# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:08:15 2020
#   Inital geometry file: a 77 line input string
#   Ligand name: 5-(cyclohexylamino)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC=C(NC2CCCCC2)C(=O)N1
#
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
 GX7  GX7  5-(cyclohexylamino)pyrimidine-2,4(1H,3H)-dione  ligand  30  15  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GX7
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
 GX7  N1   N  NR16  0  -0.672   2.2902   1.5287  -0.2222
 GX7  C4   C  CH1   0  -0.055  -1.6811  -0.1508  -0.2071
 GX7  C5   C  CH2   0  -0.459  -2.7854  -1.1191  -0.6195
 GX7  C6   C  CH2   0  -0.435  -4.0944  -0.3881  -0.8985
 GX7  C7   C  CH2   0  -0.429  -4.5315   0.4586   0.2924
 GX7  C8   C  CH2   0  -0.438  -3.4251   1.4174   0.7191
 GX7  O1   O  O     0  -0.498   4.5425   1.2223  -0.1208
 GX7  C3   C  CR6   0   0.666   3.4086   0.7770  -0.1035
 GX7  C    C  CR16  0  -0.029   1.0089   1.0214  -0.1975
 GX7  N    N  NR16  0  -0.712   3.1458  -0.5679   0.0417
 GX7  C2   C  CR6   0   0.529   1.9191  -1.1871   0.0994
 GX7  O    O  O     0  -0.459   1.8275  -2.3948   0.2324
 GX7  C1   C  CR6   0   0.123   0.7666  -0.2950  -0.0251
 GX7  N2   N  NH1   0  -0.690  -0.4696  -0.8946   0.0747
 GX7  C9   C  CH2   0  -0.431  -2.1275   0.6690   1.0060
 GX7  H1   H  HCH1  0   0.208  -1.5141   0.5411  -1.0502
 GX7  H3   H  HCH2  0   0.223  -2.9332  -1.8491   0.1842
 GX7  H4   H  HCH2  0   0.214  -3.9671   0.2578  -1.7738
 GX7  H5   H  HCH2  0   0.233  -4.8706  -1.1117  -1.1571
 GX7  H6   H  HCH2  0   0.229  -5.4404   1.0126   0.0460
 GX7  H7   H  HCH2  0   0.211  -4.7854  -0.1972   1.1324
 GX7  H8   H  HCH2  0   0.213  -3.2548   2.1524  -0.0751
 GX7  H9   H  HCH2  0   0.231  -3.7306   1.9817   1.6028
 GX7  H10  H  HCR6  0   0.306   0.2348   1.7638  -0.3110
 GX7  H11  H  HNR6  0   0.426   3.9567  -1.1674   0.1313
 GX7  H13  H  HNH1  0   0.377  -0.4720  -1.8461  -0.2620
 GX7  H15  H  HCH2  0   0.216  -2.2726  -0.0178   1.8465
 GX7  H16  H  HCH2  0   0.233  -1.3477   1.3716   1.3096
 GX7  H17  H  HNR6  0   0.432   2.4123   2.5247  -0.3219
 GX7  H2   H  HCH2  0   0.238  -2.4725  -1.6783  -1.5058

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
 GX7  O   C2   double  1.218  0.020  1.218
 GX7  N   C2   single  1.375  0.020  1.375
 GX7  N   C3   single  1.378  0.020  1.378
 GX7  O1  C3   double  1.218  0.020  1.218
 GX7  C2  C1   single  1.463  0.020  1.463
 GX7  C3  N1   single  1.353  0.020  1.353
 GX7  C1  N2   single  1.378  0.020  1.378
 GX7  C1  C    double  1.350  0.020  1.350
 GX7  N1  C    single  1.378  0.020  1.378
 GX7  N2  C4   single  1.449  0.020  1.449
 GX7  C9  C4   single  1.531  0.020  1.531
 GX7  C9  C8   single  1.525  0.020  1.525
 GX7  C4  C5   single  1.526  0.020  1.526
 GX7  C5  C6   single  1.525  0.020  1.525
 GX7  C8  C7   single  1.525  0.020  1.525
 GX7  C6  C7   single  1.525  0.020  1.525
 GX7  C4  H1   single  0.970  0.020  1.090
 GX7  C5  H2   single  0.970  0.020  1.090
 GX7  C5  H3   single  0.970  0.020  1.090
 GX7  C6  H4   single  0.970  0.020  1.090
 GX7  C6  H5   single  0.970  0.020  1.090
 GX7  C7  H6   single  0.970  0.020  1.090
 GX7  C7  H7   single  0.970  0.020  1.090
 GX7  C8  H8   single  0.970  0.020  1.090
 GX7  C8  H9   single  0.970  0.020  1.090
 GX7  C   H10  single  0.930  0.020  1.080
