# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 17:55:07 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: trans-4-methylcyclohexanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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
 4JU  4JU  trans-4-methylcyclohexanamine  ligand  23  8  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4JU
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
 4JU  N1   N  NH2   0  -0.794   2.8586  -0.1140   0.0045
 4JU  C5   C  CH1   0  -0.075   1.4437  -0.0298  -0.3373
 4JU  C6   C  CH2   0  -0.426   0.7173  -1.2752   0.1580
 4JU  C4   C  CH2   0  -0.438   0.7448   1.2288   0.1794
 4JU  C3   C  CH2   0  -0.416  -0.7360   1.2524  -0.1857
 4JU  C2   C  CH1   0  -0.227  -1.4655   0.0056   0.3096
 4JU  C1   C  CH3   0  -0.652  -2.9357   0.0242  -0.0867
 4JU  C7   C  CH2   0  -0.415  -0.7643  -1.2509  -0.2028
 4JU  H1   H  HNH2  0   0.339   3.3361   0.7125  -0.3365
 4JU  H2   H  HNH2  0   0.331   2.9554  -0.0795   1.0140
 4JU  H4   H  HCH1  0   0.206   1.3766  -0.0216  -1.4328
 4JU  H5   H  HCH2  0   0.225   1.1945  -2.1664  -0.2578
 4JU  H6   H  HCH2  0   0.204   0.8261  -1.3431   1.2479
 4JU  H7   H  HCH2  0   0.203   0.8554   1.2721   1.2702
 4JU  H8   H  HCH2  0   0.222   1.2457   2.1165  -0.2192
 4JU  H9   H  HCH2  0   0.223  -1.2097   2.1488   0.2248
 4JU  H10  H  HCH2  0   0.203  -0.8432   1.3211  -1.2754
 4JU  H11  H  HCH1  0   0.206  -1.4012  -0.0025   1.4059
 4JU  H12  H  HCH3  0   0.222  -3.4634  -0.8536   0.2916
 4JU  H13  H  HCH3  0   0.222  -3.4433   0.9097   0.3010
 4JU  H14  H  HCH3  0   0.211  -3.0454   0.0313  -1.1739
 4JU  H15  H  HCH2  0   0.204  -0.8742  -1.3021  -1.2931
 4JU  H16  H  HCH2  0   0.223  -1.2590  -2.1410   0.1963

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
 4JU  N1  C5   single  1.458  0.020  1.458
 4JU  C6  C5   single  1.524  0.020  1.524
 4JU  C6  C7   single  1.525  0.020  1.525
 4JU  C4  C5   single  1.530  0.020  1.530
 4JU  C4  C3   single  1.525  0.020  1.525
 4JU  C2  C7   single  1.527  0.020  1.527
 4JU  C2  C3   single  1.527  0.020  1.527
 4JU  C2  C1   single  1.523  0.020  1.523
 4JU  N1  H1   single  0.890  0.020  1.040
 4JU  N1  H2   single  0.890  0.020  1.040
 4JU  C5  H4   single  0.970  0.020  1.090
 4JU  C6  H5   single  0.970  0.020  1.090
 4JU  C6  H6   single  0.970  0.020  1.090
 4JU  C4  H7   single  0.970  0.020  1.090
 4JU  C4  H8   single  0.970  0.020  1.090
 4JU  C3  H9   single  0.970  0.020  1.090
 4JU  C3  H10  single  0.970  0.020  1.090
 4JU  C2  H11  single  0.970  0.020  1.090
 4JU  C1  H12  single  0.970  0.020  1.090
 4JU  C1  H13  single  0.970  0.020  1.090
 4JU  C1  H14  single  0.970  0.020  1.090
 4JU  C7  H15  single  0.970  0.020  1.090
 4JU  C7  H16  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
 4JU  H2   N1  H1   105.19  3.000
 4JU  H2   N1  C5   108.90  3.000
 4JU  H1   N1  C5   109.35  3.000
 4JU  H4   C5  C4   107.64  3.000
 4JU  H4   C5  C6   107.53  3.000
 4JU  C4   C5  C6   110.17  3.000
 4JU  H4   C5  N1   107.08  3.000
 4JU  C4   C5  N1   114.31  3.000
 4JU  C6   C5  N1   109.82  3.000
 4JU  H6   C6  H5   106.50  3.000
 4JU  H6   C6  C7   109.40  3.000
 4JU  H5   C6  C7   110.31  3.000
 4JU  H6   C6  C5   109.02  3.000
 4JU  H5   C6  C5   109.54  3.000
 4JU  C7   C6  C5   111.90  3.000
 4JU  H8   C4  H7   106.49  3.000
 4JU  H8   C4  C3   110.16  3.000
 4JU  H7   C4  C3   109.59  3.000
 4JU  H8   C4  C5   109.59  3.000
 4JU  H7   C4  C5   108.79  3.000
 4JU  C3   C4  C5   112.05  3.000
 4JU  H10  C3  H9   106.21  3.000
 4JU  H10  C3  C2   109.06  3.000
 4JU  H9   C3  C2   109.91  3.000
 4JU  H10  C3  C4   109.49  3.000
 4JU  H9   C3  C4   110.08  3.000
 4JU  C2   C3  C4   111.93  3.000
 4JU  H11  C2  C7   107.57  3.000
 4JU  H11  C2  C1   108.45  3.000
 4JU  C7   C2  C1   111.47  3.000
 4JU  H11  C2  C3   107.57  3.000
 4JU  C1   C2  C3   111.52  3.000
 4JU  C7   C2  C3   110.09  3.000
 4JU  H14  C1  H13  107.54  3.000
 4JU  H14  C1  H12  107.55  3.000
 4JU  H13  C1  H12  107.72  3.000
 4JU  H14  C1  C2   110.85  3.000
 4JU  H13  C1  C2   111.49  3.000
 4JU  H12  C1  C2   111.50  3.000
 4JU  H16  C7  H15  106.22  3.000
 4JU  H16  C7  C2   109.83  3.000
 4JU  H15  C7  C2   109.01  3.000
 4JU  H16  C7  C6   109.89  3.000
 4JU  H15  C7  C6   109.37  3.000
 4JU  C2   C7  C6   112.32  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
 4JU  Var_01  C2  C7  C6  C5  -55.52  30.0  1
 4JU  Var_02  C2  C3  C4  C5   55.72  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
 4JU  chir_01  C5  N1  C6  C4  negativ
 4JU  chir_02  C2  C7  C3  C1  negativ

