# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 14:08:01 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 6-(cyclohexylsulfanyl)-1-(ethoxymethyl)-5-(1-methylethyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOCN1C(=O)NC(=O)C(=C1SC2CCCCC2)C(C)C
#
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
 612  612  6-(cyclohexylsulfanyl)-1-(ethoxymethyl)-5-(1-methylethyl)pyrimidine-2,4(1H,3H)-dione  ligand  48  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_612
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
 612  C1    C  CH1   0  -0.386  -2.2008  -0.7891   0.0751
 612  C2    C  CH2   0  -0.400  -2.7656   0.5537   0.5099
 612  C3    C  CH2   0  -0.433  -3.9728   0.3518   1.4242
 612  C4    C  CH2   0  -0.433  -5.0423  -0.4950   0.7425
 612  C5    C  CH2   0  -0.435  -4.4713  -1.8325   0.2853
 612  C6    C  CH2   0  -0.420  -3.2575  -1.6427  -0.6226
 612  S     S  S2    0   0.038  -0.8103  -0.6172  -1.1138
 612  C7    C  CR6   0   0.170   0.4245   0.1438  -0.0950
 612  C12   C  CR6   0  -0.086   0.6897   1.4706  -0.1880
 612  CF    C  CH1   0  -0.307  -0.0185   2.4104  -1.1370
 612  CH    C  CH3   0  -0.656  -0.6114   3.6452  -0.4569
 612  CI    C  CH3   0  -0.644   0.8834   2.7902  -2.3127
 612  C11   C  CR6   0   0.573   1.7528   2.0099   0.6564
 612  O11   O  O     0  -0.441   2.1779   3.1488   0.6153
 612  N8    N  NR6   0  -0.574   1.1003  -0.7013   0.7821
 612  C9    C  CR6   0   0.710   2.0228  -0.2117   1.6842
 612  O9    O  O     0  -0.477   2.5956  -0.8995   2.5048
 612  N10   N  NR16  0  -0.718   2.2686   1.1268   1.5795
 612  CA    C  CH2   0  -0.060   1.0312  -2.1593   0.6262
 612  OB    O  O2    0  -0.464   1.6377  -2.5907  -0.5404
 612  CC    C  CH2   0  -0.165   3.0510  -2.4724  -0.5647
 612  CD    C  CH3   0  -0.686   3.5698  -3.1436  -1.8150
 612  H1    H  HCH1  0   0.272  -1.8302  -1.3325   0.9502
 612  H2    H  HCH2  0   0.246  -2.0027   1.1432   1.0222
 612  H2A   H  HCH2  0   0.226  -3.0684   1.1195  -0.3767
 612  H3    H  HCH2  0   0.218  -3.6526  -0.1371   2.3501
 612  H3A   H  HCH2  0   0.238  -4.3787   1.3243   1.7110
 612  H4    H  HCH2  0   0.233  -5.8865  -0.6549   1.4167
 612  H4A   H  HCH2  0   0.214  -5.4312   0.0484  -0.1252
 612  H5    H  HCH2  0   0.219  -4.1770  -2.4233   1.1590
 612  H5A   H  HCH2  0   0.238  -5.2301  -2.4137  -0.2426
 612  H6    H  HCH2  0   0.231  -3.5677  -1.1496  -1.5500
 612  H6A   H  HCH2  0   0.250  -2.8374  -2.6124  -0.8992
 612  HF    H  HCH1  0   0.254  -0.8598   1.8530  -1.5468
 612  HH    H  HCH3  0   0.228  -1.2386   4.1799  -1.1718
 612  HHA   H  HCH3  0   0.228  -1.2413   3.3715   0.3906
 612  HHB   H  HCH3  0   0.234   0.1505   4.3359  -0.1044
 612  HI    H  HCH3  0   0.227   1.2404   1.9025  -2.8371
 612  HIA   H  HCH3  0   0.230   0.3288   3.3991  -3.0287
 612  HIB   H  HCH3  0   0.229   1.7512   3.3641  -1.9895
 612  HN10  H  HNR6  0   0.427   2.9716   1.4917   2.2110
 612  HA    H  HCH2  0   0.265   1.4861  -2.5910   1.5178
 612  HAA   H  HCH2  0   0.267  -0.0082  -2.4711   0.5863
 612  HC    H  HCH2  0   0.210   3.3516  -1.4174  -0.5645
 612  HCA   H  HCH2  0   0.212   3.4883  -2.9344   0.3289
 612  HD    H  HCH3  0   0.232   3.1517  -2.6867  -2.7122
 612  HDA   H  HCH3  0   0.234   4.6536  -3.0409  -1.8618
 612  HDB   H  HCH3  0   0.231   3.3328  -4.2077  -1.8251

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
 612  S    C1    single  1.838  0.020  1.838
 612  C1   C6    single  1.527  0.020  1.527
 612  C1   C2    single  1.520  0.020  1.520
