# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 18:12:11 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: [2,4-dioxo-3-(2,3,4,5-tetrabromo-6-methoxybenzyl)-3,4-dihydropyrimidin-1(2H)-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(Br)c(Br)c(Br)c(Br)c1CN2C(=O)C=CN(CC(O)=O)C2=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
 F49  F49  '[2,4-dioxo-3-(2,3,4,5-tetrabromo-6-methoxybenzyl)-3,4-dihydropyrimidin-1(2H)-yl]acetic acid'  ligand  35  25  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_F49
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
 F49  O23  O   O     0  -0.480   3.9455   0.2225   1.6570
 F49  C10  C   CR6   0   0.822   3.6521   0.7552   0.6079
 F49  N12  N   NR6   0  -0.538   4.5316   0.7552  -0.4529
 F49  C19  C   CH2   0  -0.446   5.7741   0.0456  -0.2655
 F49  C20  C   C     0   0.551   5.5525  -1.4519  -0.2743
 F49  O22  O   OH1   0  -0.586   6.6190  -2.0858   0.1823
 F49  O21  O   O     0  -0.419   4.5538  -1.9832  -0.6774
 F49  C13  C   CR16  0   0.097   4.2301   1.3480  -1.6402
 F49  C11  C   CR16  0  -0.507   3.0867   2.0207  -1.8329
 F49  C9   C   CR6   0   0.610   2.1240   2.1121  -0.7662
 F49  O18  O   O     0  -0.454   1.0760   2.7274  -0.8214
 F49  N8   N   NR6   0  -0.594   2.4586   1.4123   0.3956
 F49  C7   C   CH2   0  -0.383   1.4710   1.4137   1.4699
 F49  C1   C   CR6   0   0.079   0.1648   0.7855   1.0387
 F49  C3   C   CR6   0   0.414   0.2001  -0.5248   0.5576
 F49  O24  O   O2    0  -0.466   1.3726  -1.1875   0.5300
 F49  C25  C   CH3   0  -0.421   1.6370  -2.0004   1.6765
 F49  C5   C   CR6   0  -0.185  -0.9506  -1.1376   0.0629
 F49  BR7  BR  BR    0   0.042  -0.7899  -2.8452  -0.6844
 F49  C6   C   CR6   0  -0.095  -2.1706  -0.4708   0.0978
 F49  BR6  BR  BR    0   0.052  -3.7080  -1.3031  -0.5631
 F49  C4   C   CR6   0  -0.085  -2.2336   0.8159   0.6354
 F49  BR5  BR  BR    0   0.046  -3.8788   1.7051   0.7199
 F49  C2   C   CR6   0  -0.162  -1.0667   1.4376   1.0866
 F49  BR4  BR  BR    0   0.023  -1.1813   3.1763   1.7875
 F49  H1   H   HCH2  0   0.325   6.4490   0.2996  -1.0847
 F49  H2   H   HCH2  0   0.318   6.2648   0.3598   0.6546
 F49  H3   H   HOH1  0   0.489   6.4940  -3.0454   0.1245
 F49  H4   H   HCR6  0   0.327   4.9783   1.2583  -2.4145
 F49  H5   H   HCR6  0   0.293   2.8768   2.5018  -2.7754
 F49  H6   H   HCH2  0   0.312   1.8869   0.8666   2.3120
 F49  H7   H   HCH2  0   0.300   1.3315   2.4361   1.8079
 F49  H8   H   HCH3  0   0.253   2.6083  -2.4566   1.5124
 F49  H9   H   HCH3  0   0.235   1.6711  -1.4019   2.5882
 F49  H10  H   HCH3  0   0.233   0.8863  -2.7836   1.7961

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
 F49  C11  C13  double    1.340  0.020  1.340
 F49  C11  C9   single    1.440  0.020  1.440
 F49  C13  N12  single    1.361  0.020  1.361
 F49  O18  C9   double    1.216  0.020  1.216
 F49  C9   N8   single    1.397  0.020  1.397
 F49  N12  C19  single    1.443  0.020  1.443
 F49  N12  C10  single    1.378  0.020  1.378
 F49  C19  C20  single    1.514  0.020  1.514
 F49  O21  C20  double    1.201  0.020  1.201
