# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 03:19:39 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 9-beta-D-xylofuranosyl-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(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
 XYA  XYA  9-beta-D-xylofuranosyl-9H-purin-6-amine  ligand  32  19  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XYA
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
 XYA  O5'   O  OH1   0  -0.667  -4.4211   1.5421  -1.1912
 XYA  C5'   C  CH2   0  -0.175  -3.8328   1.0317  -0.0188
 XYA  C4'   C  CH1   0   0.018  -3.0751  -0.2246  -0.3687
 XYA  O4'   O  O2    0  -0.501  -1.9784   0.0832  -1.2400
 XYA  C1'   C  CH1   0   0.188  -0.8687  -0.6962  -0.9334
 XYA  N9    N  NR5   0  -0.531   0.2037   0.1589  -0.4420
 XYA  C8    C  CR15  0   0.118   0.1326   1.4332   0.0449
 XYA  N7    N  N     0  -0.460   1.2851   1.9051   0.4243
 XYA  C5    C  CR56  0  -0.003   2.1681   0.8854   0.1815
 XYA  C6    C  CR6   0   0.451   3.5543   0.7465   0.3724
 XYA  N1    N  N     0  -0.474   4.1234  -0.4124   0.0197
 XYA  C2    C  CR16  0   0.038   3.3656  -1.3787  -0.4918
 XYA  N3    N  N     0  -0.459   2.0627  -1.3700  -0.7142
 XYA  C4    C  CR56  0   0.481   1.5129  -0.2097  -0.3596
 XYA  N6    N  NH2   0  -0.817   4.3175   1.7214   0.8734
 XYA  C2'   C  CH1   0  -0.034  -1.3199  -1.7169   0.1187
 XYA  O2'   O  OH1   0  -0.664  -1.8023  -2.8263  -0.5908
 XYA  C3'   C  CH1   0  -0.060  -2.4524  -0.9623   0.8166
 XYA  O3'   O  OH1   0  -0.659  -1.8751  -0.1096   1.7736
 XYA  H5'   H  HOH1  0   0.458  -4.8344   2.3824  -0.9744
 XYA  H5'1  H  HCH2  0   0.209  -4.5902   0.7687   0.7329
 XYA  H5'2  H  HCH2  0   0.210  -3.1588   1.7605   0.4464
 XYA  H4'   H  HCH1  0   0.243  -3.7538  -0.9125  -0.8868
 XYA  H1'   H  HCH1  0   0.277  -0.4875  -1.2014  -1.8260
 XYA  H8    H  HCR5  0   0.293  -0.7958   1.9781   0.0902
 XYA  H2    H  HCR6  0   0.251   3.8897  -2.2910  -0.7569
 XYA  HN61  H  HNH2  0   0.402   5.2849   1.5433   1.0816
 XYA  HN62  H  HNH2  0   0.409   3.9037   2.5605   1.2398
 XYA  H2'   H  HCH1  0   0.265  -0.5138  -1.9827   0.8117
 XYA  H1    H  HOH1  0   0.462  -2.1545  -3.4634   0.0391
 XYA  H3'   H  HCH1  0   0.265  -3.1744  -1.6493   1.2727
 XYA  H3    H  HOH1  0   0.463  -2.5641   0.2197   2.3586

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
 XYA  O5'  C5'   single    1.407  0.020  1.407
 XYA  O5'  H5'   single    0.850  0.020  0.980
 XYA  C5'  C4'   single    1.508  0.020  1.508
 XYA  C5'  H5'1  single    0.970  0.020  1.090
 XYA  C5'  H5'2  single    0.970  0.020  1.090
 XYA  C4'  O4'   single    1.434  0.020  1.434
 XYA  C4'  C3'   single    1.529  0.020  1.529
 XYA  C4'  H4'   single    0.970  0.020  1.090
