# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 23:24:50 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 1-beta-D-ribofuranosyl-1,3,5-triazinane-2,4,6-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C(=O)NC(=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
 RDD  RDD  1-beta-D-ribofuranosyl-1,3,5-triazinane-2,4,6-trione  ligand  29  18  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RDD
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
 RDD  C2    C  CR6   0   0.764  -1.9895  -0.6254   1.0154
 RDD  C6    C  CR6   0   0.770  -1.0572   0.6565  -0.8353
 RDD  C4    C  CR6   0   0.690  -3.4309   0.8683  -0.2846
 RDD  O6    O  O     0  -0.442  -0.1336   0.9828  -1.5385
 RDD  N5    N  NR16  0  -0.722  -2.3153   1.1683  -1.0192
 RDD  O4    O  O     0  -0.444  -4.5147   1.3539  -0.4932
 RDD  N3    N  NR16  0  -0.722  -3.1915  -0.0416   0.7112
 RDD  O2    O  O     0  -0.448  -1.8815  -1.4050   1.9295
 RDD  N1    N  NR6   0  -0.620  -0.9303  -0.2563   0.1965
 RDD  C1'   C  CH1   0   0.196   0.4000  -0.7677   0.5172
 RDD  O4'   O  O2    0  -0.492   1.1932   0.2993   0.9559
 RDD  C4'   C  CH1   0   0.020   2.5009   0.2068   0.4186
 RDD  C5'   C  CH2   0  -0.163   3.0683   1.5868   0.1974
 RDD  O5'   O  OH1   0  -0.671   3.2579   2.2218   1.4386
 RDD  C3'   C  CH1   0  -0.034   2.3651  -0.5829  -0.8827
 RDD  O3'   O  OH1   0  -0.663   3.5384  -1.3202  -1.1175
 RDD  C2'   C  CH1   0  -0.039   1.1428  -1.4876  -0.6236
 RDD  O2'   O  OH1   0  -0.675   1.5500  -2.7437  -0.1481
 RDD  HN5   H  HNR6  0   0.447  -2.4245   1.8321  -1.7753
 RDD  HN3   H  HNR6  0   0.448  -3.9756  -0.3011   1.2969
 RDD  H1'   H  HCH1  0   0.277   0.2437  -1.4880   1.3198
 RDD  H4'   H  HCH1  0   0.234   3.1508  -0.3520   1.1081
 RDD  H5'   H  HCH2  0   0.205   4.0136   1.4706  -0.3493
 RDD  H5'A  H  HCH2  0   0.202   2.3841   2.1486  -0.4521
 RDD  HO5'  H  HOH1  0   0.457   3.6288   3.0932   1.2733
 RDD  H3'   H  HCH1  0   0.258   2.1556   0.0923  -1.7141
 RDD  HO3'  H  HOH1  0   0.470   3.6665  -1.4112  -2.0668
 RDD  H2'   H  HCH1  0   0.249   0.5186  -1.5974  -1.5165
 RDD  HO2'  H  HOH1  0   0.448   2.4550  -2.8809  -0.4624

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
 RDD  C2   N3    single  1.370  0.020  1.370
 RDD  C2   O2    double  1.206  0.020  1.206
 RDD  C2   N1    single  1.389  0.020  1.389
 RDD  C6   O6    double  1.206  0.020  1.206
 RDD  C6   N5    single  1.371  0.020  1.371
 RDD  C6   N1    single  1.383  0.020  1.383
 RDD  C4   N5    single  1.369  0.020  1.369
 RDD  C4   O4    double  1.206  0.020  1.206
 RDD  C4   N3    single  1.370  0.020  1.370
 RDD  N1   C1'   single  1.461  0.020  1.461
 RDD  C1'  O4'   single  1.400  0.020  1.400
 RDD  C1'  C2'   single  1.540  0.020  1.540
 RDD  O4'  C4'   single  1.417  0.020  1.417
 RDD  C4'  C5'   single  1.508  0.020  1.508
 RDD  C4'  C3'   single  1.528  0.020  1.528
 RDD  C5'  O5'   single  1.407  0.020  1.407
 RDD  C3'  O3'   single  1.405  0.020  1.405
 RDD  C3'  C2'   single  1.543  0.020  1.543
 RDD  C2'  O2'   single  1.404  0.020  1.404
 RDD  N5   HN5   single  0.860  0.020  1.020
 RDD  N3   HN3   single  0.860  0.020  1.020
 RDD  C1'  H1'   single  0.970  0.020  1.090
 RDD  C4'  H4'   single  0.970  0.020  1.090
 RDD  C5'  H5'   single  0.970  0.020  1.090
 RDD  C5'  H5'A  single  0.970  0.020  1.090
 RDD  O5'  HO5'  single  0.850  0.020  0.980
 RDD  C3'  H3'   single  0.970  0.020  1.090
 RDD  O3'  HO3'  single  0.850  0.020  0.980
