# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 19:38:37 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 6-amino-1-methyl-5-(piperidin-1-yl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=C(N2CCCCC2)C(=O)NC1=O)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
 S0G  S0G  6-amino-1-methyl-5-(piperidin-1-yl)pyrimidine-2,4(1H,3H)-dione  ligand  32  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S0G
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
 S0G  C3   C  CR6   0  -0.067  -0.0572   0.2191  -0.0566
 S0G  C1   C  CR6   0   0.651   1.0286   1.0315   0.2500
 S0G  C6   C  CR6   0   0.552   0.1844  -1.1013  -0.5269
 S0G  C4   C  CR6   0   0.696   2.6186  -0.6663  -0.3503
 S0G  C16  C  CH2   0  -0.444  -4.0615  -0.2151  -0.1184
 S0G  C15  C  CH2   0  -0.428  -3.2273   0.0984  -1.3573
 S0G  C14  C  CH2   0  -0.425  -3.1699  -0.6478   1.0424
 S0G  C12  C  CH2   0  -0.295  -2.1431   1.1221  -1.0267
 S0G  C13  C  CH2   0  -0.296  -2.1025   0.4101   1.3077
 S0G  N5   N  NR16  0  -0.730   1.5371  -1.4354  -0.6397
 S0G  N7   N  NT    0  -0.496  -1.3341   0.7719   0.1285
 S0G  N2   N  NR6   0  -0.586   2.3274   0.6023   0.1119
 S0G  N10  N  NH2   0  -0.837   0.8320   2.2674   0.7103
 S0G  O9   O  O     0  -0.493  -0.6457  -1.9479  -0.8377
 S0G  O8   O  O     0  -0.490   3.7582  -1.0699  -0.4883
 S0G  H1   H  HCH2  0   0.203  -4.6234   0.6793   0.1758
 S0G  H2   H  HCH2  0   0.226  -4.8038  -0.9858  -0.3396
 S0G  H3   H  HCH2  0   0.222  -2.7651  -0.8160  -1.7316
 S0G  H4   H  HCH2  0   0.215  -3.8618   0.4953  -2.1546
 S0G  H5   H  HCH2  0   0.215  -3.7656  -0.7936   1.9479
 S0G  H6   H  HCH2  0   0.219  -2.6931  -1.6017   0.8090
 S0G  H7   H  HCH2  0   0.232  -1.4812   1.2762  -1.8803
 S0G  H8   H  HCH2  0   0.208  -2.6309   2.0872  -0.8308
 S0G  H9   H  HCH2  0   0.208  -2.6022   1.3113   1.6892
 S0G  H10  H  HCH2  0   0.233  -1.4134   0.0824   2.0871
 S0G  H11  H  HCH3  0   0.266   3.3814   1.7814   1.4990
 S0G  H12  H  HCH3  0   0.291   4.3657   0.9782   0.2801
 S0G  H13  H  HCH3  0   0.265   3.4097   2.3841  -0.1765
 S0G  H14  H  HNR6  0   0.415   1.7447  -2.3651  -0.9796
 S0G  H15  H  HNH2  0   0.420  -0.1243   2.5789   0.7634
 S0G  H16  H  HNH2  0   0.427   1.5647   2.9303   0.8855
 S0G  C11  C  CH3   0  -0.577   3.4284   1.4926   0.4499

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
 S0G  C16  C15  single  1.526  0.020  1.526
 S0G  C16  C14  single  1.526  0.020  1.526
 S0G  C15  C12  single  1.527  0.020  1.527
 S0G  C14  C13  single  1.526  0.020  1.526
 S0G  C12  N7   single  1.453  0.020  1.453
 S0G  C13  N7   single  1.453  0.020  1.453
 S0G  O9   C6   double  1.226  0.020  1.226
 S0G  N7   C3   single  1.404  0.020  1.404
 S0G  C6   C3   single  1.422  0.020  1.422
 S0G  C6   N5   single  1.398  0.020  1.398
 S0G  C3   C1   double  1.390  0.020  1.390
 S0G  N5   C4   single  1.358  0.020  1.358
 S0G  C1   N10  single  1.333  0.020  1.333
 S0G  C1   N2   single  1.375  0.020  1.375
 S0G  C4   N2   single  1.381  0.020  1.381
 S0G  C4   O8   double  1.217  0.020  1.217
 S0G  N2   C11  single  1.456  0.020  1.456
 S0G  C16  H1   single  0.970  0.020  1.090
 S0G  C16  H2   single  0.970  0.020  1.090
 S0G  C15  H3   single  0.970  0.020  1.090
 S0G  C15  H4   single  0.970  0.020  1.090
 S0G  C14  H5   single  0.970  0.020  1.090
 S0G  C14  H6   single  0.970  0.020  1.090
 S0G  C12  H7   single  0.970  0.020  1.090
 S0G  C12  H8   single  0.970  0.020  1.090
 S0G  C13  H9   single  0.970  0.020  1.090
 S0G  C13  H10  single  0.970  0.020  1.090
 S0G  C11  H11  single  0.970  0.020  1.090
 S0G  C11  H12  single  0.970  0.020  1.090
 S0G  C11  H13  single  0.970  0.020  1.090
 S0G  N5   H14  single  0.860  0.020  1.020
 S0G  N10  H15  single  0.860  0.020  1.020
 S0G  N10  H16  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
 S0G  N7   C3   C6   124.32  3.000
