# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 13:21:13 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 6-benzyl-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(=C1Cc2ccccc2)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
 MKC  MKC  6-benzyl-1-(ethoxymethyl)-5-(1-methylethyl)pyrimidine-2,4(1H,3H)-dione  ligand  44  22  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MKC
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
 MKC  C1    C  CR6   0   0.159   1.2755   0.5630  -1.1909
 MKC  C2    C  CR16  0  -0.297   1.8465   1.1587  -2.3141
 MKC  C3    C  CR16  0  -0.247   2.5507   0.4053  -3.2400
 MKC  C4    C  CR16  0  -0.272   2.6944  -0.9659  -3.0611
 MKC  C5    C  CR16  0  -0.244   2.1260  -1.5681  -1.9493
 MKC  C6    C  CR16  0  -0.282   1.4229  -0.8082  -1.0212
 MKC  C7    C  CR6   0   0.400  -0.3478   0.7161   0.7617
 MKC  N8    N  NR6   0  -0.597  -1.6718   0.5676   0.3676
 MKC  C9    C  CR6   0   0.708  -2.5802  -0.1440   1.1247
 MKC  O9    O  O     0  -0.484  -3.7284  -0.3528   0.7845
 MKC  N10   N  NR16  0  -0.718  -2.0992  -0.5948   2.3171
 MKC  C11   C  CR6   0   0.569  -0.8276  -0.4402   2.8287
 MKC  O11   O  O     0  -0.453  -0.5858  -0.8501   3.9507
 MKC  C12   C  CR6   0  -0.168   0.1147   0.2106   1.9363
 MKC  C13   C  CH2   0  -0.623   0.5637   1.4457  -0.1881
 MKC  C14   C  CH1   0  -0.320   1.5629   0.3031   2.3708
 MKC  C15   C  CH3   0  -0.642   1.7535   1.3108   3.5059
 MKC  C16   C  CH3   0  -0.651   2.1787  -1.0563   2.7135
 MKC  C17   C  CH2   0  -0.082  -2.1753   1.1701  -0.8736
 MKC  O17   O  O2    0  -0.461  -1.5899   0.6510  -2.0119
 MKC  C18   C  CH2   0  -0.160  -1.9104  -0.7004  -2.2953
 MKC  C19   C  CH3   0  -0.691  -1.2821  -1.0713  -3.6175
 MKC  H2    H  HCR6  0   0.248   1.7350   2.2260  -2.4670
 MKC  H3    H  HCR6  0   0.254   2.9846   0.8884  -4.1061
 MKC  H4    H  HCR6  0   0.254   3.2408  -1.5569  -3.7847
 MKC  H5    H  HCR6  0   0.253   2.2247  -2.6356  -1.7987
 MKC  H6    H  HCR6  0   0.244   0.9812  -1.3035  -0.1656
 MKC  HN1   H  HNR6  0   0.423  -2.7664  -1.0855   2.8993
 MKC  H131  H  HCH2  0   0.298   0.0301   2.2293  -0.7234
 MKC  H132  H  HCH2  0   0.297   1.3088   1.9845   0.3977
 MKC  H14   H  HCH1  0   0.243   2.1416   0.6690   1.5222
 MKC  H151  H  HCH3  0   0.228   2.8141   1.4226   3.7373
 MKC  H152  H  HCH3  0   0.227   1.3686   2.2933   3.2286
 MKC  H153  H  HCH3  0   0.230   1.2469   0.9915   4.4156
 MKC  H161  H  HCH3  0   0.234   1.7668  -1.4838   3.6244
 MKC  H162  H  HCH3  0   0.226   2.0346  -1.7733   1.9036
 MKC  H163  H  HCH3  0   0.228   3.2539  -0.9390   2.8571
 MKC  H171  H  HCH2  0   0.276  -1.9662   2.2383  -0.8557
 MKC  H172  H  HCH2  0   0.269  -3.2568   1.0365  -0.8669
 MKC  H181  H  HCH2  0   0.213  -2.9992  -0.8308  -2.3306
 MKC  H182  H  HCH2  0   0.209  -1.5282  -1.3614  -1.5085
 MKC  H191  H  HCH3  0   0.229  -1.4875  -2.1182  -3.8401
 MKC  H192  H  HCH3  0   0.227  -1.6821  -0.4694  -4.4342
 MKC  H193  H  HCH3  0   0.246  -0.2004  -0.9395  -3.5808

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
 MKC  C1   C2    aromatic  1.394  0.020  1.394
 MKC  C1   C6    aromatic  1.389  0.020  1.389
 MKC  C1   C13   single    1.514  0.020  1.514
 MKC  C2   C3    aromatic  1.386  0.020  1.386
 MKC  C2   H2    single    0.930  0.020  1.080
 MKC  C3   C4    aromatic  1.390  0.020  1.390
 MKC  C3   H3    single    0.930  0.020  1.080
 MKC  C4   C5    aromatic  1.386  0.020  1.386
 MKC  C4   H4    single    0.930  0.020  1.080