 F49  C20  O22  single    1.322  0.020  1.322
 F49  N8   C10  single    1.379  0.020  1.379
 F49  N8   C7   single    1.459  0.020  1.459
 F49  C10  O23  double    1.213  0.020  1.213
 F49  C25  O24  single    1.430  0.020  1.430
 F49  BR4  C2   single    1.878  0.020  1.878
 F49  BR5  C4   single    1.872  0.020  1.872
 F49  C2   C4   aromatic  1.397  0.020  1.397
 F49  C2   C1   aromatic  1.394  0.020  1.394
 F49  C7   C1   single    1.512  0.020  1.512
 F49  C4   C6   aromatic  1.396  0.020  1.396
 F49  C1   C3   aromatic  1.396  0.020  1.396
 F49  C6   C5   aromatic  1.391  0.020  1.391
 F49  C6   BR6  single    1.869  0.020  1.869
 F49  C3   C5   aromatic  1.394  0.020  1.394
 F49  C3   O24  single    1.347  0.020  1.347
 F49  C5   BR7  single    1.871  0.020  1.871
 F49  C19  H1   single    0.970  0.020  1.090
 F49  C19  H2   single    0.970  0.020  1.090
 F49  O22  H3   single    0.850  0.020  0.980
 F49  C13  H4   single    0.930  0.020  1.080
 F49  C11  H5   single    0.930  0.020  1.080
 F49  C7   H6   single    0.970  0.020  1.090
 F49  C7   H7   single    0.970  0.020  1.090
 F49  C25  H8   single    0.970  0.020  1.090
 F49  C25  H9   single    0.970  0.020  1.090
 F49  C25  H10  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
 F49  N8   C10  N12  115.71  3.000
 F49  N8   C10  O23  123.50  3.000
 F49  N12  C10  O23  120.77  3.000
 F49  C13  N12  C19  121.22  3.000
 F49  C19  N12  C10  116.71  3.000
 F49  C13  N12  C10  122.02  3.000
 F49  H2   C19  H1   106.77  3.000
 F49  H2   C19  C20  110.87  3.000
 F49  H1   C19  C20  108.44  3.000
 F49  H2   C19  N12  110.84  3.000
 F49  H1   C19  N12  108.69  3.000
 F49  C20  C19  N12  111.08  3.000
 F49  O21  C20  O22  125.08  3.000
 F49  O22  C20  C19  110.74  3.000
 F49  O21  C20  C19  124.15  3.000
 F49  H3   O22  C20  110.48  3.000
 F49  H4   C13  C11  121.95  3.000
 F49  H4   C13  N12  115.82  3.000
 F49  C11  C13  N12  122.21  3.000
 F49  H5   C11  C9   119.26  3.000
 F49  H5   C11  C13  121.02  3.000
 F49  C9   C11  C13  119.71  3.000
 F49  N8   C9   O18  119.83  3.000
 F49  N8   C9   C11  115.09  3.000
 F49  O18  C9   C11  125.07  3.000
 F49  C7   N8   C9   116.72  3.000
 F49  C7   N8   C10  118.22  3.000
 F49  C9   N8   C10  125.04  3.000
 F49  H7   C7   H6   106.38  3.000
 F49  H7   C7   C1   111.65  3.000
 F49  H6   C7   C1   110.02  3.000
 F49  H7   C7   N8   108.48  3.000
 F49  H6   C7   N8   108.11  3.000
 F49  C1   C7   N8   111.98  3.000
 F49  C2   C1   C3   118.23  3.000
 F49  C3   C1   C7   117.79  3.000
 F49  C2   C1   C7   123.97  3.000
 F49  C5   C3   O24  119.66  3.000
 F49  O24  C3   C1   119.39  3.000
 F49  C5   C3   C1   120.92  3.000
 F49  C25  O24  C3   115.09  3.000
 F49  H10  C25  H9   108.88  3.000
 F49  H10  C25  H8   109.30  3.000
 F49  H9   C25  H8   109.20  3.000
 F49  H10  C25  O24  111.63  3.000
 F49  H9   C25  O24  111.34  3.000
 F49  H8   C25  O24  106.44  3.000
 F49  C6   C5   BR7  121.53  3.000
 F49  BR7  C5   C3   118.16  3.000
 F49  C6   C5   C3   120.29  3.000
 F49  C4   C6   BR6  120.63  3.000
