# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 04:55:29 2021
#   Inital geometry file: a 95 line input string
#   Ligand name: N-(3-{[(2R)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyrimidin-5-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C[C@H](N1)Oc2cccc(NC(=O)Cc3cncnc3)c2
#
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
 UGD  UGD  N-(3-{[(2R)-4-oxoazetidin-2-yl]oxy}phenyl)-2-(pyrimidin-5-yl)acetamide  ligand  36  22  .  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_UGD
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
 UGD  N1   N  N     0  -0.390   6.0194   1.0589  17.5786
 UGD  N3   N  N     0  -0.646  12.7816   4.1781  21.7394
 UGD  C4   C  CR16  0   0.051   5.1082   1.7318  18.2622
 UGD  C5   C  CR16  0  -0.044   6.8435   0.2944  18.2849
 UGD  C6   C  CR6   0   0.388  11.0772  -0.0677  22.0768
 UGD  C7   C  CR16  0  -0.354  12.0844  -1.0208  22.2475
 UGD  C8   C  CR16  0  -0.239  13.2610  -0.6876  22.8941
 UGD  C10  C  CR6   0   0.364  12.4612   1.5352  23.2094
 UGD  C13  C  C     0   0.541  12.8367   5.4731  22.1353
 UGD  O2   O  O     0  -0.451  12.5392   6.5056  21.5876
 UGD  C12  C  C     0  -0.695  13.4539   5.0858  23.4749
 UGD  C11  C  C     0   0.262  13.4166   3.6508  22.9281
 UGD  O1   O  O2    0  -0.504  12.6122   2.8037  23.7043
 UGD  C9   C  CR16  0  -0.339  13.4655   0.5948  23.3834
 UGD  C14  C  CR16  0  -0.406  11.2733   1.2264  22.5588
 UGD  N2   N  NH1   0  -0.749   9.9215  -0.4907  21.4152
 UGD  C    C  C     0   0.565   8.7950   0.2022  21.1188
 UGD  O    O  O     0  -0.451   8.6189   1.3769  21.3744
 UGD  C2   C  CR6   0   0.022   6.7693   0.1889  19.6651
 UGD  N    N  N     0  -0.392   4.9358   1.7051  19.5757
 UGD  C3   C  CR16  0  -0.035   5.7651   0.9358  20.2668
 UGD  H2   H  HCR6  0   0.264   4.4347   2.3625  17.6930
 UGD  H3   H  HCR6  0   0.275   7.5939  -0.2605  17.7306
 UGD  H4   H  HCR6  0   0.274  11.9414  -2.0288  21.8772
 UGD  H5   H  HCR6  0   0.267  14.0265  -1.4410  23.0228
 UGD  H6   H  H     0   0.296  12.8190   5.2583  24.3436
 UGD  H7   H  H     0   0.297  14.4468   5.4950  23.6543
 UGD  H8   H  H     0   0.258  14.3877   3.1894  22.7302
 UGD  H9   H  HCR6  0   0.270  14.3802   0.8541  23.9010
 UGD  H10  H  HCR6  0   0.289  10.5206   1.9899  22.4501
 UGD  H11  H  HNH1  0   0.422   9.9323  -1.4591  21.1320
 UGD  H14  H  HCR6  0   0.275   5.6201   0.9016  21.3417
 UGD  C1   C  CH2   0  -0.697   7.7222  -0.6478  20.4526
 UGD  H1   H  H     0   0.395  12.5896   3.7595  20.8397
 UGD  H12  H  HCH2  0   0.318   7.1922  -1.1806  21.2488
 UGD  H13  H  HCH2  0   0.297   8.1719  -1.4150  19.8194

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
 UGD  N1   C4   aromatic  1.323  0.020  1.323
 UGD  N1   C5   aromatic  1.328  0.020  1.328
 UGD  C4   N    aromatic  1.325  0.020  1.325
 UGD  C5   C2   aromatic  1.386  0.020  1.386
 UGD  N    C3   aromatic  1.326  0.020  1.326
 UGD  C2   C3   aromatic  1.389  0.020  1.389
 UGD  C2   C1   single    1.493  0.020  1.493
 UGD  C1   C    single    1.522  0.020  1.522
 UGD  O    C    double    1.215  0.020  1.215
 UGD  C    N2   single    1.355  0.020  1.355
 UGD  N2   C6   single    1.397  0.020  1.397
 UGD  C6   C7   aromatic  1.397  0.020  1.397
