# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 18:22:34 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 1-deoxy-1-(2,6,8-trioxo-1,2,3,6,7,8-hexahydro-9H-purin-9-yl)-D-arabinitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@H](O)CN1C(=O)NC2=C1NC(=O)NC2=O
#
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
 PUG  PUG  1-deoxy-1-(2,6,8-trioxo-1,2,3,6,7,8-hexahydro-9H-purin-9-yl)-D-arabinitol  ligand  35  21  .  2022-07-22  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_PUG
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
 PUG  O1    O  OC    0  -0.470  -3.2054   3.1983   0.4033
 PUG  C2    C  CR6   0   0.671  -3.0864   2.0052   0.2220
 PUG  N3    N  NR16  0  -0.734  -4.0724   1.2317  -0.3405
 PUG  C4    C  CR6   0   0.541  -4.0779  -0.1433  -0.5961
 PUG  O2    O  OC    0  -0.465  -5.0453  -0.6891  -1.0966
 PUG  N1    N  NR16  0  -0.741  -1.9436   1.3191   0.5650
 PUG  C8    C  CR56  0   0.647  -1.8501  -0.0133   0.3468
 PUG  C9    C  CR56  0   0.090  -2.8546  -0.7440  -0.2034
 PUG  N5    N  NR15  0  -0.736  -2.4113  -2.0579  -0.2442
 PUG  N7    N  NR5   0  -0.557  -0.8208  -0.8390   0.6505
 PUG  C6    C  CR5   0   0.669  -1.1571  -2.1436   0.2639
 PUG  O4    O  OC    0  -0.495  -0.4383  -3.1174   0.3825
 PUG  C10   C  CH2   0  -0.361   0.4807  -0.4840   1.1741
 PUG  C11   C  CH1   0   0.030   1.4682  -0.1833   0.0468
 PUG  O19   O  OH1   0  -0.657   1.0062   0.8702  -0.7650
 PUG  C12   C  CH1   0  -0.049   2.8676   0.0620   0.6167
 PUG  O21   O  OH1   0  -0.665   2.8702   1.1724   1.4923
 PUG  C13   C  CH1   0  -0.027   3.9388   0.2046  -0.4777
 PUG  O23   O  OH1   0  -0.655   3.8413  -0.8217  -1.4341
 PUG  C14   C  CH2   0  -0.158   5.3293   0.2742   0.1364
 PUG  O26   O  OH1   0  -0.669   6.2585   0.5568  -0.8821
 PUG  H3    H  HNR6  0   0.431  -4.9109   1.7341  -0.6033
 PUG  H1    H  HNR6  0   0.438  -1.1950   1.8454   0.9913
 PUG  H5    H  HNR5  0   0.427  -2.9234  -2.8443  -0.6102
 PUG  H101  H  HCH2  0   0.290   0.8352  -1.3214   1.7741
 PUG  H102  H  HCH2  0   0.278   0.3688   0.3621   1.8551
 PUG  H11   H  HCH1  0   0.258   1.5126  -1.0650  -0.5967
 PUG  H19   H  HOH1  0   0.438   1.0941   1.7034  -0.2891
 PUG  H12   H  HCH1  0   0.242   3.1183  -0.8107   1.2330
 PUG  H21   H  HOH1  0   0.452   3.0331   1.9812   0.9950
 PUG  H13   H  HCH1  0   0.232   3.7513   1.1365  -1.0256
 PUG  H23   H  HOH1  0   0.448   4.1148  -1.6525  -1.0293
 PUG  H141  H  HCH2  0   0.196   5.5451  -0.6869   0.6287
 PUG  H142  H  HCH2  0   0.206   5.3457   1.0393   0.9205
 PUG  H26   H  HOH1  0   0.456   7.1334   0.5871  -0.4850

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
 PUG  O1   C2    double    1.213  0.020  1.213
 PUG  C2   N3    aromatic  1.374  0.020  1.374
 PUG  C2   N1    aromatic  1.376  0.020  1.376
 PUG  N3   C4    aromatic  1.399  0.020  1.399
 PUG  N3   H3    single    0.860  0.020  1.020
 PUG  C4   O2    double    1.218  0.020  1.218
 PUG  C4   C9    aromatic  1.418  0.020  1.418