 XYA  O4'  C1'   single    1.390  0.020  1.390
 XYA  C1'  N9    single    1.457  0.020  1.457
 XYA  C1'  C2'   single    1.534  0.020  1.534
 XYA  C1'  H1'   single    0.970  0.020  1.090
 XYA  N9   C8    aromatic  1.366  0.020  1.366
 XYA  N9   C4    aromatic  1.363  0.020  1.363
 XYA  C8   N7    aromatic  1.302  0.020  1.302
 XYA  C8   H8    single    0.930  0.020  1.080
 XYA  N7   C5    aromatic  1.371  0.020  1.371
 XYA  C5   C6    aromatic  1.406  0.020  1.406
 XYA  C5   C4    aromatic  1.386  0.020  1.386
 XYA  C6   N1    aromatic  1.338  0.020  1.338
 XYA  C6   N6    single    1.336  0.020  1.336
 XYA  N1   C2    aromatic  1.330  0.020  1.330
 XYA  C2   N3    aromatic  1.322  0.020  1.322
 XYA  C2   H2    single    0.930  0.020  1.080
 XYA  N3   C4    aromatic  1.332  0.020  1.332
 XYA  N6   HN61  single    0.860  0.020  1.020
 XYA  N6   HN62  single    0.860  0.020  1.020
 XYA  C2'  O2'   single    1.403  0.020  1.403
 XYA  C2'  C3'   single    1.529  0.020  1.529
 XYA  C2'  H2'   single    0.970  0.020  1.090
 XYA  O2'  H1    single    0.850  0.020  0.980
 XYA  C3'  O3'   single    1.406  0.020  1.406
 XYA  C3'  H3'   single    0.970  0.020  1.090
 XYA  O3'  H3    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
 XYA  H5'   O5'  C5'   107.99  3.000
 XYA  H5'2  C5'  H5'1  107.01  3.000
 XYA  H5'2  C5'  C4'   110.08  3.000
 XYA  H5'1  C5'  C4'   107.79  3.000
 XYA  H5'2  C5'  O5'   111.68  3.000
 XYA  H5'1  C5'  O5'   111.62  3.000
 XYA  C4'   C5'  O5'   108.59  3.000
 XYA  H4'   C4'  C3'   108.40  3.000
 XYA  H4'   C4'  O4'   108.72  3.000
 XYA  C3'   C4'  O4'   105.26  3.000
 XYA  H4'   C4'  C5'   108.74  3.000
 XYA  C3'   C4'  C5'   115.26  3.000
 XYA  O4'   C4'  C5'   110.27  3.000
 XYA  C1'   O4'  C4'   110.86  3.000
 XYA  H1'   C1'  C2'   110.78  3.000
 XYA  H1'   C1'  N9    106.84  3.000
 XYA  C2'   C1'  N9    112.07  3.000
 XYA  H1'   C1'  O4'   110.92  3.000
 XYA  C2'   C1'  O4'   106.83  3.000
 XYA  N9    C1'  O4'   109.44  3.000
 XYA  C4    N9   C8    106.31  3.000
 XYA  C4    N9   C1'   124.67  3.000
 XYA  C8    N9   C1'   129.01  3.000
 XYA  H8    C8   N7    124.56  3.000
 XYA  H8    C8   N9    122.11  3.000
 XYA  N7    C8   N9    113.32  3.000
 XYA  C5    N7   C8    104.42  3.000
 XYA  C4    C5   C6    116.16  3.000
 XYA  C4    C5   N7    110.64  3.000
 XYA  C6    C5   N7    133.20  3.000
 XYA  N6    C6   N1    119.21  3.000
 XYA  N6    C6   C5    122.82  3.000
 XYA  N1    C6   C5    117.97  3.000
 XYA  C2    N1   C6    119.22  3.000
 XYA  H2    C2   N3    116.14  3.000
 XYA  H2    C2   N1    115.44  3.000
 XYA  N3    C2   N1    128.42  3.000
 XYA  C4    N3   C2    111.58  3.000
 XYA  N3    C4   C5    126.66  3.000
 XYA  N3    C4   N9    128.03  3.000
 XYA  C5    C4   N9    105.31  3.000
