# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 10:20:51 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-[4-(morpholin-4-yl)-6-oxo-1,6-dihydropyrimidin-2-yl]-N-phenylacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CC1=NC(=CC(=O)N1)N2CCOCC2)Nc3ccccc3
#
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
 0W7  0W7  2-[4-(morpholin-4-yl)-6-oxo-1,6-dihydropyrimidin-2-yl]-N-phenylacetamide  ligand  41  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0W7
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
 0W7  O17  O  O     0  -0.455  -1.6655   1.5273   2.1301
 0W7  C14  C  C     0   0.535  -1.5288   1.8134   0.9561
 0W7  N15  N  NH1   0  -0.728  -2.2579   1.2971  -0.0581
 0W7  C16  C  CR6   0   0.377  -3.2548   0.3155  -0.0281
 0W7  C19  C  CR16  0  -0.314  -3.6590  -0.3653   1.1210
 0W7  C20  C  CR16  0  -0.245  -4.6562  -1.3285   1.0298
 0W7  C23  C  CR16  0  -0.346  -3.8654   0.0130  -1.2483
 0W7  C22  C  CR16  0  -0.245  -4.8578  -0.9486  -1.3226
 0W7  C21  C  CR16  0  -0.272  -5.2622  -1.6286  -0.1807
 0W7  C13  C  CH2   0  -0.683  -0.4742   2.8119   0.5123
 0W7  C2   C  CR6   0   0.542   0.8648   2.1389   0.4436
 0W7  N3   N  NR16  0  -0.698   1.9532   2.8972   0.6427
 0W7  C4   C  CR6   0   0.530   3.2558   2.3951   0.5448
 0W7  O18  O  O     0  -0.509   4.2056   3.1528   0.7143
 0W7  C5   C  CR16  0  -0.581   3.3085   1.0104   0.2387
 0W7  N1   N  N     0  -0.495   0.9170   0.8796   0.1737
 0W7  C6   C  CR6   0   0.589   2.1415   0.2825   0.0798
 0W7  N7   N  NT    0  -0.507   2.1078  -1.0495  -0.1631
 0W7  C8   C  CH2   0  -0.319   0.9222  -1.6774  -0.7327
 0W7  C12  C  CH2   0  -0.321   3.3284  -1.8048  -0.3719
 0W7  C11  C  CH2   0  -0.185   3.1226  -3.2589   0.0175
 0W7  O10  O  O2    0  -0.480   2.0152  -3.8342  -0.6326
 0W7  C9   C  CH2   0  -0.194   0.8397  -3.1285  -0.3061
 0W7  H1   H  HNH1  0   0.418  -2.0290   1.6324  -0.9811
 0W7  H2   H  HCR6  0   0.280  -3.2100  -0.1584   2.0780
 0W7  H3   H  HCR6  0   0.259  -4.9571  -1.8516   1.9286
 0W7  H4   H  HCR6  0   0.271  -3.5594   0.5390  -2.1455
 0W7  H5   H  HCR6  0   0.260  -5.3163  -1.1637  -2.2790
 0W7  H6   H  HCR6  0   0.256  -6.0380  -2.3803  -0.2346
 0W7  H7   H  HCH2  0   0.318  -0.6939   3.2414  -0.4690
 0W7  H8   H  HCH2  0   0.313  -0.4533   3.6373   1.2251
 0W7  H9   H  HNR6  0   0.424   1.8474   3.8816   0.8506
 0W7  H10  H  HCR6  0   0.271   4.2884   0.5733   0.1244
 0W7  H11  H  HCH2  0   0.275   0.0322  -1.1515  -0.3994
 0W7  H12  H  HCH2  0   0.236   0.9581  -1.6121  -1.8274
 0W7  H13  H  HCH2  0   0.242   3.6536  -1.7294  -1.4172
 0W7  H14  H  HCH2  0   0.266   4.1296  -1.4123   0.2519
 0W7  H15  H  HCH2  0   0.248   4.0074  -3.8326  -0.2607
 0W7  H16  H  HCH2  0   0.210   3.0036  -3.3265   1.1080
 0W7  H17  H  HCH2  0   0.210   0.6473  -3.1835   0.7746
 0W7  H18  H  HCH2  0   0.247   0.0084  -3.6107  -0.8217

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
 0W7  C22  C21  aromatic  1.389  0.020  1.389
 0W7  C22  C23  aromatic  1.384  0.020  1.384
 0W7  C21  C20  aromatic  1.387  0.020  1.387
 0W7  C23  C16  aromatic  1.398  0.020  1.398
 0W7  C20  C19  aromatic  1.389  0.020  1.389
 0W7  C16  C19  aromatic  1.395  0.020  1.395
 0W7  C16  N15  single    1.399  0.020  1.399
 0W7  O17  C14  double    1.216  0.020  1.216
 0W7  N15  C14  single    1.352  0.020  1.352
 0W7  C14  C13  single    1.519  0.020  1.519
 0W7  C13  C2   single    1.500  0.020  1.500
