# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  8 18:36:23 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-(beta-D-ribofuranosyl)pyrimidin-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=CC=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
 ZE8  ZE8  1-(beta-D-ribofuranosyl)pyrimidin-2(1H)-one  ligand  28  16  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZE8
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
 ZE8  N1   N  NR6   0  -0.535   1.3711   0.1402   0.3788
 ZE8  C2   C  CR6   0   0.623   1.5251  -0.5628  -0.8237
 ZE8  O2   O  O     0  -0.486   0.5736  -0.7165  -1.5680
 ZE8  N3   N  N     0  -0.469   2.7660  -1.0512  -1.1158
 ZE8  C4   C  CR16  0  -0.000   3.7598  -0.8379  -0.3029
 ZE8  C5   C  CR16  0  -0.426   3.6529  -0.1230   0.9031
 ZE8  C6   C  CR16  0   0.114   2.4159   0.3441   1.2083
 ZE8  C1'  C  CH1   0   0.205   0.0534   0.6365   0.7760
 ZE8  C2'  C  CH1   0  -0.044  -0.6242   1.6075  -0.2074
 ZE8  O2'  O  OH1   0  -0.675  -1.0347   2.7358   0.5211
 ZE8  C3'  C  CH1   0  -0.035  -1.8454   0.8120  -0.7085
 ZE8  O3'  O  OH1   0  -0.663  -2.9883   1.6152  -0.8643
 ZE8  C4'  C  CH1   0   0.021  -2.0767  -0.2009   0.4110
 ZE8  O4'  O  O2    0  -0.488  -0.8007  -0.4468   0.9807
 ZE8  C5'  C  CH2   0  -0.163  -2.6808  -1.4909  -0.0845
 ZE8  O5'  O  OH1   0  -0.671  -2.9592  -2.3264   1.0131
 ZE8  H1   H  HCR6  0   0.286   4.7206  -1.2509  -0.5942
 ZE8  H2   H  HCR6  0   0.291   4.4955   0.0376   1.5559
 ZE8  H3   H  HCR6  0   0.329   2.2100   0.8936   2.1164
 ZE8  H4   H  HCH1  0   0.259   0.2274   1.1742   1.7131
 ZE8  H5   H  HCH1  0   0.250   0.0443   1.8967  -1.0261
 ZE8  H6   H  HOH1  0   0.448  -1.9251   2.9575   0.2144
 ZE8  H7   H  HCH1  0   0.260  -1.5905   0.3008  -1.6370
 ZE8  H8   H  HOH1  0   0.470  -3.0121   1.9501  -1.7663
 ZE8  H9   H  HCH1  0   0.234  -2.7399   0.2478   1.1655
 ZE8  H10  H  HCH2  0   0.205  -3.5908  -1.2333  -0.6421
 ZE8  H11  H  HCH2  0   0.203  -1.9845  -1.9579  -0.7932
 ZE8  H12  H  HOH1  0   0.457  -3.3668  -3.1314   0.6811

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
 ZE8  O2   C2   double  1.218  0.020  1.218
 ZE8  N3   C2   single  1.365  0.020  1.365
 ZE8  N3   C4   double  1.302  0.020  1.302
 ZE8  C2   N1   single  1.401  0.020  1.401
 ZE8  O2'  C2'  single  1.404  0.020  1.404
 ZE8  C4   C5   single  1.406  0.020  1.406
 ZE8  N1   C1'  single  1.463  0.020  1.463
 ZE8  N1   C6   single  1.350  0.020  1.350
 ZE8  C2'  C1'  single  1.539  0.020  1.539
 ZE8  C2'  C3'  single  1.541  0.020  1.541
 ZE8  C1'  O4'  single  1.395  0.020  1.395
 ZE8  O4'  C4'  single  1.419  0.020  1.419
 ZE8  C6   C5   double  1.357  0.020  1.357
 ZE8  C3'  O3'  single  1.406  0.020  1.406
 ZE8  C3'  C4'  single  1.527  0.020  1.527
 ZE8  C4'  C5'  single  1.508  0.020  1.508
 ZE8  C5'  O5'  single  1.407  0.020  1.407
 ZE8  C4   H1   single  0.930  0.020  1.080
 ZE8  C5   H2   single  0.930  0.020  1.080
 ZE8  C6   H3   single  0.930  0.020  1.080
 ZE8  C1'  H4   single  0.970  0.020  1.090