 XYA  HN62  N6   HN61  117.95  3.000
 XYA  HN62  N6   C6    120.73  3.000
 XYA  HN61  N6   C6    119.87  3.000
 XYA  H2'   C2'  C3'   112.08  3.000
 XYA  H2'   C2'  O2'   112.40  3.000
 XYA  C3'   C2'  O2'   111.50  3.000
 XYA  H2'   C2'  C1'   112.26  3.000
 XYA  C3'   C2'  C1'   101.68  3.000
 XYA  O2'   C2'  C1'   106.29  3.000
 XYA  H1    O2'  C2'   108.56  3.000
 XYA  H3'   C3'  O3'   111.55  3.000
 XYA  H3'   C3'  C2'   111.62  3.000
 XYA  O3'   C3'  C2'   107.81  3.000
 XYA  H3'   C3'  C4'   110.91  3.000
 XYA  O3'   C3'  C4'   113.73  3.000
 XYA  C2'   C3'  C4'   100.72  3.000
 XYA  H3    O3'  C3'   109.12  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
 XYA  CONST_01  C5    N7  C8  N9     0.00  0.0  0
 XYA  CONST_02  N7    C5  C4  N9     0.00  0.0  0
 XYA  CONST_03  C6    C5  C4  N9   180.00  0.0  0
 XYA  CONST_04  C2    N3  C4  N9   180.00  0.0  0
 XYA  CONST_05  C5    C4  N9  C8     0.00  0.0  0
 XYA  CONST_06  N3    C4  N9  C8   180.00  0.0  0
 XYA  CONST_07  C6    C5  N7  C8   180.00  0.0  0
 XYA  CONST_08  C4    C5  N7  C8     0.00  0.0  0
 XYA  CONST_09  C4    N9  C8  N7     0.00  0.0  0
 XYA  CONST_10  N1    C6  C5  N7   180.00  0.0  0
 XYA  CONST_11  N3    C4  C5  N7   180.00  0.0  0
 XYA  CONST_12  C2    N1  C6  C5     0.00  0.0  0
 XYA  CONST_13  C2    N3  C4  C5     0.00  0.0  0
 XYA  CONST_14  N3    C4  C5  C6     0.00  0.0  0
 XYA  CONST_15  N3    C2  N1  C6     0.00  0.0  0
 XYA  CONST_16  C4    C5  C6  N1     0.00  0.0  0
 XYA  CONST_17  C4    N3  C2  N1     0.00  0.0  0
 XYA  CONST_18  N7    C8  N9  C1'  180.00  0.0  0
 XYA  CONST_19  C5    C4  N9  C1'  180.00  0.0  0
 XYA  CONST_20  N3    C4  N9  C1'    0.00  0.0  0
 XYA  CONST_21  N6    C6  C5  N7     0.00  0.0  0
 XYA  CONST_22  N6    C6  N1  C2   180.00  0.0  0
 XYA  CONST_23  N6    C6  C5  C4   180.00  0.0  0
 XYA  CONST_24  H8    C8  N9  C1'    0.00  0.0  0
 XYA  CONST_25  H2    C2  N1  C6   180.00  0.0  0
 XYA  CONST_26  HN61  N6  C6  C5   180.00  0.0  0
 XYA  CONST_27  HN62  N6  C6  C5     0.00  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
 XYA  chir_01  C4'  C5'  O4'  C3'  negativ
 XYA  chir_02  C1'  O4'  N9   C2'  negativ
 XYA  chir_03  C2'  O2'  C1'  C3'  negativ
 XYA  chir_04  C3'  O3'  C4'  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
 XYA  plan-1  C1'   0.020
 XYA  plan-1  N9    0.020
 XYA  plan-1  C8    0.020
 XYA  plan-1  N7    0.020
 XYA  plan-1  C5    0.020
 XYA  plan-1  C6    0.020
 XYA  plan-1  N1    0.020
 XYA  plan-1  C2    0.020
 XYA  plan-1  N3    0.020
 XYA  plan-1  C4    0.020
 XYA  plan-1  N6    0.020
 XYA  plan-1  H8    0.020
 XYA  plan-1  H2    0.020
 XYA  plan-2  C6    0.020
 XYA  plan-2  N6    0.020
 XYA  plan-2  HN61  0.020
 XYA  plan-2  HN62  0.020

