# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 14:01:40 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: 5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-3,6-dihydropyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(CCNC(=O)C2=C(O)C(=O)N=C(N2)c3ccccc3C(F)(F)F)ccn1
#
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
 U3A  U3A  5-hydroxy-N-[2-(2-methoxypyridin-4-yl)ethyl]-6-oxo-2-[2-(trifluoromethyl)phenyl]-3,6-dihydropyrimidine-4-carboxamide  ligand  48  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U3A
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
 U3A  C11  C  CR6   0   0.113  -14.2815  -40.5097  -16.3074
 U3A  C12  C  CR6   0   0.188  -15.3537  -40.2447  -17.0857
 U3A  C25  C  CT    0   1.071  -14.4211  -36.1245  -14.3514
 U3A  C29  C  CR16  0  -0.388  -12.6181  -41.9054  -10.8419
 U3A  F27  F  F     0  -0.309  -15.3398  -35.4825  -15.0815
 U3A  F28  F  F     0  -0.301  -14.3584  -35.4984  -13.1730
 U3A  C01  C  CH3   0  -0.443  -10.4686  -37.9520  -12.9149
 U3A  C03  C  CR6   0   0.510  -11.6227  -39.4630  -11.4984
 U3A  C04  C  CR16  0  -0.501  -11.4981  -40.5071  -12.4193
 U3A  C05  C  CR6   0   0.205  -12.0052  -41.7544  -12.0841
 U3A  C06  C  CH2   0  -0.514  -11.9558  -42.8899  -13.0642
 U3A  C07  C  CH2   0  -0.298  -13.3077  -43.1002  -13.7499
 U3A  C09  C  C     0   0.518  -13.9309  -41.8769  -15.8001
 U3A  C14  C  CR6   0   0.378  -15.6291  -38.8630  -17.4892
 U3A  C17  C  CR6   0   0.374  -13.7348  -38.2099  -16.3566
 U3A  C19  C  CR6   0   0.026  -12.7669  -37.1555  -15.9613
 U3A  C20  C  CR16  0  -0.252  -11.5147  -37.1573  -16.5635
 U3A  C21  C  CR16  0  -0.231  -10.5914  -36.1641  -16.2714
 U3A  C22  C  CR16  0  -0.233  -10.9174  -35.1647  -15.3701
 U3A  C23  C  CR16  0  -0.278  -12.1585  -35.1650  -14.7510
 U3A  C24  C  CR6   0  -0.216  -13.0861  -36.1576  -15.0378
 U3A  C30  C  CR16  0  -0.057  -12.6910  -40.8036  -10.0101
 U3A  F26  F  F     0  -0.311  -14.8960  -37.3530  -14.1086
 U3A  N08  N  NH1   0  -0.627  -13.7362  -41.9231  -14.4734
 U3A  N16  N  N     0  -0.447  -14.7582  -37.8930  -17.0897
 U3A  N18  N  NR16  0  -0.645  -13.4687  -39.4551  -15.9554
 U3A  N31  N  N     0  -0.438  -12.2088  -39.6069  -10.3228
 U3A  O10  O  O     0  -0.447  -13.8385  -42.8219  -16.5606
 U3A  O13  O  OH1   0  -0.596  -16.2149  -41.1818  -17.4702
 U3A  O15  O  O     0  -0.474  -16.6262  -38.6271  -18.1622
 U3A  H1   H  HCR6  0   0.261  -13.0281  -42.8566  -10.5282
 U3A  H2   H  HCH3  0   0.263  -10.1785  -36.9056  -12.8716
 U3A  H3   H  HCH3  0   0.234   -9.5690  -38.5647  -13.0096
 U3A  H4   H  HCH3  0   0.232  -11.0958  -38.1049  -13.7963
 U3A  H5   H  HCR6  0   0.282  -11.0152  -40.3693  -13.3777
 U3A  H6   H  HCH2  0   0.268  -11.6946  -43.8162  -12.5483
 U3A  H7   H  HCH2  0   0.262  -11.1895  -42.7079  -13.8196
 U3A  H8   H  HCH2  0   0.262  -14.0655  -43.3556  -13.0068
 U3A  H9   H  HCH2  0   0.271  -13.2410  -43.9317  -14.4475
 U3A  H10  H  HCR6  0   0.281  -11.2654  -37.9340  -17.2753
 U3A  H11  H  HCR6  0   0.278   -9.6229  -36.1732  -16.7527
