# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 05:42:38 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: 6-benzyl-1-[(benzyloxy)methyl]-5-(1-methylethyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C1=C(Cc2ccccc2)N(COCc3ccccc3)C(=O)NC1=O
#
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
 TNK  TNK  6-benzyl-1-[(benzyloxy)methyl]-5-(1-methylethyl)pyrimidine-2,4(1H,3H)-dione  ligand  51  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TNK
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
 TNK  C1    C  CR6   0   0.106   -1.5882  -34.8652  26.4531
 TNK  C2    C  CR16  0  -0.293   -2.2733  -34.6087  27.6399
 TNK  C3    C  CR16  0  -0.241   -1.7839  -33.6930  28.5582
 TNK  C4    C  CR16  0  -0.265   -0.6008  -33.0108  28.3004
 TNK  C5    C  CR16  0  -0.238    0.0848  -33.2562  27.1204
 TNK  C6    C  CR16  0  -0.282   -0.4056  -34.1779  26.2021
 TNK  C7    C  CR6   0   0.395   -1.6503  -35.8153  24.0862
 TNK  N8    N  NR6   0  -0.600   -2.3200  -34.9202  23.2586
 TNK  C9    C  CR6   0   0.717   -2.0881  -34.8643  21.8990
 TNK  O9    O  O     0  -0.474   -2.7155  -34.1504  21.1451
 TNK  N10   N  NR16  0  -0.726   -1.0842  -35.6766  21.4635
 TNK  C11   C  CR6   0   0.569   -0.2851  -36.5131  22.2183
 TNK  O11   O  O     0  -0.443    0.5988  -37.1428  21.6662
 TNK  C12   C  CR6   0  -0.161   -0.6179  -36.5706  23.6339
 TNK  C13   C  CH2   0  -0.646   -2.1528  -35.8966  25.5013
 TNK  C14   C  CH1   0  -0.321    0.1969  -37.4828  24.5253
 TNK  C15   C  CH3   0  -0.642   -0.0161  -38.9618  24.2008
 TNK  C16   C  CH3   0  -0.649    1.6828  -37.1121  24.5437
 TNK  C17   C  CH2   0  -0.042   -3.3236  -34.0181  23.7712
 TNK  O17   O  O2    0  -0.475   -4.5647  -34.6626  23.7548
 TNK  C18   C  CH2   0  -0.205   -5.5962  -33.8428  24.2637
 TNK  C19   C  CR6   0   0.071   -6.8197  -34.6782  24.5051
 TNK  C20   C  CR16  0  -0.296   -6.7302  -35.8776  25.2096
 TNK  C21   C  CR16  0  -0.238   -7.8674  -36.6295  25.4638
 TNK  C22   C  CR16  0  -0.264   -9.1101  -36.1922  25.0196
 TNK  C23   C  CR16  0  -0.239   -9.2068  -34.9995  24.3182
 TNK  C24   C  CR16  0  -0.304   -8.0652  -34.2500  24.0599
 TNK  H2    H  HCR6  0   0.253   -3.2023  -35.1287  27.8445
 TNK  H3    H  HCR6  0   0.255   -2.3300  -33.5069  29.4741
 TNK  H4    H  HCR6  0   0.255   -0.2191  -32.2921  29.0138
 TNK  H5    H  HCR6  0   0.255    1.0059  -32.7292  26.9069
 TNK  H6    H  HCR6  0   0.251    0.1443  -34.3520  25.2850
 TNK  HN1   H  HNR6  0   0.422   -0.8917  -35.6412  20.4697
 TNK  H131  H  HCH2  0   0.308   -1.9411  -36.8923  25.8900
 TNK  H132  H  HCH2  0   0.317   -3.2418  -35.8328  25.5048
 TNK  H14   H  HCH1  0   0.243   -0.1469  -37.3355  25.5493
 TNK  H151  H  HCH3  0   0.228    0.5242  -39.5829  24.9169
 TNK  H152  H  HCH3  0   0.227   -1.0720  -39.2299  24.2602
 TNK  H153  H  HCH3  0   0.229    0.3428  -39.2147  23.2048
 TNK  H161  H  HCH3  0   0.228    2.1885  -37.6806  25.3255
 TNK  H162  H  HCH3  0   0.231    2.1770  -37.3321  23.6004
 TNK  H163  H  HCH3  0   0.229    1.8229  -36.0530  24.7642
 TNK  H171  H  HCH2  0   0.254   -3.0483  -33.7083  24.7830
 TNK  H172  H  HCH2  0   0.262   -3.3270  -33.1204  23.1494
 TNK  H181  H  HCH2  0   0.228   -5.2793  -33.3758  25.2074
