# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 21:31:35 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1ncn(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
 RBV  RBV  1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide  ligand  29  17  .  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_RBV
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
 RBV  N1    N  NR5   0  -0.304   0.4924  -0.6990  -0.6090
 RBV  N2    N  N     0  -0.247   1.0219   0.2149   0.1965
 RBV  C3    C  CR5   0   0.242   2.2943   0.1789  -0.1168
 RBV  N3    N  NH2   0  -0.803   4.5372   0.9035   0.0944
 RBV  O3    O  O     0  -0.472   2.9552   1.8513   1.4162
 RBV  N4    N  N     0  -0.469   2.6058  -0.7116  -1.0848
 RBV  C5    C  CR15  0   0.132   1.4466  -1.2443  -1.3763
 RBV  C6    C  C     0   0.458   3.2901   1.0642   0.5462
 RBV  C1'   C  CR15  0   0.243  -0.9306  -0.9622  -0.6427
 RBV  C2'   C  CR15  0  -0.067  -1.5146  -1.2505   0.7430
 RBV  O2'   O  OH1   0  -0.656  -1.4620  -2.6224   1.0042
 RBV  C3'   C  CR15  0  -0.019  -2.9281  -0.6789   0.6005
 RBV  O3'   O  OH1   0  -0.669  -3.7574  -1.5663  -0.1025
 RBV  C4'   C  CR15  0  -0.048  -2.6668   0.5376  -0.2732
 RBV  O4'   O  O     0  -0.483  -1.6044   0.1461  -1.1479
 RBV  C5'   C  CH2   0  -0.146  -2.3010   1.7729   0.5240
 RBV  O5'   O  OH1   0  -0.669  -2.0310   2.8138  -0.3809
 RBV  HN3   H  HNH2  0   0.415   4.7492   0.2457  -0.6373
 RBV  HN3A  H  HNH2  0   0.411   5.2864   1.4721   0.4531
 RBV  H5    H  HCR5  0   0.317   1.2512  -2.0076  -2.1133
 RBV  H1'   H  HCR5  0   0.267  -1.0489  -1.8285  -1.3018
 RBV  H2'   H  HCR5  0   0.264  -0.9694  -0.6749   1.4992
 RBV  HO2'  H  HOH1  0   0.471  -1.5285  -2.7592   1.9546
 RBV  H3'   H  HCR5  0   0.251  -3.3558  -0.4048   1.5735
 RBV  HO3'  H  HOH1  0   0.449  -3.6106  -2.4516   0.2507
 RBV  H4'   H  HCR5  0   0.263  -3.5390   0.7644  -0.8937
 RBV  H5'   H  HCH2  0   0.206  -3.1502   2.0084   1.1794
 RBV  H5'A  H  HCH2  0   0.204  -1.4410   1.5705   1.1743
 RBV  HO5'  H  HOH1  0   0.458  -1.7287   3.5749   0.1220

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
 RBV  N1   N2    aromatic  1.328  0.020  1.328
 RBV  N1   C5    aromatic  1.340  0.020  1.340
 RBV  N1   C1'   single    1.448  0.020  1.448
 RBV  N2   C3    aromatic  1.311  0.020  1.311
 RBV  C3   N4    aromatic  1.352  0.020  1.352
 RBV  C3   C6    single    1.488  0.020  1.488
 RBV  N3   C6    single    1.336  0.020  1.336
 RBV  O3   C6    double    1.220  0.020  1.220
 RBV  N4   C5    aromatic  1.309  0.020  1.309
 RBV  C1'  C2'   single    1.531  0.020  1.531
 RBV  C1'  O4'   single    1.392  0.020  1.392
 RBV  C2'  O2'   single    1.398  0.020  1.398
 RBV  C2'  C3'   single    1.531  0.020  1.531
 RBV  C3'  O3'   single    1.403  0.020  1.403
 RBV  C3'  C4'   single    1.520  0.020  1.520
 RBV  C4'  O4'   single    1.431  0.020  1.431
 RBV  C4'  C5'   single    1.515  0.020  1.515
 RBV  C5'  O5'   single    1.405  0.020  1.405
 RBV  N3   HN3   single    0.860  0.020  1.020
 RBV  N3   HN3A  single    0.860  0.020  1.020
 RBV  C5   H5    single    0.930  0.020  1.080
 RBV  C1'  H1'   single    0.970  0.020  1.090
 RBV  C2'  H2'   single    0.970  0.020  1.090
 RBV  O2'  HO2'  single    0.850  0.020  0.980
 RBV  C3'  H3'   single    0.970  0.020  1.090
 RBV  O3'  HO3'  single    0.850  0.020  0.980