 0W7  C2   N3   single    1.341  0.020  1.341
 0W7  C2   N1   double    1.289  0.020  1.289
 0W7  N3   C4   single    1.399  0.020  1.399
 0W7  N1   C6   single    1.365  0.020  1.365
 0W7  C4   O18  double    1.227  0.020  1.227
 0W7  C4   C5   single    1.419  0.020  1.419
 0W7  C6   C5   double    1.385  0.020  1.385
 0W7  C6   N7   single    1.354  0.020  1.354
 0W7  C8   N7   single    1.458  0.020  1.458
 0W7  C8   C9   single    1.515  0.020  1.515
 0W7  N7   C12  single    1.450  0.020  1.450
 0W7  C9   O10  single    1.409  0.020  1.409
 0W7  C12  C11  single    1.519  0.020  1.519
 0W7  O10  C11  single    1.407  0.020  1.407
 0W7  N15  H1   single    0.860  0.020  1.020
 0W7  C19  H2   single    0.930  0.020  1.080
 0W7  C20  H3   single    0.930  0.020  1.080
 0W7  C23  H4   single    0.930  0.020  1.080
 0W7  C22  H5   single    0.930  0.020  1.080
 0W7  C21  H6   single    0.930  0.020  1.080
 0W7  C13  H7   single    0.970  0.020  1.090
 0W7  C13  H8   single    0.970  0.020  1.090
 0W7  N3   H9   single    0.860  0.020  1.020
 0W7  C5   H10  single    0.930  0.020  1.080
 0W7  C8   H11  single    0.970  0.020  1.090
 0W7  C8   H12  single    0.970  0.020  1.090
 0W7  C12  H13  single    0.970  0.020  1.090
 0W7  C12  H14  single    0.970  0.020  1.090
 0W7  C11  H15  single    0.970  0.020  1.090
 0W7  C11  H16  single    0.970  0.020  1.090
 0W7  C9   H17  single    0.970  0.020  1.090
 0W7  C9   H18  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
 0W7  C13  C14  N15  113.99  3.000
 0W7  C13  C14  O17  120.99  3.000
 0W7  N15  C14  O17  125.02  3.000
 0W7  H1   N15  C16  114.49  3.000
 0W7  H1   N15  C14  115.94  3.000
 0W7  C16  N15  C14  129.51  3.000
 0W7  C23  C16  C19  119.13  3.000
 0W7  C19  C16  N15  124.49  3.000
 0W7  C23  C16  N15  116.38  3.000
 0W7  H2   C19  C20  119.38  3.000
 0W7  H2   C19  C16  121.14  3.000
 0W7  C20  C19  C16  119.48  3.000
 0W7  H3   C20  C21  119.91  3.000
 0W7  H3   C20  C19  118.69  3.000
 0W7  C21  C20  C19  121.40  3.000
 0W7  H4   C23  C22  119.68  3.000
 0W7  H4   C23  C16  119.62  3.000
 0W7  C22  C23  C16  120.70  3.000
 0W7  H5   C22  C21  120.38  3.000
 0W7  H5   C22  C23  119.30  3.000
 0W7  C21  C22  C23  120.32  3.000
 0W7  H6   C21  C22  120.53  3.000
 0W7  H6   C21  C20  120.49  3.000
 0W7  C22  C21  C20  118.97  3.000
 0W7  H8   C13  H7   107.04  3.000
 0W7  H8   C13  C2   110.63  3.000
 0W7  H7   C13  C2   108.33  3.000
 0W7  H8   C13  C14  108.66  3.000
 0W7  H7   C13  C14  112.39  3.000
 0W7  C2   C13  C14  109.78  3.000
 0W7  N1   C2   N3   123.40  3.000
 0W7  N1   C2   C13  118.95  3.000
 0W7  N3   C2   C13  117.64  3.000
 0W7  H9   N3   C4   117.44  3.000
 0W7  H9   N3   C2   119.72  3.000
 0W7  C4   N3   C2   122.82  3.000
 0W7  C5   C4   O18  127.14  3.000
 0W7  C5   C4   N3   113.56  3.000
 0W7  O18  C4   N3   119.30  3.000
 0W7  H10  C5   C6   122.71  3.000
 0W7  H10  C5   C4   116.86  3.000
 0W7  C6   C5   C4   120.42  3.000
 0W7  C6   N1   C2   118.55  3.000
 0W7  N7   C6   N1   114.84  3.000
 0W7  N7   C6   C5   123.95  3.000
 0W7  N1   C6   C5   121.21  3.000
 0W7  C12  N7   C8   113.82  3.000
 0W7  C12  N7   C6   121.13  3.000
 0W7  C8   N7   C6   120.93  3.000
 0W7  H12  C8   H11  107.71  3.000
 0W7  H12  C8   C9   109.87  3.000
 0W7  H11  C8   C9   109.44  3.000
 0W7  H12  C8   N7   109.74  3.000
 0W7  H11  C8   N7   109.75  3.000
