# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 31 13:07:14 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolane-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@H](O)[C@H](O[C@H]1N2C=CC(=O)NC2=O)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
 UUA  UUA  '(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolane-2-carboxylic acid'  ligand  28  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UUA
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
 UUA  N1   N  NR6   0  -0.579   1.1609   0.3963   0.2964
 UUA  C4   C  CR15  0   0.225  -0.1902   0.8967   0.4791
 UUA  C5   C  C     0   0.532  -2.5998  -1.4107   0.1080
 UUA  C6   C  CR6   0   0.750   1.4078  -0.7251  -0.4793
 UUA  C7   C  CR6   0   0.568   3.8143  -0.5246   0.0980
 UUA  C8   C  CR16  0  -0.511   3.4658   0.6293   0.8893
 UUA  O8   O  OH1   0  -0.592  -3.7403  -1.3845  -0.5694
 UUA  O2   O  O     0  -0.422  -1.9459  -2.3993   0.2935
 UUA  C1   C  CR15  0  -0.112  -2.2864  -0.0455   0.6957
 UUA  C2   C  CR15  0  -0.049  -2.4073   1.1551  -0.2614
 UUA  O3   O  OH1   0  -0.664  -2.6791   2.3367   0.4416
 UUA  C3   C  CR15  0  -0.026  -0.9750   1.2370  -0.7884
 UUA  O4   O  OH1   0  -0.655  -0.5612   2.4803  -1.2594
 UUA  O1   O  O     0  -0.476  -0.9645  -0.0268   1.1937
 UUA  O6   O  O     0  -0.460   0.5445  -1.3267  -1.0766
 UUA  C9   C  CR16  0   0.100   2.1853   1.0230   0.9542
 UUA  N2   N  NR16  0  -0.734   2.7234  -1.1077  -0.5275
 UUA  O5   O  O     0  -0.462   4.9301  -0.9879  -0.0432
 UUA  H1   H  HCR5  0   0.260  -0.0715   1.8170   1.0606
 UUA  H2   H  HCR6  0   0.295   4.2314   1.1642   1.4290
 UUA  H3   H  HOH1  0   0.487  -3.9687  -2.2763  -0.8737
 UUA  H4   H  HCR5  0   0.304  -2.9889   0.0815   1.5297
 UUA  H5   H  HCR5  0   0.269  -3.1351   0.9851  -1.0599
 UUA  H6   H  HOH1  0   0.461  -3.5865   2.3017   0.7608
 UUA  H7   H  HCR5  0   0.271  -0.8515   0.4539  -1.5399
 UUA  H8   H  HOH1  0   0.465  -0.8645   2.5835  -2.1664
 UUA  H9   H  HCR6  0   0.330   1.8979   1.8813   1.5447
 UUA  H10  H  HNR6  0   0.427   2.9068  -1.9274  -1.0934

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
 UUA  O6  C6   double  1.210  0.020  1.210
 UUA  N2  C6   single  1.371  0.020  1.371
 UUA  N2  C7   single  1.386  0.020  1.386
 UUA  C6  N1   single  1.386  0.020  1.386
 UUA  O5  C7   double  1.216  0.020  1.216
 UUA  C7  C8   single  1.442  0.020  1.442
 UUA  N1  C4   single  1.452  0.020  1.452
 UUA  N1  C9   single  1.369  0.020  1.369
 UUA  O4  C3   single  1.392  0.020  1.392
 UUA  C4  C3   single  1.529  0.020  1.529
 UUA  C4  O1   single  1.401  0.020  1.401
 UUA  O3  C2   single  1.401  0.020  1.401
 UUA  C8  C9   double  1.341  0.020  1.341
 UUA  C3  C2   single  1.528  0.020  1.528
 UUA  O1  C1   single  1.413  0.020  1.413
 UUA  C2  C1   single  1.540  0.020  1.540
 UUA  C1  C5   single  1.519  0.020  1.519
 UUA  C5  O2   double  1.200  0.020  1.200
 UUA  C5  O8   single  1.327  0.020  1.327
 UUA  C4  H1   single  0.970  0.020  1.090
 UUA  C8  H2   single  0.930  0.020  1.080
 UUA  O8  H3   single  0.850  0.020  0.980
 UUA  C1  H4   single  0.970  0.020  1.090
 UUA  C2  H5   single  0.970  0.020  1.090
 UUA  O3  H6   single  0.850  0.020  0.980
 UUA  C3  H7   single  0.970  0.020  1.090
 UUA  O4  H8   single  0.850  0.020  0.980
 UUA  C9  H9   single  0.930  0.020  1.080
 UUA  N2  H10  single  0.860  0.020  1.020

