# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 15:21:51 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 7-[(2S)-2,3-dihydroxypropyl]-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2ncn(C[C@H](O)CO)c2C1=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
 X0T  X0T  7-[(2S)-2,3-dihydroxypropyl]-1,3-dimethyl-3,7-dihydro-1H-purine-2,6-dione  ligand  32  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X0T
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
 X0T  CAB   C  CH3   0  -0.535   3.5436  -1.7570  -0.6556
 X0T  N3    N  NR6   0  -0.587   2.5416  -0.7771  -0.2695
 X0T  C2    C  CR6   0   0.724   2.8470   0.5587  -0.1990
 X0T  O2    O  O     0  -0.487   3.9614   0.9750  -0.4508
 X0T  N1    N  NR6   0  -0.601   1.8164   1.4216   0.1789
 X0T  CAA   C  CH3   0  -0.531   2.1192   2.8472   0.2700
 X0T  C6    C  CR6   0   0.587   0.4997   1.0706   0.4724
 X0T  O6    O  O     0  -0.484  -0.3210   1.9195   0.7893
 X0T  C5    C  CR56  0   0.148   0.2742  -0.3277   0.3533
 X0T  C4    C  CR56  0   0.437   1.2727  -1.1968   0.0022
 X0T  N9    N  N     0  -0.470   0.8381  -2.4681  -0.0254
 X0T  C8    C  CR15  0   0.133  -0.4339  -2.3756   0.3184
 X0T  N7    N  NR5   0  -0.474  -0.8301  -1.1208   0.5650
 X0T  CAI   C  CH2   0  -0.359  -2.1715  -0.7022   0.9186
 X0T  CAO   C  CH1   0  -0.007  -2.9851  -0.2678  -0.3029
 X0T  OAF   O  OH1   0  -0.657  -2.2933   0.6448  -1.1139
 X0T  CAH   C  CH2   0  -0.159  -4.3315   0.2614   0.1640
 X0T  OAE   O  OH1   0  -0.667  -5.1380   0.4987  -0.9622
 X0T  HAB1  H  HCH3  0   0.272   4.5101  -1.2739  -0.7295
 X0T  HAB2  H  HCH3  0   0.260   3.5970  -2.5457   0.0914
 X0T  HAB3  H  HCH3  0   0.259   3.2915  -2.1985  -1.6185
 X0T  HAA1  H  HCH3  0   0.271   3.1614   3.0087   0.0296
 X0T  HAA2  H  HCH3  0   0.256   1.5050   3.4098  -0.4298
 X0T  HAA3  H  HCH3  0   0.256   1.9283   3.2103   1.2775
 X0T  H8    H  HCR5  0   0.303  -1.1096  -3.2129   0.4091
 X0T  HAI1  H  HCH2  0   0.289  -2.6620  -1.5433   1.4076
 X0T  HAI2  H  HCH2  0   0.279  -2.0981   0.0991   1.6540
 X0T  HAO   H  HCH1  0   0.243  -3.1553  -1.1509  -0.9277
 X0T  HAF   H  HOH1  0   0.445  -2.0534   1.4167  -0.5864
 X0T  HAH1  H  HCH2  0   0.203  -4.7843  -0.4743   0.8423
 X0T  HAH2  H  HCH2  0   0.199  -4.1713   1.1771   0.7522
 X0T  HAE   H  HOH1  0   0.457  -5.9727   0.8674  -0.6596

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
 X0T  CAB  N3    single    1.454  0.020  1.454
 X0T  N3   C2    single    1.372  0.020  1.372
 X0T  N3   C4    single    1.364  0.020  1.364
 X0T  C2   O2    double    1.216  0.020  1.216
 X0T  C2   N1    single    1.396  0.020  1.396