 0W7  C9   C8   N7   110.30  3.000
 0W7  H14  C12  H13  107.64  3.000
 0W7  H14  C12  C11  107.33  3.000
 0W7  H13  C12  C11  110.49  3.000
 0W7  H14  C12  N7   110.43  3.000
 0W7  H13  C12  N7   110.53  3.000
 0W7  C11  C12  N7   110.33  3.000
 0W7  H16  C11  H15  107.98  3.000
 0W7  H16  C11  O10  110.37  3.000
 0W7  H15  C11  O10  107.80  3.000
 0W7  H16  C11  C12  109.13  3.000
 0W7  H15  C11  C12  109.16  3.000
 0W7  O10  C11  C12  112.30  3.000
 0W7  C9   O10  C11  110.16  3.000
 0W7  H18  C9   H17  108.02  3.000
 0W7  H18  C9   O10  107.75  3.000
 0W7  H17  C9   O10  110.41  3.000
 0W7  H18  C9   C8   109.39  3.000
 0W7  H17  C9   C8   109.54  3.000
 0W7  O10  C9   C8   111.65  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
 0W7  CONST_01  C21  C22  C23  C16     0.00   0.0  0
 0W7  CONST_02  C21  C20  C19  C16     0.00   0.0  0
 0W7  CONST_03  C22  C21  C20  C19     0.00   0.0  0
 0W7  CONST_04  C22  C23  C16  C19     0.00   0.0  0
 0W7  CONST_05  C23  C22  C21  C20     0.00   0.0  0
 0W7  CONST_06  C23  C16  C19  C20     0.00   0.0  0
 0W7  CONST_07  C5   C4   N3   C2      0.00   0.0  0
 0W7  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 0W7  CONST_09  N7   C6   N1   C2    180.00   0.0  0
 0W7  CONST_10  C6   N1   C2   N3      0.00   0.0  0
 0W7  CONST_11  N1   C2   N3   C4      0.00   0.0  0
 0W7  CONST_13  C12  N7   C6   C5      0.00   0.0  0
 0W7  CONST_15  C12  N7   C6   N1    180.00   0.0  0
 0W7  CONST_16  C22  C23  C16  N15   180.00   0.0  0
 0W7  CONST_17  C20  C19  C16  N15   180.00   0.0  0
 0W7  CONST_18  C4   N3   C2   C13   180.00   0.0  0
 0W7  CONST_19  C6   N1   C2   C13   180.00   0.0  0
 0W7  CONST_20  O18  C4   N3   C2    180.00   0.0  0
 0W7  CONST_21  H5   C22  C23  C16   180.00   0.0  0
 0W7  CONST_22  H3   C20  C19  C16   180.00   0.0  0
 0W7  CONST_23  H6   C21  C20  C19   180.00   0.0  0
 0W7  CONST_24  H4   C23  C16  C19   180.00   0.0  0
 0W7  CONST_25  H2   C19  C16  C23   180.00   0.0  0
 0W7  CONST_26  H9   N3   C4   C5    180.00   0.0  0
 0W7  CONST_27  C23  C16  N15  C14   180.00   0.0  0
 0W7  CONST_28  C19  C16  N15  C14     0.00   0.0  0
 0W7  CONST_29  H1   N15  C16  C19   180.00   0.0  0
 0W7  CONST_30  C16  N15  C14  O17     0.00   0.0  0
 0W7  CONST_31  C13  C14  N15  C16   180.00   0.0  0
 0W7  Var_01    C9   C8   N7   C6   -152.66  30.0  1
 0W7  Var_02    C11  C12  N7   C6    153.61  30.0  1
 0W7  Var_03    O10  C9   C8   N7    -54.98  30.0  1
 0W7  Var_04    O10  C11  C12  N7     53.61  30.0  1
 0W7  Var_05    N3   C2   C13  C14  -151.83  30.0  3
 0W7  Var_06    C2   C13  C14  O17    80.35  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
 0W7  plan-1  N15  0.020
 0W7  plan-1  C16  0.020
 0W7  plan-1  C19  0.020
 0W7  plan-1  C20  0.020
 0W7  plan-1  C23  0.020
 0W7  plan-1  C22  0.020
 0W7  plan-1  C21  0.020
 0W7  plan-1  H2   0.020
 0W7  plan-1  H3   0.020
 0W7  plan-1  H4   0.020
 0W7  plan-1  H5   0.020
 0W7  plan-1  H6   0.020
 0W7  plan-2  C13  0.020
 0W7  plan-2  C2   0.020
 0W7  plan-2  N3   0.020
 0W7  plan-2  C4   0.020
 0W7  plan-2  O18  0.020
 0W7  plan-2  C5   0.020
 0W7  plan-2  N1   0.020
 0W7  plan-2  C6   0.020
 0W7  plan-2  N7   0.020
 0W7  plan-2  C8   0.020
 0W7  plan-2  C12  0.020
 0W7  plan-2  H9   0.020
 0W7  plan-2  H10  0.020
 0W7  plan-3  O17  0.020
 0W7  plan-3  C14  0.020
 0W7  plan-3  N15  0.020
 0W7  plan-3  C16  0.020
 0W7  plan-3  C13  0.020
 0W7  plan-3  H1   0.020

