# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:47:35 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 1-beta-D-ribofuranosyl-1H-imidazo[4,5-c]pyridin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
#
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
 AD3  AD3  1-beta-D-ribofuranosyl-1H-imidazo[4,5-c]pyridin-4-amine  ligand  33  19  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AD3
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
 AD3  O5'   O  OH1   0  -0.667   2.1134  -0.8162  -4.2322
 AD3  C5'   C  CH2   0  -0.155   1.4311   0.2543  -3.6292
 AD3  C4'   C  CH1   0   0.011   0.1233  -0.2477  -3.0709
 AD3  O4'   O  O2    0  -0.494   0.3516  -1.1870  -2.0185
 AD3  C3'   C  CH1   0  -0.042  -0.7243   0.8527  -2.4384
 AD3  O3'   O  OH1   0  -0.655  -1.5031   1.4847  -3.4138
 AD3  C2'   C  CH1   0  -0.043  -1.5412   0.0631  -1.4101
 AD3  O2'   O  OH1   0  -0.663  -2.5880  -0.6331  -2.0270
 AD3  C1'   C  CH1   0   0.168  -0.5100  -0.9648  -0.9465
 AD3  N9    N  NR5   0  -0.549   0.2536  -0.4748   0.1959
 AD3  C8    C  CR15  0   0.091   1.5420  -0.0197   0.2270
 AD3  N7    N  N     0  -0.453   1.9253   0.3497   1.4131
 AD3  C5    C  CR56  0  -0.024   0.8353   0.1264   2.2152
 AD3  C6    C  CR6   0   0.392   0.6580   0.3378   3.5973
 AD3  N6    N  NH2   0  -0.827   1.6712   0.8048   4.3687
 AD3  N1    N  N     0  -0.471  -0.5019   0.0404   4.1658
 AD3  C2    C  CR16  0  -0.087  -1.4992  -0.4644   3.4219
 AD3  C3    C  CR16  0  -0.397  -1.4476  -0.7111   2.0681
 AD3  C4    C  CR56  0   0.429  -0.2216  -0.3917   1.4743
 AD3  HO5'  H  HOH1  0   0.459   2.9374  -0.4808  -4.5968
 AD3  H5'1  H  HCH2  0   0.215   1.1980   1.0506  -4.3482
 AD3  H5'2  H  HCH2  0   0.198   2.0178   0.7165  -2.8240
 AD3  H4'   H  HCH1  0   0.246  -0.4472  -0.7366  -3.8706
 AD3  H3'   H  HCH1  0   0.244  -0.0788   1.5704  -1.9140
 AD3  HO3'  H  HOH1  0   0.469  -1.8026   2.3335  -3.0724
 AD3  H2'   H  HCH1  0   0.261  -1.8991   0.6898  -0.5837
 AD3  HO2'  H  HOH1  0   0.453  -2.9713  -0.0547  -2.6981
 AD3  H1'   H  HCH1  0   0.285  -0.9861  -1.9015  -0.6396
 AD3  H8    H  HCR5  0   0.296   2.1640   0.0048  -0.6535
 AD3  HN61  H  HNH2  0   0.387   1.4260   1.1750   5.2721
 AD3  HN62  H  HNH2  0   0.393   2.4352   1.2709   3.9095
 AD3  H2    H  HCR6  0   0.255  -2.4125  -0.6854   3.9631
 AD3  H3    H  HCR6  0   0.273  -2.2954  -1.1164   1.5344

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
 AD3  O5'  C5'   single    1.405  0.020  1.405
 AD3  O5'  HO5'  single    0.850  0.020  0.980
 AD3  C5'  C4'   single    1.508  0.020  1.508
 AD3  C5'  H5'1  single    0.970  0.020  1.090
 AD3  C5'  H5'2  single    0.970  0.020  1.090
 AD3  C4'  O4'   single    1.429  0.020  1.429
 AD3  C4'  C3'   single    1.526  0.020  1.526
 AD3  C4'  H4'   single    0.970  0.020  1.090