 612  C1   H1    single  0.970  0.020  1.090
 612  C2   C3    single  1.528  0.020  1.528
 612  C2   H2    single  0.970  0.020  1.090
 612  C2   H2A   single  0.970  0.020  1.090
 612  C3   C4    single  1.525  0.020  1.525
 612  C3   H3    single  0.970  0.020  1.090
 612  C3   H3A   single  0.970  0.020  1.090
 612  C5   C4    single  1.524  0.020  1.524
 612  C4   H4    single  0.970  0.020  1.090
 612  C4   H4A   single  0.970  0.020  1.090
 612  C6   C5    single  1.528  0.020  1.528
 612  C5   H5    single  0.970  0.020  1.090
 612  C5   H5A   single  0.970  0.020  1.090
 612  C6   H6    single  0.970  0.020  1.090
 612  C6   H6A   single  0.970  0.020  1.090
 612  C7   S     single  1.773  0.020  1.773
 612  N8   C7    single  1.393  0.020  1.393
 612  C12  C7    double  1.356  0.020  1.356
 612  C11  C12   single  1.461  0.020  1.461
 612  C12  CF    single  1.512  0.020  1.512
 612  CF   CI    single  1.530  0.020  1.530
 612  CF   CH    single  1.529  0.020  1.529
 612  CF   HF    single  0.970  0.020  1.090
 612  CH   HH    single  0.970  0.020  1.090
 612  CH   HHA   single  0.970  0.020  1.090
 612  CH   HHB   single  0.970  0.020  1.090
 612  CI   HI    single  0.970  0.020  1.090
 612  CI   HIA   single  0.970  0.020  1.090
 612  CI   HIB   single  0.970  0.020  1.090
 612  O11  C11   double  1.216  0.020  1.216
 612  N10  C11   single  1.378  0.020  1.378
 612  C9   N8    single  1.380  0.020  1.380
 612  N8   CA    single  1.468  0.020  1.468
 612  O9   C9    double  1.214  0.020  1.214
 612  N10  C9    single  1.365  0.020  1.365
 612  N10  HN10  single  0.860  0.020  1.020
 612  CA   OB    single  1.384  0.020  1.384
 612  CA   HA    single  0.970  0.020  1.090
 612  CA   HAA   single  0.970  0.020  1.090
 612  CC   OB    single  1.418  0.020  1.418
 612  CC   CD    single  1.511  0.020  1.511
 612  CC   HC    single  0.970  0.020  1.090
 612  CC   HCA   single  0.970  0.020  1.090
 612  CD   HD    single  0.970  0.020  1.090
 612  CD   HDA   single  0.970  0.020  1.090
 612  CD   HDB   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
 612  H1    C1   S    107.91  3.000
 612  H1    C1   C6   108.78  3.000
 612  S     C1   C6   106.28  3.000
 612  H1    C1   C2   109.61  3.000
 612  C6    C1   C2   111.55  3.000
 612  S     C1   C2   112.56  3.000
 612  H2A   C2   H2   107.12  3.000
 612  H2A   C2   C3   109.54  3.000
 612  H2    C2   C3   110.04  3.000
 612  H2A   C2   C1   109.13  3.000
 612  H2    C2   C1   110.58  3.000
 612  C3    C2   C1   110.36  3.000
 612  H3A   C3   H3   106.51  3.000
 612  H3A   C3   C4   110.56  3.000
 612  H3    C3   C4   109.58  3.000
 612  H3A   C3   C2   109.46  3.000
 612  H3    C3   C2   109.51  3.000
 612  C4    C3   C2   111.10  3.000
 612  H4A   C4   H4   106.69  3.000
 612  H4A   C4   C5   109.32  3.000
 612  H4    C4   C5   110.25  3.000
 612  H4A   C4   C3   109.13  3.000
 612  H4    C4   C3   110.33  3.000
 612  C5    C4   C3   111.01  3.000
 612  H5A   C5   H5   106.58  3.000
 612  H5A   C5   C6   109.33  3.000
 612  H5    C5   C6   109.13  3.000
 612  H5A   C5   C4   110.59  3.000
 612  H5    C5   C4   109.56  3.000
 612  C6    C5   C4   111.52  3.000
 612  H6A   C6   H6   107.11  3.000
 612  H6A   C6   C5   110.22  3.000
 612  H6    C6   C5   109.52  3.000
 612  H6A   C6   C1   110.23  3.000
 612  H6    C6   C1   109.34  3.000
 612  C5    C6   C1   110.35  3.000
 612  C7    S    C1   101.27  3.000
 612  N8    C7   C12  122.81  3.000
