# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:46:59 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: 3-(4-amino-2-oxopyrimidin-1(2H)-yl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CN1C=CC(=NC1=O)N)C(O)=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
 CUD  CUD  3-(4-amino-2-oxopyrimidin-1(2H)-yl)-D-alanine  D-peptide  23  14  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_CUD
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
 CUD  C2    C  CR6    0   0.581  1.1990  -13.1130  4.9989
 CUD  C4    C  CR6    0   0.505  1.5331  -14.4207  3.1026
 CUD  C5    C  CR16   0  -0.476  2.6090  -13.5988  2.6532
 CUD  C6    C  CR16   0   0.098  2.9115  -12.5416  3.4368
 CUD  N     N  NH2    0  -0.777  0.5956   -9.9055  4.5874
 CUD  CA    C  CH1    0  -0.230  2.0362   -9.8039  4.7203
 CUD  N1    N  NR6    0  -0.496  2.2468  -12.2812  4.5805
 CUD  N4    N  NH2    0  -0.814  1.1672  -15.4850  2.3830
 CUD  N3    N  N      0  -0.541  0.8792  -14.1708  4.2186
 CUD  O2    O  O      0  -0.517  0.6153  -12.8773  6.0484
 CUD  C     C  C      0   0.391  2.5772   -8.5790  5.5139
 CUD  O     O  O      0  -0.591  1.7421   -7.7703  5.9565
 CUD  OXT   O  OC    -1  -0.611  3.8198   -8.5169  5.6221
 CUD  HA    H  HCH1   0   0.226  2.4493   -9.7197  3.7060
 CUD  H6    H  HCR6   0   0.306  3.7099  -11.8563  3.1826
 CUD  H5    H  HCR6   0   0.279  3.1535  -13.8020  1.7436
 CUD  HN4   H  HNH2   0   0.397  0.4050  -16.0636  2.6917
 CUD  HN4A  H  HNH2   0   0.409  1.6193  -15.7183  1.5167
 CUD  CB    C  CH2    0  -0.320  2.6008  -11.0840  5.3358
 CUD  HN    H  HNH2   0   0.325  0.1826   -9.8879  5.5126
 CUD  HB    H  HCH2   0   0.259  3.6860  -11.0187  5.3788
 CUD  HBA   H  HCH2   0   0.259  2.2390  -11.2142  6.3539
 CUD  HNA   H  HNH2   0   0.337  0.2547   -9.0643  4.1390

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
 CUD  N3    C2   single  1.353  0.020  1.353
 CUD  N1    C2   single  1.402  0.020  1.402
 CUD  C2    O2   double  1.224  0.020  1.224
 CUD  N4    C4   single  1.336  0.020  1.336
 CUD  C5    C4   single  1.426  0.020  1.426
 CUD  C4    N3   double  1.317  0.020  1.317
 CUD  H5    C5   single  0.930  0.020  1.080
 CUD  C5    C6   double  1.350  0.020  1.350
 CUD  H6    C6   single  0.930  0.020  1.080
 CUD  C6    N1   single  1.348  0.020  1.348
 CUD  CA    N    single  1.458  0.019  1.458
 CUD  N     HN   single  0.890  0.020  1.040
 CUD  N     HNA  single  0.890  0.020  1.040
 CUD  HA    CA   single  0.970  0.020  0.970
 CUD  CA    CB   single  1.521  0.033  1.521
 CUD  CA    C    single  1.525  0.021  1.525
 CUD  N1    CB   single  1.459  0.020  1.459
 CUD  CB    HB   single  0.970  0.020  1.090
 CUD  CB    HBA  single  0.970  0.020  1.090
 CUD  HN4A  N4   single  0.860  0.020  1.020
 CUD  N4    HN4  single  0.860  0.020  1.020
 CUD  OXT   C    deloc   1.249  0.020  1.249
 CUD  C     O    deloc   1.231  0.020  1.231

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
 CUD  O2    C2  N3   122.17  3.000
 CUD  O2    C2  N1   119.88  3.000
 CUD  N3    C2  N1   117.94  3.000
 CUD  N3    C4  N4   118.13  3.000
 CUD  N3    C4  C5   122.14  3.000
 CUD  N4    C4  C5   119.73  3.000
 CUD  H5    C5  C6   121.56  3.000
 CUD  C6    C5  C4   115.93  3.000
 CUD  H5    C5  C4   122.52  3.000
 CUD  H6    C6  N1   116.14  3.000
 CUD  N1    C6  C5   122.21  3.000
 CUD  H6    C6  C5   121.65  3.000
 CUD  HNA   N   HN   104.64  3.000
 CUD  HNA   N   CA   108.48  3.000
 CUD  HN    N   CA   108.66  3.000
 CUD  HA    CA  C    110.00  3.000
 CUD  C     CA  CB   110.50  1.500
 CUD  HA    CA  CB   109.00  3.000
 CUD  C     CA  N    111.00  2.800
 CUD  CB    CA  N    110.40  1.500
 CUD  HA    CA  N    110.00  3.000
 CUD  CB    N1  C6   118.56  3.000
 CUD  CB    N1  C2   120.91  3.000
 CUD  C6    N1  C2   120.47  3.000
 CUD  HN4A  N4  HN4  118.18  3.000
 CUD  HN4   N4  C4   120.05  3.000
 CUD  HN4A  N4  C4   121.75  3.000
 CUD  C4    N3  C2   121.30  3.000
 CUD  OXT   C   O    127.22  3.000
 CUD  O     C   CA   120.80  1.700
 CUD  OXT   C   CA   120.80  1.700
 CUD  HBA   CB  HB   107.57  3.000
 CUD  HBA   CB  N1   107.78  3.000
 CUD  HB    CB  N1   108.16  3.000
 CUD  HBA   CB  CA   110.74  3.000
 CUD  HB    CB  CA   109.52  3.000
 CUD  N1    CB  CA   112.90  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
 CUD  CONST_01  C5    C4  N3  C2     0.00   0.0  0
 CUD  CONST_02  N1    C2  N3  C4     0.00   0.0  0
 CUD  CONST_03  N3    C2  N1  C6     0.00   0.0  0
 CUD  CONST_04  N4    C4  N3  C2   180.00   0.0  0
 CUD  CONST_05  O2    C2  N3  C4   180.00   0.0  0
 CUD  CONST_06  O2    C2  N1  C6   180.00   0.0  0
 CUD  CONST_07  N3    C2  N1  CB   180.00   0.0  0
 CUD  CONST_08  O2    C2  N1  CB     0.00   0.0  0
 CUD  CONST_09  HN4A  N4  C4  C5     0.00   0.0  0
 CUD  CONST_10  HN4   N4  C4  C5   180.00   0.0  0
 CUD  Var_01    CA    CB  N1  C2  -100.29  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
 CUD  chir_01  CA  N  CB  C  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
 CUD  plan-1  C2    0.020
 CUD  plan-1  C4    0.020
 CUD  plan-1  C5    0.020
 CUD  plan-1  C6    0.020
 CUD  plan-1  N1    0.020
 CUD  plan-1  N4    0.020
 CUD  plan-1  N3    0.020
 CUD  plan-1  O2    0.020
 CUD  plan-1  H6    0.020
 CUD  plan-1  H5    0.020
 CUD  plan-1  HN4   0.020
 CUD  plan-1  HN4A  0.020
 CUD  plan-1  CB    0.020
 CUD  plan-2  CA    0.020
 CUD  plan-2  C     0.020
 CUD  plan-2  O     0.020
 CUD  plan-2  OXT   0.020

