# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 23:18:39 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-(5-deoxy-beta-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@@H]([C@@H](O)[C@@H]1O)N2C=CC(=O)NC2=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
 D3Z  D3Z  1-(5-deoxy-beta-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione  ligand  28  16  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D3Z
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
 D3Z  N1    N  NR6   0  -0.569   0.6064   0.1815  -0.5147
 D3Z  C2    C  CR6   0   0.726   0.8799  -1.0478   0.0550
 D3Z  N3    N  NR16  0  -0.730   2.1284  -1.1260   0.6387
 D3Z  C4    C  CR6   0   0.566   3.1298  -0.1751   0.6898
 D3Z  C5    C  CR16  0  -0.505   2.7752   1.0524   0.0242
 D3Z  C6    C  CR16  0   0.092   1.5579   1.1622  -0.5291
 D3Z  O2    O  O     0  -0.459   0.1440  -2.0061   0.0563
 D3Z  O4    O  O     0  -0.471   4.1871  -0.4087   1.2484
 D3Z  C1'   C  CH1   0   0.189  -0.7035   0.6047  -1.0866
 D3Z  C2'   C  CH1   0  -0.036  -1.4528   1.5372  -0.1202
 D3Z  O2'   O  OH1   0  -0.664  -2.1776   2.4292  -0.9244
 D3Z  C3'   C  CH1   0  -0.048  -2.3668   0.5529   0.6043
 D3Z  C4'   C  CH1   0   0.059  -2.7199  -0.4024  -0.5356
 D3Z  O3'   O  OH1   0  -0.660  -1.6173  -0.0232   1.6413
 D3Z  O4'   O  O2    0  -0.487  -1.5522  -0.4375  -1.3734
 D3Z  C5'   C  CH3   0  -0.718  -3.1440  -1.7963  -0.1387
 D3Z  HN3   H  HNR6  0   0.421   2.3324  -2.0216   1.0652
 D3Z  H5    H  HCR6  0   0.292   3.4817   1.8658  -0.0280
 D3Z  H6    H  HCR6  0   0.323   1.2686   2.0728  -1.0371
 D3Z  H1'   H  HCH1  0   0.280  -0.4414   1.1363  -2.0076
 D3Z  H2'   H  HCH1  0   0.262  -0.7792   2.0574   0.5712
 D3Z  HO2'  H  HOH1  0   0.462  -2.7386   2.9691  -0.3582
 D3Z  H3'   H  HCH1  0   0.249  -3.2729   1.0425   0.9846
 D3Z  H4'   H  HCH1  0   0.233  -3.5306   0.0598  -1.1101
 D3Z  HO3'  H  HOH1  0   0.461  -2.1126  -0.7573   2.0182
 D3Z  H5'   H  HCH3  0   0.237  -4.0547  -1.7424   0.4599
 D3Z  H5'A  H  HCH3  0   0.249  -3.3754  -2.3938  -1.0205
 D3Z  H5'B  H  HCH3  0   0.244  -2.3784  -2.3192   0.4301

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
 D3Z  N1   C2    single  1.382  0.020  1.382
 D3Z  N1   C6    single  1.367  0.020  1.367
 D3Z  N1   C1'   single  1.491  0.020  1.491
 D3Z  C2   N3    single  1.380  0.020  1.380
 D3Z  C2   O2    double  1.208  0.020  1.208
 D3Z  N3   C4    single  1.382  0.020  1.382
 D3Z  C4   C5    single  1.441  0.020  1.441
 D3Z  C4   O4    double  1.218  0.020  1.218
 D3Z  C5   C6    double  1.342  0.020  1.342
 D3Z  C1'  C2'   single  1.538  0.020  1.538
 D3Z  C1'  O4'   single  1.374  0.020  1.374
 D3Z  C2'  O2'   single  1.403  0.020  1.403
 D3Z  C2'  C3'   single  1.526  0.020  1.526
 D3Z  C3'  C4'   single  1.529  0.020  1.529
 D3Z  C3'  O3'   single  1.403  0.020  1.403
 D3Z  C4'  O4'   single  1.438  0.020  1.438
 D3Z  C4'  C5'   single  1.510  0.020  1.510
 D3Z  N3   HN3   single  0.860  0.020  1.020
 D3Z  C5   H5    single  0.930  0.020  1.080
 D3Z  C6   H6    single  0.930  0.020  1.080
 D3Z  C1'  H1'   single  0.970  0.020  1.090
 D3Z  C2'  H2'   single  0.970  0.020  1.090
 D3Z  O2'  HO2'  single  0.850  0.020  0.980
 D3Z  C3'  H3'   single  0.970  0.020  1.090