 MKC  C5   C6    aromatic  1.390  0.020  1.390
 MKC  C5   H5    single    0.930  0.020  1.080
 MKC  C6   H6    single    0.930  0.020  1.080
 MKC  C7   N8    single    1.389  0.020  1.389
 MKC  C7   C12   double    1.360  0.020  1.360
 MKC  C7   C13   single    1.505  0.020  1.505
 MKC  N8   C9    single    1.380  0.020  1.380
 MKC  N8   C17   single    1.469  0.020  1.469
 MKC  C9   O9    double    1.216  0.020  1.216
 MKC  C9   N10   single    1.362  0.020  1.362
 MKC  N10  C11   single    1.379  0.020  1.379
 MKC  N10  HN1   single    0.860  0.020  1.020
 MKC  C11  O11   double    1.219  0.020  1.219
 MKC  C11  C12   single    1.452  0.020  1.452
 MKC  C12  C14   single    1.515  0.020  1.515
 MKC  C13  H131  single    0.970  0.020  1.090
 MKC  C13  H132  single    0.970  0.020  1.090
 MKC  C14  C15   single    1.530  0.020  1.530
 MKC  C14  C16   single    1.531  0.020  1.531
 MKC  C14  H14   single    0.970  0.020  1.090
 MKC  C15  H151  single    0.970  0.020  1.090
 MKC  C15  H152  single    0.970  0.020  1.090
 MKC  C15  H153  single    0.970  0.020  1.090
 MKC  C16  H161  single    0.970  0.020  1.090
 MKC  C16  H162  single    0.970  0.020  1.090
 MKC  C16  H163  single    0.970  0.020  1.090
 MKC  C17  O17   single    1.381  0.020  1.381
 MKC  C17  H171  single    0.970  0.020  1.090
 MKC  C17  H172  single    0.970  0.020  1.090
 MKC  O17  C18   single    1.418  0.020  1.418
 MKC  C18  C19   single    1.510  0.020  1.510
 MKC  C18  H181  single    0.970  0.020  1.090
 MKC  C18  H182  single    0.970  0.020  1.090
 MKC  C19  H191  single    0.970  0.020  1.090
 MKC  C19  H192  single    0.970  0.020  1.090
 MKC  C19  H193  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
 MKC  C13   C1   C6    122.99  3.000
 MKC  C13   C1   C2    118.51  3.000
 MKC  C6    C1   C2    118.47  3.000
 MKC  H2    C2   C3    119.56  3.000
 MKC  H2    C2   C1    119.49  3.000
 MKC  C3    C2   C1    120.95  3.000
 MKC  H3    C3   C4    120.11  3.000
 MKC  H3    C3   C2    119.71  3.000
 MKC  C4    C3   C2    120.18  3.000
 MKC  H4    C4   C5    120.40  3.000
 MKC  H4    C4   C3    120.31  3.000
 MKC  C5    C4   C3    119.29  3.000
 MKC  H5    C5   C6    119.49  3.000
 MKC  H5    C5   C4    120.17  3.000
 MKC  C6    C5   C4    120.35  3.000
 MKC  H6    C6   C5    118.92  3.000
 MKC  H6    C6   C1    120.31  3.000
 MKC  C5    C6   C1    120.77  3.000
 MKC  C13   C7   C12   121.29  3.000
 MKC  C13   C7   N8    116.74  3.000
 MKC  C12   C7   N8    121.97  3.000
 MKC  C17   N8   C9    116.71  3.000
 MKC  C17   N8   C7    121.50  3.000
 MKC  C9    N8   C7    121.78  3.000
 MKC  N10   C9   O9    121.44  3.000
 MKC  N10   C9   N8    114.73  3.000
 MKC  O9    C9   N8    123.83  3.000
 MKC  HN1   N10  C11   116.65  3.000
 MKC  HN1   N10  C9    115.53  3.000
 MKC  C11   N10  C9    127.81  3.000
 MKC  C12   C11  O11   126.01  3.000
 MKC  C12   C11  N10   114.87  3.000
 MKC  O11   C11  N10   119.12  3.000
 MKC  C14   C12  C11   118.14  3.000
 MKC  C14   C12  C7    123.38  3.000
 MKC  C11   C12  C7    118.48  3.000
 MKC  H132  C13  H131  104.09  3.000
 MKC  H132  C13  C7    108.32  3.000
 MKC  H131  C13  C7    111.24  3.000
 MKC  H132  C13  C1    108.83  3.000
 MKC  H131  C13  C1    108.93  3.000
 MKC  C7    C13  C1    114.85  3.000
 MKC  H14   C14  C16   104.99  3.000
 MKC  H14   C14  C15   106.88  3.000
 MKC  C16   C14  C15   111.64  3.000
 MKC  H14   C14  C12   107.74  3.000
 MKC  C16   C14  C12   113.23  3.000
 MKC  C15   C14  C12   111.85  3.000