 AD3  O4'  C1'   single    1.393  0.020  1.393
 AD3  C3'  O3'   single    1.399  0.020  1.399
 AD3  C3'  C2'   single    1.532  0.020  1.532
 AD3  C3'  H3'   single    0.970  0.020  1.090
 AD3  O3'  HO3'  single    0.850  0.020  0.980
 AD3  C2'  O2'   single    1.400  0.020  1.400
 AD3  C2'  C1'   single    1.528  0.020  1.528
 AD3  C2'  H2'   single    0.970  0.020  1.090
 AD3  O2'  HO2'  single    0.850  0.020  0.980
 AD3  C1'  N9    single    1.459  0.020  1.459
 AD3  C1'  H1'   single    0.970  0.020  1.090
 AD3  N9   C8    aromatic  1.367  0.020  1.367
 AD3  N9   C4    aromatic  1.366  0.020  1.366
 AD3  C8   N7    aromatic  1.300  0.020  1.300
 AD3  C8   H8    single    0.930  0.020  1.080
 AD3  N7   C5    aromatic  1.372  0.020  1.372
 AD3  C5   C6    aromatic  1.409  0.020  1.409
 AD3  C5   C4    aromatic  1.391  0.020  1.391
 AD3  C6   N6    single    1.356  0.020  1.356
 AD3  C6   N1    aromatic  1.326  0.020  1.326
 AD3  N6   HN61  single    0.890  0.020  1.040
 AD3  N6   HN62  single    0.890  0.020  1.040
 AD3  N1   C2    aromatic  1.343  0.020  1.343
 AD3  C2   C3    aromatic  1.377  0.020  1.377
 AD3  C2   H2    single    0.930  0.020  1.080
 AD3  C3   C4    aromatic  1.399  0.020  1.399
 AD3  C3   H3    single    0.930  0.020  1.080

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
 AD3  HO5'  O5'  C5'   108.25  3.000
 AD3  H5'2  C5'  H5'1  106.76  3.000
 AD3  H5'2  C5'  C4'   109.39  3.000
 AD3  H5'1  C5'  C4'   107.45  3.000
 AD3  H5'2  C5'  O5'   112.07  3.000
 AD3  H5'1  C5'  O5'   112.00  3.000
 AD3  C4'   C5'  O5'   109.05  3.000
 AD3  H4'   C4'  C3'   109.54  3.000
 AD3  H4'   C4'  O4'   109.08  3.000
 AD3  C3'   C4'  O4'   104.92  3.000
 AD3  H4'   C4'  C5'   109.23  3.000
 AD3  C3'   C4'  C5'   113.27  3.000
 AD3  O4'   C4'  C5'   110.67  3.000
 AD3  C1'   O4'  C4'   111.29  3.000
 AD3  H3'   C3'  C2'   109.25  3.000
 AD3  H3'   C3'  O3'   111.39  3.000
 AD3  C2'   C3'  O3'   113.82  3.000
 AD3  H3'   C3'  C4'   110.03  3.000
 AD3  C2'   C3'  C4'   101.69  3.000
 AD3  O3'   C3'  C4'   110.24  3.000
 AD3  HO3'  O3'  C3'   108.92  3.000
 AD3  H2'   C2'  C1'   112.08  3.000
 AD3  H2'   C2'  O2'   111.84  3.000
 AD3  C1'   C2'  O2'   107.68  3.000
 AD3  H2'   C2'  C3'   112.64  3.000
 AD3  C1'   C2'  C3'   100.98  3.000
 AD3  O2'   C2'  C3'   111.04  3.000
 AD3  HO2'  O2'  C2'   107.77  3.000
 AD3  H1'   C1'  N9    107.19  3.000
 AD3  H1'   C1'  C2'   111.54  3.000
 AD3  N9    C1'  C2'   111.40  3.000
 AD3  H1'   C1'  O4'   110.38  3.000
 AD3  N9    C1'  O4'   109.42  3.000
 AD3  C2'   C1'  O4'   106.93  3.000
 AD3  C4    N9   C8    106.63  3.000
 AD3  C4    N9   C1'   124.83  3.000
 AD3  C8    N9   C1'   128.54  3.000
 AD3  H8    C8   N7    124.64  3.000
 AD3  H8    C8   N9    122.19  3.000
