# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:39:46 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-deoxy-1-[6-(hydroxymethyl)-2,4-dioxo-3,4-dihydropteridin-8(2H)-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=C(CO)N=C2C(=O)NC(=O)N=C12
#
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
 1XL  1XL  1-deoxy-1-[6-(hydroxymethyl)-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl]-D-arabinitol  ligand  39  23  .  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_1XL
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
 1XL  OAD  O  OH1   0  -0.670  -6.6280   0.2177  -0.7962
 1XL  CAJ  C  CH2   0  -0.158  -5.6427   0.2554   0.2090
 1XL  CAT  C  CH1   0  -0.026  -4.2725   0.2822  -0.4509
 1XL  OAE  O  OH1   0  -0.659  -4.1221   1.3996  -1.2961
 1XL  CAV  C  CH1   0  -0.026  -3.1562   0.2300   0.6069
 1XL  OAG  O  OH1   0  -0.662  -3.2667  -0.9165   1.4189
 1XL  CAU  C  CH1   0   0.031  -1.7614   0.3218  -0.0262
 1XL  OAF  O  OH1   0  -0.682  -1.5142  -0.7870  -0.8566
 1XL  CAK  C  CH2   0  -0.388  -0.7245   0.4701   1.0846
 1XL  N8   N  NR6   0  -0.460   0.6385   0.6214   0.5582
 1XL  C7   C  CR16  0   0.023   1.1360   1.8525   0.3617
 1XL  C8A  C  CR66  0   0.613   1.3910  -0.4826   0.2818
 1XL  N1   N  N     0  -0.602   0.8578  -1.6692   0.4220
 1XL  C2   C  CR6   0   0.592   1.6263  -2.7662   0.1904
 1XL  O2   O  O     0  -0.469   1.2028  -3.8998   0.2969
 1XL  N3   N  NR16  0  -0.719   2.9574  -2.5724  -0.1847
 1XL  C4   C  CR6   0   0.556   3.5937  -1.3826  -0.3910
 1XL  O4   O  O     0  -0.425   4.7501  -1.3003  -0.7399
 1XL  C4A  C  CR66  0  -0.025   2.7253  -0.2135  -0.1407
 1XL  N5   N  N     0  -0.325   3.2027   0.9816  -0.3305
 1XL  C6   C  CR6   0   0.132   2.4149   2.0384  -0.1006
 1XL  CAI  C  CH2   0  -0.213   2.9740   3.4049  -0.3485
 1XL  OAC  O  OH1   0  -0.660   4.0711   3.5962   0.5102
 1XL  H1   H  HOH1  0   0.455  -7.4871   0.1800  -0.3671
 1XL  H2   H  HCH2  0   0.190  -5.7467   1.1486   0.8456
 1XL  H3   H  HCH2  0   0.207  -5.7077  -0.6137   0.8719
 1XL  H4   H  HCH1  0   0.233  -4.1785  -0.5952  -1.1011
 1XL  H5   H  HOH1  0   0.446  -4.2721   2.1994  -0.7795
 1XL  H6   H  HCH1  0   0.241  -3.2819   1.0876   1.2795
 1XL  H7   H  HOH1  0   0.445  -3.1973  -1.6962   0.8556
 1XL  H8   H  HCH1  0   0.248  -1.7224   1.2237  -0.6460
 1XL  H9   H  HOH1  0   0.460  -0.9479  -1.4211  -0.3887
 1XL  H10  H  HCH2  0   0.307  -0.9392   1.3607   1.6717
 1XL  H11  H  HCH2  0   0.304  -0.7262  -0.3854   1.7575
 1XL  H12  H  HCR6  0   0.346   0.4808   2.6793   0.5959
 1XL  H14  H  HNR6  0   0.424   3.4985  -3.4134  -0.3465
 1XL  H15  H  HCH2  0   0.234   3.2677   3.4708  -1.4022
 1XL  H16  H  HCH2  0   0.221   2.1859   4.1505  -0.1913
 1XL  H17  H  HOH1  0   0.463   4.5690   4.3535   0.1878

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
 1XL  O2   C2   double  1.215  0.020  1.215
 1XL  C2   N3   single  1.397  0.020  1.397
 1XL  C2   N1   single  1.359  0.020  1.359
 1XL  N3   C4   single  1.365  0.020  1.365
