# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 10:52:31 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-beta-D-ribofuranosyl-3,4-dihydropyrimidin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CCNC2=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
 DHZ  DHZ  1-beta-D-ribofuranosyl-3,4-dihydropyrimidin-2(1H)-one  ligand  30  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 PERFECT
;

data_comp_DHZ
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
 DHZ  N1    N  NT    0  -0.587  -0.1949   0.3124  -1.2073
 DHZ  C2    C  C     0   0.720   0.7743  -0.6324  -1.5057
 DHZ  O2    O  O     0  -0.514   1.2440  -1.3740  -0.6553
 DHZ  N3    N  NH1   0  -0.678   1.1863  -0.6783  -2.7902
 DHZ  C4    C  CH2   0  -0.253   0.6459   0.0247  -3.9367
 DHZ  C5    C  C1    0  -0.387  -0.2616   1.1086  -3.4714
 DHZ  C6    C  C1    0   0.026  -0.6234   1.1988  -2.1994
 DHZ  C1'   C  CH1   0   0.234  -0.6442   0.5296   0.1439
 DHZ  C2'   C  CH1   0  -0.023  -1.2523  -0.6647   0.8795
 DHZ  O2'   O  OH1   0  -0.663  -2.5607  -0.8602   0.4317
 DHZ  C3'   C  CH1   0  -0.046  -1.0983  -0.2174   2.3342
 DHZ  O3'   O  OH1   0  -0.671  -2.1498   0.6661   2.6332
 DHZ  C4'   C  CH1   0  -0.027   0.2631   0.4848   2.2858
 DHZ  O4'   O  O2    0  -0.495   0.3946   1.0033   0.9638
 DHZ  C5'   C  CH2   0  -0.154   1.4072  -0.4462   2.6329
 DHZ  O5'   O  OH1   0  -0.673   2.6151   0.2703   2.5355
 DHZ  HN3   H  HNH1  0   0.403   1.8712  -1.3936  -2.9762
 DHZ  H41   H  HCH2  0   0.242   0.1151  -0.6702  -4.5985
 DHZ  H42   H  HCH2  0   0.249   1.4707   0.4379  -4.5236
 DHZ  H5    H  H     0   0.266  -0.6353   1.8232  -4.1897
 DHZ  H6    H  H     0   0.288  -1.2908   1.9781  -1.8579
 DHZ  H1'   H  HCH1  0   0.234  -1.4287   1.2916   0.0576
 DHZ  H2'   H  HCH1  0   0.254  -0.6376  -1.5553   0.7310
 DHZ  HO2   H  HOH1  0   0.459  -2.8785  -1.7014   0.7726
 DHZ  H3'   H  HCH1  0   0.241  -1.0851  -1.0693   3.0268
 DHZ  HO3   H  HOH1  0   0.453  -2.0050   1.0180   3.5169
 DHZ  H4'   H  HCH1  0   0.241   0.2804   1.3272   2.9889
 DHZ  H5'1  H  HCH2  0   0.211   1.3996  -1.3169   1.9689
 DHZ  H5'2  H  HCH2  0   0.194   1.2349  -0.8128   3.6541
 DHZ  HO5   H  HOH1  0   0.455   3.3389  -0.3496   2.6591

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
 DHZ  N1   C2    single  1.386  0.020  1.386
 DHZ  N1   C6    single  1.398  0.020  1.398
 DHZ  N1   C1'   single  1.440  0.020  1.440
 DHZ  C2   O2    double  1.222  0.020  1.222
 DHZ  C2   N3    single  1.350  0.020  1.350
 DHZ  N3   C4    single  1.449  0.020  1.449
 DHZ  N3   HN3   single  0.860  0.020  1.020
 DHZ  C4   C5    single  1.488  0.020  1.488
 DHZ  C4   H41   single  0.970  0.020  1.090
 DHZ  C4   H42   single  0.970  0.020  1.090
 DHZ  C5   C6    double  1.326  0.020  1.326
 DHZ  C5   H5    single  0.930  0.020  1.080
 DHZ  C6   H6    single  0.930  0.020  1.080
 DHZ  C1'  C2'   single  1.529  0.020  1.529
 DHZ  C1'  O4'   single  1.406  0.020  1.406
 DHZ  C1'  H1'   single  0.970  0.020  1.090
 DHZ  C2'  O2'   single  1.397  0.020  1.397
 DHZ  C2'  C3'   single  1.530  0.020  1.530
 DHZ  C2'  H2'   single  0.970  0.020  1.090
 DHZ  O2'  HO2   single  0.850  0.020  0.980
 DHZ  C3'  O3'   single  1.406  0.020  1.406
 DHZ  C3'  C4'   single  1.533  0.020  1.533
 DHZ  C3'  H3'   single  0.970  0.020  1.090
 DHZ  O3'  HO3   single  0.850  0.020  0.980
 DHZ  C4'  O4'   single  1.426  0.020  1.426
 DHZ  C4'  C5'   single  1.515  0.020  1.515
 DHZ  C4'  H4'   single  0.970  0.020  1.090
 DHZ  C5'  O5'   single  1.408  0.020  1.408
 DHZ  C5'  H5'1  single  0.970  0.020  1.090
 DHZ  C5'  H5'2  single  0.970  0.020  1.090
 DHZ  O5'  HO5   single  0.850  0.020  0.980