 F49  BR6  C6   C5   119.95  3.000
 F49  C4   C6   C5   119.41  3.000
 F49  C2   C4   BR5  120.54  3.000
 F49  C2   C4   C6   119.80  3.000
 F49  BR5  C4   C6   119.66  3.000
 F49  BR4  C2   C4   118.79  3.000
 F49  C4   C2   C1   121.23  3.000
 F49  BR4  C2   C1   119.98  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
 F49  CONST_01  C6   C4   C2   C1      0.00   0.0  0
 F49  CONST_02  C6   C5   C3   C1      0.00   0.0  0
 F49  CONST_03  C4   C2   C1   C3      0.00   0.0  0
 F49  CONST_04  C4   C6   C5   C3      0.00   0.0  0
 F49  CONST_05  C2   C4   C6   C5      0.00   0.0  0
 F49  CONST_06  C2   C1   C3   C5      0.00   0.0  0
 F49  CONST_07  C11  C9   N8   C10     0.00   0.0  0
 F49  CONST_08  C9   N8   C10  N12     0.00   0.0  0
 F49  CONST_09  N8   C10  N12  C13     0.00   0.0  0
 F49  CONST_10  C4   C2   C1   C7    180.00   0.0  0
 F49  CONST_11  C5   C3   C1   C7    180.00   0.0  0
 F49  CONST_12  BR5  C4   C2   C1    180.00   0.0  0
 F49  CONST_13  BR7  C5   C3   C1    180.00   0.0  0
 F49  CONST_14  BR4  C2   C1   C3    180.00   0.0  0
 F49  CONST_15  BR6  C6   C5   C3    180.00   0.0  0
 F49  CONST_16  C2   C1   C3   O24   180.00   0.0  0
 F49  CONST_17  C6   C5   C3   O24   180.00   0.0  0
 F49  CONST_18  BR5  C4   C6   C5    180.00   0.0  0
 F49  CONST_19  C4   C6   C5   BR7   180.00   0.0  0
 F49  CONST_20  BR4  C2   C4   C6    180.00   0.0  0
 F49  CONST_21  C2   C4   C6   BR6   180.00   0.0  0
 F49  CONST_22  C13  N12  C10  O23   180.00   0.0  0
 F49  CONST_23  C9   N8   C10  O23   180.00   0.0  0
 F49  CONST_24  O18  C9   N8   C10   180.00   0.0  0
 F49  CONST_25  C7   N8   C10  N12   180.00   0.0  0
 F49  CONST_26  N8   C10  N12  C19   180.00   0.0  0
 F49  CONST_27  C7   N8   C9   C11   180.00   0.0  0
 F49  CONST_28  C19  N12  C10  O23     0.00   0.0  0
 F49  CONST_29  C7   N8   C10  O23     0.00   0.0  0
 F49  CONST_30  C7   N8   C9   O18     0.00   0.0  0
 F49  CONST_31  H3   O22  C20  C19   180.00   0.0  0
 F49  Var_01    C1   C7   N8   C10  -120.66  30.0  3
 F49  Var_02    C2   C1   C7   N8   -122.60  30.0  2
 F49  Var_03    C20  C19  N12  C10    72.50  30.0  3
 F49  Var_04    C5   C3   O24  C25   -88.35  30.0  1
 F49  Var_05    O21  C20  C19  N12    15.55  30.0  3
 F49  Var_06    H8   C25  O24  C3   -179.51  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
 F49  plan-1  O23  0.020
 F49  plan-1  C10  0.020
 F49  plan-1  N12  0.020
 F49  plan-1  C19  0.020
 F49  plan-1  C13  0.020
 F49  plan-1  C11  0.020
 F49  plan-1  C9   0.020
 F49  plan-1  O18  0.020
 F49  plan-1  N8   0.020
 F49  plan-1  C7   0.020
 F49  plan-1  H4   0.020
 F49  plan-1  H5   0.020
 F49  plan-2  C7   0.020
 F49  plan-2  C1   0.020
 F49  plan-2  C3   0.020
 F49  plan-2  O24  0.020
 F49  plan-2  C5   0.020
 F49  plan-2  BR7  0.020
 F49  plan-2  C6   0.020
 F49  plan-2  BR6  0.020
 F49  plan-2  C4   0.020
 F49  plan-2  BR5  0.020
 F49  plan-2  C2   0.020
 F49  plan-2  BR4  0.020
 F49  plan-3  C19  0.020
 F49  plan-3  C20  0.020
 F49  plan-3  O22  0.020
 F49  plan-3  O21  0.020
 F49  plan-3  H3   0.020