 UGD  C6   C14  aromatic  1.395  0.020  1.395
 UGD  N3   C11  single    1.447  0.020  1.447
 UGD  N3   C13  single    1.355  0.020  1.355
 UGD  C7   C8   aromatic  1.383  0.020  1.383
 UGD  C14  C10  aromatic  1.389  0.020  1.389
 UGD  O2   C13  double    1.206  0.020  1.206
 UGD  C11  O1   single    1.402  0.020  1.402
 UGD  C11  C12  single    1.536  0.020  1.536
 UGD  C13  C12  single    1.525  0.020  1.525
 UGD  C8   C9   aromatic  1.388  0.020  1.388
 UGD  C10  C9   aromatic  1.387  0.020  1.387
 UGD  C10  O1   single    1.370  0.020  1.370
 UGD  N3   H1   single    0.860  0.020  1.020
 UGD  C4   H2   single    0.930  0.020  1.080
 UGD  C5   H3   single    0.930  0.020  1.080
 UGD  C7   H4   single    0.930  0.020  1.080
 UGD  C8   H5   single    0.930  0.020  1.080
 UGD  C12  H6   single    0.970  0.020  1.090
 UGD  C12  H7   single    0.970  0.020  1.090
 UGD  C11  H8   single    0.970  0.020  1.090
 UGD  C9   H9   single    0.930  0.020  1.080
 UGD  C14  H10  single    0.930  0.020  1.080
 UGD  N2   H11  single    0.860  0.020  1.020
 UGD  C1   H12  single    0.970  0.020  1.090
 UGD  C1   H13  single    0.970  0.020  1.090
 UGD  C3   H14  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
 UGD  C5   N1   C4   116.45  3.000
 UGD  H1   N3   C11  131.57  3.000
 UGD  H1   N3   C13  131.57  3.000
 UGD  C11  N3   C13   95.18  3.000
 UGD  H2   C4   N    116.83  3.000
 UGD  H2   C4   N1   116.90  3.000
 UGD  N    C4   N1   126.27  3.000
 UGD  H3   C5   C2   120.43  3.000
 UGD  H3   C5   N1   116.86  3.000
 UGD  C2   C5   N1   122.71  3.000
 UGD  N2   C6   C14  124.11  3.000
 UGD  C14  C6   C7   119.30  3.000
 UGD  N2   C6   C7   116.59  3.000
 UGD  H4   C7   C8   119.75  3.000
 UGD  H4   C7   C6   119.86  3.000
 UGD  C8   C7   C6   120.39  3.000
 UGD  H5   C8   C9   119.82  3.000
 UGD  H5   C8   C7   119.32  3.000
 UGD  C9   C8   C7   120.85  3.000
 UGD  C14  C10  C9   121.82  3.000
 UGD  C9   C10  O1   120.18  3.000
 UGD  C14  C10  O1   117.99  3.000
 UGD  C12  C13  O2   135.75  3.000
 UGD  C12  C13  N3    91.74  3.000
 UGD  O2   C13  N3   132.47  3.000
 UGD  H7   C12  H6   109.90  3.000
 UGD  H7   C12  C11  115.59  3.000
 UGD  H6   C12  C11  114.68  3.000
 UGD  H7   C12  C13  114.73  3.000
 UGD  H6   C12  C13  115.11  3.000
 UGD  C11  C12  C13   85.11  3.000
 UGD  H8   C11  O1   110.78  3.000
 UGD  H8   C11  C12  115.92  3.000
 UGD  O1   C11  C12  112.40  3.000
 UGD  H8   C11  N3   113.26  3.000
 UGD  C12  C11  N3    87.86  3.000
 UGD  O1   C11  N3   115.02  3.000
 UGD  C11  O1   C10  115.00  3.000
 UGD  H9   C9   C10  120.63  3.000
 UGD  H9   C9   C8   120.96  3.000
 UGD  C10  C9   C8   118.40  3.000
 UGD  H10  C14  C10  119.15  3.000
 UGD  H10  C14  C6   121.62  3.000
 UGD  C10  C14  C6   119.23  3.000
 UGD  H11  N2   C    115.98  3.000
 UGD  H11  N2   C6   114.50  3.000
 UGD  C    N2   C6   129.51  3.000
 UGD  C1   C    O    121.99  3.000
 UGD  O    C    N2   124.66  3.000
 UGD  C1   C    N2   113.33  3.000
 UGD  C3   C2   C1   122.31  3.000
 UGD  C1   C2   C5   122.26  3.000
 UGD  C3   C2   C5   115.42  3.000
 UGD  C3   N    C4   116.56  3.000
 UGD  H14  C3   N    116.82  3.000
 UGD  H14  C3   C2   120.59  3.000
 UGD  N    C3   C2   122.59  3.000
 UGD  H13  C1   H12  106.22  3.000
