# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:06:04 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (1S)-1,4-anhydro-1-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)c2c[nH]c3C(=O)NC=Nc23
#
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
 9DI  9DI  (1S)-1,4-anhydro-1-(4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-D-ribitol  ligand  32  19  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9DI
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
 9DI  C9    C  CR5   0  -0.063   0.3107   0.4310  -0.2347
 9DI  C4    C  CR56  0   0.150  -0.1806   0.2844  -1.5555
 9DI  N3    N  N     0  -0.445  -1.4147   0.5888  -2.0577
 9DI  C2    C  CR16  0   0.123  -1.5584   0.3419  -3.3119
 9DI  N1    N  NR16  0  -0.661  -0.5943  -0.1802  -4.1177
 9DI  C6    C  CR6   0   0.521   0.6898  -0.5238  -3.7160
 9DI  O6    O  O     0  -0.481   1.5151  -0.9858  -4.4901
 9DI  C5    C  CR56  0   0.157   0.8468  -0.2504  -2.3257
 9DI  N7    N  NR15  0  -0.652   1.9270  -0.4232  -1.5214
 9DI  C8    C  CR15  0  -0.051   1.6137  -0.0136  -0.2676
 9DI  C5'   C  CH2   0  -0.154   1.3915  -0.3329   3.6517
 9DI  O5'   O  OH1   0  -0.670   2.1420   0.6916   4.2576
 9DI  C4'   C  CH1   0   0.009   0.1242   0.2514   3.0789
 9DI  O4'   O  O2    0  -0.502   0.4267   1.1712   2.0399
 9DI  C1'   C  CH1   0  -0.065  -0.4440   0.9841   0.9321
 9DI  C2'   C  CH1   0  -0.018  -1.5480   0.0462   1.4157
 9DI  O2'   O  OH1   0  -0.671  -2.5468   0.8196   2.0333
 9DI  C3'   C  CH1   0  -0.023  -0.7860  -0.7982   2.4328
 9DI  O3'   O  OH1   0  -0.667  -1.6674  -1.4296   3.3197
 9DI  H2    H  HCR6  0   0.292  -2.5002   0.5489  -3.8038
 9DI  HN1   H  HNR6  0   0.431  -0.8262  -0.3303  -5.0910
 9DI  HN7   H  HNR5  0   0.420   2.8202  -0.7916  -1.8055
 9DI  H8    H  HCR5  0   0.293   2.3474  -0.0594   0.5200
 9DI  H5'1  H  HCH2  0   0.195   1.9520  -0.8333   2.8505
 9DI  H5'2  H  HCH2  0   0.198   1.1101  -1.1102   4.3756
 9DI  HO5'  H  HOH1  0   0.457   2.9414   0.3030   4.6241
 9DI  H1'   H  HCH1  0   0.256  -0.8817   1.9495   0.6509
 9DI  H2'   H  HCH1  0   0.248  -1.9564  -0.5575   0.5969
 9DI  HO2'  H  HOH1  0   0.452  -3.1220   0.2308   2.5337
 9DI  H3'   H  HCH1  0   0.232  -0.1739  -1.5318   1.8898
 9DI  HO3'  H  HOH1  0   0.463  -1.2212  -2.1708   3.7380
 9DI  H4'   H  HCH1  0   0.222  -0.4307   0.7608   3.8794

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
 9DI  C9   C4    aromatic  1.417  0.020  1.417
 9DI  C9   C8    aromatic  1.377  0.020  1.377
 9DI  C9   C1'   single    1.496  0.020  1.496
 9DI  C4   N3    single    1.367  0.020  1.367
 9DI  C4   C5    aromatic  1.391  0.020  1.391
 9DI  N3   C2    double    1.286  0.020  1.286
 9DI  C2   N1    single    1.361  0.020  1.361
 9DI  C2   H2    single    0.930  0.020  1.080
 9DI  N1   C6    single    1.389  0.020  1.389
 9DI  N1   HN1   single    0.860  0.020  1.020
 9DI  C6   O6    double    1.222  0.020  1.222
 9DI  C6   C5    single    1.426  0.020  1.426
 9DI  C5   N7    aromatic  1.358  0.020  1.358
 9DI  N7   C8    aromatic  1.356  0.020  1.356
 9DI  N7   HN7   single    0.860  0.020  1.020
 9DI  C8   H8    single    0.930  0.020  1.080
 9DI  C5'  O5'   single    1.407  0.020  1.407
 9DI  C5'  C4'   single    1.509  0.020  1.509
 9DI  C5'  H5'1  single    0.970  0.020  1.090
 9DI  C5'  H5'2  single    0.970  0.020  1.090
 9DI  O5'  HO5'  single    0.850  0.020  0.980
 9DI  C4'  O4'   single    1.420  0.020  1.420
 9DI  C4'  C3'   single    1.532  0.020  1.532
 9DI  C4'  H4'   single    0.970  0.020  1.090
 9DI  O4'  C1'   single    1.421  0.020  1.421
 9DI  C1'  C2'   single    1.527  0.020  1.527
 9DI  C1'  H1'   single    0.970  0.020  1.090
 9DI  C2'  O2'   single    1.406  0.020  1.406
 9DI  C2'  C3'   single    1.526  0.020  1.526
 9DI  C2'  H2'   single    0.970  0.020  1.090