 TNK  H182  H  HCH2  0   0.236   -5.8226  -33.0257  23.5672
 TNK  H20   H  HCR6  0   0.262   -5.7699  -36.2258  25.5703
 TNK  H21   H  HCR6  0   0.254   -7.7852  -37.5595  26.0117
 TNK  H22   H  HCR6  0   0.254   -9.9966  -36.7803  25.2188
 TNK  H23   H  HCR6  0   0.255  -10.1692  -34.6526  23.9645
 TNK  H24   H  HCR6  0   0.253   -8.1456  -33.3237  23.5030

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
 TNK  C1   C2    aromatic  1.394  0.020  1.394
 TNK  C1   C6    aromatic  1.391  0.020  1.391
 TNK  C1   C13   single    1.513  0.020  1.513
 TNK  C2   C3    aromatic  1.386  0.020  1.386
 TNK  C2   H2    single    0.930  0.020  1.080
 TNK  C3   C4    aromatic  1.390  0.020  1.390
 TNK  C3   H3    single    0.930  0.020  1.080
 TNK  C4   C5    aromatic  1.387  0.020  1.387
 TNK  C4   H4    single    0.930  0.020  1.080
 TNK  C5   C6    aromatic  1.390  0.020  1.390
 TNK  C5   H5    single    0.930  0.020  1.080
 TNK  C6   H6    single    0.930  0.020  1.080
 TNK  C7   N8    single    1.391  0.020  1.391
 TNK  C7   C12   double    1.357  0.020  1.357
 TNK  C7   C13   single    1.504  0.020  1.504
 TNK  N8   C9    single    1.380  0.020  1.380
 TNK  N8   C17   single    1.444  0.020  1.444
 TNK  C9   O9    double    1.213  0.020  1.213
 TNK  C9   N10   single    1.363  0.020  1.363
 TNK  N10  C11   single    1.381  0.020  1.381
 TNK  N10  HN1   single    0.860  0.020  1.020
 TNK  C11  O11   double    1.218  0.020  1.218
 TNK  C11  C12   single    1.455  0.020  1.455
 TNK  C12  C14   single    1.513  0.020  1.513
 TNK  C13  H131  single    0.970  0.020  1.090
 TNK  C13  H132  single    0.970  0.020  1.090
 TNK  C14  C15   single    1.529  0.020  1.529
 TNK  C14  C16   single    1.532  0.020  1.532
 TNK  C14  H14   single    0.970  0.020  1.090
 TNK  C15  H151  single    0.970  0.020  1.090
 TNK  C15  H152  single    0.970  0.020  1.090
 TNK  C15  H153  single    0.970  0.020  1.090
 TNK  C16  H161  single    0.970  0.020  1.090
 TNK  C16  H162  single    0.970  0.020  1.090
 TNK  C16  H163  single    0.970  0.020  1.090
 TNK  C17  O17   single    1.399  0.020  1.399
 TNK  C17  H171  single    0.970  0.020  1.090
 TNK  C17  H172  single    0.970  0.020  1.090
 TNK  O17  C18   single    1.413  0.020  1.413
 TNK  C18  C19   single    1.501  0.020  1.501
 TNK  C18  H181  single    0.970  0.020  1.090
 TNK  C18  H182  single    0.970  0.020  1.090
 TNK  C19  C20   aromatic  1.394  0.020  1.394
 TNK  C19  C24   aromatic  1.390  0.020  1.390
 TNK  C20  C21   aromatic  1.387  0.020  1.387
 TNK  C20  H20   single    0.930  0.020  1.080
 TNK  C21  C22   aromatic  1.390  0.020  1.390
 TNK  C21  H21   single    0.930  0.020  1.080
 TNK  C22  C23   aromatic  1.387  0.020  1.387
 TNK  C22  H22   single    0.930  0.020  1.080
 TNK  C23  C24   aromatic  1.390  0.020  1.390
 TNK  C23  H23   single    0.930  0.020  1.080
 TNK  C24  H24   single    0.930  0.020  1.080

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
 TNK  C13   C1   C6    122.74  3.000
 TNK  C13   C1   C2    118.53  3.000
 TNK  C6    C1   C2    118.72  3.000
 TNK  H2    C2   C3    119.63  3.000
 TNK  H2    C2   C1    119.57  3.000
 TNK  C3    C2   C1    120.80  3.000
 TNK  H3    C3   C4    120.14  3.000
