# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 05:45:07 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: [azanyl(piperidin-1-yl)methylidene]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])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
 D86  D86  '[azanyl(piperidin-1-yl)methylidene]azanium'  ligand  23  9  .  2021-08-08  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D86
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
 D86  C1   C  CH2   0  -0.449   2.4907   0.0192  -0.2254
 D86  C6   C  CH2   0  -0.432   1.6735  -1.2675  -0.1611
 D86  C5   C  CH2   0  -0.348   0.5039  -1.0980   0.7971
 D86  N4   N  NT    0  -0.445  -0.3197   0.0446   0.4111
 D86  C3   C  CH2   0  -0.328   0.4195   1.3058   0.4137
 D86  C2   C  CH2   0  -0.432   1.6004   1.2145  -0.5462
 D86  C7   C  C     0   0.820  -1.5429  -0.0829  -0.0916
 D86  N8   N  NH2   0  -0.817  -2.0203  -1.2754  -0.4401
 D86  N9   N  NC2   1  -0.818  -2.3309   0.9791  -0.2460
 D86  H1   H  HCH2  0   0.225   2.9825   0.1818   0.7391
 D86  H2   H  HCH2  0   0.247   3.2831  -0.0704  -0.9702
 D86  H3   H  HCH2  0   0.233   1.2988  -1.5287  -1.1552
 D86  H4   H  HCH2  0   0.252   2.2899  -2.1014   0.1785
 D86  H6   H  HCH2  0   0.275  -0.0998  -1.9994   0.8703
 D86  H5   H  HCH2  0   0.270   0.8764  -0.8969   1.8053
 D86  H7   H  HCH2  0   0.271  -0.2240   2.1363   0.1385
 D86  H8   H  HCH2  0   0.261   0.7652   1.4900   1.4340
 D86  H9   H  HCH2  0   0.251   2.1673   2.1457  -0.4890
 D86  H10  H  HCH2  0   0.234   1.2182   1.1363  -1.5682
 D86  H11  H  HNH2  0   0.433  -1.4142  -2.0407  -0.6802
 D86  H12  H  HNH2  0   0.431  -2.9823  -1.3688  -0.7206
 D86  H13  H  HNC2  0   0.434  -2.1993   1.8141   0.2986
 D86  H14  H  HNC2  0   0.431  -3.2248   0.8777  -0.6965

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
 D86  N9  C7   double  1.331  0.020  1.331
 D86  N8  C7   single  1.331  0.020  1.331
 D86  C7  N4   single  1.329  0.020  1.329
 D86  N4  C3   single  1.462  0.020  1.462
 D86  N4  C5   single  1.460  0.020  1.460
 D86  C3  C2   single  1.525  0.020  1.525
 D86  C5  C6   single  1.521  0.020  1.521
 D86  C2  C1   single  1.525  0.020  1.525
 D86  C6  C1   single  1.526  0.020  1.526
 D86  C1  H1   single  0.970  0.020  1.090
 D86  C1  H2   single  0.970  0.020  1.090
 D86  C6  H3   single  0.970  0.020  1.090
 D86  C6  H4   single  0.970  0.020  1.090
 D86  C5  H6   single  0.970  0.020  1.090
 D86  C5  H5   single  0.970  0.020  1.090
 D86  C3  H7   single  0.970  0.020  1.090
 D86  C3  H8   single  0.970  0.020  1.090
 D86  C2  H9   single  0.970  0.020  1.090
 D86  C2  H10  single  0.970  0.020  1.090
 D86  N8  H11  single  0.860  0.020  1.020
 D86  N8  H12  single  0.860  0.020  1.020
 D86  N9  H13  single  0.860  0.020  1.020
 D86  N9  H14  single  0.860  0.020  1.020

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
 D86  H2   C1  H1   106.70  3.000
 D86  H2   C1  C2   110.17  3.000
 D86  H1   C1  C2   109.34  3.000
 D86  H2   C1  C6   110.40  3.000
 D86  H1   C1  C6   109.20  3.000
 D86  C2   C1  C6   110.94  3.000
 D86  H4   C6  H3   107.08  3.000
 D86  H4   C6  C5   108.86  3.000
 D86  H3   C6  C5   109.61  3.000
 D86  H4   C6  C1   110.80  3.000
 D86  H3   C6  C1   110.28  3.000
 D86  C5   C6  C1   110.14  3.000
 D86  H5   C5  H6   106.23  3.000
 D86  H5   C5  N4   106.97  3.000
 D86  H6   C5  N4   110.68  3.000
 D86  H5   C5  C6   109.84  3.000
 D86  H6   C5  C6   112.14  3.000
 D86  N4   C5  C6   110.74  3.000
 D86  C7   N4  C3   123.30  3.000
 D86  C3   N4  C5   112.91  3.000
 D86  C7   N4  C5   122.97  3.000
 D86  H8   C3  H7   107.16  3.000
 D86  H8   C3  C2   110.67  3.000
 D86  H7   C3  C2   110.19  3.000
 D86  H8   C3  N4   107.88  3.000
 D86  H7   C3  N4   111.08  3.000
 D86  C2   C3  N4   109.81  3.000
 D86  H10  C2  H9   106.94  3.000
 D86  H10  C2  C3   108.78  3.000
 D86  H9   C2  C3   108.55  3.000
 D86  H10  C2  C1   110.16  3.000
 D86  H9   C2  C1   110.76  3.000
 D86  C3   C2  C1   111.52  3.000
 D86  N9   C7  N8   118.17  3.000
 D86  N8   C7  N4   121.01  3.000
 D86  N9   C7  N4   120.81  3.000
 D86  H12  N8  H11  116.05  3.000
 D86  H12  N8  C7   119.94  3.000
 D86  H11  N8  C7   121.89  3.000
 D86  H14  N9  H13  116.26  3.000
 D86  H14  N9  C7   119.83  3.000
 D86  H13  N9  C7   121.48  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
 D86  CONST_01  N9   C7  N4  C5  180.00   0.0  0
 D86  CONST_02  N8   C7  N4  C5    0.00   0.0  0
 D86  CONST_06  H14  N9  C7  N4  180.00   0.0  0
 D86  CONST_08  H12  N8  C7  N4  180.00   0.0  0
 D86  Var_01    N4   C3  C2  C1  -54.76  30.0  1
 D86  Var_02    N4   C5  C6  C1   56.01  30.0  1
 D86  Var_03    C3   N4  C5  C6  -60.10  30.0  1
 D86  Var_04    C3   C2  C1  C6   53.08  30.0  1
 D86  Var_05    C2   C3  N4  C5   58.78  30.0  1
 D86  Var_06    C2   C1  C6  C5  -53.08  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
 D86  plan-1  C5   0.020
 D86  plan-1  N4   0.020
 D86  plan-1  C3   0.020
 D86  plan-1  C7   0.020
 D86  plan-1  N8   0.020
 D86  plan-1  N9   0.020
 D86  plan-1  H11  0.020
 D86  plan-1  H12  0.020
 D86  plan-1  H13  0.020
 D86  plan-1  H14  0.020

