# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 21:34:00 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1O[C@H]([C@H](O)[C@H]1O)n2cc(CN3C=CC(=O)NC3=O)nn2
#
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
 0EY  0EY  1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidine  ligand  38  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0EY
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
 0EY  C4   C  CR6   0   0.567   4.6031  -1.5804  -0.2362
 0EY  C5   C  CR16  0  -0.507   4.3321  -0.8986  -1.4776
 0EY  C6   C  CR16  0   0.100   3.6203   0.2411  -1.4642
 0EY  C8   C  CR5   0   0.158   0.8590   1.6881  -0.3522
 0EY  C9   C  CR15  0  -0.037  -0.0015   1.6123   0.7097
 0EY  N1   N  NR6   0  -0.511   3.1386   0.8074  -0.3224
 0EY  N3   N  NR16  0  -0.730   4.0623  -0.9443   0.8725
 0EY  C2   C  CR6   0   0.741   3.3256   0.2097   0.9044
 0EY  O4   O  O     0  -0.466   5.2345  -2.6132  -0.1079
 0EY  N5   N  N     0  -0.292   0.1660   1.3725  -1.4702
 0EY  N6   N  N     0  -0.088  -1.0516   1.1135  -1.1557
 0EY  N7   N  NR5   0  -0.292  -1.1737   1.2598   0.1555
 0EY  C1'  C  CH1   0   0.134  -2.4107   0.9331   0.8517
 0EY  O4'  O  O2    0  -0.475  -2.4841  -0.4280   1.1203
 0EY  C4'  C  CH1   0   0.012  -3.0592  -1.0812  -0.0052
 0EY  C5'  C  CH2   0  -0.173  -3.7004  -2.3749   0.4283
 0EY  O5'  O  OH1   0  -0.669  -2.7027  -3.2585   0.8754
 0EY  C3'  C  CH1   0  -0.037  -4.0629  -0.0800  -0.5923
 0EY  O3'  O  OH1   0  -0.660  -4.0037  -0.1446  -1.9881
 0EY  C2'  C  CH1   0   0.014  -3.6568   1.2794   0.0295
 0EY  O2'  O  OH1   0  -0.668  -4.6006   1.7602   0.9536
 0EY  H1   H  HCR6  0   0.293   4.6999  -1.3067  -2.4058
 0EY  H2   H  HCR6  0   0.321   3.3990   0.7771  -2.3763
 0EY  H3   H  HCH2  0   0.303   2.5607   2.5271  -1.3089
 0EY  H4   H  HCH2  0   0.303   2.5825   2.6706   0.4379
 0EY  H5   H  HCR5  0   0.320   0.1283   1.7796   1.7649
 0EY  H6   H  HNR6  0   0.426   4.2107  -1.3880   1.7709
 0EY  H7   H  HCH1  0   0.294  -2.3769   1.4802   1.7937
 0EY  H8   H  HCH1  0   0.244  -2.2871  -1.2861  -0.7588
 0EY  H9   H  HCH2  0   0.204  -4.4449  -2.1620   1.2075
 0EY  H10  H  HCH2  0   0.210  -4.2464  -2.7756  -0.4359
 0EY  H11  H  HOH1  0   0.459  -3.1285  -4.0658   1.1774
 0EY  H12  H  HCH1  0   0.241  -5.0723  -0.3193  -0.2283
 0EY  H13  H  HOH1  0   0.458  -4.7674   0.3142  -2.3510
 0EY  H14  H  HCH1  0   0.255  -3.4452   2.0145  -0.7542
 0EY  H15  H  HOH1  0   0.460  -5.4155   1.9594   0.4817
 0EY  C7   C  CH2   0  -0.436   2.3109   2.0115  -0.3833
 0EY  O2   O  O     0  -0.476   2.8736   0.6713   1.9318

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
 0EY  O2   C2   double    1.214  0.020  1.214
 0EY  N3   C2   single    1.370  0.020  1.370
 0EY  N3   C4   single    1.388  0.020  1.388
 0EY  C2   N1   single    1.377  0.020  1.377
 0EY  N5   N6   aromatic  1.284  0.020  1.284
 0EY  N5   C8   aromatic  1.353  0.020  1.353
