# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:12:31 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: trans-N-(3-aminopropyl)cyclohexane-1,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCN[C@@H]1CC[C@@H](N)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
 JFQ  JFQ  trans-N-(3-aminopropyl)cyclohexane-1,4-diamine  ligand  33  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JFQ
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
 JFQ  C1    C  CH2   0  -0.274  -4.3744   0.5311  -0.3189
 JFQ  N1    N  NH2   0  -0.799  -5.6592   0.0867   0.2030
 JFQ  C2    C  CH2   0  -0.450  -3.2396  -0.3201   0.2287
 JFQ  N2    N  NH1   0  -0.603  -0.8173  -0.7058   0.2394
 JFQ  C3    C  CH2   0  -0.258  -1.8792   0.1432  -0.2682
 JFQ  N3    N  NH2   0  -0.807   4.7457   0.4785  -0.2458
 JFQ  C4    C  CH1   0  -0.053   0.5202  -0.3468  -0.2075
 JFQ  C5    C  CH2   0  -0.438   1.4997  -1.4545   0.1710
 JFQ  C6    C  CH2   0  -0.436   2.9201  -1.1429  -0.2868
 JFQ  C7    C  CH1   0  -0.052   3.4104   0.1912   0.2618
 JFQ  C8    C  CH2   0  -0.431   2.4471   1.2994  -0.1451
 JFQ  C9    C  CH2   0  -0.450   1.0246   1.0016   0.3164
 JFQ  H1    H  HCH2  0   0.188  -4.3229   0.5284  -1.4177
 JFQ  H1A   H  HCH2  0   0.212  -4.2236   1.5697  -0.0114
 JFQ  HN1   H  HNH2  0   0.345  -6.3913   0.6881  -0.1526
 JFQ  HN1A  H  HNH2  0   0.337  -5.8658  -0.8346  -0.1635
 JFQ  H2    H  HCH2  0   0.215  -3.2655  -0.2831   1.3228
 JFQ  H2A   H  HCH2  0   0.215  -3.3889  -1.3668  -0.0555
 JFQ  HN2   H  HNH1  0   0.328  -0.8380  -0.6917   1.2541
 JFQ  H3    H  HCH2  0   0.210  -1.8538   0.0936  -1.3621
 JFQ  H3A   H  HCH2  0   0.188  -1.7536   1.2060  -0.0108
 JFQ  HN3A  H  HNH2  0   0.339   5.3851  -0.2430   0.0663
 JFQ  H4    H  HCH1  0   0.207   0.4831  -0.2921  -1.3038
 JFQ  H5    H  HCH2  0   0.208   1.4851  -1.5864   1.2599
 JFQ  H5A   H  HCH2  0   0.229   1.1615  -2.3995  -0.2605
 JFQ  H6    H  HCH2  0   0.227   3.5966  -1.9461   0.0215
 JFQ  H6A   H  HCH2  0   0.208   2.9575  -1.1045  -1.3815
 JFQ  H7    H  HCH1  0   0.183   3.3892   0.1237   1.3630
 JFQ  H8    H  HCH2  0   0.226   2.7812   2.2564   0.2672
 JFQ  H8A   H  HCH2  0   0.209   2.4719   1.4039  -1.2358
 JFQ  H9    H  HCH2  0   0.232   0.3592   1.8085  -0.0004
 JFQ  H9A   H  HCH2  0   0.205   0.9909   0.9824   1.4131
 JFQ  HN3   H  HNH2  0   0.339   5.0850   1.3368   0.1723

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
 JFQ  C1  N1    single  1.456  0.020  1.456
 JFQ  C1  C2    single  1.521  0.020  1.521
 JFQ  C2  C3    single  1.521  0.020  1.521
 JFQ  N2  C3    single  1.451  0.020  1.451
 JFQ  N2  C4    single  1.455  0.020  1.455
 JFQ  N3  C7    single  1.457  0.020  1.457
 JFQ  C4  C5    single  1.526  0.020  1.526
 JFQ  C4  C9    single  1.532  0.020  1.532
 JFQ  C5  C6    single  1.525  0.020  1.525
 JFQ  C6  C7    single  1.524  0.020  1.524
 JFQ  C7  C8    single  1.524  0.020  1.524
 JFQ  C8  C9    single  1.525  0.020  1.525
 JFQ  C1  H1    single  0.970  0.020  1.090
 JFQ  C1  H1A   single  0.970  0.020  1.090
 JFQ  N1  HN1   single  0.890  0.020  1.040
 JFQ  N1  HN1A  single  0.890  0.020  1.040
 JFQ  C2  H2    single  0.970  0.020  1.090
 JFQ  C2  H2A   single  0.970  0.020  1.090
 JFQ  N2  HN2   single  0.890  0.020  1.040
