# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 22:17:12 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: methyl 3-(5-bromo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alaninate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)CN1C=C(Br)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
 D5Y  D5Y  'methyl 3-(5-bromo-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-L-alaninate'  ligand  26  16  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D5Y
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
 D5Y  O3   O   O     0  -0.459  -3.5706   3.2103   5.3703
 D5Y  C4   C   CR16  0   0.118  -3.0877   1.6043   8.4514
 D5Y  C5   C   CR6   0  -0.370  -2.9172   2.6367   9.2951
 D5Y  C6   C   CR6   0   0.600  -2.9970   3.9976   8.8012
 D5Y  N1   N   NR16  0  -0.731  -3.2307   4.0550   7.4409
 D5Y  C7   C   CR6   0   0.737  -3.3997   3.0219   6.5526
 D5Y  N2   N   NH2   0  -0.767  -5.8697   0.9914   5.5222
 D5Y  BR   BR  BR    0   0.011  -2.5583   2.3820  11.1066
 D5Y  O2   O   O     0  -0.431  -2.8668   5.0027   9.4655
 D5Y  N    N   NR6   0  -0.530  -3.3548   1.7633   7.1243
 D5Y  C3   C   CH2   0  -0.336  -3.5628   0.5764   6.2936
 D5Y  C2   C   CH1   0  -0.208  -5.0174   0.0911   6.2532
 D5Y  C1   C   C     0   0.550  -5.5218  -0.2264   7.6602
 D5Y  O1   O   O     0  -0.428  -6.4043   0.3744   8.2158
 D5Y  O    O   O2    0  -0.453  -4.8620  -1.2391   8.2042
 D5Y  C    C   CH3   0  -0.428  -5.2320  -1.6366   9.5280
 D5Y  H1   H   HCR6  0   0.335  -3.0005   0.5793   8.7846
 D5Y  H2   H   HNR6  0   0.436  -3.2779   4.9819   7.0339
 D5Y  H4   H   HNH2  0   0.350  -6.0488   1.8386   6.0459
 D5Y  H6   H   HCH2  0   0.297  -2.9112  -0.2089   6.6729
 D5Y  H7   H   HCH2  0   0.302  -3.2465   0.8016   5.2791
 D5Y  H8   H   HCH1  0   0.300  -4.9788  -0.8556   5.7054
 D5Y  H9   H   HCH3  0   0.258  -4.5740  -2.4602   9.7868
 D5Y  H10  H   HCH3  0   0.237  -5.0932  -0.8243  10.2415
 D5Y  H11  H   HCH3  0   0.249  -6.2674  -1.9721   9.5634
 D5Y  H3   H   HNH2  0   0.363  -6.7734   0.5606   5.3759

