# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 19:02:33 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-beta-D-ribofuranosyl-1H-imidazol-5-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cncn1[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
 AIS  AIS  1-beta-D-ribofuranosyl-1H-imidazol-5-amine  ligand  28  15  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AIS
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
 AIS  O2'   O  OH1   0  -0.664  -0.8321   2.5288   0.8506
 AIS  C2'   C  CR15  0  -0.046  -0.3638   1.5294  -0.0123
 AIS  C3'   C  CR15  0  -0.038  -1.5264   0.8400  -0.7346
 AIS  O3'   O  OH1   0  -0.657  -2.5284   1.7198  -1.1594
 AIS  C4'   C  CR15  0   0.013  -2.0564  -0.0894   0.3534
 AIS  C5'   C  CH2   0  -0.158  -2.7537  -1.3088  -0.1958
 AIS  O5'   O  OH1   0  -0.667  -3.2546  -2.0733   0.8723
 AIS  O4'   O  O     0  -0.495  -0.9054  -0.4633   1.1085
 AIS  C1'   C  CR15  0   0.173   0.1728   0.3874   0.8505
 AIS  N1    N  NR5   0  -0.471   1.2302  -0.3569   0.1873
 AIS  C2    C  CR15  0   0.080   1.1401  -1.5273  -0.5003
 AIS  N3    N  N     0  -0.452   2.3058  -1.9237  -0.9267
 AIS  C4    C  CR15  0  -0.248   3.1995  -0.9691  -0.5219
 AIS  C5    C  CR5   0   0.391   2.5514   0.0139   0.1765
 AIS  N6    N  NH2   0  -0.861   2.9841   1.1375   0.8686
 AIS  H1    H  HOH1  0   0.452  -1.5199   3.0223   0.3868
 AIS  H2'   H  HCR5  0   0.256   0.3923   1.9126  -0.7098
 AIS  H3'   H  HCR5  0   0.242  -1.1333   0.2477  -1.5717
 AIS  H3    H  HOH1  0   0.469  -2.2932   2.0628  -2.0274
 AIS  H4'   H  HCR5  0   0.242  -2.7513   0.4619   1.0006
 AIS  H5'1  H  HCH2  0   0.212  -3.5544  -0.9576  -0.8602
 AIS  H5'2  H  HCH2  0   0.201  -2.0529  -1.8818  -0.8178
 AIS  H5'   H  HOH1  0   0.459  -3.7049  -2.8401   0.5071
 AIS  H1'   H  HCR5  0   0.276   0.5957   0.7695   1.7852
 AIS  H2    H  HCR5  0   0.277   0.2079  -2.0470  -0.6527
 AIS  H4    H  HCR5  0   0.251   4.2560  -1.0360  -0.7338
 AIS  HN61  H  HNH2  0   0.383   3.9920   1.1678   0.9205
 AIS  HN62  H  HNH2  0   0.381   2.6679   2.0102   0.4643

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
 AIS  O2'  C2'   single    1.401  0.020  1.401
 AIS  O2'  H1    single    0.850  0.020  0.980
 AIS  C2'  C3'   single    1.532  0.020  1.532
 AIS  C2'  C1'   single    1.529  0.020  1.529
 AIS  C2'  H2'   single    0.970  0.020  1.090
 AIS  C3'  O3'   single    1.400  0.020  1.400
 AIS  C3'  C4'   single    1.526  0.020  1.526
 AIS  C3'  H3'   single    0.970  0.020  1.090
 AIS  O3'  H3    single    0.850  0.020  0.980
 AIS  C4'  C5'   single    1.508  0.020  1.508
 AIS  C4'  O4'   single    1.426  0.020  1.426
 AIS  C4'  H4'   single    0.970  0.020  1.090
 AIS  C5'  O5'   single    1.406  0.020  1.406
 AIS  C5'  H5'1  single    0.970  0.020  1.090
 AIS  C5'  H5'2  single    0.970  0.020  1.090
 AIS  O5'  H5'   single    0.850  0.020  0.980
 AIS  O4'  C1'   single    1.397  0.020  1.397
 AIS  C1'  N1    single    1.453  0.020  1.453
 AIS  C1'  H1'   single    0.970  0.020  1.090
 AIS  N1   C2    aromatic  1.360  0.020  1.360
 AIS  N1   C5    aromatic  1.372  0.020  1.372
 AIS  C2   N3    aromatic  1.303  0.020  1.303
 AIS  C2   H2    single    0.930  0.020  1.080
 AIS  N3   C4    aromatic  1.369  0.020  1.369
 AIS  C4   C5    aromatic  1.369  0.020  1.369
 AIS  C4   H4    single    0.930  0.020  1.080