 0EY  N6   N7   aromatic  1.325  0.020  1.325
 0EY  O4   C4   double    1.217  0.020  1.217
 0EY  C4   C5   single    1.442  0.020  1.442
 0EY  N1   C7   single    1.462  0.020  1.462
 0EY  N1   C6   single    1.362  0.020  1.362
 0EY  C7   C8   single    1.488  0.020  1.488
 0EY  C8   C9   aromatic  1.369  0.020  1.369
 0EY  O5'  C5'  single    1.406  0.020  1.406
 0EY  O3'  C3'  single    1.399  0.020  1.399
 0EY  C4'  C5'  single    1.508  0.020  1.508
 0EY  C4'  O4'  single    1.423  0.020  1.423
 0EY  C4'  C3'  single    1.534  0.020  1.534
 0EY  N7   C9   aromatic  1.344  0.020  1.344
 0EY  N7   C1'  single    1.457  0.020  1.457
 0EY  C5   C6   double    1.344  0.020  1.344
 0EY  O4'  C1'  single    1.389  0.020  1.389
 0EY  C3'  C2'  single    1.549  0.020  1.549
 0EY  C1'  C2'  single    1.533  0.020  1.533
 0EY  C2'  O2'  single    1.406  0.020  1.406
 0EY  C5   H1   single    0.930  0.020  1.080
 0EY  C6   H2   single    0.930  0.020  1.080
 0EY  C7   H3   single    0.970  0.020  1.090
 0EY  C7   H4   single    0.970  0.020  1.090
 0EY  C9   H5   single    0.930  0.020  1.080
 0EY  N3   H6   single    0.860  0.020  1.020
 0EY  C1'  H7   single    0.970  0.020  1.090
 0EY  C4'  H8   single    0.970  0.020  1.090
 0EY  C5'  H9   single    0.970  0.020  1.090
 0EY  C5'  H10  single    0.970  0.020  1.090
 0EY  O5'  H11  single    0.850  0.020  0.980
 0EY  C3'  H12  single    0.970  0.020  1.090
 0EY  O3'  H13  single    0.850  0.020  0.980
 0EY  C2'  H14  single    0.970  0.020  1.090
 0EY  O2'  H15  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
 0EY  O4   C4   N3   120.45  3.000
 0EY  O4   C4   C5   126.11  3.000
 0EY  N3   C4   C5   113.44  3.000
 0EY  H1   C5   C6   120.67  3.000
 0EY  H1   C5   C4   119.86  3.000
 0EY  C6   C5   C4   119.47  3.000
 0EY  H2   C6   N1   115.38  3.000
 0EY  H2   C6   C5   121.38  3.000
 0EY  N1   C6   C5   123.24  3.000
 0EY  N5   C8   C9   107.83  3.000
 0EY  C9   C8   C7   129.92  3.000
 0EY  N5   C8   C7   122.23  3.000
 0EY  H5   C9   N7   123.40  3.000
 0EY  H5   C9   C8   132.54  3.000
 0EY  N7   C9   C8   104.06  3.000
 0EY  C2   N1   C7   118.11  3.000
 0EY  C7   N1   C6   120.49  3.000
 0EY  C2   N1   C6   121.20  3.000
 0EY  H6   N3   C2   115.30  3.000
 0EY  H6   N3   C4   116.79  3.000
 0EY  C2   N3   C4   127.91  3.000
 0EY  O2   C2   N3   122.72  3.000
 0EY  N3   C2   N1   114.70  3.000
 0EY  O2   C2   N1   122.58  3.000
 0EY  N6   N5   C8   109.30  3.000
 0EY  N7   N6   N5   107.91  3.000
 0EY  C1'  N7   N6   121.77  3.000
 0EY  C1'  N7   C9   127.05  3.000
 0EY  N6   N7   C9   110.91  3.000
 0EY  H7   C1'  C2'  112.05  3.000
 0EY  H7   C1'  O4'  109.05  3.000
 0EY  C2'  C1'  O4'  106.39  3.000
 0EY  H7   C1'  N7   105.91  3.000
 0EY  C2'  C1'  N7   112.55  3.000
 0EY  O4'  C1'  N7   110.92  3.000
 0EY  C4'  O4'  C1'  108.56  3.000
 0EY  H8   C4'  C3'  108.60  3.000
 0EY  H8   C4'  C5'  109.65  3.000