 9DI  O2'  HO2'  single    0.850  0.020  0.980
 9DI  C3'  O3'   single    1.401  0.020  1.401
 9DI  C3'  H3'   single    0.970  0.020  1.090
 9DI  O3'  HO3'  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
 9DI  C1'   C9   C8    127.99  3.000
 9DI  C1'   C9   C4    126.19  3.000
 9DI  C8    C9   C4    105.81  3.000
 9DI  C5    C4   N3    123.31  3.000
 9DI  C5    C4   C9    107.45  3.000
 9DI  N3    C4   C9    129.25  3.000
 9DI  C2    N3   C4    114.61  3.000
 9DI  H2    C2   N1    114.88  3.000
 9DI  H2    C2   N3    120.24  3.000
 9DI  N1    C2   N3    124.88  3.000
 9DI  HN1   N1   C6    116.97  3.000
 9DI  HN1   N1   C2    117.66  3.000
 9DI  C6    N1   C2    125.37  3.000
 9DI  C5    C6   O6    128.01  3.000
 9DI  C5    C6   N1    109.66  3.000
 9DI  O6    C6   N1    122.32  3.000
 9DI  N7    C5   C6    129.86  3.000
 9DI  N7    C5   C4    107.97  3.000
 9DI  C6    C5   C4    122.17  3.000
 9DI  HN7   N7   C8    125.20  3.000
 9DI  HN7   N7   C5    125.80  3.000
 9DI  C8    N7   C5    109.00  3.000
 9DI  H8    C8   N7    120.39  3.000
 9DI  H8    C8   C9    129.83  3.000
 9DI  N7    C8   C9    109.77  3.000
 9DI  H5'2  C5'  H5'1  106.80  3.000
 9DI  H5'2  C5'  C4'   108.00  3.000
 9DI  H5'1  C5'  C4'   109.15  3.000
 9DI  H5'2  C5'  O5'   111.59  3.000
 9DI  H5'1  C5'  O5'   111.94  3.000
 9DI  C4'   C5'  O5'   109.24  3.000
 9DI  HO5'  O5'  C5'   108.26  3.000
 9DI  H4'   C4'  C3'   108.95  3.000
 9DI  H4'   C4'  O4'   109.88  3.000
 9DI  C3'   C4'  O4'   105.17  3.000
 9DI  H4'   C4'  C5'   109.09  3.000
 9DI  C3'   C4'  C5'   113.20  3.000
 9DI  O4'   C4'  C5'   110.47  3.000
 9DI  C1'   O4'  C4'   110.76  3.000
 9DI  H1'   C1'  C2'   109.47  3.000
 9DI  H1'   C1'  O4'   109.18  3.000
 9DI  C2'   C1'  O4'   106.08  3.000
 9DI  H1'   C1'  C9    109.08  3.000
 9DI  C2'   C1'  C9    112.62  3.000
 9DI  O4'   C1'  C9    110.34  3.000
 9DI  H2'   C2'  C3'   112.28  3.000
 9DI  H2'   C2'  O2'   111.49  3.000
 9DI  C3'   C2'  O2'   111.49  3.000
 9DI  H2'   C2'  C1'   111.78  3.000
 9DI  C3'   C2'  C1'   100.95  3.000
 9DI  O2'   C2'  C1'   108.34  3.000
 9DI  HO2'  O2'  C2'   108.42  3.000
 9DI  H3'   C3'  O3'   111.25  3.000
 9DI  H3'   C3'  C2'   108.56  3.000
 9DI  O3'   C3'  C2'   110.93  3.000
 9DI  H3'   C3'  C4'   109.56  3.000
 9DI  O3'   C3'  C4'   114.56  3.000
 9DI  C2'   C3'  C4'   101.46  3.000
 9DI  HO3'  O3'  C3'   109.33  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
 9DI  CONST_01  N7   C5  C4  C9    0.00  0.0  0
 9DI  CONST_02  C5   N7  C8  C9    0.00  0.0  0
 9DI  CONST_03  N7   C8  C9  C4    0.00  0.0  0
 9DI  CONST_04  C8   N7  C5  C4    0.00  0.0  0
 9DI  CONST_05  C8   C9  C4  C5    0.00  0.0  0
 9DI  CONST_06  C1'  C9  C4  N3    0.00  0.0  0
 9DI  CONST_07  C1'  C9  C4  C5  180.00  0.0  0
 9DI  CONST_08  C1'  C9  C8  N7  180.00  0.0  0
 9DI  CONST_09  N1   C2  N3  C4    0.00  0.0  0
 9DI  CONST_10  C6   N1  C2  N3    0.00  0.0  0
 9DI  CONST_11  C5   C6  N1  C2    0.00  0.0  0
 9DI  CONST_12  O6   C6  N1  C2  180.00  0.0  0
 9DI  CONST_13  HN7  N7  C8  C9  180.00  0.0  0
 9DI  CONST_14  H8   C8  C9  C4  180.00  0.0  0
 9DI  CONST_15  H2   C2  N3  C4  180.00  0.0  0
 9DI  CONST_16  HN1  N1  C2  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
 9DI  chir_01  C4'  C5'  O4'  C3'  negativ
 9DI  chir_02  C1'  O4'  C9   C2'  negativ
 9DI  chir_03  C2'  O2'  C1'  C3'  negativ
 9DI  chir_04  C3'  O3'  C4'  C2'  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
 9DI  plan-1  C9   0.020
 9DI  plan-1  C4   0.020
 9DI  plan-1  N3   0.020
 9DI  plan-1  C2   0.020
 9DI  plan-1  N1   0.020
 9DI  plan-1  C6   0.020
 9DI  plan-1  O6   0.020
 9DI  plan-1  C5   0.020
 9DI  plan-1  N7   0.020
 9DI  plan-1  C8   0.020
 9DI  plan-1  C1'  0.020
 9DI  plan-1  H2   0.020
 9DI  plan-1  HN1  0.020
 9DI  plan-1  HN7  0.020
 9DI  plan-1  H8   0.020