 U3A  H12  H  HCR6  0   0.278  -10.2051  -34.3848  -15.1378
 U3A  H13  H  HCR6  0   0.282  -12.3886  -34.3857  -14.0375
 U3A  H14  H  HCR6  0   0.263  -13.1613  -40.8874   -9.0363
 U3A  H15  H  HNH1  0   0.417  -13.9663  -41.1079  -13.9241
 U3A  H16  H  HNR6  0   0.450  -12.6444  -39.6300  -15.3942
 U3A  H17  H  HOH1  0   0.473  -16.9157  -40.7383  -17.9758
 U3A  O02  O  O2    0  -0.441  -11.1682  -38.2236  -11.7150

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
 U3A  O15  C14  double    1.226  0.020  1.226
 U3A  O13  C12  single    1.330  0.020  1.330
 U3A  C14  C12  single    1.466  0.020  1.466
 U3A  C14  N16  single    1.363  0.020  1.363
 U3A  C12  C11  double    1.351  0.020  1.351
 U3A  N16  C17  double    1.298  0.020  1.298
 U3A  C11  N18  single    1.377  0.020  1.377
 U3A  C11  C09  single    1.500  0.020  1.500
 U3A  C17  N18  single    1.335  0.020  1.335
 U3A  C17  C19  single    1.485  0.020  1.485
 U3A  F27  C25  single    1.338  0.020  1.338
 U3A  O10  C09  double    1.216  0.020  1.216
 U3A  C09  N08  single    1.342  0.020  1.342
 U3A  C19  C20  aromatic  1.389  0.020  1.389
 U3A  C19  C24  aromatic  1.397  0.020  1.397
 U3A  C20  C21  aromatic  1.387  0.020  1.387
 U3A  C25  C24  single    1.501  0.020  1.501
 U3A  C25  F26  single    1.339  0.020  1.339
 U3A  C25  F28  single    1.336  0.020  1.336
 U3A  C24  C23  aromatic  1.388  0.020  1.388
 U3A  C21  C22  aromatic  1.385  0.020  1.385
 U3A  N08  C07  single    1.447  0.020  1.447
 U3A  C23  C22  aromatic  1.387  0.020  1.387
 U3A  C07  C06  single    1.530  0.020  1.530
 U3A  C01  O02  single    1.415  0.020  1.415
 U3A  C06  C05  single    1.501  0.020  1.501
 U3A  C04  C05  aromatic  1.388  0.020  1.388
 U3A  C04  C03  aromatic  1.398  0.020  1.398
 U3A  O02  C03  single    1.338  0.020  1.338
 U3A  C05  C29  aromatic  1.393  0.020  1.393
 U3A  C03  N31  aromatic  1.321  0.020  1.321
 U3A  C29  C30  aromatic  1.382  0.020  1.382
 U3A  N31  C30  aromatic  1.328  0.020  1.328
 U3A  C29  H1   single    0.930  0.020  1.080
 U3A  C01  H2   single    0.970  0.020  1.090
 U3A  C01  H3   single    0.970  0.020  1.090
 U3A  C01  H4   single    0.970  0.020  1.090
 U3A  C04  H5   single    0.930  0.020  1.080
 U3A  C06  H6   single    0.970  0.020  1.090
 U3A  C06  H7   single    0.970  0.020  1.090
 U3A  C07  H8   single    0.970  0.020  1.090
 U3A  C07  H9   single    0.970  0.020  1.090
 U3A  C20  H10  single    0.930  0.020  1.080
 U3A  C21  H11  single    0.930  0.020  1.080
 U3A  C22  H12  single    0.930  0.020  1.080
 U3A  C23  H13  single    0.930  0.020  1.080
 U3A  C30  H14  single    0.930  0.020  1.080
 U3A  N08  H15  single    0.860  0.020  1.020
 U3A  N18  H16  single    0.860  0.020  1.020
 U3A  O13  H17  single    0.850  0.020  0.980

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
 U3A  N18  C11  C09  118.27  3.000
 U3A  C09  C11  C12  124.00  3.000
 U3A  N18  C11  C12  117.73  3.000
 U3A  O13  C12  C14  117.59  3.000
 U3A  C14  C12  C11  119.52  3.000
 U3A  O13  C12  C11  122.84  3.000