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
 DHZ  C1'   N1   C6    118.33  3.000
 DHZ  C1'   N1   C2    121.53  3.000
 DHZ  C6    N1   C2    119.59  3.000
 DHZ  N3    C2   O2    121.61  3.000
 DHZ  N3    C2   N1    116.20  3.000
 DHZ  O2    C2   N1    122.18  3.000
 DHZ  HN3   N3   C4    116.86  3.000
 DHZ  HN3   N3   C2    114.03  3.000
 DHZ  C4    N3   C2    128.50  3.000
 DHZ  H42   C4   H41   106.29  3.000
 DHZ  H42   C4   C5    110.64  3.000
 DHZ  H41   C4   C5    110.80  3.000
 DHZ  H42   C4   N3    109.06  3.000
 DHZ  H41   C4   N3    110.52  3.000
 DHZ  C5    C4   N3    109.47  3.000
 DHZ  H5    C5   C6    119.92  3.000
 DHZ  H5    C5   C4    119.01  3.000
 DHZ  C6    C5   C4    121.06  3.000
 DHZ  H6    C6   C5    121.37  3.000
 DHZ  H6    C6   N1    114.97  3.000
 DHZ  C5    C6   N1    123.66  3.000
 DHZ  H1'   C1'  O4'   109.89  3.000
 DHZ  H1'   C1'  C2'   107.22  3.000
 DHZ  O4'   C1'  C2'   106.06  3.000
 DHZ  H1'   C1'  N1    104.71  3.000
 DHZ  O4'   C1'  N1    111.56  3.000
 DHZ  C2'   C1'  N1    117.24  3.000
 DHZ  H2'   C2'  C3'   108.12  3.000
 DHZ  H2'   C2'  O2'   111.69  3.000
 DHZ  C3'   C2'  O2'   116.11  3.000
 DHZ  H2'   C2'  C1'   110.35  3.000
 DHZ  C3'   C2'  C1'   100.90  3.000
 DHZ  O2'   C2'  C1'   109.13  3.000
 DHZ  HO2   O2'  C2'   108.56  3.000
 DHZ  H3'   C3'  C4'   111.39  3.000
 DHZ  H3'   C3'  O3'   111.25  3.000
 DHZ  C4'   C3'  O3'   112.53  3.000
 DHZ  H3'   C3'  C2'   111.98  3.000
 DHZ  C4'   C3'  C2'   101.15  3.000
 DHZ  O3'   C3'  C2'   108.11  3.000
 DHZ  HO3   O3'  C3'   108.23  3.000
 DHZ  H4'   C4'  C5'   108.23  3.000
 DHZ  H4'   C4'  O4'   108.27  3.000
 DHZ  C5'   C4'  O4'   111.47  3.000
 DHZ  H4'   C4'  C3'   110.22  3.000
 DHZ  C5'   C4'  C3'   112.45  3.000
 DHZ  O4'   C4'  C3'   106.12  3.000
 DHZ  C4'   O4'  C1'   110.49  3.000
 DHZ  H5'2  C5'  H5'1  107.30  3.000
 DHZ  H5'2  C5'  O5'   111.64  3.000
 DHZ  H5'1  C5'  O5'   111.63  3.000
 DHZ  H5'2  C5'  C4'   107.43  3.000
 DHZ  H5'1  C5'  C4'   110.14  3.000
 DHZ  O5'   C5'  C4'   108.62  3.000
 DHZ  HO5   O5'  C5'   108.00  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
 DHZ  CONST_01  C4   N3  C2  N1    0.00   0.0  0
 DHZ  CONST_02  C6   N1  C2  N3    0.00   0.0  0
 DHZ  CONST_03  C1'  N1  C2  N3  180.00   0.0  0
 DHZ  CONST_04  C6   N1  C2  O2  180.00   0.0  0
 DHZ  CONST_05  C1'  N1  C2  O2    0.00   0.0  0
 DHZ  CONST_06  C4   N3  C2  O2  180.00   0.0  0
 DHZ  CONST_07  HN3  N3  C2  N1  180.00   0.0  0
 DHZ  Var_01    C4   C5  C6  N1    0.20  30.0  1
 DHZ  Var_02    C5   C6  N1  C2    7.45  30.0  1
 DHZ  Var_03    C5   C4  N3  C2   14.02  30.0  1
 DHZ  Var_04    C6   C5  C4  N3   -9.60  30.0  1

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
 DHZ  chir_01  C1'  N1   C2'  O4'  negativ
 DHZ  chir_02  C2'  O2'  C3'  C1'  positiv
 DHZ  chir_03  C3'  O3'  C2'  C4'  negativ
 DHZ  chir_04  C4'  O4'  C3'  C5'  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
 DHZ  plan-1  N1   0.020
 DHZ  plan-1  C2   0.020
 DHZ  plan-1  O2   0.020
 DHZ  plan-1  N3   0.020
 DHZ  plan-1  C4   0.020
 DHZ  plan-1  C6   0.020
 DHZ  plan-1  C1'  0.020
 DHZ  plan-1  HN3  0.020