 D3Z  C4'  H4'   single  0.970  0.020  1.090
 D3Z  O3'  HO3'  single  0.850  0.020  0.980
 D3Z  C5'  H5'   single  0.970  0.020  1.090
 D3Z  C5'  H5'A  single  0.970  0.020  1.090
 D3Z  C5'  H5'B  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
 D3Z  C1'   N1   C6    113.83  3.000
 D3Z  C1'   N1   C2    125.77  3.000
 D3Z  C6    N1   C2    120.32  3.000
 D3Z  O2    C2   N3    120.36  3.000
 D3Z  O2    C2   N1    125.83  3.000
 D3Z  N3    C2   N1    113.81  3.000
 D3Z  HN3   N3   C4    116.55  3.000
 D3Z  HN3   N3   C2    114.23  3.000
 D3Z  C4    N3   C2    129.20  3.000
 D3Z  O4    C4   C5    126.07  3.000
 D3Z  O4    C4   N3    120.92  3.000
 D3Z  C5    C4   N3    113.01  3.000
 D3Z  H5    C5   C6    120.84  3.000
 D3Z  H5    C5   C4    120.24  3.000
 D3Z  C6    C5   C4    118.92  3.000
 D3Z  H6    C6   C5    120.33  3.000
 D3Z  H6    C6   N1    115.01  3.000
 D3Z  C5    C6   N1    124.66  3.000
 D3Z  H1'   C1'  O4'   109.90  3.000
 D3Z  H1'   C1'  C2'   110.53  3.000
 D3Z  O4'   C1'  C2'   106.86  3.000
 D3Z  H1'   C1'  N1    104.49  3.000
 D3Z  O4'   C1'  N1    114.04  3.000
 D3Z  C2'   C1'  N1    111.05  3.000
 D3Z  H2'   C2'  C3'   112.00  3.000
 D3Z  H2'   C2'  O2'   112.16  3.000
 D3Z  C3'   C2'  O2'   111.89  3.000
 D3Z  H2'   C2'  C1'   112.62  3.000
 D3Z  C3'   C2'  C1'   101.48  3.000
 D3Z  O2'   C2'  C1'   106.08  3.000
 D3Z  HO2'  O2'  C2'   108.69  3.000
 D3Z  H3'   C3'  O3'   111.59  3.000
 D3Z  H3'   C3'  C4'   110.27  3.000
 D3Z  O3'   C3'  C4'   114.70  3.000
 D3Z  H3'   C3'  C2'   111.78  3.000
 D3Z  O3'   C3'  C2'   107.20  3.000
 D3Z  C4'   C3'  C2'   100.80  3.000
 D3Z  H4'   C4'  C5'   108.62  3.000
 D3Z  H4'   C4'  O4'   107.80  3.000
 D3Z  C5'   C4'  O4'   111.02  3.000
 D3Z  H4'   C4'  C3'   107.35  3.000
 D3Z  C5'   C4'  C3'   116.47  3.000
 D3Z  O4'   C4'  C3'   105.20  3.000
 D3Z  HO3'  O3'  C3'   109.13  3.000
 D3Z  C4'   O4'  C1'   111.19  3.000
 D3Z  H5'B  C5'  H5'A  108.00  3.000
 D3Z  H5'B  C5'  H5'   108.93  3.000
 D3Z  H5'A  C5'  H5'   107.08  3.000
 D3Z  H5'B  C5'  C4'   112.55  3.000
 D3Z  H5'A  C5'  C4'   110.67  3.000
 D3Z  H5'   C5'  C4'   109.45  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
 D3Z  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 D3Z  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 D3Z  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 D3Z  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 D3Z  CONST_05  O4   C4  N3  C2  180.00  0.0  0
 D3Z  CONST_06  O2   C2  N3  C4  180.00  0.0  0
 D3Z  CONST_07  O2   C2  N1  C6  180.00  0.0  0
 D3Z  CONST_08  C1'  N1  C2  O2    0.00  0.0  0
 D3Z  CONST_09  HN3  N3  C2  N1  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
 D3Z  chir_01  C1'  N1   C2'  O4'  positiv
 D3Z  chir_02  C2'  O2'  C3'  C1'  negativ
 D3Z  chir_03  C3'  O3'  C2'  C4'  negativ
 D3Z  chir_04  C4'  O4'  C3'  C5'  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
 D3Z  plan-1  N1   0.020
 D3Z  plan-1  C2   0.020
 D3Z  plan-1  N3   0.020
 D3Z  plan-1  C4   0.020
 D3Z  plan-1  C5   0.020
 D3Z  plan-1  C6   0.020
 D3Z  plan-1  O2   0.020
 D3Z  plan-1  O4   0.020
 D3Z  plan-1  C1'  0.020
 D3Z  plan-1  HN3  0.020
 D3Z  plan-1  H5   0.020
 D3Z  plan-1  H6   0.020