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
 D5Y  O3  C7   double  1.209  0.020  1.209
 D5Y  N2  C2   single  1.439  0.020  1.439
 D5Y  C2  C3   single  1.534  0.020  1.534
 D5Y  C2  C1   single  1.528  0.020  1.528
 D5Y  C3  N    single  1.464  0.020  1.464
 D5Y  C7  N    single  1.383  0.020  1.383
 D5Y  C7  N1   single  1.373  0.020  1.373
 D5Y  N   C4   single  1.363  0.020  1.363
 D5Y  N1  C6   single  1.381  0.020  1.381
 D5Y  C1  O1   double  1.204  0.020  1.204
 D5Y  C1  O    single  1.325  0.020  1.325
 D5Y  O   C    single  1.431  0.020  1.431
 D5Y  C4  C5   double  1.344  0.020  1.344
 D5Y  C6  C5   single  1.450  0.020  1.450
 D5Y  C6  O2   double  1.212  0.020  1.212
 D5Y  C5  BR   single  1.864  0.020  1.864
 D5Y  C4  H1   single  0.930  0.020  1.080
 D5Y  N1  H2   single  0.860  0.020  1.020
 D5Y  N2  H3   single  0.890  0.020  1.040
 D5Y  N2  H4   single  0.890  0.020  1.040
 D5Y  C3  H6   single  0.970  0.020  1.090
 D5Y  C3  H7   single  0.970  0.020  1.090
 D5Y  C2  H8   single  0.970  0.020  1.090
 D5Y  C   H9   single  0.970  0.020  1.090
 D5Y  C   H10  single  0.970  0.020  1.090
 D5Y  C   H11  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
 D5Y  H1   C4  N    115.24  3.000
 D5Y  H1   C4  C5   121.63  3.000
 D5Y  N    C4  C5   123.12  3.000
 D5Y  BR   C5  C6   118.02  3.000
 D5Y  BR   C5  C4   121.97  3.000
 D5Y  C6   C5  C4   120.00  3.000
 D5Y  O2   C6  N1   121.57  3.000
 D5Y  O2   C6  C5   125.86  3.000
 D5Y  N1   C6  C5   112.56  3.000
 D5Y  H2   N1  C7   115.01  3.000
 D5Y  H2   N1  C6   116.19  3.000
 D5Y  C7   N1  C6   128.80  3.000
 D5Y  N    C7  N1   114.42  3.000
 D5Y  N1   C7  O3   122.19  3.000
 D5Y  N    C7  O3   123.40  3.000
 D5Y  H4   N2  H3   105.86  3.000
 D5Y  H4   N2  C2   111.45  3.000
 D5Y  H3   N2  C2   109.64  3.000
 D5Y  C3   N   C7   119.92  3.000
 D5Y  C7   N   C4   120.99  3.000
 D5Y  C3   N   C4   119.06  3.000
 D5Y  H7   C3  H6   107.49  3.000
 D5Y  H7   C3  C2   108.49  3.000
 D5Y  H6   C3  C2   110.40  3.000
 D5Y  H7   C3  N    108.69  3.000
 D5Y  H6   C3  N    107.59  3.000
 D5Y  C2   C3  N    113.97  3.000
 D5Y  H8   C2  C1   107.02  3.000
 D5Y  H8   C2  C3   104.68  3.000
 D5Y  C1   C2  C3   110.76  3.000
 D5Y  H8   C2  N2   107.93  3.000
 D5Y  C1   C2  N2   113.71  3.000
 D5Y  C3   C2  N2   112.15  3.000
 D5Y  O    C1  O1   123.84  3.000
 D5Y  O    C1  C2   111.87  3.000
 D5Y  O1   C1  C2   124.29  3.000
 D5Y  C    O   C1   117.60  3.000
 D5Y  H11  C   H10  109.23  3.000
 D5Y  H11  C   H9   109.56  3.000
 D5Y  H10  C   H9   109.40  3.000
 D5Y  H11  C   O    111.19  3.000
 D5Y  H10  C   O    111.44  3.000
 D5Y  H9   C   O    105.94  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
 D5Y  CONST_01  N1  C7  N   C4     0.00   0.0  0
 D5Y  CONST_02  C7  N1  C6  C5     0.00   0.0  0
 D5Y  CONST_03  N   C7  N1  C6     0.00   0.0  0
 D5Y  CONST_04  C4  N   C7  O3   180.00   0.0  0
 D5Y  CONST_05  C6  N1  C7  O3   180.00   0.0  0
 D5Y  CONST_06  C3  N   C7  N1   180.00   0.0  0
 D5Y  CONST_07  O2  C6  N1  C7   180.00   0.0  0
 D5Y  CONST_08  H2  N1  C6  C5   180.00   0.0  0
 D5Y  CONST_09  C3  N   C7  O3     0.00   0.0  0
 D5Y  Var_01    C2  C3  N   C4    88.36  30.0  2
 D5Y  Var_02    H9  C   O   C1  -179.36  30.0  3

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
 D5Y  chir_01  C2  N2  C3  C1  negativ

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
 D5Y  plan-1  O3  0.020
 D5Y  plan-1  C4  0.020
 D5Y  plan-1  C5  0.020
 D5Y  plan-1  C6  0.020
 D5Y  plan-1  N1  0.020
 D5Y  plan-1  C7  0.020
 D5Y  plan-1  BR  0.020
 D5Y  plan-1  O2  0.020
 D5Y  plan-1  N   0.020
 D5Y  plan-1  C3  0.020
 D5Y  plan-1  H1  0.020
 D5Y  plan-1  H2  0.020
 D5Y  plan-2  C2  0.020
 D5Y  plan-2  C1  0.020
 D5Y  plan-2  O1  0.020
 D5Y  plan-2  O   0.020