 ZE8  C2'  H5   single  0.970  0.020  1.090
 ZE8  O2'  H6   single  0.850  0.020  0.980
 ZE8  C3'  H7   single  0.970  0.020  1.090
 ZE8  O3'  H8   single  0.850  0.020  0.980
 ZE8  C4'  H9   single  0.970  0.020  1.090
 ZE8  C5'  H10  single  0.970  0.020  1.090
 ZE8  C5'  H11  single  0.970  0.020  1.090
 ZE8  O5'  H12  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
 ZE8  C1'  N1   C6   118.63  3.000
 ZE8  C6   N1   C2   121.21  3.000
 ZE8  C1'  N1   C2   120.14  3.000
 ZE8  N3   C2   O2   122.30  3.000
 ZE8  N3   C2   N1   117.57  3.000
 ZE8  O2   C2   N1   120.13  3.000
 ZE8  C4   N3   C2   120.12  3.000
 ZE8  H1   C4   C5   119.40  3.000
 ZE8  H1   C4   N3   116.48  3.000
 ZE8  C5   C4   N3   124.12  3.000
 ZE8  H2   C5   C6   121.67  3.000
 ZE8  H2   C5   C4   122.40  3.000
 ZE8  C6   C5   C4   115.93  3.000
 ZE8  H3   C6   C5   122.51  3.000
 ZE8  H3   C6   N1   116.46  3.000
 ZE8  C5   C6   N1   121.03  3.000
 ZE8  H4   C1'  O4'  110.69  3.000
 ZE8  H4   C1'  C2'  107.88  3.000
 ZE8  O4'  C1'  C2'  108.31  3.000
 ZE8  H4   C1'  N1   104.83  3.000
 ZE8  O4'  C1'  N1   109.15  3.000
 ZE8  C2'  C1'  N1   115.91  3.000
 ZE8  H5   C2'  C3'  112.13  3.000
 ZE8  H5   C2'  O2'  110.73  3.000
 ZE8  C3'  C2'  O2'  110.59  3.000
 ZE8  H5   C2'  C1'  112.04  3.000
 ZE8  C3'  C2'  C1'  103.35  3.000
 ZE8  O2'  C2'  C1'  107.70  3.000
 ZE8  H6   O2'  C2'  106.78  3.000
 ZE8  H7   C3'  C4'  110.41  3.000
 ZE8  H7   C3'  O3'  111.33  3.000
 ZE8  C4'  C3'  O3'  109.70  3.000
 ZE8  H7   C3'  C2'  109.49  3.000
 ZE8  C4'  C3'  C2'  102.94  3.000
 ZE8  O3'  C3'  C2'  112.67  3.000
 ZE8  H8   O3'  C3'  108.84  3.000
 ZE8  H9   C4'  C5'  109.43  3.000
 ZE8  H9   C4'  O4'  109.72  3.000
 ZE8  C5'  C4'  O4'  110.11  3.000
 ZE8  H9   C4'  C3'  108.87  3.000
 ZE8  C5'  C4'  C3'  112.77  3.000
 ZE8  O4'  C4'  C3'  105.85  3.000
 ZE8  C4'  O4'  C1'  110.93  3.000
 ZE8  H11  C5'  H10  107.32  3.000
 ZE8  H11  C5'  O5'  112.12  3.000
 ZE8  H10  C5'  O5'  111.81  3.000
 ZE8  H11  C5'  C4'  108.78  3.000
 ZE8  H10  C5'  C4'  107.35  3.000
 ZE8  O5'  C5'  C4'  109.32  3.000
 ZE8  H12  O5'  C5'  108.16  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
 ZE8  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 ZE8  CONST_02  C1'  N1  C2  N3  180.00  0.0  0
 ZE8  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 ZE8  CONST_04  C4   N3  C2  O2  180.00  0.0  0
 ZE8  CONST_05  C1'  N1  C2  O2    0.00  0.0  0
 ZE8  CONST_06  C6   N1  C2  O2  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
 ZE8  chir_01  C1'  N1   C2'  O4'  negativ
 ZE8  chir_02  C2'  O2'  C3'  C1'  positiv
 ZE8  chir_03  C3'  O3'  C4'  C2'  positiv
 ZE8  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
 ZE8  plan-1  N1   0.020
 ZE8  plan-1  C2   0.020
 ZE8  plan-1  O2   0.020
 ZE8  plan-1  N3   0.020
 ZE8  plan-1  C4   0.020
 ZE8  plan-1  C5   0.020
 ZE8  plan-1  C6   0.020
 ZE8  plan-1  C1'  0.020
 ZE8  plan-1  H1   0.020
 ZE8  plan-1  H2   0.020
 ZE8  plan-1  H3   0.020

