# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 08:50:48 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: 6-(3,5-dimethylbenzyl)-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(=C1Cc2cc(C)cc(C)c2)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
 GCA  GCA  6-(3,5-dimethylbenzyl)-1-(ethoxymethyl)-5-(1-methylethyl)pyrimidine-2,4(1H,3H)-dione  ligand  50  24  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GCA
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
 GCA  C1   C  CR6   0   0.194   0.4197   0.7828  -1.2431
 GCA  C2   C  CR16  0  -0.367   0.4585   1.4553  -2.4604
 GCA  C3   C  CR6   0   0.128   0.9009   0.8281  -3.6192
 GCA  C4   C  CR16  0  -0.368   1.3020  -0.5038  -3.5453
 GCA  C5   C  CR6   0   0.129   1.2747  -1.1992  -2.3421
 GCA  C6   C  CR16  0  -0.350   0.8330  -0.5416  -1.1958
 GCA  CP   C  CH3   0  -0.725   0.9611   1.5809  -4.9174
 GCA  CQ   C  CH3   0  -0.723   1.7230  -2.6303  -2.2685
 GCA  CG   C  CH2   0  -0.625  -0.0418   1.5471  -0.0199
 GCA  C7   C  CR6   0   0.395  -0.2993   0.6926   1.1911
 GCA  C12  C  CR6   0  -0.163   0.7005   0.3809   2.0575
 GCA  CF   C  CH1   0  -0.317   2.1316   0.8419   1.8762
 GCA  CH   C  CH3   0  -0.643   2.5213   1.9078   2.9017
 GCA  CI   C  CH3   0  -0.649   3.1368  -0.3118   1.8509
 GCA  C11  C  CR6   0   0.567   0.3822  -0.4303   3.2183
 GCA  O11  O  O     0  -0.453   1.1446  -0.7164   4.1252
 GCA  N8   N  NR6   0  -0.595  -1.5917   0.2085   1.3528
 GCA  C9   C  CR6   0   0.706  -1.9204  -0.6597   2.3735
 GCA  O9   O  O     0  -0.484  -3.0198  -1.1605   2.5079
 GCA  N10  N  NR16  0  -0.718  -0.9102  -0.9127   3.2524
 GCA  CA   C  CH2   0  -0.081  -2.6800   0.6175   0.4550
 GCA  OB   O  O2    0  -0.461  -2.5080   0.1905  -0.8473
 GCA  CC   C  CH2   0  -0.159  -2.6341  -1.2075  -1.0443
 GCA  CD   C  CH3   0  -0.691  -2.4856  -1.4982  -2.5188
 GCA  H21  H  HCR6  0   0.237   0.1303   2.4888  -2.5080
 GCA  H41  H  HCR6  0   0.235   1.6359  -1.0083  -4.4460
 GCA  H61  H  HCR6  0   0.231   0.8011  -1.0962  -0.2649
 GCA  HP1  H  HCH3  0   0.247   1.8576   2.2027  -4.9656
 GCA  HP2  H  HCH3  0   0.242   0.9868   0.9066  -5.7726
 GCA  HP3  H  HCH3  0   0.242   0.1041   2.2445  -5.0357
 GCA  HQ1  H  HCH3  0   0.246   2.7930  -2.6975  -2.0598
 GCA  HQ2  H  HCH3  0   0.240   1.2055  -3.1689  -1.4747
 GCA  HQ3  H  HCH3  0   0.242   1.5429  -3.1562  -3.2056
 GCA  HG1  H  HCH2  0   0.296  -0.9137   2.1427  -0.2836
 GCA  HG2  H  HCH2  0   0.296   0.7161   2.2875   0.2370
 GCA  HF1  H  HCH1  0   0.243   2.2064   1.3059   0.8932
 GCA  HH1  H  HCH3  0   0.227   3.5171   2.2973   2.6826
 GCA  HH2  H  HCH3  0   0.227   1.8247   2.7475   2.8818
 GCA  HH3  H  HCH3  0   0.229   2.5361   1.5050   3.9134
 GCA  HI1  H  HCH3  0   0.233   3.2505  -0.7853   2.8231
 GCA  HI2  H  HCH3  0   0.225   2.8448  -1.0766   1.1295
 GCA  HI3  H  HCH3  0   0.227   4.1145   0.0661   1.5480