 TNK  H3    C3   C2    119.73  3.000
 TNK  C4    C3   C2    120.13  3.000
 TNK  H4    C4   C5    120.27  3.000
 TNK  H4    C4   C3    120.26  3.000
 TNK  C5    C4   C3    119.47  3.000
 TNK  H5    C5   C6    119.52  3.000
 TNK  H5    C5   C4    120.16  3.000
 TNK  C6    C5   C4    120.33  3.000
 TNK  H6    C6   C5    119.11  3.000
 TNK  H6    C6   C1    120.33  3.000
 TNK  C5    C6   C1    120.56  3.000
 TNK  C13   C7   C12   122.54  3.000
 TNK  C13   C7   N8    115.71  3.000
 TNK  C12   C7   N8    121.75  3.000
 TNK  C17   N8   C9    116.18  3.000
 TNK  C17   N8   C7    121.71  3.000
 TNK  C9    N8   C7    122.09  3.000
 TNK  N10   C9   O9    122.22  3.000
 TNK  N10   C9   N8    114.48  3.000
 TNK  O9    C9   N8    123.31  3.000
 TNK  HN1   N10  C11   116.57  3.000
 TNK  HN1   N10  C9    115.65  3.000
 TNK  C11   N10  C9    127.77  3.000
 TNK  C12   C11  O11   125.92  3.000
 TNK  C12   C11  N10   115.04  3.000
 TNK  O11   C11  N10   119.04  3.000
 TNK  C14   C12  C11   118.27  3.000
 TNK  C14   C12  C7    123.28  3.000
 TNK  C11   C12  C7    118.44  3.000
 TNK  H132  C13  H131  104.25  3.000
 TNK  H132  C13  C7    109.48  3.000
 TNK  H131  C13  C7    108.67  3.000
 TNK  H132  C13  C1    109.31  3.000
 TNK  H131  C13  C1    109.03  3.000
 TNK  C7    C13  C1    115.50  3.000
 TNK  H14   C14  C16   105.19  3.000
 TNK  H14   C14  C15   106.62  3.000
 TNK  C16   C14  C15   111.83  3.000
 TNK  H14   C14  C12   107.58  3.000
 TNK  C16   C14  C12   112.55  3.000
 TNK  C15   C14  C12   112.51  3.000
 TNK  H153  C15  H152  108.17  3.000
 TNK  H153  C15  H151  107.75  3.000
 TNK  H152  C15  H151  107.67  3.000
 TNK  H153  C15  C14   111.90  3.000
 TNK  H152  C15  C14   111.16  3.000
 TNK  H151  C15  C14   110.02  3.000
 TNK  H163  C16  H162  108.27  3.000
 TNK  H163  C16  H161  107.55  3.000
 TNK  H162  C16  H161  107.79  3.000
 TNK  H163  C16  C14   111.22  3.000
 TNK  H162  C16  C14   112.43  3.000
 TNK  H161  C16  C14   109.40  3.000
 TNK  H172  C17  H171  107.15  3.000
 TNK  H172  C17  O17   111.67  3.000
 TNK  H171  C17  O17   111.40  3.000
 TNK  H172  C17  N8    108.28  3.000
 TNK  H171  C17  N8    109.31  3.000
 TNK  O17   C17  N8    108.95  3.000
 TNK  C18   O17  C17   112.11  3.000
 TNK  H182  C18  H181  106.74  3.000
 TNK  H182  C18  C19   110.39  3.000
 TNK  H181  C18  C19   109.47  3.000
 TNK  H182  C18  O17   110.74  3.000
 TNK  H181  C18  O17   110.20  3.000
 TNK  C19   C18  O17   109.28  3.000
 TNK  C24   C19  C20   118.97  3.000
 TNK  C24   C19  C18   120.48  3.000
 TNK  C20   C19  C18   120.52  3.000
 TNK  H20   C20  C21   119.45  3.000
 TNK  H20   C20  C19   120.12  3.000
 TNK  C21   C20  C19   120.43  3.000
 TNK  H21   C21  C22   119.99  3.000
 TNK  H21   C21  C20   119.75  3.000
 TNK  C22   C21  C20   120.26  3.000
 TNK  H22   C22  C23   120.21  3.000
 TNK  H22   C22  C21   120.16  3.000
 TNK  C23   C22  C21   119.63  3.000
 TNK  H23   C23  C24   119.79  3.000
 TNK  H23   C23  C22   120.19  3.000
 TNK  C24   C23  C22   120.03  3.000
 TNK  H24   C24  C23   119.70  3.000
 TNK  H24   C24  C19   119.62  3.000
 TNK  C23   C24  C19   120.68  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