 MKC  H153  C15  H152  108.19  3.000
 MKC  H153  C15  H151  107.76  3.000
 MKC  H152  C15  H151  107.73  3.000
 MKC  H153  C15  C14   111.63  3.000
 MKC  H152  C15  C14   111.14  3.000
 MKC  H151  C15  C14   110.23  3.000
 MKC  H163  C16  H162  107.37  3.000
 MKC  H163  C16  H161  107.78  3.000
 MKC  H162  C16  H161  108.27  3.000
 MKC  H163  C16  C14   109.28  3.000
 MKC  H162  C16  C14   111.36  3.000
 MKC  H161  C16  C14   112.59  3.000
 MKC  H172  C17  H171  108.11  3.000
 MKC  H172  C17  O17   112.31  3.000
 MKC  H171  C17  O17   107.51  3.000
 MKC  H172  C17  N8    106.55  3.000
 MKC  H171  C17  N8    108.83  3.000
 MKC  O17   C17  N8    113.39  3.000
 MKC  C18   O17  C17   115.29  3.000
 MKC  H182  C18  H181  107.30  3.000
 MKC  H182  C18  C19   109.59  3.000
 MKC  H181  C18  C19   110.83  3.000
 MKC  H182  C18  O17   110.64  3.000
 MKC  H181  C18  O17   110.13  3.000
 MKC  C19   C18  O17   108.37  3.000
 MKC  H193  C19  H192  108.80  3.000
 MKC  H193  C19  H191  108.06  3.000
 MKC  H192  C19  H191  107.95  3.000
 MKC  H193  C19  C18   110.71  3.000
 MKC  H192  C19  C18   111.56  3.000
 MKC  H191  C19  C18   109.65  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
 MKC  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 MKC  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 MKC  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 MKC  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 MKC  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 MKC  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 MKC  CONST_07  N10   C9   N8   C7      0.00   0.0  0
 MKC  CONST_08  C11   N10  C9   N8      0.00   0.0  0
 MKC  CONST_09  C12   C11  N10  C9      0.00   0.0  0
 MKC  CONST_10  C13   C1   C2   C3    180.00   0.0  0
 MKC  CONST_11  C13   C1   C6   C5    180.00   0.0  0
 MKC  CONST_12  O9    C9   N8   C7    180.00   0.0  0
 MKC  CONST_13  O11   C11  N10  C9    180.00   0.0  0
 MKC  CONST_14  C11   N10  C9   O9    180.00   0.0  0
 MKC  CONST_15  C17   N8   C9   N10   180.00   0.0  0
 MKC  CONST_16  H3    C3   C2   C1    180.00   0.0  0
 MKC  CONST_17  H5    C5   C6   C1    180.00   0.0  0
 MKC  CONST_18  H6    C6   C1   C2    180.00   0.0  0
 MKC  CONST_19  H4    C4   C3   C2    180.00   0.0  0
 MKC  CONST_20  H2    C2   C3   C4    180.00   0.0  0
 MKC  CONST_21  HN1   N10  C9   N8    180.00   0.0  0
 MKC  CONST_22  C17   N8   C9   O9      0.00   0.0  0
 MKC  Var_01    N8    C7   C13  C1    -90.62  30.0  2
 MKC  Var_02    C7    C13  C1   C2    163.19  30.0  2
 MKC  Var_03    O17   C17  N8   C7     64.46  30.0  3
 MKC  Var_04    C15   C14  C12  C7    107.54  30.0  3
 MKC  Var_05    H151  C15  C14  C12  -174.95  30.0  3
 MKC  Var_06    H161  C16  C14  C12   -69.48  30.0  3
 MKC  Var_07    C19   C18  O17  C17   175.59  30.0  3
 MKC  Var_08    H191  C19  C18  O17   178.10  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
 MKC  plan-1  C1   0.020
 MKC  plan-1  C2   0.020
 MKC  plan-1  C3   0.020
 MKC  plan-1  C4   0.020
 MKC  plan-1  C5   0.020
 MKC  plan-1  C6   0.020
 MKC  plan-1  C13  0.020
 MKC  plan-1  H2   0.020
 MKC  plan-1  H3   0.020
 MKC  plan-1  H4   0.020
 MKC  plan-1  H5   0.020
 MKC  plan-1  H6   0.020
 MKC  plan-2  C7   0.020
 MKC  plan-2  N8   0.020
 MKC  plan-2  C9   0.020
 MKC  plan-2  O9   0.020
 MKC  plan-2  N10  0.020
 MKC  plan-2  C11  0.020
 MKC  plan-2  O11  0.020
 MKC  plan-2  C12  0.020
 MKC  plan-2  C13  0.020
 MKC  plan-2  C14  0.020
 MKC  plan-2  C17  0.020
 MKC  plan-2  HN1  0.020