 X0T  N1   CAA   single    1.460  0.020  1.460
 X0T  N1   C6    single    1.394  0.020  1.394
 X0T  C6   O6    double    1.222  0.020  1.222
 X0T  C6   C5    single    1.421  0.020  1.421
 X0T  C5   C4    aromatic  1.370  0.020  1.370
 X0T  C5   N7    aromatic  1.376  0.020  1.376
 X0T  C4   N9    aromatic  1.344  0.020  1.344
 X0T  N9   C8    aromatic  1.321  0.020  1.321
 X0T  C8   N7    aromatic  1.339  0.020  1.339
 X0T  N7   CAI   single    1.449  0.020  1.449
 X0T  CAI  CAO   single    1.531  0.020  1.531
 X0T  CAO  OAF   single    1.403  0.020  1.403
 X0T  CAO  CAH   single    1.520  0.020  1.520
 X0T  CAH  OAE   single    1.405  0.020  1.405
 X0T  CAB  HAB1  single    0.970  0.020  1.090
 X0T  CAB  HAB2  single    0.970  0.020  1.090
 X0T  CAB  HAB3  single    0.970  0.020  1.090
 X0T  CAA  HAA1  single    0.970  0.020  1.090
 X0T  CAA  HAA2  single    0.970  0.020  1.090
 X0T  CAA  HAA3  single    0.970  0.020  1.090
 X0T  C8   H8    single    0.930  0.020  1.080
 X0T  CAI  HAI1  single    0.970  0.020  1.090
 X0T  CAI  HAI2  single    0.970  0.020  1.090
 X0T  CAO  HAO   single    0.970  0.020  1.090
 X0T  OAF  HAF   single    0.850  0.020  0.980
 X0T  CAH  HAH1  single    0.970  0.020  1.090
 X0T  CAH  HAH2  single    0.970  0.020  1.090
 X0T  OAE  HAE   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
 X0T  HAB3  CAB  HAB2  108.95  3.000
 X0T  HAB3  CAB  HAB1  109.10  3.000
 X0T  HAB2  CAB  HAB1  109.06  3.000
 X0T  HAB3  CAB  N3    110.40  3.000
 X0T  HAB2  CAB  N3    109.89  3.000
 X0T  HAB1  CAB  N3    109.42  3.000
 X0T  C4    N3   C2    119.76  3.000
 X0T  C4    N3   CAB   119.13  3.000
 X0T  C2    N3   CAB   121.10  3.000
 X0T  N1    C2   O2    121.40  3.000
 X0T  N1    C2   N3    116.83  3.000
 X0T  O2    C2   N3    121.78  3.000
 X0T  C6    N1   CAA   115.37  3.000
 X0T  C6    N1   C2    126.77  3.000
 X0T  CAA   N1   C2    117.85  3.000
 X0T  HAA3  CAA  HAA2  108.91  3.000
 X0T  HAA3  CAA  HAA1  108.98  3.000
 X0T  HAA2  CAA  HAA1  108.89  3.000
 X0T  HAA3  CAA  N1    110.32  3.000
 X0T  HAA2  CAA  N1    110.34  3.000
 X0T  HAA1  CAA  N1    109.37  3.000
 X0T  C5    C6   O6    126.75  3.000
 X0T  C5    C6   N1    112.33  3.000
 X0T  O6    C6   N1    120.92  3.000
 X0T  N7    C5   C4    105.00  3.000
 X0T  N7    C5   C6    132.96  3.000
 X0T  C4    C5   C6    122.01  3.000
 X0T  N9    C4   C5    111.70  3.000
 X0T  N9    C4   N3    126.01  3.000
 X0T  C5    C4   N3    122.28  3.000
 X0T  C8    N9   C4    103.88  3.000
 X0T  H8    C8   N7    121.75  3.000
 X0T  H8    C8   N9    124.77  3.000
 X0T  N7    C8   N9    113.48  3.000
 X0T  CAI   N7   C8    126.13  3.000