 TNK  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 TNK  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 TNK  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 TNK  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 TNK  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 TNK  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 TNK  CONST_07  C22   C21  C20  C19     0.00   0.0  0
 TNK  CONST_08  C22   C23  C24  C19     0.00   0.0  0
 TNK  CONST_09  C23   C24  C19  C20     0.00   0.0  0
 TNK  CONST_10  C23   C22  C21  C20     0.00   0.0  0
 TNK  CONST_11  C24   C19  C20  C21     0.00   0.0  0
 TNK  CONST_12  C24   C23  C22  C21     0.00   0.0  0
 TNK  CONST_13  N10   C9   N8   C7      0.00   0.0  0
 TNK  CONST_14  C11   N10  C9   N8      0.00   0.0  0
 TNK  CONST_15  C12   C11  N10  C9      0.00   0.0  0
 TNK  CONST_16  C13   C1   C2   C3    180.00   0.0  0
 TNK  CONST_17  C13   C1   C6   C5    180.00   0.0  0
 TNK  CONST_18  C21   C20  C19  C18   180.00   0.0  0
 TNK  CONST_19  C23   C24  C19  C18   180.00   0.0  0
 TNK  CONST_20  O9    C9   N8   C7    180.00   0.0  0
 TNK  CONST_21  O11   C11  N10  C9    180.00   0.0  0
 TNK  CONST_22  C11   N10  C9   O9    180.00   0.0  0
 TNK  CONST_23  C17   N8   C9   N10   180.00   0.0  0
 TNK  CONST_24  H3    C3   C2   C1    180.00   0.0  0
 TNK  CONST_25  H5    C5   C6   C1    180.00   0.0  0
 TNK  CONST_26  H6    C6   C1   C2    180.00   0.0  0
 TNK  CONST_27  H4    C4   C3   C2    180.00   0.0  0
 TNK  CONST_28  H2    C2   C3   C4    180.00   0.0  0
 TNK  CONST_29  H21   C21  C20  C19   180.00   0.0  0
 TNK  CONST_30  H23   C23  C24  C19   180.00   0.0  0
 TNK  CONST_31  H24   C24  C19  C20   180.00   0.0  0
 TNK  CONST_32  H22   C22  C21  C20   180.00   0.0  0
 TNK  CONST_33  H20   C20  C21  C22   180.00   0.0  0
 TNK  CONST_34  HN1   N10  C9   N8    180.00   0.0  0
 TNK  CONST_35  C17   N8   C9   O9      0.00   0.0  0
 TNK  Var_01    N8    C7   C13  C1    -84.96  30.0  2
 TNK  Var_02    C7    C13  C1   C2    160.97  30.0  2
 TNK  Var_03    O17   C17  N8   C7    -87.65  30.0  3
 TNK  Var_04    C15   C14  C12  C7    112.30  30.0  3
 TNK  Var_05    C20   C19  C18  O17    49.15  30.0  2
 TNK  Var_06    C19   C18  O17  C17  -167.46  30.0  3
 TNK  Var_07    H151  C15  C14  C12  -175.39  30.0  3
 TNK  Var_08    H161  C16  C14  C12   170.18  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
 TNK  plan-1  C1   0.020
 TNK  plan-1  C2   0.020
 TNK  plan-1  C3   0.020
 TNK  plan-1  C4   0.020
 TNK  plan-1  C5   0.020
 TNK  plan-1  C6   0.020
 TNK  plan-1  C13  0.020
 TNK  plan-1  H2   0.020
 TNK  plan-1  H3   0.020
 TNK  plan-1  H4   0.020
 TNK  plan-1  H5   0.020
 TNK  plan-1  H6   0.020
 TNK  plan-2  C7   0.020
 TNK  plan-2  N8   0.020
 TNK  plan-2  C9   0.020
 TNK  plan-2  O9   0.020
 TNK  plan-2  N10  0.020
 TNK  plan-2  C11  0.020
 TNK  plan-2  O11  0.020
 TNK  plan-2  C12  0.020
 TNK  plan-2  C13  0.020
 TNK  plan-2  C14  0.020
 TNK  plan-2  C17  0.020
 TNK  plan-2  HN1  0.020
 TNK  plan-3  C18  0.020
 TNK  plan-3  C19  0.020
 TNK  plan-3  C20  0.020
 TNK  plan-3  C21  0.020
 TNK  plan-3  C22  0.020
 TNK  plan-3  C23  0.020
 TNK  plan-3  C24  0.020
 TNK  plan-3  H20  0.020
 TNK  plan-3  H21  0.020
 TNK  plan-3  H22  0.020
 TNK  plan-3  H23  0.020
 TNK  plan-3  H24  0.020