 GCA  HN1  H  HNR6  0   0.423  -1.1489  -1.5143   4.0311
 GCA  HA1  H  HCH2  0   0.274  -2.7302   1.7048   0.4399
 GCA  HA2  H  HCH2  0   0.268  -3.6037   0.2426   0.8958
 GCA  HC1  H  HCH2  0   0.213  -3.6082  -1.5533  -0.6757
 GCA  HC2  H  HCH2  0   0.207  -1.8635  -1.7476  -0.4820
 GCA  HD1  H  HCH3  0   0.228  -2.5769  -2.5705  -2.6909
 GCA  HD2  H  HCH3  0   0.226  -3.2586  -0.9995  -3.1047
 GCA  HD3  H  HCH3  0   0.248  -1.5079  -1.1798  -2.8818

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
 GCA  C1   C2   aromatic  1.391  0.020  1.391
 GCA  C1   C6   aromatic  1.388  0.020  1.388
 GCA  C1   CG   single    1.514  0.020  1.514
 GCA  C2   C3   aromatic  1.390  0.020  1.390
 GCA  C2   H21  single    0.930  0.020  1.080
 GCA  C3   C4   aromatic  1.393  0.020  1.393
 GCA  C3   CP   single    1.502  0.020  1.502
 GCA  C4   C5   aromatic  1.390  0.020  1.390
 GCA  C4   H41  single    0.930  0.020  1.080
 GCA  C5   C6   aromatic  1.393  0.020  1.393
 GCA  C5   CQ   single    1.502  0.020  1.502
 GCA  C6   H61  single    0.930  0.020  1.080
 GCA  CP   HP1  single    0.970  0.020  1.090
 GCA  CP   HP2  single    0.970  0.020  1.090
 GCA  CP   HP3  single    0.970  0.020  1.090
 GCA  CQ   HQ1  single    0.970  0.020  1.090
 GCA  CQ   HQ2  single    0.970  0.020  1.090
 GCA  CQ   HQ3  single    0.970  0.020  1.090
 GCA  CG   C7   single    1.504  0.020  1.504
 GCA  CG   HG1  single    0.970  0.020  1.090
 GCA  CG   HG2  single    0.970  0.020  1.090
 GCA  C7   C12  double    1.359  0.020  1.359
 GCA  C7   N8   single    1.389  0.020  1.389
 GCA  C12  CF   single    1.514  0.020  1.514
 GCA  C12  C11  single    1.452  0.020  1.452
 GCA  CF   CH   single    1.530  0.020  1.530
 GCA  CF   CI   single    1.530  0.020  1.530
 GCA  CF   HF1  single    0.970  0.020  1.090
 GCA  CH   HH1  single    0.970  0.020  1.090
 GCA  CH   HH2  single    0.970  0.020  1.090
 GCA  CH   HH3  single    0.970  0.020  1.090
 GCA  CI   HI1  single    0.970  0.020  1.090
 GCA  CI   HI2  single    0.970  0.020  1.090
 GCA  CI   HI3  single    0.970  0.020  1.090
 GCA  C11  O11  double    1.219  0.020  1.219
 GCA  C11  N10  single    1.380  0.020  1.380
 GCA  N8   C9   single    1.380  0.020  1.380
 GCA  N8   CA   single    1.469  0.020  1.469
 GCA  C9   O9   double    1.216  0.020  1.216
 GCA  C9   N10  single    1.363  0.020  1.363
 GCA  N10  HN1  single    0.860  0.020  1.020
 GCA  CA   OB   single    1.381  0.020  1.381
 GCA  CA   HA1  single    0.970  0.020  1.090
 GCA  CA   HA2  single    0.970  0.020  1.090
 GCA  OB   CC   single    1.417  0.020  1.417
 GCA  CC   CD   single    1.510  0.020  1.510
 GCA  CC   HC1  single    0.970  0.020  1.090
 GCA  CC   HC2  single    0.970  0.020  1.090
 GCA  CD   HD1  single    0.970  0.020  1.090
 GCA  CD   HD2  single    0.970  0.020  1.090
 GCA  CD   HD3  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
