  N4   108.76  3.000
 MRZ  H6   C5  C6   109.56  3.000
 MRZ  H5   C5  C6   110.24  3.000
 MRZ  N4   C5  C6   110.86  3.000
 MRZ  C7   N4  C3   121.07  3.000
 MRZ  C7   N4  C5   117.87  3.000
 MRZ  C3   N4  C5   113.29  3.000
 MRZ  H8   C3  H7   106.45  3.000
 MRZ  H8   C3  C2   109.23  3.000
 MRZ  H7   C3  C2   109.57  3.000
 MRZ  H8   C3  N4   109.84  3.000
 MRZ  H7   C3  N4   110.65  3.000
 MRZ  C2   C3  N4   110.99  3.000
 MRZ  H10  C2  H9   107.03  3.000
 MRZ  H10  C2  C3   109.17  3.000
 MRZ  H9   C2  C3   108.73  3.000
 MRZ  H10  C2  C1   109.96  3.000
 MRZ  H9   C2  C1   110.86  3.000
 MRZ  C3   C2  C1   111.00  3.000
 MRZ  N9   C7  N8   124.52  3.000
 MRZ  N8   C7  N4   114.89  3.000
 MRZ  N9   C7  N4   120.58  3.000
 MRZ  H12  N8  H11  111.13  3.000
 MRZ  H12  N8  C7   114.19  3.000
 MRZ  H11  N8  C7   116.61  3.000
 MRZ  H13  N9  C7   110.42  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
 MRZ  CONST_01  N9   C7  N4  C5    0.00   0.0  0
 MRZ  CONST_02  N8   C7  N4  C5  180.00   0.0  0
 MRZ  CONST_05  H13  N9  C7  N4  180.00   0.0  0
 MRZ  CONST_07  H12  N8  C7  N4  180.00   0.0  0
 MRZ  Var_01    N4   C3  C2  C1  -55.45  30.0  1
 MRZ  Var_02    N4   C5  C6  C1   54.53  30.0  1
 MRZ  Var_03    C3   C2  C1  C6   53.53  30.0  1
 MRZ  Var_04    C3   N4  C5  C6  -56.98  30.0  1
 MRZ  Var_05    C2   C3  N4  C5   57.70  30.0  1
 MRZ  Var_06    C2   C1  C6  C5  -53.23  30.0  1

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
 MRZ  plan-1  C5   0.020
 MRZ  plan-1  N4   0.020
 MRZ  plan-1  C3   0.020
 MRZ  plan-1  C7   0.020
 MRZ  plan-1  N8   0.020
 MRZ  plan-1  N9   0.020
 MRZ  plan-1  H11  0.020
 MRZ  plan-1  H12  0.020
 MRZ  plan-1  H13  0.020