 U3A  F26  C25  C24  112.21  3.000
 U3A  F26  C25  F28  106.65  3.000
 U3A  C24  C25  F28  111.83  3.000
 U3A  F28  C25  F27  106.78  3.000
 U3A  F26  C25  F27  107.20  3.000
 U3A  C24  C25  F27  111.82  3.000
 U3A  H1   C29  C30  120.41  3.000
 U3A  H1   C29  C05  121.35  3.000
 U3A  C30  C29  C05  118.24  3.000
 U3A  H4   C01  H3   108.92  3.000
 U3A  H4   C01  H2   108.67  3.000
 U3A  H3   C01  H2   108.88  3.000
 U3A  H4   C01  O02  111.92  3.000
 U3A  H3   C01  O02  111.89  3.000
 U3A  H2   C01  O02  106.44  3.000
 U3A  O02  C03  N31  113.31  3.000
 U3A  N31  C03  C04  122.98  3.000
 U3A  O02  C03  C04  123.72  3.000
 U3A  H5   C04  C05  119.45  3.000
 U3A  H5   C04  C03  121.89  3.000
 U3A  C05  C04  C03  118.67  3.000
 U3A  C06  C05  C04  120.68  3.000
 U3A  C04  C05  C29  118.27  3.000
 U3A  C06  C05  C29  120.98  3.000
 U3A  H7   C06  H6   107.49  3.000
 U3A  H7   C06  C07  109.45  3.000
 U3A  H6   C06  C07  107.85  3.000
 U3A  H7   C06  C05  110.42  3.000
 U3A  H6   C06  C05  109.95  3.000
 U3A  C07  C06  C05  111.56  3.000
 U3A  H9   C07  H8   107.48  3.000
 U3A  H9   C07  N08  108.64  3.000
 U3A  H8   C07  N08  108.98  3.000
 U3A  H9   C07  C06  109.77  3.000
 U3A  H8   C07  C06  109.90  3.000
 U3A  N08  C07  C06  111.96  3.000
 U3A  O10  C09  N08  125.48  3.000
 U3A  N08  C09  C11  113.56  3.000
 U3A  O10  C09  C11  120.96  3.000
 U3A  O15  C14  N16  122.93  3.000
 U3A  N16  C14  C12  118.03  3.000
 U3A  O15  C14  C12  119.04  3.000
 U3A  N18  C17  N16  123.68  3.000
 U3A  N18  C17  C19  116.90  3.000
 U3A  N16  C17  C19  119.40  3.000
 U3A  C24  C19  C20  119.57  3.000
 U3A  C24  C19  C17  122.31  3.000
 U3A  C20  C19  C17  118.10  3.000
 U3A  H10  C20  C21  119.91  3.000
 U3A  H10  C20  C19  119.57  3.000
 U3A  C21  C20  C19  120.51  3.000
 U3A  H11  C21  C22  120.43  3.000
 U3A  H11  C21  C20  119.76  3.000
 U3A  C22  C21  C20  119.81  3.000
 U3A  H12  C22  C23  119.58  3.000
 U3A  H12  C22  C21  120.35  3.000
 U3A  C23  C22  C21  120.07  3.000
 U3A  H13  C23  C24  120.62  3.000
 U3A  H13  C23  C22  119.00  3.000
 U3A  C24  C23  C22  120.38  3.000
 U3A  C23  C24  C19  119.65  3.000
 U3A  C23  C24  C25  118.93  3.000
 U3A  C19  C24  C25  121.41  3.000
 U3A  H14  C30  N31  116.01  3.000
 U3A  H14  C30  C29  120.10  3.000
 U3A  N31  C30  C29  123.89  3.000
 U3A  H15  N08  C09  118.50  3.000
 U3A  H15  N08  C07  116.90  3.000
 U3A  C09  N08  C07  124.44  3.000
 U3A  C17  N16  C14  119.70  3.000
 U3A  H16  N18  C17  119.34  3.000
 U3A  H16  N18  C11  119.34  3.000
 U3A  C17  N18  C11  121.32  3.000
 U3A  C30  N31  C03  117.96  3.000
 U3A  H17  O13  C12  107.22  3.000
 U3A  C03  O02  C01  118.88  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
 U3A  CONST_01  C03  C04  C05  C29     0.00   0.0  0
 U3A  CONST_02  C03  N31  C30  C29     0.00   0.0  0
 U3A  CONST_03  C30  C29  C05  C04     0.00   0.0  0
 U3A  CONST_04  C30  N31  C03  C04     0.00   0.0  0
 U3A  CONST_05  N31  C03  C04  C05     0.00   0.0  0
 U3A  CONST_06  N31  C30  C29  C05     0.00   0.0  0