 0EY  C3'  C4'  C5'  113.06  3.000
 0EY  H8   C4'  O4'  110.14  3.000
 0EY  C3'  C4'  O4'  105.52  3.000
 0EY  C5'  C4'  O4'  109.79  3.000
 0EY  H10  C5'  H9   106.99  3.000
 0EY  H10  C5'  O5'  111.95  3.000
 0EY  H9   C5'  O5'  112.16  3.000
 0EY  H10  C5'  C4'  107.36  3.000
 0EY  H9   C5'  C4'  109.02  3.000
 0EY  O5'  C5'  C4'  109.20  3.000
 0EY  H11  O5'  C5'  108.26  3.000
 0EY  H12  C3'  C2'  107.38  3.000
 0EY  H12  C3'  O3'  111.06  3.000
 0EY  C2'  C3'  O3'  115.47  3.000
 0EY  H12  C3'  C4'  109.38  3.000
 0EY  C2'  C3'  C4'  104.33  3.000
 0EY  O3'  C3'  C4'  108.91  3.000
 0EY  H13  O3'  C3'  108.71  3.000
 0EY  H14  C2'  O2'  111.75  3.000
 0EY  H14  C2'  C3'  110.64  3.000
 0EY  O2'  C2'  C3'  112.83  3.000
 0EY  H14  C2'  C1'  112.24  3.000
 0EY  O2'  C2'  C1'  105.70  3.000
 0EY  C3'  C2'  C1'  103.31  3.000
 0EY  H15  O2'  C2'  108.47  3.000
 0EY  H4   C7   H3   107.32  3.000
 0EY  H4   C7   N1   109.04  3.000
 0EY  H3   C7   N1   107.19  3.000
 0EY  H4   C7   C8   111.08  3.000
 0EY  H3   C7   C8   110.16  3.000
 0EY  N1   C7   C8   111.88  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
 0EY  CONST_01  N7   N6  N5  C8    0.00   0.0  0
 0EY  CONST_02  N6   N7  C9  C8    0.00   0.0  0
 0EY  CONST_03  N6   N5  C8  C9    0.00   0.0  0
 0EY  CONST_04  N5   N6  N7  C9    0.00   0.0  0
 0EY  CONST_05  N7   C9  C8  N5    0.00   0.0  0
 0EY  CONST_06  C1'  N7  C9  C8  180.00   0.0  0
 0EY  CONST_07  C1'  N7  N6  N5  180.00   0.0  0
 0EY  CONST_08  N1   C2  N3  C4    0.00   0.0  0
 0EY  CONST_09  C2   N3  C4  C5    0.00   0.0  0
 0EY  CONST_10  N3   C2  N1  C6    0.00   0.0  0
 0EY  CONST_11  N6   N5  C8  C7  180.00   0.0  0
 0EY  CONST_12  N7   C9  C8  C7  180.00   0.0  0
 0EY  CONST_13  O2   C2  N3  C4  180.00   0.0  0
 0EY  CONST_14  O2   C2  N1  C6  180.00   0.0  0
 0EY  CONST_15  N3   C2  N1  C7  180.00   0.0  0
 0EY  CONST_16  O4   C4  N3  C2  180.00   0.0  0
 0EY  CONST_17  H5   C9  C8  N5  180.00   0.0  0
 0EY  CONST_18  H6   N3  C4  C5  180.00   0.0  0
 0EY  CONST_19  O2   C2  N1  C7    0.00   0.0  0
 0EY  Var_01    C8   C7  N1  C6   95.97  30.0  3
 0EY  Var_02    N1   C7  C8  C9   93.12  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
 0EY  chir_01  C1'  N7   O4'  C2'  positiv
 0EY  chir_02  C4'  O4'  C5'  C3'  negativ
 0EY  chir_03  C3'  O3'  C2'  C4'  positiv
 0EY  chir_04  C2'  O2'  C1'  C3'  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
 0EY  plan-1  C8   0.020
 0EY  plan-1  C9   0.020
 0EY  plan-1  N5   0.020
 0EY  plan-1  N6   0.020
 0EY  plan-1  N7   0.020
 0EY  plan-1  C1'  0.020
 0EY  plan-1  H5   0.020
 0EY  plan-1  C7   0.020
 0EY  plan-2  C4   0.020
 0EY  plan-2  C5   0.020
 0EY  plan-2  C6   0.020
 0EY  plan-2  N1   0.020
 0EY  plan-2  N3   0.020
 0EY  plan-2  C2   0.020
 0EY  plan-2  O4   0.020
 0EY  plan-2  H1   0.020
 0EY  plan-2  H2   0.020
 0EY  plan-2  H6   0.020
 0EY  plan-2  C7   0.020
 0EY  plan-2  O2   0.020