 AIS  C5   N6    single    1.389  0.020  1.389
 AIS  N6   HN61  single    0.890  0.020  1.040
 AIS  N6   HN62  single    0.890  0.020  1.040

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
 AIS  H1    O2'  C2'   107.87  3.000
 AIS  H2'   C2'  C1'   112.19  3.000
 AIS  H2'   C2'  C3'   112.34  3.000
 AIS  C1'   C2'  C3'   101.32  3.000
 AIS  H2'   C2'  O2'   111.87  3.000
 AIS  C1'   C2'  O2'   107.62  3.000
 AIS  C3'   C2'  O2'   110.95  3.000
 AIS  H3'   C3'  C4'   109.84  3.000
 AIS  H3'   C3'  O3'   111.34  3.000
 AIS  C4'   C3'  O3'   110.53  3.000
 AIS  H3'   C3'  C2'   109.29  3.000
 AIS  C4'   C3'  C2'   101.62  3.000
 AIS  O3'   C3'  C2'   113.79  3.000
 AIS  H3    O3'  C3'   108.83  3.000
 AIS  H4'   C4'  O4'   109.28  3.000
 AIS  H4'   C4'  C5'   109.15  3.000
 AIS  O4'   C4'  C5'   110.73  3.000
 AIS  H4'   C4'  C3'   109.53  3.000
 AIS  O4'   C4'  C3'   104.88  3.000
 AIS  C5'   C4'  C3'   113.17  3.000
 AIS  H5'2  C5'  H5'1  106.83  3.000
 AIS  H5'2  C5'  O5'   111.95  3.000
 AIS  H5'1  C5'  O5'   111.95  3.000
 AIS  H5'2  C5'  C4'   109.45  3.000
 AIS  H5'1  C5'  C4'   107.39  3.000
 AIS  O5'   C5'  C4'   109.13  3.000
 AIS  H5'   O5'  C5'   108.18  3.000
 AIS  C1'   O4'  C4'   111.42  3.000
 AIS  H1'   C1'  N1    106.69  3.000
 AIS  H1'   C1'  O4'   110.66  3.000
 AIS  N1    C1'  O4'   109.50  3.000
 AIS  H1'   C1'  C2'   110.90  3.000
 AIS  N1    C1'  C2'   112.37  3.000
 AIS  O4'   C1'  C2'   106.75  3.000
 AIS  C5    N1   C2    106.99  3.000
 AIS  C5    N1   C1'   124.45  3.000
 AIS  C2    N1   C1'   128.54  3.000
 AIS  H2    C2   N3    125.49  3.000
 AIS  H2    C2   N1    122.92  3.000
 AIS  N3    C2   N1    111.59  3.000
 AIS  C4    N3   C2    105.97  3.000
 AIS  H4    C4   C5    127.44  3.000
 AIS  H4    C4   N3    122.52  3.000
 AIS  C5    C4   N3    110.03  3.000
 AIS  N6    C5   C4    133.44  3.000
 AIS  N6    C5   N1    120.98  3.000
 AIS  C4    C5   N1    105.41  3.000
 AIS  HN62  N6   HN61  107.85  3.000
 AIS  HN62  N6   C5    113.65  3.000
 AIS  HN61  N6   C5    111.16  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
 AIS  CONST_01  C4    N3  C2  N1     0.00  0.0  0
 AIS  CONST_02  N3    C4  C5  N1     0.00  0.0  0
 AIS  CONST_03  C4    C5  N1  C2     0.00  0.0  0
 AIS  CONST_04  C5    C4  N3  C2     0.00  0.0  0
 AIS  CONST_05  C5    N1  C2  N3     0.00  0.0  0
 AIS  CONST_06  N3    C2  N1  C1'  180.00  0.0  0
 AIS  CONST_07  C4    C5  N1  C1'  180.00  0.0  0
 AIS  CONST_08  N6    C5  N1  C1'    0.00  0.0  0
 AIS  CONST_09  N6    C5  N1  C2   180.00  0.0  0
 AIS  CONST_10  N6    C5  C4  N3   180.00  0.0  0
 AIS  CONST_11  H2    C2  N1  C1'    0.00  0.0  0
 AIS  CONST_12  H4    C4  C5  N1   180.00  0.0  0
 AIS  CONST_13  HN61  N6  C5  N1   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
 AIS  chir_01  C2'  O2'  C3'  C1'  positiv
 AIS  chir_02  C3'  O3'  C4'  C2'  positiv
 AIS  chir_03  C4'  O4'  C3'  C5'  negativ
 AIS  chir_04  C1'  O4'  N1   C2'  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
 AIS  plan-1  C1'   0.020
 AIS  plan-1  N1    0.020
 AIS  plan-1  C2    0.020
 AIS  plan-1  N3    0.020
 AIS  plan-1  C4    0.020
 AIS  plan-1  C5    0.020
 AIS  plan-1  N6    0.020
 AIS  plan-1  H2    0.020
 AIS  plan-1  H4    0.020
 AIS  plan-2  C5    0.020
 AIS  plan-2  N6    0.020
 AIS  plan-2  HN61  0.020
 AIS  plan-2  HN62  0.020

