# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:02:53 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: 4-amino-1-(beta-D-ribofuranosyl)-1,3,5-triazin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)N(C=N1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O
#
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
 5AE  5AE  4-amino-1-(beta-D-ribofuranosyl)-1,3,5-triazin-2(1H)-one  ligand  29  17  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5AE
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
 5AE  O2   O  O     0  -0.491  -1.7728  -2.0496   1.0233
 5AE  C2   C  CR6   0   0.615  -1.9388  -0.9429   0.5460
 5AE  N3   N  N     0  -0.521  -3.1465  -0.4185   0.2709
 5AE  C4   C  CR6   0   0.555  -3.2249   0.7918  -0.2403
 5AE  N4   N  NH2   0  -0.794  -4.4184   1.2983  -0.5210
 5AE  N5   N  N     0  -0.472  -2.1633   1.6095  -0.5134
 5AE  N1   N  NR6   0  -0.539  -0.8169  -0.1303   0.2517
 5AE  C6   C  CR16  0   0.206  -1.0091   1.1003  -0.2495
 5AE  C1'  C  CH1   0   0.212   0.5333  -0.6385   0.4906
 5AE  O4'  O  O2    0  -0.494   1.3331   0.3921   0.9909
 5AE  C4'  C  CH1   0  -0.048   2.6090   0.4082   0.3394
 5AE  C5'  C  CH2   0  -0.168   2.7428   1.5998  -0.5889
 5AE  O5'  O  OH1   0  -0.668   2.4814   2.7699   0.1439
 5AE  C3'  C  CH1   0  -0.039   2.6997  -0.9222  -0.4072
 5AE  O3'  O  OH1   0  -0.667   3.0871  -1.9819   0.4257
 5AE  C2'  C  CH1   0  -0.003   1.2317  -1.1322  -0.7785
 5AE  O2'  O  OH1   0  -0.649   0.8401  -2.4337  -1.0688
 5AE  H1   H  HNH2  0   0.412  -5.2531   0.7631  -0.3548
 5AE  H2   H  HNH2  0   0.413  -4.5025   2.2165  -0.9212
 5AE  H3   H  HCR6  0   0.311  -0.1287   1.7078  -0.4216
 5AE  H4   H  HCH1  0   0.270   0.4300  -1.4503   1.2130
 5AE  H5   H  HCH1  0   0.263   3.3758   0.4820   1.1174
 5AE  H6   H  HCH2  0   0.228   3.7616   1.5861  -0.9978
 5AE  H7   H  HCH2  0   0.197   2.0609   1.4999  -1.4454
 5AE  H8   H  HOH1  0   0.460   2.5653   3.5208  -0.4504
 5AE  H9   H  HCH1  0   0.255   3.3442  -0.8458  -1.2928
 5AE  H10  H  HOH1  0   0.458   3.9888  -1.8220   0.7217
 5AE  H11  H  HCH1  0   0.237   0.9920  -0.4465  -1.6044
 5AE  H12  H  HOH1  0   0.463   1.1838  -2.6716  -1.9357

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
 5AE  N4   C4   single  1.327  0.020  1.327
 5AE  N3   C4   double  1.316  0.020  1.316
 5AE  N3   C2   single  1.345  0.020  1.345
 5AE  O2   C2   double  1.217  0.020  1.217
 5AE  C4   N5   single  1.368  0.020  1.368
 5AE  C2   N1   single  1.416  0.020  1.416
 5AE  N5   C6   double  1.289  0.020  1.289
 5AE  N1   C6   single  1.343  0.020  1.343
 5AE  N1   C1'  single  1.462  0.020  1.462
 5AE  O4'  C1'  single  1.397  0.020  1.397
 5AE  O4'  C4'  single  1.433  0.020  1.433
 5AE  C1'  C2'  single  1.530  0.020  1.530
 5AE  C4'  C5'  single  1.516  0.020  1.516
 5AE  C4'  C3'  single  1.528  0.020  1.528
 5AE  C5'  O5'  single  1.405  0.020  1.405
 5AE  C2'  O2'  single  1.390  0.020  1.390
 5AE  C2'  C3'  single  1.529  0.020  1.529
 5AE  C3'  O3'  single  1.403  0.020  1.403
 5AE  N4   H1   single  0.860  0.020  1.020
 5AE  N4   H2   single  0.860  0.020  1.020
 5AE  C6   H3   single  0.930  0.020  1.080
 5AE  C1'  H4   single  0.970  0.020  1.090
 5AE  C4'  H5   single  0.970  0.020  1.090
 5AE  C5'  H6   single  0.970  0.020  1.090
 5AE  C5'  H7   single  0.970  0.020  1.090