 PUG  N1   C8    aromatic  1.353  0.020  1.353
 PUG  N1   H1    single    0.860  0.020  1.020
 PUG  C8   C9    aromatic  1.359  0.020  1.359
 PUG  C8   N7    aromatic  1.354  0.020  1.354
 PUG  C9   N5    aromatic  1.387  0.020  1.387
 PUG  N5   C6    aromatic  1.356  0.020  1.356
 PUG  N5   H5    single    0.860  0.020  1.020
 PUG  N7   C6    aromatic  1.402  0.020  1.402
 PUG  N7   C10   single    1.447  0.020  1.447
 PUG  C6   O4    double    1.216  0.020  1.216
 PUG  C10  C11   single    1.529  0.020  1.529
 PUG  C10  H101  single    0.970  0.020  1.090
 PUG  C10  H102  single    0.970  0.020  1.090
 PUG  C11  O19   single    1.408  0.020  1.408
 PUG  C11  C12   single    1.531  0.020  1.531
 PUG  C11  H11   single    0.970  0.020  1.090
 PUG  O19  H19   single    0.850  0.020  0.980
 PUG  C12  O21   single    1.414  0.020  1.414
 PUG  C12  C13   single    1.538  0.020  1.538
 PUG  C12  H12   single    0.970  0.020  1.090
 PUG  O21  H21   single    0.850  0.020  0.980
 PUG  C13  O23   single    1.406  0.020  1.406
 PUG  C13  C14   single    1.522  0.020  1.522
 PUG  C13  H13   single    0.970  0.020  1.090
 PUG  O23  H23   single    0.850  0.020  0.980
 PUG  C14  O26   single    1.407  0.020  1.407
 PUG  C14  H141  single    0.970  0.020  1.090
 PUG  C14  H142  single    0.970  0.020  1.090
 PUG  O26  H26   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
 PUG  N1    C2   N3    114.66  3.000
 PUG  N1    C2   O1    122.32  3.000
 PUG  N3    C2   O1    123.01  3.000
 PUG  H3    N3   C4    115.93  3.000
 PUG  H3    N3   C2    114.93  3.000
 PUG  C4    N3   C2    129.15  3.000
 PUG  C9    C4   O2    127.51  3.000
 PUG  C9    C4   N3    111.25  3.000
 PUG  O2    C4   N3    121.24  3.000
 PUG  H1    N1   C8    122.01  3.000
 PUG  H1    N1   C2    117.45  3.000
 PUG  C8    N1   C2    120.53  3.000
 PUG  N7    C8   C9    108.96  3.000
 PUG  N7    C8   N1    128.08  3.000
 PUG  C9    C8   N1    122.94  3.000
 PUG  N5    C9   C8    106.56  3.000
 PUG  N5    C9   C4    131.96  3.000
 PUG  C8    C9   C4    121.47  3.000
 PUG  H5    N5   C6    123.86  3.000
 PUG  H5    N5   C9    125.99  3.000
 PUG  C6    N5   C9    110.14  3.000
 PUG  C10   N7   C6    122.95  3.000
 PUG  C10   N7   C8    127.97  3.000
 PUG  C6    N7   C8    108.86  3.000
 PUG  O4    C6   N7    125.21  3.000
 PUG  O4    C6   N5    129.33  3.000
 PUG  N7    C6   N5    105.46  3.000
 PUG  H102  C10  H101  106.59  3.000
 PUG  H102  C10  C11   111.95  3.000
 PUG  H101  C10  C11   110.31  3.000
 PUG  H102  C10  N7    108.88  3.000
 PUG  H101  C10  N7    107.66  3.000
 PUG  C11   C10  N7    111.25  3.000
 PUG  H11   C11  C12   108.14  3.000
 PUG  H11   C11  O19   106.12  3.000
 PUG  C12   C11  O19   113.25  3.000
 PUG  H11   C11  C10   107.57  3.000
 PUG  C12   C11  C10   110.34  3.000
 PUG  O19   C11  C10   111.13  3.000
 PUG  H19   O19  C11   109.41  3.000
 PUG  H12   C12  C13   108.31  3.000
 PUG  H12   C12  O21   106.04  3.000