 JFQ  C3  H3    single  0.970  0.020  1.090
 JFQ  C3  H3A   single  0.970  0.020  1.090
 JFQ  N3  HN3   single  0.890  0.020  1.040
 JFQ  N3  HN3A  single  0.890  0.020  1.040
 JFQ  C4  H4    single  0.970  0.020  1.090
 JFQ  C5  H5    single  0.970  0.020  1.090
 JFQ  C5  H5A   single  0.970  0.020  1.090
 JFQ  C6  H6    single  0.970  0.020  1.090
 JFQ  C6  H6A   single  0.970  0.020  1.090
 JFQ  C7  H7    single  0.970  0.020  1.090
 JFQ  C8  H8    single  0.970  0.020  1.090
 JFQ  C8  H8A   single  0.970  0.020  1.090
 JFQ  C9  H9    single  0.970  0.020  1.090
 JFQ  C9  H9A   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
 JFQ  H1A   C1  H1   106.07  3.000
 JFQ  H1A   C1  C2   109.11  3.000
 JFQ  H1    C1  C2   108.87  3.000
 JFQ  H1A   C1  N1   108.10  3.000
 JFQ  H1    C1  N1   113.49  3.000
 JFQ  C2    C1  N1   111.01  3.000
 JFQ  HN1A  N1  HN1  105.42  3.000
 JFQ  HN1A  N1  C1   109.14  3.000
 JFQ  HN1   N1  C1   109.33  3.000
 JFQ  H2A   C2  H2   106.76  3.000
 JFQ  H2A   C2  C3   109.18  3.000
 JFQ  H2    C2  C3   109.72  3.000
 JFQ  H2A   C2  C1   109.87  3.000
 JFQ  H2    C2  C1   108.86  3.000
 JFQ  C3    C2  C1   112.30  3.000
 JFQ  HN2   N2  C4   108.80  3.000
 JFQ  HN2   N2  C3   109.06  3.000
 JFQ  C4    N2  C3   114.88  3.000
 JFQ  H3A   C3  H3   105.94  3.000
 JFQ  H3A   C3  N2   113.56  3.000
 JFQ  H3    C3  N2   107.81  3.000
 JFQ  H3A   C3  C2   108.66  3.000
 JFQ  H3    C3  C2   109.47  3.000
 JFQ  N2    C3  C2   111.23  3.000
 JFQ  HN3A  N3  HN3  105.35  3.000
 JFQ  HN3A  N3  C7   109.30  3.000
 JFQ  HN3   N3  C7   109.27  3.000
 JFQ  H4    C4  C9   107.98  3.000
 JFQ  H4    C4  C5   107.78  3.000
 JFQ  C9    C4  C5   110.04  3.000
 JFQ  H4    C4  N2   106.72  3.000
 JFQ  C9    C4  N2   114.50  3.000
 JFQ  C5    C4  N2   109.55  3.000
 JFQ  H5A   C5  H5   106.49  3.000
 JFQ  H5A   C5  C6   110.28  3.000
 JFQ  H5    C5  C6   109.57  3.000
 JFQ  H5A   C5  C4   109.34  3.000
 JFQ  H5    C5  C4   108.96  3.000
 JFQ  C6    C5  C4   112.03  3.000
 JFQ  H6A   C6  H6   106.62  3.000
 JFQ  H6A   C6  C7   108.54  3.000
 JFQ  H6    C6  C7   110.02  3.000
 JFQ  H6A   C6  C5   109.81  3.000
 JFQ  H6    C6  C5   109.96  3.000
 JFQ  C7    C6  C5   111.76  3.000
 JFQ  H7    C7  C8   107.38  3.000
 JFQ  H7    C7  C6   107.43  3.000
 JFQ  C8    C7  C6   109.71  3.000
 JFQ  H7    C7  N3   112.17  3.000
 JFQ  C8    C7  N3   110.06  3.000
 JFQ  C6    C7  N3   110.01  3.000
 JFQ  H8A   C8  H8   106.54  3.000
 JFQ  H8A   C8  C9   109.93  3.000
 JFQ  H8    C8  C9   109.97  3.000
 JFQ  H8A   C8  C7   108.71  3.000
 JFQ  H8    C8  C7   110.02  3.000
 JFQ  C9    C8  C7   111.53  3.000
 JFQ  H9A   C9  H9   106.49  3.000
 JFQ  H9A   C9  C8   109.54  3.000
 JFQ  H9    C9  C8   109.64  3.000
 JFQ  H9A   C9  C4   108.44  3.000
 JFQ  H9    C9  C4   110.50  3.000
 JFQ  C8    C9  C4   112.06  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
 JFQ  Var_01  C7   C6  C5  C4    56.21  30.0  1
 JFQ  Var_02  C7   C8  C9  C4   -56.29  30.0  1
 JFQ  Var_03  C4   N2  C3  C2   178.97  30.0  1
 JFQ  Var_04  N2   C3  C2  C1  -178.47  30.0  3
 JFQ  Var_05  C3   C2  C1  N1  -178.43  30.0  3
 JFQ  Var_06  HN1  N1  C1  C2   178.13  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
 JFQ  chir_01  C4  N2  C5  C9  positiv
 JFQ  chir_02  C7  N3  C6  C8  positiv