 5AE  O5'  H8   single  0.850  0.020  0.980
 5AE  C3'  H9   single  0.970  0.020  1.090
 5AE  O3'  H10  single  0.850  0.020  0.980
 5AE  C2'  H11  single  0.970  0.020  1.090
 5AE  O2'  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
 5AE  N1   C2   N3   116.43  3.000
 5AE  N1   C2   O2   119.70  3.000
 5AE  N3   C2   O2   123.87  3.000
 5AE  C4   N3   C2   119.43  3.000
 5AE  N5   C4   N4   115.33  3.000
 5AE  N5   C4   N3   125.53  3.000
 5AE  N4   C4   N3   119.14  3.000
 5AE  H2   N4   H1   118.86  3.000
 5AE  H2   N4   C4   120.55  3.000
 5AE  H1   N4   C4   120.57  3.000
 5AE  C6   N5   C4   114.71  3.000
 5AE  C1'  N1   C6   120.78  3.000
 5AE  C1'  N1   C2   119.88  3.000
 5AE  C6   N1   C2   119.35  3.000
 5AE  H3   C6   N1   117.19  3.000
 5AE  H3   C6   N5   118.27  3.000
 5AE  N1   C6   N5   124.53  3.000
 5AE  H4   C1'  C2'  110.61  3.000
 5AE  H4   C1'  O4'  111.45  3.000
 5AE  C2'  C1'  O4'  105.88  3.000
 5AE  H4   C1'  N1   106.22  3.000
 5AE  C2'  C1'  N1   113.45  3.000
 5AE  O4'  C1'  N1   109.32  3.000
 5AE  C4'  O4'  C1'  110.81  3.000
 5AE  H5   C4'  C3'  111.36  3.000
 5AE  H5   C4'  C5'  108.68  3.000
 5AE  C3'  C4'  C5'  112.32  3.000
 5AE  H5   C4'  O4'  107.54  3.000
 5AE  C3'  C4'  O4'  105.38  3.000
 5AE  C5'  C4'  O4'  111.46  3.000
 5AE  H7   C5'  H6   106.52  3.000
 5AE  H7   C5'  O5'  111.51  3.000
 5AE  H6   C5'  O5'  112.16  3.000
 5AE  H7   C5'  C4'  110.54  3.000
 5AE  H6   C5'  C4'  107.46  3.000
 5AE  O5'  C5'  C4'  108.59  3.000
 5AE  H8   O5'  C5'  108.17  3.000
 5AE  H9   C3'  C2'  112.17  3.000
 5AE  H9   C3'  O3'  111.68  3.000
 5AE  C2'  C3'  O3'  107.80  3.000
 5AE  H9   C3'  C4'  111.61  3.000
 5AE  O3'  C3'  C4'  112.58  3.000
 5AE  C2'  C3'  C4'  100.44  3.000
 5AE  H10  O3'  C3'  108.41  3.000
 5AE  H11  C2'  O2'  111.45  3.000
 5AE  H11  C2'  C3'  107.81  3.000
 5AE  O2'  C2'  C3'  116.74  3.000
 5AE  H11  C2'  C1'  108.79  3.000
 5AE  C3'  C2'  C1'  101.10  3.000
 5AE  O2'  C2'  C1'  110.29  3.000
 5AE  H12  O2'  C2'  108.60  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
 5AE  CONST_01  N5   C4  N3  C2    0.00  0.0  0
 5AE  CONST_02  N5   C6  N1  C2    0.00  0.0  0
 5AE  CONST_03  C6   N5  C4  N3    0.00  0.0  0
 5AE  CONST_04  C6   N1  C2  N3    0.00  0.0  0
 5AE  CONST_05  C1'  N1  C2  N3  180.00  0.0  0
 5AE  CONST_06  N1   C2  N3  C4    0.00  0.0  0
 5AE  CONST_07  N1   C6  N5  C4    0.00  0.0  0
 5AE  CONST_08  C1'  N1  C6  N5  180.00  0.0  0
 5AE  CONST_09  C4   N3  C2  O2  180.00  0.0  0
 5AE  CONST_10  C6   N1  C2  O2  180.00  0.0  0
 5AE  CONST_11  C1'  N1  C2  O2    0.00  0.0  0
 5AE  CONST_12  N4   C4  N3  C2  180.00  0.0  0
 5AE  CONST_13  C6   N5  C4  N4  180.00  0.0  0
 5AE  CONST_14  H3   C6  N1  C2  180.00  0.0  0
 5AE  CONST_15  H1   N4  C4  N3    0.00  0.0  0
 5AE  CONST_16  H2   N4  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
 5AE  chir_01  C1'  N1   O4'  C2'  positiv
 5AE  chir_02  C4'  O4'  C5'  C3'  positiv
 5AE  chir_03  C3'  O3'  C4'  C2'  positiv
 5AE  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
 5AE  plan-1  O2   0.020
 5AE  plan-1  C2   0.020
 5AE  plan-1  N3   0.020
 5AE  plan-1  C4   0.020
 5AE  plan-1  N4   0.020
 5AE  plan-1  N5   0.020
 5AE  plan-1  N1   0.020
 5AE  plan-1  C6   0.020
 5AE  plan-1  C1'  0.020
 5AE  plan-1  H1   0.020
 5AE  plan-1  H2   0.020
 5AE  plan-1  H3   0.020