 S0G  C6   C3   C1   118.86  3.000
 S0G  N7   C3   C1   116.82  3.000
 S0G  N10  C1   N2   117.60  3.000
 S0G  N2   C1   C3   122.23  3.000
 S0G  N10  C1   C3   120.17  3.000
 S0G  O9   C6   N5   118.02  3.000
 S0G  N5   C6   C3   114.39  3.000
 S0G  O9   C6   C3   127.59  3.000
 S0G  O8   C4   N2   122.68  3.000
 S0G  O8   C4   N5   122.26  3.000
 S0G  N2   C4   N5   115.06  3.000
 S0G  H2   C16  H1   106.35  3.000
 S0G  H2   C16  C14  110.54  3.000
 S0G  H1   C16  C14  109.06  3.000
 S0G  H2   C16  C15  110.60  3.000
 S0G  H1   C16  C15  109.29  3.000
 S0G  C14  C16  C15  110.87  3.000
 S0G  H4   C15  H3   107.46  3.000
 S0G  H4   C15  C12  109.05  3.000
 S0G  H3   C15  C12  109.60  3.000
 S0G  H4   C15  C16  110.44  3.000
 S0G  H3   C15  C16  109.75  3.000
 S0G  C12  C15  C16  110.49  3.000
 S0G  H6   C14  H5   107.36  3.000
 S0G  H6   C14  C13  109.72  3.000
 S0G  H5   C14  C13  109.24  3.000
 S0G  H6   C14  C16  109.90  3.000
 S0G  H5   C14  C16  110.45  3.000
 S0G  C13  C14  C16  110.14  3.000
 S0G  H8   C12  H7   106.54  3.000
 S0G  H8   C12  N7   108.49  3.000
 S0G  H7   C12  N7   108.56  3.000
 S0G  H8   C12  C15  108.19  3.000
 S0G  H7   C12  C15  110.85  3.000
 S0G  N7   C12  C15  113.94  3.000
 S0G  H10  C13  H9   106.60  3.000
 S0G  H10  C13  N7   108.70  3.000
 S0G  H9   C13  N7   108.54  3.000
 S0G  H10  C13  C14  110.97  3.000
 S0G  H9   C13  C14  108.11  3.000
 S0G  N7   C13  C14  113.67  3.000
 S0G  H14  N5   C4   115.38  3.000
 S0G  H14  N5   C6   116.45  3.000
 S0G  C4   N5   C6   128.17  3.000
 S0G  C13  N7   C12  114.25  3.000
 S0G  C13  N7   C3   119.34  3.000
 S0G  C12  N7   C3   119.77  3.000
 S0G  C11  N2   C4   118.69  3.000
 S0G  C11  N2   C1   120.02  3.000
 S0G  C4   N2   C1   121.29  3.000
 S0G  H16  N10  H15  118.67  3.000
 S0G  H16  N10  C1   124.40  3.000
 S0G  H15  N10  C1   116.42  3.000
 S0G  H13  C11  H12  108.27  3.000
 S0G  H13  C11  H11  109.64  3.000
 S0G  H12  C11  H11  108.32  3.000
 S0G  H13  C11  N2   110.73  3.000
 S0G  H12  C11  N2   109.14  3.000
 S0G  H11  C11  N2   110.68  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
 S0G  CONST_01  C4   N5   C6   C3      0.00   0.0  0
 S0G  CONST_02  C4   N2   C1   C3      0.00   0.0  0
 S0G  CONST_03  N5   C4   N2   C1      0.00   0.0  0
 S0G  CONST_04  N2   C4   N5   C6      0.00   0.0  0
 S0G  CONST_05  C11  N2   C1   C3    180.00   0.0  0
 S0G  CONST_06  O8   C4   N2   C1    180.00   0.0  0
 S0G  CONST_07  O8   C4   N5   C6    180.00   0.0  0
 S0G  CONST_08  O9   C6   N5   C4    180.00   0.0  0
 S0G  CONST_09  N10  C1   N2   C4    180.00   0.0  0
 S0G  CONST_10  N5   C4   N2   C11   180.00   0.0  0
 S0G  CONST_11  H14  N5   C6   C3    180.00   0.0  0
 S0G  CONST_12  N10  C1   N2   C11     0.00   0.0  0
 S0G  CONST_13  O8   C4   N2   C11     0.00   0.0  0
 S0G  CONST_14  H15  N10  C1   C3      0.00   0.0  0
 S0G  CONST_15  H16  N10  C1   C3    180.00   0.0  0
 S0G  Var_01    C15  C12  N7   C3    101.03  30.0  1
 S0G  Var_02    C14  C13  N7   C3   -100.36  30.0  1
 S0G  Var_03    C12  N7   C3   C1    108.46  30.0  2
 S0G  Var_04    N7   C12  C15  C16    51.54  30.0  1
 S0G  Var_05    N7   C13  C14  C16   -53.05  30.0  1
 S0G  Var_06    C13  C14  C16  C15    54.75  30.0  1
 S0G  Var_07    C12  C15  C16  C14   -54.04  30.0  1
 S0G  Var_08    H11  C11  N2   C1     60.66  30.0  3

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
 S0G  plan-1  C3   0.020
 S0G  plan-1  C1   0.020
 S0G  plan-1  C6   0.020
 S0G  plan-1  C4   0.020
 S0G  plan-1  N5   0.020
 S0G  plan-1  N7   0.020
 S0G  plan-1  N2   0.020
 S0G  plan-1  N10  0.020
 S0G  plan-1  O9   0.020
 S0G  plan-1  O8   0.020
 S0G  plan-1  H14  0.020
 S0G  plan-1  H15  0.020
 S0G  plan-1  H16  0.020
 S0G  plan-1  C11  0.020
 S0G  plan-2  C3   0.020
 S0G  plan-2  C12  0.020
 S0G  plan-2  C13  0.020
 S0G  plan-2  N7   0.020