 PUG  C13   C12  O21   111.50  3.000
 PUG  H12   C12  C11   106.89  3.000
 PUG  C13   C12  C11   112.74  3.000
 PUG  O21   C12  C11   110.98  3.000
 PUG  H21   O21  C12   109.87  3.000
 PUG  H13   C13  C14   108.59  3.000
 PUG  H13   C13  O23   105.57  3.000
 PUG  C14   C13  O23   111.79  3.000
 PUG  H13   C13  C12   108.37  3.000
 PUG  C14   C13  C12   110.70  3.000
 PUG  O23   C13  C12   111.59  3.000
 PUG  H23   O23  C13   108.89  3.000
 PUG  H142  C14  H141  106.65  3.000
 PUG  H142  C14  O26   111.58  3.000
 PUG  H141  C14  O26   111.68  3.000
 PUG  H142  C14  C13   109.54  3.000
 PUG  H141  C14  C13   108.64  3.000
 PUG  O26   C14  C13   108.70  3.000
 PUG  H26   O26  C14   107.97  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
 PUG  CONST_01  C9   C4   N3  C2    0.00   0.0  0
 PUG  CONST_02  C9   C8   N1  C2    0.00   0.0  0
 PUG  CONST_03  N7   C8   N1  C2  180.00   0.0  0
 PUG  CONST_04  C8   N1   C2  N3    0.00   0.0  0
 PUG  CONST_05  C8   C9   C4  N3    0.00   0.0  0
 PUG  CONST_06  N5   C9   C4  N3  180.00   0.0  0
 PUG  CONST_07  N1   C2   N3  C4    0.00   0.0  0
 PUG  CONST_08  N1   C8   C9  C4    0.00   0.0  0
 PUG  CONST_09  N7   C8   C9  C4  180.00   0.0  0
 PUG  CONST_10  C6   N5   C9  C4  180.00   0.0  0
 PUG  CONST_11  N5   C9   C8  N1  180.00   0.0  0
 PUG  CONST_12  C6   N7   C8  N1  180.00   0.0  0
 PUG  CONST_13  C6   N5   C9  C8    0.00   0.0  0
 PUG  CONST_14  N5   C6   N7  C8    0.00   0.0  0
 PUG  CONST_15  C6   N7   C8  C9    0.00   0.0  0
 PUG  CONST_16  N7   C6   N5  C9    0.00   0.0  0
 PUG  CONST_17  N7   C8   C9  N5    0.00   0.0  0
 PUG  CONST_18  C4   N3   C2  O1  180.00   0.0  0
 PUG  CONST_19  C8   N1   C2  O1  180.00   0.0  0
 PUG  CONST_20  O2   C4   N3  C2  180.00   0.0  0
 PUG  CONST_21  C8   C9   C4  O2  180.00   0.0  0
 PUG  CONST_22  N5   C9   C4  O2    0.00   0.0  0
 PUG  CONST_23  C10  N7   C8  N1    0.00   0.0  0
 PUG  CONST_24  O4   C6   N7  C8  180.00   0.0  0
 PUG  CONST_25  C10  N7   C8  C9  180.00   0.0  0
 PUG  CONST_26  O4   C6   N5  C9  180.00   0.0  0
 PUG  CONST_27  C10  N7   C6  N5  180.00   0.0  0
 PUG  CONST_28  H1   N1   C2  N3  180.00   0.0  0
 PUG  CONST_29  H5   N5   C9  C4    0.00   0.0  0
 PUG  CONST_30  H3   N3   C2  N1  180.00   0.0  0
 PUG  CONST_31  C10  N7   C6  O4    0.00   0.0  0
 PUG  Var_01    C11  C10  N7  C8  -88.65  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
 PUG  chir_01  C11  C10  O19  C12  negativ
 PUG  chir_02  C12  O21  C11  C13  negativ
 PUG  chir_03  C13  O23  C12  C14  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
 PUG  plan-1  O1   0.020
 PUG  plan-1  C2   0.020
 PUG  plan-1  N3   0.020
 PUG  plan-1  C4   0.020
 PUG  plan-1  O2   0.020
 PUG  plan-1  N1   0.020
 PUG  plan-1  C8   0.020
 PUG  plan-1  C9   0.020
 PUG  plan-1  N5   0.020
 PUG  plan-1  N7   0.020
 PUG  plan-1  C6   0.020
 PUG  plan-1  O4   0.020
 PUG  plan-1  C10  0.020
 PUG  plan-1  H3   0.020
 PUG  plan-1  H1   0.020
 PUG  plan-1  H5   0.020