 GCA  CG   C1   C6   123.01  3.000
 GCA  CG   C1   C2   118.12  3.000
 GCA  C6   C1   C2   118.86  3.000
 GCA  H21  C2   C3   119.29  3.000
 GCA  H21  C2   C1   119.36  3.000
 GCA  C3   C2   C1   121.35  3.000
 GCA  CP   C3   C4   120.91  3.000
 GCA  CP   C3   C2   120.48  3.000
 GCA  C4   C3   C2   118.61  3.000
 GCA  H41  C4   C5   119.48  3.000
 GCA  H41  C4   C3   119.28  3.000
 GCA  C5   C4   C3   121.24  3.000
 GCA  CQ   C5   C6   120.27  3.000
 GCA  CQ   C5   C4   120.89  3.000
 GCA  C6   C5   C4   118.83  3.000
 GCA  H61  C6   C5   118.31  3.000
 GCA  H61  C6   C1   120.57  3.000
 GCA  C5   C6   C1   121.11  3.000
 GCA  HP3  CP   HP2  108.06  3.000
 GCA  HP3  CP   HP1  107.09  3.000
 GCA  HP2  CP   HP1  107.36  3.000
 GCA  HP3  CP   C3   111.55  3.000
 GCA  HP2  CP   C3   111.67  3.000
 GCA  HP1  CP   C3   110.88  3.000
 GCA  HQ3  CQ   HQ2  108.03  3.000
 GCA  HQ3  CQ   HQ1  107.25  3.000
 GCA  HQ2  CQ   HQ1  107.19  3.000
 GCA  HQ3  CQ   C5   111.63  3.000
 GCA  HQ2  CQ   C5   111.41  3.000
 GCA  HQ1  CQ   C5   111.13  3.000
 GCA  HG2  CG   HG1  104.03  3.000
 GCA  HG2  CG   C7   108.37  3.000
 GCA  HG1  CG   C7   111.64  3.000
 GCA  HG2  CG   C1   108.74  3.000
 GCA  HG1  CG   C1   108.94  3.000
 GCA  C7   CG   C1   114.56  3.000
 GCA  N8   C7   C12  122.01  3.000
 GCA  N8   C7   CG   116.80  3.000
 GCA  C12  C7   CG   121.16  3.000
 GCA  C11  C12  CF   118.24  3.000
 GCA  C11  C12  C7   118.46  3.000
 GCA  CF   C12  C7   123.30  3.000
 GCA  HF1  CF   CI   105.12  3.000
 GCA  HF1  CF   CH   106.90  3.000
 GCA  CI   CF   CH   111.66  3.000
 GCA  HF1  CF   C12  107.61  3.000
 GCA  CI   CF   C12  113.15  3.000
 GCA  CH   CF   C12  111.88  3.000
 GCA  HH3  CH   HH2  108.08  3.000
 GCA  HH3  CH   HH1  107.83  3.000
 GCA  HH2  CH   HH1  107.71  3.000
 GCA  HH3  CH   CF   111.62  3.000
 GCA  HH2  CH   CF   111.18  3.000
 GCA  HH1  CH   CF   110.27  3.000
 GCA  HI3  CI   HI2  107.40  3.000
 GCA  HI3  CI   HI1  107.78  3.000
 GCA  HI2  CI   HI1  108.29  3.000
 GCA  HI3  CI   CF   109.40  3.000
 GCA  HI2  CI   CF   111.32  3.000
 GCA  HI1  CI   CF   112.47  3.000
 GCA  N10  C11  O11  119.04  3.000
 GCA  N10  C11  C12  114.87  3.000
 GCA  O11  C11  C12  126.09  3.000
 GCA  CA   N8   C9   116.80  3.000
 GCA  CA   N8   C7   121.40  3.000
 GCA  C9   N8   C7   121.80  3.000
 GCA  N10  C9   O9   121.51  3.000
 GCA  N10  C9   N8   114.67  3.000
 GCA  O9   C9   N8   123.82  3.000
 GCA  HN1  N10  C9   115.57  3.000
 GCA  HN1  N10  C11  116.58  3.000
 GCA  C9   N10  C11  127.84  3.000
 GCA  HA2  CA   HA1  108.06  3.000
 GCA  HA2  CA   OB   112.37  3.000
 GCA  HA1  CA   OB   107.54  3.000
 GCA  HA2  CA   N8   106.56  3.000
 GCA  HA1  CA   N8   108.70  3.000
 GCA  OB   CA   N8   113.45  3.000
 GCA  CC   OB   CA   115.14  3.000
 GCA  HC2  CC   HC1  107.24  3.000
 GCA  HC2  CC   CD   109.69  3.000