 U3A  CONST_07  C22  C21  C20  C19     0.00   0.0  0
 U3A  CONST_08  C22  C23  C24  C19     0.00   0.0  0
 U3A  CONST_09  C23  C24  C19  C20     0.00   0.0  0
 U3A  CONST_10  C23  C22  C21  C20     0.00   0.0  0
 U3A  CONST_11  C24  C19  C20  C21     0.00   0.0  0
 U3A  CONST_12  C24  C23  C22  C21     0.00   0.0  0
 U3A  CONST_13  C21  C20  C19  C17   180.00   0.0  0
 U3A  CONST_14  C23  C24  C19  C17   180.00   0.0  0
 U3A  CONST_15  N16  C17  N18  C11     0.00   0.0  0
 U3A  CONST_16  C19  C17  N18  C11   180.00   0.0  0
 U3A  CONST_17  N18  C17  N16  C14     0.00   0.0  0
 U3A  CONST_18  C19  C17  N16  C14   180.00   0.0  0
 U3A  CONST_19  C17  C19  C24  C25     0.00   0.0  0
 U3A  CONST_20  C20  C19  C24  C25   180.00   0.0  0
 U3A  CONST_21  C22  C23  C24  C25   180.00   0.0  0
 U3A  CONST_22  C06  C05  C04  C03   180.00   0.0  0
 U3A  CONST_23  O02  C03  C04  C05   180.00   0.0  0
 U3A  CONST_24  C30  C29  C05  C06   180.00   0.0  0
 U3A  CONST_25  O02  C03  N31  C30   180.00   0.0  0
 U3A  CONST_26  H5   C04  C05  C29   180.00   0.0  0
 U3A  CONST_27  H14  C30  N31  C03   180.00   0.0  0
 U3A  CONST_28  H1   C29  C05  C04   180.00   0.0  0
 U3A  CONST_29  H10  C20  C19  C17     0.00   0.0  0
 U3A  CONST_30  H11  C21  C20  C19   180.00   0.0  0
 U3A  CONST_31  H13  C23  C24  C19   180.00   0.0  0
 U3A  CONST_32  H12  C22  C21  C20   180.00   0.0  0
 U3A  CONST_33  H16  N18  C17  C19     0.00   0.0  0
 U3A  CONST_34  C07  N08  C09  C11   180.00   0.0  0
 U3A  CONST_35  H15  N08  C09  C11     0.00   0.0  0
 U3A  CONST_36  O10  C09  N08  C07     0.00   0.0  0
 U3A  Var_01    N16  C17  C19  C20  -107.79  30.0  3
 U3A  Var_02    O10  C09  C11  C12    52.27  30.0  2
 U3A  Var_03    C07  C06  C05  C29    75.98  30.0  2
 U3A  Var_04    C19  C24  C25  F27   -86.04  30.0  2
 U3A  Var_05    C04  C03  O02  C01    -2.85  30.0  2
 U3A  Var_06    N08  C07  C06  C05    59.62  30.0  2
 U3A  Var_07    H2   C01  O02  C03  -178.85  30.0  3
 U3A  Var_08    C09  N08  C07  C06   117.65  30.0  2

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
 U3A  plan-1  C29  0.020
 U3A  plan-1  C03  0.020
 U3A  plan-1  C04  0.020
 U3A  plan-1  C05  0.020
 U3A  plan-1  C06  0.020
 U3A  plan-1  C30  0.020
 U3A  plan-1  N31  0.020
 U3A  plan-1  H1   0.020
 U3A  plan-1  H5   0.020
 U3A  plan-1  H14  0.020
 U3A  plan-1  O02  0.020
 U3A  plan-2  C11  0.020
 U3A  plan-2  C12  0.020
 U3A  plan-2  C09  0.020
 U3A  plan-2  C14  0.020
 U3A  plan-2  C17  0.020
 U3A  plan-2  C19  0.020
 U3A  plan-2  N16  0.020
 U3A  plan-2  N18  0.020
 U3A  plan-2  O13  0.020
 U3A  plan-2  O15  0.020
 U3A  plan-2  H16  0.020
 U3A  plan-3  C25  0.020
 U3A  plan-3  C17  0.020
 U3A  plan-3  C19  0.020
 U3A  plan-3  C20  0.020
 U3A  plan-3  C21  0.020
 U3A  plan-3  C22  0.020
 U3A  plan-3  C23  0.020
 U3A  plan-3  C24  0.020
 U3A  plan-3  H10  0.020
 U3A  plan-3  H11  0.020
 U3A  plan-3  H12  0.020
 U3A  plan-3  H13  0.020
 U3A  plan-4  C11  0.020
 U3A  plan-4  C07  0.020
 U3A  plan-4  C09  0.020
 U3A  plan-4  N08  0.020
 U3A  plan-4  O10  0.020
 U3A  plan-4  H15  0.020