 X0T  CAI   N7   C5    127.88  3.000
 X0T  C8    N7   C5    105.93  3.000
 X0T  HAI2  CAI  HAI1  107.16  3.000
 X0T  HAI2  CAI  CAO   111.44  3.000
 X0T  HAI1  CAI  CAO   109.76  3.000
 X0T  HAI2  CAI  N7    108.34  3.000
 X0T  HAI1  CAI  N7    107.65  3.000
 X0T  CAO   CAI  N7    112.29  3.000
 X0T  HAO   CAO  CAH   108.56  3.000
 X0T  HAO   CAO  OAF   105.75  3.000
 X0T  CAH   CAO  OAF   112.82  3.000
 X0T  HAO   CAO  CAI   108.00  3.000
 X0T  CAH   CAO  CAI   108.93  3.000
 X0T  OAF   CAO  CAI   112.57  3.000
 X0T  HAF   OAF  CAO   109.08  3.000
 X0T  HAH2  CAH  HAH1  106.70  3.000
 X0T  HAH2  CAH  OAE   111.81  3.000
 X0T  HAH1  CAH  OAE   111.79  3.000
 X0T  HAH2  CAH  CAO   108.97  3.000
 X0T  HAH1  CAH  CAO   108.77  3.000
 X0T  OAE   CAH  CAO   108.72  3.000
 X0T  HAE   OAE  CAH   108.10  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
 X0T  CONST_01  C8    N9   C4  C5     0.00   0.0  0
 X0T  CONST_02  N9    C8   N7  C5     0.00   0.0  0
 X0T  CONST_03  C8    N7   C5  C4     0.00   0.0  0
 X0T  CONST_04  N7    C8   N9  C4     0.00   0.0  0
 X0T  CONST_05  N7    C5   C4  N9     0.00   0.0  0
 X0T  CONST_06  C6    N1   C2  N3     0.00   0.0  0
 X0T  CONST_07  C5    C6   N1  C2     0.00   0.0  0
 X0T  CONST_08  C4    N3   C2  N1     0.00   0.0  0
 X0T  CONST_09  CAI   N7   C5  C6     0.00   0.0  0
 X0T  CONST_10  CAI   N7   C5  C4   180.00   0.0  0
 X0T  CONST_11  CAI   N7   C8  N9   180.00   0.0  0
 X0T  CONST_12  N1    C2   N3  CAB  180.00   0.0  0
 X0T  CONST_13  CAA   N1   C2  N3   180.00   0.0  0
 X0T  CONST_14  O6    C6   N1  C2   180.00   0.0  0
 X0T  CONST_15  C4    N3   C2  O2   180.00   0.0  0
 X0T  CONST_16  C6    N1   C2  O2   180.00   0.0  0
 X0T  CONST_17  C5    C6   N1  CAA  180.00   0.0  0
 X0T  CONST_18  H8    C8   N7  C5   180.00   0.0  0
 X0T  CONST_19  O2    C2   N3  CAB    0.00   0.0  0
 X0T  CONST_20  CAA   N1   C2  O2     0.00   0.0  0
 X0T  CONST_21  O6    C6   N1  CAA    0.00   0.0  0
 X0T  Var_01    CAO   CAI  N7  C5    82.71  30.0  2
 X0T  Var_02    HAB1  CAB  N3  C2     7.24  30.0  3
 X0T  Var_03    HAA1  CAA  N1  C2    -0.92  30.0  3

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
 X0T  chir_01  CAO  CAI  OAF  CAH  positiv

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
 X0T  plan-1  CAB  0.020
 X0T  plan-1  N3   0.020
 X0T  plan-1  C2   0.020
 X0T  plan-1  O2   0.020
 X0T  plan-1  N1   0.020
 X0T  plan-1  CAA  0.020
 X0T  plan-1  C6   0.020
 X0T  plan-1  O6   0.020
 X0T  plan-1  C5   0.020
 X0T  plan-1  C4   0.020
 X0T  plan-1  N9   0.020
 X0T  plan-1  C8   0.020
 X0T  plan-1  N7   0.020
 X0T  plan-1  CAI  0.020
 X0T  plan-1  H8   0.020

