# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 23:54:40 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (1R,2R)-cyclohexane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCCC[C@H]1N
#
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
 DNH  DNH  (1R,2R)-cyclohexane-1,2-diamine  ligand  22  8  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DNH
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
 DNH  C7   C  CH2   0  -0.434   0.6829  -0.2760  -1.9392
 DNH  C8   C  CH2   0  -0.434  -0.7229   0.3109  -1.9276
 DNH  C3   C  CH1   0  -0.074   0.6962  -0.3068   0.6077
 DNH  C4   C  CH1   0  -0.074  -0.7100   0.2976   0.6197
 DNH  C5   C  CH2   0  -0.440   1.4359   0.1034  -0.6703
 DNH  C6   C  CH2   0  -0.440  -1.4628  -0.0900  -0.6575
 DNH  N1   N  NH2   0  -0.787   1.4183   0.0343   1.8266
 DNH  N2   N  NH2   0  -0.787  -1.4211  -0.0649   1.8392
 DNH  H71  H  HCH2  0   0.226   1.2330   0.0647  -2.8198
 DNH  H72  H  HCH2  0   0.210   0.6211  -1.3669  -2.0162
 DNH  H81  H  HCH2  0   0.210  -0.6622   1.4030  -1.9878
 DNH  H82  H  HCH2  0   0.226  -1.2819  -0.0161  -2.8078
 DNH  H3   H  HCH1  0   0.202   0.5810  -1.4004   0.5932
 DNH  H4   H  HCH1  0   0.202  -0.5949   1.3913   0.6244
 DNH  H51  H  HCH2  0   0.205   1.5919   1.1892  -0.6486
 DNH  H52  H  HCH2  0   0.224   2.4306  -0.3523  -0.6680
 DNH  H61  H  HCH2  0   0.224  -2.4575   0.3653  -0.6364
 DNH  H62  H  HCH2  0   0.205  -1.6184  -1.1759  -0.6534
 DNH  H11  H  HNH2  0   0.338   2.3787  -0.2765   1.7342
 DNH  H12  H  HNH2  0   0.329   1.4725   1.0444   1.9042
 DNH  H21  H  HNH2  0   0.338  -2.3810   0.2518   1.7618
 DNH  H22  H  HNH2  0   0.329  -1.4796  -1.0761   1.8970

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
 DNH  C7  C8   single  1.523  0.020  1.523
 DNH  C7  C5   single  1.524  0.020  1.524
 DNH  C7  H71  single  0.970  0.020  1.090
 DNH  C7  H72  single  0.970  0.020  1.090
 DNH  C8  C6   single  1.524  0.020  1.524
 DNH  C8  H81  single  0.970  0.020  1.090
 DNH  C8  H82  single  0.970  0.020  1.090
 DNH  C3  C4   single  1.531  0.020  1.531
 DNH  C3  C5   single  1.533  0.020  1.533
 DNH  C3  N1   single  1.457  0.020  1.457
 DNH  C3  H3   single  0.970  0.020  1.090
 DNH  C4  C6   single  1.532  0.020  1.532
 DNH  C4  N2   single  1.457  0.020  1.457
 DNH  C4  H4   single  0.970  0.020  1.090
 DNH  C5  H51  single  0.970  0.020  1.090
 DNH  C5  H52  single  0.970  0.020  1.090
 DNH  C6  H61  single  0.970  0.020  1.090
 DNH  C6  H62  single  0.970  0.020  1.090
 DNH  N1  H11  single  0.890  0.020  1.040
 DNH  N1  H12  single  0.890  0.020  1.040
 DNH  N2  H21  single  0.890  0.020  1.040
 DNH  N2  H22  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
 DNH  H72  C7  H71  106.40  3.000
 DNH  H72  C7  C5   109.54  3.000
 DNH  H71  C7  C5   110.17  3.000
 DNH  H72  C7  C8   109.40  3.000
 DNH  H71  C7  C8   110.52  3.000
 DNH  C5   C7  C8   110.72  3.000
 DNH  H82  C8  H81  106.40  3.000
 DNH  H82  C8  C6   110.14  3.000
 DNH  H81  C8  C6   109.58  3.000
 DNH  H82  C8  C7   110.53  3.000
 DNH  H81  C8  C7   109.42  3.000
 DNH  C6   C8  C7   110.68  3.000
 DNH  H3   C3  N1   107.20  3.000
 DNH  H3   C3  C5   107.80  3.000
 DNH  N1   C3  C5   113.31  3.000
 DNH  H3   C3  C4   107.25  3.000
 DNH  N1   C3  C4   110.87  3.000
 DNH  C5   C3  C4   110.14  3.000
 DNH  H4   C4  N2   107.15  3.000
 DNH  H4   C4  C6   107.85  3.000
 DNH  N2   C4  C6   113.25  3.000
 DNH  H4   C4  C3   107.25  3.000
 DNH  N2   C4  C3   110.89  3.000
 DNH  C6   C4  C3   110.17  3.000
 DNH  H52  C5  H51  106.43  3.000
 DNH  H52  C5  C3   109.00  3.000
 DNH  H51  C5  C3   108.49  3.000
 DNH  H52  C5  C7   110.33  3.000
 DNH  H51  C5  C7   109.46  3.000
 DNH  C3   C5  C7   112.91  3.000
 DNH  H62  C6  H61  106.43  3.000
 DNH  H62  C6  C4   108.48  3.000
 DNH  H61  C6  C4   108.98  3.000
 DNH  H62  C6  C8   109.42  3.000
 DNH  H61  C6  C8   110.37  3.000
 DNH  C4   C6  C8   112.94  3.000
 DNH  H12  N1  H11  105.16  3.000
 DNH  H12  N1  C3   108.87  3.000
 DNH  H11  N1  C3   108.75  3.000
 DNH  H22  N2  H21  105.14  3.000
 DNH  H22  N2  C4   108.89  3.000
 DNH  H21  N2  C4   108.69  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
 DNH  Var_01  C4  C6  C8  C7   55.57  30.0  1
 DNH  Var_02  C3  C5  C7  C8   55.63  30.0  1
 DNH  Var_03  C6  C8  C7  C5  -54.05  30.0  1

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
 DNH  chir_01  C3  C4  C5  N1  negativ
 DNH  chir_02  C4  N2  C6  C3  positiv