 UGD  H13  C1   C2   110.54  3.000
 UGD  H12  C1   C2   110.33  3.000
 UGD  H13  C1   C    110.85  3.000
 UGD  H12  C1   C    107.14  3.000
 UGD  C2   C1   C    111.58  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
 UGD  CONST_01  C3   N    C4   N1      0.00   0.0  0
 UGD  CONST_02  C3   C2   C5   N1      0.00   0.0  0
 UGD  CONST_03  C2   C5   N1   C4      0.00   0.0  0
 UGD  CONST_04  C2   C3   N    C4      0.00   0.0  0
 UGD  CONST_05  N    C4   N1   C5      0.00   0.0  0
 UGD  CONST_06  N    C3   C2   C5      0.00   0.0  0
 UGD  CONST_07  C9   C8   C7   C6      0.00   0.0  0
 UGD  CONST_08  C9   C10  C14  C6      0.00   0.0  0
 UGD  CONST_09  C10  C14  C6   C7      0.00   0.0  0
 UGD  CONST_10  C10  C9   C8   C7      0.00   0.0  0
 UGD  CONST_11  C14  C6   C7   C8      0.00   0.0  0
 UGD  CONST_12  C14  C10  C9   C8      0.00   0.0  0
 UGD  CONST_13  C11  C12  C13  N3      0.00   0.0  0
 UGD  CONST_14  C1   C2   C5   N1    180.00   0.0  0
 UGD  CONST_15  O1   C10  C14  C6    180.00   0.0  0
 UGD  CONST_16  N2   C6   C7   C8    180.00   0.0  0
 UGD  CONST_17  O1   C10  C9   C8    180.00   0.0  0
 UGD  CONST_18  N2   C6   C14  C10   180.00   0.0  0
 UGD  CONST_19  N    C3   C2   C1    180.00   0.0  0
 UGD  CONST_20  C11  N3   C13  O2    180.00   0.0  0
 UGD  CONST_21  C11  C12  C13  O2    180.00   0.0  0
 UGD  CONST_22  H3   C5   N1   C4    180.00   0.0  0
 UGD  CONST_23  H14  C3   N    C4    180.00   0.0  0
 UGD  CONST_24  H2   C4   N1   C5    180.00   0.0  0
 UGD  CONST_25  H5   C8   C7   C6    180.00   0.0  0
 UGD  CONST_26  H10  C14  C6   C7    180.00   0.0  0
 UGD  CONST_27  H9   C9   C8   C7    180.00   0.0  0
 UGD  CONST_28  H4   C7   C8   C9    180.00   0.0  0
 UGD  CONST_29  H1   N3   C13  C12   180.00   0.0  0
 UGD  CONST_30  C    N2   C6   C7    180.00   0.0  0
 UGD  CONST_31  C    N2   C6   C14     0.00   0.0  0
 UGD  CONST_32  H11  N2   C6   C7      0.00   0.0  0
 UGD  CONST_33  C1   C    N2   C6    180.00   0.0  0
 UGD  CONST_34  O    C    N2   C6      0.00   0.0  0
 UGD  Var_01    C14  C10  O1   C11  -102.06  30.0  2
 UGD  Var_02    H6   C12  C13  N3   -112.58  30.0  1
 UGD  Var_03    C    C1   C2   C5    101.68  30.0  2
 UGD  Var_04    C2   C1   C    N2   -157.14  30.0  1

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
 UGD  chir_01  C11  N3  O1  C12  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
 UGD  plan-1  N1   0.020
 UGD  plan-1  C4   0.020
 UGD  plan-1  C5   0.020
 UGD  plan-1  C2   0.020
 UGD  plan-1  N    0.020
 UGD  plan-1  C3   0.020
 UGD  plan-1  H2   0.020
 UGD  plan-1  H3   0.020
 UGD  plan-1  H14  0.020
 UGD  plan-1  C1   0.020
 UGD  plan-2  C6   0.020
 UGD  plan-2  C7   0.020
 UGD  plan-2  C8   0.020
 UGD  plan-2  C10  0.020
 UGD  plan-2  O1   0.020
 UGD  plan-2  C9   0.020
 UGD  plan-2  C14  0.020
 UGD  plan-2  N2   0.020
 UGD  plan-2  H4   0.020
 UGD  plan-2  H5   0.020
 UGD  plan-2  H9   0.020
 UGD  plan-2  H10  0.020
 UGD  plan-3  C6   0.020
 UGD  plan-3  N2   0.020
 UGD  plan-3  C    0.020
 UGD  plan-3  O    0.020
 UGD  plan-3  H11  0.020
 UGD  plan-3  C1   0.020
 UGD  plan-4  N3   0.020
 UGD  plan-4  C13  0.020
 UGD  plan-4  O2   0.020
 UGD  plan-4  C12  0.020
 UGD  plan-4  C11  0.020
 UGD  plan-4  H1   0.020

