# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 11:08:32 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 4-(aminomethyl)piperidine-1-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC1CCN(CC1)C(N)=N
#
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
 03N  03N  4-(aminomethyl)piperidine-1-carboximidamide  ligand  27  11  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_03N
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
 03N  N24   N  NH2   0  -0.806   4.0090  -0.6072  -0.0233
 03N  C25   C  CH2   0  -0.267   3.0801   0.4502  -0.3968
 03N  C26   C  CH1   0  -0.241   1.7118   0.2614   0.2457
 03N  C27   C  CH2   0  -0.433   1.0389  -1.0413  -0.1770
 03N  C28   C  CH2   0  -0.271  -0.3618  -1.1788   0.4018
 03N  N29   N  NT    0  -0.469  -1.1805  -0.0304   0.0615
 03N  C30   C  CH2   0  -0.296  -0.6011   1.2312   0.5022
 03N  C31   C  CH2   0  -0.419   0.7862   1.4263  -0.0870
 03N  C32   C  C     0   0.554  -2.5469  -0.2050   0.0239
 03N  N33   N  NH2   0  -0.839  -3.2673   0.9289  -0.2980
 03N  N34   N  N     0  -0.713  -3.0660  -1.3465   0.2954
 03N  HN24  H  HNH2  0   0.343   3.7598  -1.4632  -0.5024
 03N  H125  H  HCH2  0   0.220   3.4972   1.4009  -0.0526
 03N  H225  H  HCH2  0   0.184   2.9444   0.5510  -1.4850
 03N  H26   H  HCH1  0   0.210   1.8525   0.2351   1.3345
 03N  H127  H  HCH2  0   0.213   0.9849  -1.0878  -1.2709
 03N  H227  H  HCH2  0   0.232   1.6233  -1.9047   0.1513
 03N  H128  H  HCH2  0   0.249  -0.8389  -2.0758   0.0151
 03N  H228  H  HCH2  0   0.204  -0.2989  -1.3000   1.4931
 03N  H130  H  HCH2  0   0.250  -1.2355   2.0657   0.2156
 03N  H230  H  HCH2  0   0.215  -0.5363   1.2503   1.6001
 03N  H131  H  HCH2  0   0.232   1.2000   2.3630   0.2957
 03N  H231  H  HCH2  0   0.215   0.7024   1.5354  -1.1737
 03N  H133  H  HNH2  0   0.385  -2.8529   1.5473  -0.9782
 03N  H233  H  HNH2  0   0.384  -4.2385   0.7579  -0.5051
 03N  H134  H  H     0   0.316  -4.0624  -1.3369   0.1089
 03N  H2    H  HNH2  0   0.347   4.9334  -0.3731  -0.3615

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
 03N  N24  HN24  single  0.890  0.020  1.040
 03N  C25  N24   single  1.456  0.020  1.456
 03N  C25  H125  single  0.970  0.020  1.090
 03N  C25  H225  single  0.970  0.020  1.090
 03N  C26  C25   single  1.523  0.020  1.523
 03N  C26  C31   single  1.525  0.020  1.525
 03N  C26  H26   single  0.970  0.020  1.090
 03N  C27  C26   single  1.526  0.020  1.526
 03N  C27  H127  single  0.970  0.020  1.090
 03N  C27  H227  single  0.970  0.020  1.090
 03N  C28  C27   single  1.522  0.020  1.522
 03N  C28  N29   single  1.451  0.020  1.451
 03N  C28  H128  single  0.970  0.020  1.090
 03N  C28  H228  single  0.970  0.020  1.090
 03N  N29  C30   single  1.457  0.020  1.457
 03N  C30  C31   single  1.520  0.020  1.520
 03N  C30  H130  single  0.970  0.020  1.090
 03N  C30  H230  single  0.970  0.020  1.090
 03N  C31  H131  single  0.970  0.020  1.090
 03N  C31  H231  single  0.970  0.020  1.090
 03N  C32  N29   single  1.378  0.020  1.378