 612  C12   C7   S    121.12  3.000
 612  N8    C7   S    116.07  3.000
 612  C11   C12  CF   118.32  3.000
 612  CF    C12  C7   124.03  3.000
 612  C11   C12  C7   117.63  3.000
 612  HF    CF   CI   107.06  3.000
 612  HF    CF   CH   106.32  3.000
 612  CI    CF   CH   111.71  3.000
 612  HF    CF   C12  106.25  3.000
 612  CH    CF   C12  113.85  3.000
 612  CI    CF   C12  111.14  3.000
 612  HHB   CH   HHA  108.19  3.000
 612  HHB   CH   HH   107.69  3.000
 612  HHA   CH   HH   107.46  3.000
 612  HHB   CH   CF   112.67  3.000
 612  HHA   CH   CF   111.52  3.000
 612  HH    CH   CF   109.10  3.000
 612  HIB   CI   HIA  107.79  3.000
 612  HIB   CI   HI   108.09  3.000
 612  HIA   CI   HI   107.75  3.000
 612  HIB   CI   CF   111.87  3.000
 612  HIA   CI   CF   110.07  3.000
 612  HI    CI   CF   111.12  3.000
 612  N10   C11  O11  119.47  3.000
 612  N10   C11  C12  115.04  3.000
 612  O11   C11  C12  125.48  3.000
 612  CA    N8   C9   116.95  3.000
 612  CA    N8   C7   120.86  3.000
 612  C9    N8   C7   121.38  3.000
 612  N10   C9   O9   121.49  3.000
 612  N10   C9   N8   114.71  3.000
 612  O9    C9   N8   123.79  3.000
 612  HN10  N10  C9   115.49  3.000
 612  HN10  N10  C11  116.53  3.000
 612  C9    N10  C11  127.78  3.000
 612  HAA   CA   HA   108.41  3.000
 612  HAA   CA   OB   107.40  3.000
 612  HA    CA   OB   112.53  3.000
 612  HAA   CA   N8   109.52  3.000
 612  HA    CA   N8   106.67  3.000
 612  OB    CA   N8   112.25  3.000
 612  CC    OB   CA   115.16  3.000
 612  HCA   CC   HC   107.20  3.000
 612  HCA   CC   CD   110.49  3.000
 612  HC    CC   CD   109.47  3.000
 612  HCA   CC   OB   110.37  3.000
 612  HC    CC   OB   110.69  3.000
 612  CD    CC   OB   108.62  3.000
 612  HDB   CD   HDA  107.93  3.000
 612  HDB   CD   HD   108.54  3.000
 612  HDA   CD   HD   107.86  3.000
 612  HDB   CD   CC   111.51  3.000
 612  HDA   CD   CC   109.59  3.000
 612  HD    CD   CC   111.29  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
 612  CONST_01  N10   C9   N8   C7      0.00   0.0  0
 612  CONST_02  C9    N10  C11  C12     0.00   0.0  0
 612  CONST_03  N8    C9   N10  C11     0.00   0.0  0
 612  CONST_04  O9    C9   N8   C7    180.00   0.0  0
 612  CONST_05  O9    C9   N10  C11   180.00   0.0  0
 612  CONST_06  C9    N10  C11  O11   180.00   0.0  0
 612  CONST_07  CA    N8   C9   N10   180.00   0.0  0
 612  CONST_08  HN10  N10  C11  C12   180.00   0.0  0
 612  CONST_09  CA    N8   C9   O9      0.00   0.0  0
 612  Var_01    C4    C5   C6   C1     55.36  30.0  1
 612  Var_02    C4    C3   C2   C1    -56.47  30.0  1
 612  Var_03    C5    C4   C3   C2     55.88  30.0  1
 612  Var_04    C6    C5   C4   C3    -55.49  30.0  1
 612  Var_05    N8    C7   S    C1     78.02  30.0  2
 612  Var_06    OB    CA   N8   C7     66.00  30.0  3
 612  Var_07    CI    CF   C12  C7   -105.69  30.0  3
 612  Var_08    HI    CI   CF   C12    55.94  30.0  3
 612  Var_09    HH    CH   CF   C12  -170.74  30.0  3
 612  Var_10    CD    CC   OB   CA    172.73  30.0  1
 612  Var_11    HD    CD   CC   OB     59.44  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
 612  chir_01  C1  S  C6  C2  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
 612  plan-1  S     0.020
 612  plan-1  C7    0.020
 612  plan-1  C12   0.020
 612  plan-1  CF    0.020
 612  plan-1  C11   0.020
 612  plan-1  O11   0.020
 612  plan-1  N8    0.020
 612  plan-1  C9    0.020
 612  plan-1  O9    0.020
 612  plan-1  N10   0.020
 612  plan-1  CA    0.020
 612  plan-1  HN10  0.020