 GCA  HC1  CC   CD   110.77  3.000
 GCA  HC2  CC   OB   110.62  3.000
 GCA  HC1  CC   OB   110.06  3.000
 GCA  CD   CC   OB   108.47  3.000
 GCA  HD3  CD   HD2  108.86  3.000
 GCA  HD3  CD   HD1  108.05  3.000
 GCA  HD2  CD   HD1  107.80  3.000
 GCA  HD3  CD   CC   110.92  3.000
 GCA  HD2  CD   CC   111.52  3.000
 GCA  HD1  CD   CC   109.59  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
 GCA  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 GCA  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 GCA  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 GCA  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 GCA  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 GCA  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 GCA  CONST_07  N10  C9   N8   C7      0.00   0.0  0
 GCA  CONST_08  C9   N10  C11  C12     0.00   0.0  0
 GCA  CONST_09  N8   C9   N10  C11     0.00   0.0  0
 GCA  CONST_10  CP   C3   C2   C1    180.00   0.0  0
 GCA  CONST_11  CQ   C5   C6   C1    180.00   0.0  0
 GCA  CONST_12  CG   C1   C2   C3    180.00   0.0  0
 GCA  CONST_13  CQ   C5   C4   C3    180.00   0.0  0
 GCA  CONST_14  CP   C3   C4   C5    180.00   0.0  0
 GCA  CONST_15  CG   C1   C6   C5    180.00   0.0  0
 GCA  CONST_16  O9   C9   N8   C7    180.00   0.0  0
 GCA  CONST_17  O9   C9   N10  C11   180.00   0.0  0
 GCA  CONST_18  C9   N10  C11  O11   180.00   0.0  0
 GCA  CONST_19  CA   N8   C9   N10   180.00   0.0  0
 GCA  CONST_20  H61  C6   C1   C2    180.00   0.0  0
 GCA  CONST_21  H41  C4   C3   C2    180.00   0.0  0
 GCA  CONST_22  H21  C2   C3   C4    180.00   0.0  0
 GCA  CONST_23  HN1  N10  C11  C12   180.00   0.0  0
 GCA  CONST_24  CA   N8   C9   O9      0.00   0.0  0
 GCA  Var_01    C12  C7   CG   C1     87.04  30.0  3
 GCA  Var_02    C7   CG   C1   C2    169.14  30.0  2
 GCA  Var_03    CH   CF   C12  C7    108.83  30.0  3
 GCA  Var_04    OB   CA   N8   C7     65.46  30.0  3
 GCA  Var_05    HP1  CP   C3   C2     80.01  30.0  2
 GCA  Var_06    HQ1  CQ   C5   C4     89.41  30.0  2
 GCA  Var_07    HH1  CH   CF   C12  -173.98  30.0  3
 GCA  Var_08    HI1  CI   CF   C12   -69.97  30.0  3
 GCA  Var_09    CD   CC   OB   CA    177.32  30.0  3
 GCA  Var_10    HD1  CD   CC   OB    179.84  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
 GCA  plan-1  C1   0.020
 GCA  plan-1  C2   0.020
 GCA  plan-1  C3   0.020
 GCA  plan-1  C4   0.020
 GCA  plan-1  C5   0.020
 GCA  plan-1  C6   0.020
 GCA  plan-1  CP   0.020
 GCA  plan-1  CQ   0.020
 GCA  plan-1  CG   0.020
 GCA  plan-1  H21  0.020
 GCA  plan-1  H41  0.020
 GCA  plan-1  H61  0.020
 GCA  plan-2  CG   0.020
 GCA  plan-2  C7   0.020
 GCA  plan-2  C12  0.020
 GCA  plan-2  CF   0.020
 GCA  plan-2  C11  0.020
 GCA  plan-2  O11  0.020
 GCA  plan-2  N8   0.020
 GCA  plan-2  C9   0.020
 GCA  plan-2  O9   0.020
 GCA  plan-2  N10  0.020
 GCA  plan-2  CA   0.020
 GCA  plan-2  HN1  0.020