 RDD  C2'  H2'   single  0.970  0.020  1.090
 RDD  O2'  HO2'  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
 RDD  N1    C2   O2   123.39  3.000
 RDD  N1    C2   N3   115.14  3.000
 RDD  O2    C2   N3   121.47  3.000
 RDD  N1    C6   N5   115.51  3.000
 RDD  N1    C6   O6   122.90  3.000
 RDD  N5    C6   O6   121.59  3.000
 RDD  N3    C4   O4   123.39  3.000
 RDD  N3    C4   N5   113.15  3.000
 RDD  O4    C4   N5   123.46  3.000
 RDD  HN5   N5   C4   117.18  3.000
 RDD  HN5   N5   C6   116.37  3.000
 RDD  C4    N5   C6   126.45  3.000
 RDD  HN3   N3   C4   117.09  3.000
 RDD  HN3   N3   C2   116.21  3.000
 RDD  C4    N3   C2   126.70  3.000
 RDD  C1'   N1   C6   118.57  3.000
 RDD  C1'   N1   C2   118.16  3.000
 RDD  C6    N1   C2   123.04  3.000
 RDD  H1'   C1'  C2'  107.81  3.000
 RDD  H1'   C1'  O4'  110.74  3.000
 RDD  C2'   C1'  O4'  108.37  3.000
 RDD  H1'   C1'  N1   105.22  3.000
 RDD  C2'   C1'  N1   116.12  3.000
 RDD  O4'   C1'  N1   108.54  3.000
 RDD  C4'   O4'  C1'  110.75  3.000
 RDD  H4'   C4'  C3'  108.89  3.000
 RDD  H4'   C4'  C5'  109.54  3.000
 RDD  C3'   C4'  C5'  112.42  3.000
 RDD  H4'   C4'  O4'  109.92  3.000
 RDD  C3'   C4'  O4'  105.94  3.000
 RDD  C5'   C4'  O4'  110.07  3.000
 RDD  H5'A  C5'  H5'  107.21  3.000
 RDD  H5'A  C5'  O5'  112.01  3.000
 RDD  H5'   C5'  O5'  111.77  3.000
 RDD  H5'A  C5'  C4'  108.69  3.000
 RDD  H5'   C5'  C4'  107.46  3.000
 RDD  O5'   C5'  C4'  109.53  3.000
 RDD  HO5'  O5'  C5'  108.02  3.000
 RDD  H3'   C3'  C2'  109.80  3.000
 RDD  H3'   C3'  O3'  110.95  3.000
 RDD  C2'   C3'  O3'  112.45  3.000
 RDD  H3'   C3'  C4'  110.24  3.000
 RDD  C2'   C3'  C4'  103.32  3.000
 RDD  O3'   C3'  C4'  109.82  3.000
 RDD  HO3'  O3'  C3'  109.00  3.000
 RDD  H2'   C2'  O2'  110.60  3.000
 RDD  H2'   C2'  C3'  111.94  3.000
 RDD  O2'   C2'  C3'  110.60  3.000
 RDD  H2'   C2'  C1'  112.09  3.000
 RDD  O2'   C2'  C1'  107.90  3.000
 RDD  C3'   C2'  C1'  103.44  3.000
 RDD  HO2'  O2'  C2'  106.74  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
 RDD  CONST_01  N5   C4  N3  C2    0.00  0.0  0
 RDD  CONST_02  N5   C6  N1  C2    0.00  0.0  0
 RDD  CONST_03  N3   C4  N5  C6    0.00  0.0  0
 RDD  CONST_04  N3   C2  N1  C6    0.00  0.0  0
 RDD  CONST_05  N1   C6  N5  C4    0.00  0.0  0
 RDD  CONST_06  N1   C2  N3  C4    0.00  0.0  0
 RDD  CONST_07  C1'  N1  C6  N5  180.00  0.0  0
 RDD  CONST_08  C1'  N1  C2  N3  180.00  0.0  0
 RDD  CONST_09  O4   C4  N3  C2  180.00  0.0  0
 RDD  CONST_10  O6   C6  N1  C2  180.00  0.0  0
 RDD  CONST_11  O4   C4  N5  C6  180.00  0.0  0
 RDD  CONST_12  O2   C2  N1  C6  180.00  0.0  0
 RDD  CONST_13  O6   C6  N5  C4  180.00  0.0  0
 RDD  CONST_14  O2   C2  N3  C4  180.00  0.0  0
 RDD  CONST_15  C1'  N1  C6  O6    0.00  0.0  0
 RDD  CONST_16  C1'  N1  C2  O2    0.00  0.0  0
 RDD  CONST_17  HN3  N3  C4  N5  180.00  0.0  0
 RDD  CONST_18  HN5  N5  C4  N3  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
 RDD  chir_01  C1'  N1   O4'  C2'  positiv
 RDD  chir_02  C4'  O4'  C5'  C3'  positiv
 RDD  chir_03  C3'  O3'  C4'  C2'  positiv
 RDD  chir_04  C2'  O2'  C3'  C1'  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
 RDD  plan-1  C2   0.020
 RDD  plan-1  C6   0.020
 RDD  plan-1  C4   0.020
 RDD  plan-1  O6   0.020
 RDD  plan-1  N5   0.020
 RDD  plan-1  O4   0.020
 RDD  plan-1  N3   0.020
 RDD  plan-1  O2   0.020
 RDD  plan-1  N1   0.020
 RDD  plan-1  C1'  0.020
 RDD  plan-1  HN5  0.020
 RDD  plan-1  HN3  0.020