 AD3  N7    C8   N9    113.16  3.000
 AD3  C5    N7   C8    104.65  3.000
 AD3  C4    C5   C6    118.86  3.000
 AD3  C4    C5   N7    110.67  3.000
 AD3  C6    C5   N7    130.47  3.000
 AD3  N1    C6   N6    119.14  3.000
 AD3  N1    C6   C5    119.80  3.000
 AD3  N6    C6   C5    121.02  3.000
 AD3  HN62  N6   HN61  115.11  3.000
 AD3  HN62  N6   C6    117.86  3.000
 AD3  HN61  N6   C6    117.07  3.000
 AD3  C2    N1   C6    119.78  3.000
 AD3  H2    C2   C3    119.06  3.000
 AD3  H2    C2   N1    115.19  3.000
 AD3  C3    C2   N1    125.75  3.000
 AD3  H3    C3   C4    124.30  3.000
 AD3  H3    C3   C2    121.56  3.000
 AD3  C4    C3   C2    114.14  3.000
 AD3  C3    C4   C5    121.66  3.000
 AD3  C3    C4   N9    133.46  3.000
 AD3  C5    C4   N9    104.88  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
 AD3  CONST_01  C5  N7  C8  N9     0.00  0.0  0
 AD3  CONST_02  N7  C5  C4  N9     0.00  0.0  0
 AD3  CONST_03  C6  C5  C4  N9   180.00  0.0  0
 AD3  CONST_04  C2  C3  C4  N9   180.00  0.0  0
 AD3  CONST_05  C5  C4  N9  C8     0.00  0.0  0
 AD3  CONST_06  C3  C4  N9  C8   180.00  0.0  0
 AD3  CONST_07  C6  C5  N7  C8   180.00  0.0  0
 AD3  CONST_08  C4  C5  N7  C8     0.00  0.0  0
 AD3  CONST_09  C4  N9  C8  N7     0.00  0.0  0
 AD3  CONST_10  N1  C6  C5  N7   180.00  0.0  0
 AD3  CONST_11  C3  C4  C5  N7   180.00  0.0  0
 AD3  CONST_12  C2  N1  C6  C5     0.00  0.0  0
 AD3  CONST_13  C2  C3  C4  C5     0.00  0.0  0
 AD3  CONST_14  C3  C4  C5  C6     0.00  0.0  0
 AD3  CONST_15  C3  C2  N1  C6     0.00  0.0  0
 AD3  CONST_16  C4  C5  C6  N1     0.00  0.0  0
 AD3  CONST_17  C4  C3  C2  N1     0.00  0.0  0
 AD3  CONST_18  N7  C8  N9  C1'  180.00  0.0  0
 AD3  CONST_19  C5  C4  N9  C1'  180.00  0.0  0
 AD3  CONST_20  C3  C4  N9  C1'    0.00  0.0  0
 AD3  CONST_21  N6  C6  C5  N7     0.00  0.0  0
 AD3  CONST_22  C4  C5  C6  N6   180.00  0.0  0
 AD3  CONST_23  C2  N1  C6  N6   180.00  0.0  0
 AD3  CONST_24  H8  C8  N9  C1'    0.00  0.0  0
 AD3  CONST_25  H3  C3  C4  N9     0.00  0.0  0
 AD3  CONST_26  H2  C2  N1  C6   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
 AD3  chir_01  C4'  C5'  O4'  C3'  negativ
 AD3  chir_02  C3'  O3'  C4'  C2'  positiv
 AD3  chir_03  C2'  O2'  C3'  C1'  positiv
 AD3  chir_04  C1'  O4'  N9   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
 AD3  plan-1  C1'   0.020
 AD3  plan-1  N9    0.020
 AD3  plan-1  C8    0.020
 AD3  plan-1  N7    0.020
 AD3  plan-1  C5    0.020
 AD3  plan-1  C6    0.020
 AD3  plan-1  N6    0.020
 AD3  plan-1  N1    0.020
 AD3  plan-1  C2    0.020
 AD3  plan-1  C3    0.020
 AD3  plan-1  C4    0.020
 AD3  plan-1  H8    0.020
 AD3  plan-1  H2    0.020
 AD3  plan-1  H3    0.020
 AD3  plan-2  C6    0.020
 AD3  plan-2  N6    0.020
 AD3  plan-2  HN61  0.020
 AD3  plan-2  HN62  0.020