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
 UUA  C9   N1  C6  120.41  3.000
 UUA  C9   N1  C4  118.54  3.000
 UUA  C6   N1  C4  120.99  3.000
 UUA  H1   C4  O1  110.06  3.000
 UUA  H1   C4  C3  107.99  3.000
 UUA  O1   C4  C3  106.61  3.000
 UUA  H1   C4  N1  104.80  3.000
 UUA  O1   C4  N1  110.55  3.000
 UUA  C3   C4  N1  116.74  3.000
 UUA  C1   C5  O2  124.64  3.000
 UUA  O2   C5  O8  124.31  3.000
 UUA  C1   C5  O8  110.93  3.000
 UUA  N2   C6  O6  121.91  3.000
 UUA  N2   C6  N1  114.61  3.000
 UUA  O6   C6  N1  123.48  3.000
 UUA  O5   C7  N2  120.62  3.000
 UUA  O5   C7  C8  126.17  3.000
 UUA  N2   C7  C8  113.21  3.000
 UUA  H2   C8  C9  120.52  3.000
 UUA  H2   C8  C7  119.99  3.000
 UUA  C9   C8  C7  119.49  3.000
 UUA  H3   O8  C5  110.16  3.000
 UUA  H4   C1  O1  109.23  3.000
 UUA  H4   C1  C2  109.37  3.000
 UUA  O1   C1  C2  106.39  3.000
 UUA  H4   C1  C5  105.42  3.000
 UUA  C2   C1  C5  116.36  3.000
 UUA  O1   C1  C5  109.95  3.000
 UUA  H5   C2  C3  112.35  3.000
 UUA  H5   C2  O3  111.60  3.000
 UUA  C3   C2  O3  108.03  3.000
 UUA  H5   C2  C1  112.63  3.000
 UUA  C3   C2  C1  100.52  3.000
 UUA  O3   C2  C1  111.15  3.000
 UUA  H6   O3  C2  108.57  3.000
 UUA  H7   C3  O4  111.95  3.000
 UUA  H7   C3  C2  107.74  3.000
 UUA  O4   C3  C2  116.30  3.000
 UUA  H7   C3  C4  110.65  3.000
 UUA  C2   C3  C4  100.56  3.000
 UUA  O4   C3  C4  109.06  3.000
 UUA  H8   O4  C3  108.73  3.000
 UUA  C1   O1  C4  110.24  3.000
 UUA  H9   C9  C8  120.90  3.000
 UUA  H9   C9  N1  115.28  3.000
 UUA  C8   C9  N1  123.82  3.000
 UUA  H10  N2  C7  116.75  3.000
 UUA  H10  N2  C6  114.79  3.000
 UUA  C7   N2  C6  128.46  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
 UUA  CONST_01  C7   N2  C6  N1    0.00  0.0  0
 UUA  CONST_02  N2   C6  N1  C4  180.00  0.0  0
 UUA  CONST_03  C8   C7  N2  C6    0.00  0.0  0
 UUA  CONST_04  N2   C6  N1  C9    0.00  0.0  0
 UUA  CONST_05  O6   C6  N1  C4    0.00  0.0  0
 UUA  CONST_06  O5   C7  N2  C6  180.00  0.0  0
 UUA  CONST_07  O6   C6  N2  C7  180.00  0.0  0
 UUA  CONST_08  C9   N1  C6  O6  180.00  0.0  0
 UUA  CONST_09  H10  N2  C6  N1  180.00  0.0  0
 UUA  CONST_10  H3   O8  C5  C1  180.00  0.0  0

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
 UUA  chir_01  C4  N1  C3  O1  negativ
 UUA  chir_02  C1  O1  C2  C5  negativ
 UUA  chir_03  C2  O3  C1  C3  positiv
 UUA  chir_04  C3  O4  C2  C4  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
 UUA  plan-1  N1   0.020
 UUA  plan-1  C4   0.020
 UUA  plan-1  C6   0.020
 UUA  plan-1  C7   0.020
 UUA  plan-1  C8   0.020
 UUA  plan-1  O6   0.020
 UUA  plan-1  C9   0.020
 UUA  plan-1  N2   0.020
 UUA  plan-1  O5   0.020
 UUA  plan-1  H2   0.020
 UUA  plan-1  H9   0.020
 UUA  plan-1  H10  0.020
 UUA  plan-2  C5   0.020
 UUA  plan-2  O8   0.020
 UUA  plan-2  O2   0.020
 UUA  plan-2  C1   0.020
 UUA  plan-2  H3   0.020