 GX7  N   H11  single  0.860  0.020  1.020
 GX7  N2  H13  single  0.890  0.020  1.040
 GX7  C9  H15  single  0.970  0.020  1.090
 GX7  C9  H16  single  0.970  0.020  1.090
 GX7  N1  H17  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
 GX7  H17  N1  C    118.54  3.000
 GX7  H17  N1  C3   117.22  3.000
 GX7  C    N1  C3   124.23  3.000
 GX7  H1   C4  C9   108.30  3.000
 GX7  H1   C4  N2   110.11  3.000
 GX7  C9   C4  N2   111.38  3.000
 GX7  H1   C4  C5   107.52  3.000
 GX7  C9   C4  C5   110.06  3.000
 GX7  N2   C4  C5   109.39  3.000
 GX7  H3   C5  H2   107.00  3.000
 GX7  H3   C5  C6   109.74  3.000
 GX7  H2   C5  C6   110.03  3.000
 GX7  H3   C5  C4   108.79  3.000
 GX7  H2   C5  C4   109.66  3.000
 GX7  C6   C5  C4   111.50  3.000
 GX7  H5   C6  H4   106.51  3.000
 GX7  H5   C6  C7   110.42  3.000
 GX7  H4   C6  C7   109.27  3.000
 GX7  H5   C6  C5   109.62  3.000
 GX7  H4   C6  C5   109.22  3.000
 GX7  C7   C6  C5   111.67  3.000
 GX7  H7   C7  H6   106.48  3.000
 GX7  H7   C7  C8   109.27  3.000
 GX7  H6   C7  C8   110.35  3.000
 GX7  H7   C7  C6   109.44  3.000
 GX7  H6   C7  C6   110.11  3.000
 GX7  C8   C7  C6   111.08  3.000
 GX7  H9   C8  H8   106.47  3.000
 GX7  H9   C8  C9   109.83  3.000
 GX7  H8   C8  C9   109.47  3.000
 GX7  H9   C8  C7   110.39  3.000
 GX7  H8   C8  C7   109.38  3.000
 GX7  C9   C8  C7   111.18  3.000
 GX7  N    C3  O1   122.39  3.000
 GX7  O1   C3  N1   124.41  3.000
 GX7  N    C3  N1   113.19  3.000
 GX7  H10  C   C1   123.78  3.000
 GX7  H10  C   N1   114.33  3.000
 GX7  C1   C   N1   121.88  3.000
 GX7  H11  N   C2   116.37  3.000
 GX7  H11  N   C3   115.75  3.000
 GX7  C2   N   C3   127.88  3.000
 GX7  C1   C2  O    123.69  3.000
 GX7  C1   C2  N    115.12  3.000
 GX7  O    C2  N    121.19  3.000
 GX7  N2   C1  C2   115.81  3.000
 GX7  N2   C1  C    126.51  3.000
 GX7  C2   C1  C    117.67  3.000
 GX7  H13  N2  C1   112.85  3.000
 GX7  H13  N2  C4   114.64  3.000
 GX7  C1   N2  C4   120.84  3.000
 GX7  H16  C9  H15  106.54  3.000
 GX7  H16  C9  C8   110.12  3.000
 GX7  H15  C9  C8   109.84  3.000
 GX7  H16  C9  C4   110.88  3.000
 GX7  H15  C9  C4   108.12  3.000
 GX7  C8   C9  C4   111.21  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
 GX7  CONST_01  C2   N   C3  N1     0.00   0.0  0
 GX7  CONST_02  C1   C2  N   C3     0.00   0.0  0
 GX7  CONST_03  N    C3  N1  C      0.00   0.0  0
 GX7  CONST_04  C2   N   C3  O1   180.00   0.0  0
 GX7  CONST_05  C    N1  C3  O1   180.00   0.0  0
 GX7  CONST_06  O    C2  N   C3   180.00   0.0  0
 GX7  CONST_07  H11  N   C3  N1   180.00   0.0  0
 GX7  CONST_08  H17  N1  C3  N    180.00   0.0  0
 GX7  Var_01    C7   C8  C9  C4    56.67  30.0  1
 GX7  Var_02    C7   C6  C5  C4   -55.37  30.0  1
 GX7  Var_03    C8   C7  C6  C5    54.36  30.0  1
 GX7  Var_04    C9   C8  C7  C6   -54.98  30.0  1
 GX7  Var_05    C2   C1  N2  C4  -171.77  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
 GX7  chir_01  C4  N2  C9  C5  positiv

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
 GX7  plan-1  N1   0.020
 GX7  plan-1  O1   0.020
 GX7  plan-1  C3   0.020
 GX7  plan-1  C    0.020
 GX7  plan-1  N    0.020
 GX7  plan-1  C2   0.020
 GX7  plan-1  O    0.020
 GX7  plan-1  C1   0.020
 GX7  plan-1  N2   0.020
 GX7  plan-1  H10  0.020
 GX7  plan-1  H11  0.020
 GX7  plan-1  H17  0.020