 03N  C32  N33   single  1.381  0.020  1.381
 03N  N33  H133  single  0.890  0.020  1.040
 03N  N33  H233  single  0.890  0.020  1.040
 03N  N34  C32   double  1.283  0.020  1.283
 03N  N34  H134  single  0.890  0.020  1.040
 03N  N24  H2    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
 03N  H2    N24  HN24  105.21  3.000
 03N  H2    N24  C25   109.22  3.000
 03N  HN24  N24  C25   109.61  3.000
 03N  H225  C25  H125  106.16  3.000
 03N  H225  C25  C26   108.51  3.000
 03N  H125  C25  C26   108.51  3.000
 03N  C26   C25  N24   112.01  3.000
 03N  H225  C25  N24   113.49  3.000
 03N  H125  C25  N24   107.89  3.000
 03N  H26   C26  C31   108.21  3.000
 03N  H26   C26  C27   108.10  3.000
 03N  C31   C26  C27   108.91  3.000
 03N  C27   C26  C25   112.65  3.000
 03N  H26   C26  C25   107.82  3.000
 03N  C31   C26  C25   111.01  3.000
 03N  H227  C27  H127  107.01  3.000
 03N  H227  C27  C28   107.85  3.000
 03N  H127  C27  C28   109.29  3.000
 03N  C28   C27  C26   112.19  3.000
 03N  H227  C27  C26   110.81  3.000
 03N  H127  C27  C26   109.53  3.000
 03N  H228  C28  H128  106.68  3.000
 03N  H228  C28  N29   110.62  3.000
 03N  H128  C28  N29   108.79  3.000
 03N  H228  C28  C27   109.56  3.000
 03N  H128  C28  C27   110.07  3.000
 03N  N29   C28  C27   111.02  3.000
 03N  C32   N29  C30   120.83  3.000
 03N  C32   N29  C28   117.75  3.000
 03N  C30   N29  C28   112.97  3.000
 03N  H230  C30  H130  106.52  3.000
 03N  H230  C30  C31   109.32  3.000
 03N  H130  C30  C31   109.39  3.000
 03N  H230  C30  N29   109.91  3.000
 03N  H130  C30  N29   110.68  3.000
 03N  C31   C30  N29   110.91  3.000
 03N  H231  C31  H131  106.91  3.000
 03N  H231  C31  C30   109.12  3.000
 03N  H131  C31  C30   108.65  3.000
 03N  H231  C31  C26   109.82  3.000
 03N  H131  C31  C26   110.39  3.000
 03N  C30   C31  C26   111.81  3.000
 03N  N34   C32  N33   124.65  3.000
 03N  N34   C32  N29   120.54  3.000
 03N  N33   C32  N29   114.80  3.000
 03N  H233  N33  H133  111.20  3.000
 03N  H233  N33  C32   114.28  3.000
 03N  H133  N33  C32   116.50  3.000
 03N  H134  N34  C32   110.50  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
 03N  CONST_01  N33   C32  N29  C28  180.00   0.0  0
 03N  CONST_02  N34   C32  N29  C28    0.00   0.0  0
 03N  CONST_06  H233  N33  C32  N29  180.00   0.0  0
 03N  CONST_07  H134  N34  C32  N29  180.00   0.0  0
 03N  Var_01    N29   C30  C31  C26  -55.85  30.0  1
 03N  Var_02    N29   C28  C27  C26   54.87  30.0  1
 03N  Var_03    C30   N29  C28  C27  -56.91  30.0  1
 03N  Var_04    C31   C30  N29  C28   57.52  30.0  1
 03N  Var_05    HN24  N24  C25  C26   73.22  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
 03N  chir_01  C26  C25  C31  C27  negativ

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
 03N  plan-1  C28   0.020
 03N  plan-1  N29   0.020
 03N  plan-1  C30   0.020
 03N  plan-1  C32   0.020
 03N  plan-1  N33   0.020
 03N  plan-1  N34   0.020
 03N  plan-1  H133  0.020
 03N  plan-1  H233  0.020
 03N  plan-1  H134  0.020