 RBV  C4'  H4'   single    0.970  0.020  1.090
 RBV  C5'  H5'   single    0.970  0.020  1.090
 RBV  C5'  H5'A  single    0.970  0.020  1.090
 RBV  O5'  HO5'  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
 RBV  C1'   N1   C5   127.77  3.000
 RBV  C1'   N1   N2   122.08  3.000
 RBV  C5    N1   N2   110.07  3.000
 RBV  C3    N2   N1   102.89  3.000
 RBV  C6    C3   N4   123.83  3.000
 RBV  C6    C3   N2   121.78  3.000
 RBV  N4    C3   N2   114.39  3.000
 RBV  HN3A  N3   HN3  118.13  3.000
 RBV  HN3A  N3   C6   120.41  3.000
 RBV  HN3   N3   C6   121.41  3.000
 RBV  C5    N4   C3   102.92  3.000
 RBV  H5    C5   N4   126.91  3.000
 RBV  H5    C5   N1   123.36  3.000
 RBV  N4    C5   N1   109.73  3.000
 RBV  O3    C6   N3   125.10  3.000
 RBV  O3    C6   C3   121.18  3.000
 RBV  N3    C6   C3   113.72  3.000
 RBV  H1'   C1'  O4'  111.05  3.000
 RBV  H1'   C1'  C2'  110.77  3.000
 RBV  O4'   C1'  C2'  107.08  3.000
 RBV  H1'   C1'  N1   105.32  3.000
 RBV  O4'   C1'  N1   109.85  3.000
 RBV  C2'   C1'  N1   112.84  3.000
 RBV  H2'   C2'  C3'  109.12  3.000
 RBV  H2'   C2'  O2'  111.59  3.000
 RBV  C3'   C2'  O2'  114.74  3.000
 RBV  H2'   C2'  C1'  109.63  3.000
 RBV  C3'   C2'  C1'  101.39  3.000
 RBV  O2'   C2'  C1'  109.85  3.000
 RBV  HO2'  O2'  C2'  108.76  3.000
 RBV  H3'   C3'  C4'  112.12  3.000
 RBV  H3'   C3'  O3'  111.83  3.000
 RBV  C4'   C3'  O3'  108.64  3.000
 RBV  H3'   C3'  C2'  111.74  3.000
 RBV  C4'   C3'  C2'  101.15  3.000
 RBV  O3'   C3'  C2'  110.86  3.000
 RBV  HO3'  O3'  C3'  107.88  3.000
 RBV  H4'   C4'  C5'  108.77  3.000
 RBV  H4'   C4'  O4'  107.57  3.000
 RBV  C5'   C4'  O4'  111.44  3.000
 RBV  H4'   C4'  C3'  110.78  3.000
 RBV  C5'   C4'  C3'  113.05  3.000
 RBV  O4'   C4'  C3'  105.07  3.000
 RBV  C4'   O4'  C1'  110.82  3.000
 RBV  H5'A  C5'  H5'  106.98  3.000
 RBV  H5'A  C5'  O5'  111.57  3.000
 RBV  H5'   C5'  O5'  111.97  3.000
 RBV  H5'A  C5'  C4'  110.53  3.000
 RBV  H5'   C5'  C4'  107.59  3.000
 RBV  O5'   C5'  C4'  108.15  3.000
 RBV  HO5'  O5'  C5'  108.06  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
 RBV  CONST_01  N4    C3  N2  N1     0.00   0.0  0
 RBV  CONST_02  C3    N4  C5  N1     0.00   0.0  0
 RBV  CONST_03  N4    C5  N1  N2     0.00   0.0  0
 RBV  CONST_04  C5    N4  C3  N2     0.00   0.0  0
 RBV  CONST_05  C5    N1  N2  C3     0.00   0.0  0
 RBV  CONST_06  C1'   N1  N2  C3   180.00   0.0  0
 RBV  CONST_07  C1'   N1  C5  N4   180.00   0.0  0
 RBV  CONST_08  C6    C3  N2  N1   180.00   0.0  0
 RBV  CONST_09  C6    C3  N4  C5   180.00   0.0  0
 RBV  CONST_10  H5    C5  N1  N2   180.00   0.0  0
 RBV  CONST_11  HN3   N3  C6  C3     0.00   0.0  0
 RBV  CONST_12  HN3A  N3  C6  C3   180.00   0.0  0
 RBV  Var_01    N3    C6  C3  N2  -179.34  30.0  2

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
 RBV  chir_01  C1'  N1   C2'  O4'  negativ
 RBV  chir_02  C2'  O2'  C3'  C1'  positiv
 RBV  chir_03  C3'  O3'  C4'  C2'  positiv
 RBV  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
 RBV  plan-1  N1    0.020
 RBV  plan-1  N2    0.020
 RBV  plan-1  C3    0.020
 RBV  plan-1  N4    0.020
 RBV  plan-1  C5    0.020
 RBV  plan-1  C6    0.020
 RBV  plan-1  C1'   0.020
 RBV  plan-1  H5    0.020
 RBV  plan-2  C3    0.020
 RBV  plan-2  N3    0.020
 RBV  plan-2  O3    0.020
 RBV  plan-2  C6    0.020
 RBV  plan-2  HN3   0.020
 RBV  plan-2  HN3A  0.020