 1XL  N1   C8A  double  1.308  0.020  1.308
 1XL  C4   O4   double  1.211  0.020  1.211
 1XL  C4   C4A  single  1.478  0.020  1.478
 1XL  C8A  C4A  single  1.425  0.020  1.425
 1XL  C8A  N8   single  1.364  0.020  1.364
 1XL  CAK  N8   single  1.469  0.020  1.469
 1XL  CAK  CAU  single  1.527  0.020  1.527
 1XL  C4A  N5   double  1.301  0.020  1.301
 1XL  N8   C7   single  1.342  0.020  1.342
 1XL  N5   C6   single  1.338  0.020  1.338
 1XL  OAF  CAU  single  1.407  0.020  1.407
 1XL  OAG  CAV  single  1.409  0.020  1.409
 1XL  C7   C6   double  1.373  0.020  1.373
 1XL  C6   CAI  single  1.497  0.020  1.497
 1XL  CAU  CAV  single  1.535  0.020  1.535
 1XL  OAC  CAI  single  1.406  0.020  1.406
 1XL  CAV  CAT  single  1.539  0.020  1.539
 1XL  OAE  CAT  single  1.409  0.020  1.409
 1XL  CAT  CAJ  single  1.521  0.020  1.521
 1XL  CAJ  OAD  single  1.408  0.020  1.408
 1XL  OAD  H1   single  0.850  0.020  0.980
 1XL  CAJ  H2   single  0.970  0.020  1.090
 1XL  CAJ  H3   single  0.970  0.020  1.090
 1XL  CAT  H4   single  0.970  0.020  1.090
 1XL  OAE  H5   single  0.850  0.020  0.980
 1XL  CAV  H6   single  0.970  0.020  1.090
 1XL  OAG  H7   single  0.850  0.020  0.980
 1XL  CAU  H8   single  0.970  0.020  1.090
 1XL  OAF  H9   single  0.850  0.020  0.980
 1XL  CAK  H10  single  0.970  0.020  1.090
 1XL  CAK  H11  single  0.970  0.020  1.090
 1XL  C7   H12  single  0.930  0.020  1.080
 1XL  N3   H14  single  0.860  0.020  1.020
 1XL  CAI  H15  single  0.970  0.020  1.090
 1XL  CAI  H16  single  0.970  0.020  1.090
 1XL  OAC  H17  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
 1XL  H1   OAD  CAJ  107.92  3.000
 1XL  H3   CAJ  H2   106.75  3.000
 1XL  H3   CAJ  CAT  109.27  3.000
 1XL  H2   CAJ  CAT  108.75  3.000
 1XL  H3   CAJ  OAD  111.68  3.000
 1XL  H2   CAJ  OAD  111.60  3.000
 1XL  CAT  CAJ  OAD  108.73  3.000
 1XL  H4   CAT  CAV  108.57  3.000
 1XL  H4   CAT  OAE  105.65  3.000
 1XL  CAV  CAT  OAE  111.21  3.000
 1XL  H4   CAT  CAJ  108.69  3.000
 1XL  OAE  CAT  CAJ  111.73  3.000
 1XL  CAV  CAT  CAJ  110.77  3.000
 1XL  H5   OAE  CAT  108.66  3.000
 1XL  H6   CAV  CAU  108.08  3.000
 1XL  H6   CAV  OAG  105.89  3.000
 1XL  CAU  CAV  OAG  110.96  3.000
 1XL  H6   CAV  CAT  108.17  3.000
 1XL  CAU  CAV  CAT  111.95  3.000
 1XL  OAG  CAV  CAT  111.52  3.000
 1XL  H7   OAG  CAV  108.40  3.000
 1XL  H8   CAU  CAK  107.92  3.000
 1XL  H8   CAU  OAF  107.98  3.000
 1XL  CAK  CAU  OAF  112.74  3.000
 1XL  H8   CAU  CAV  108.37  3.000
 1XL  OAF  CAU  CAV  110.85  3.000
 1XL  CAK  CAU  CAV  108.84  3.000
 1XL  H9   OAF  CAU  109.44  3.000
 1XL  H11  CAK  H10  108.02  3.000
 1XL  H11  CAK  N8   107.69  3.000
 1XL  H10  CAK  N8   106.98  3.000
 1XL  H11  CAK  CAU  111.86  3.000
 1XL  H10  CAK  CAU  109.76  3.000
 1XL  N8   CAK  CAU  112.30  3.000
 1XL  C8A  N8   C7   120.54  3.000
 1XL  C7   N8   CAK  119.40  3.000
 1XL  C8A  N8   CAK  120.07  3.000
 1XL  H12  C7   C6   122.29  3.000
 1XL  H12  C7   N8   116.45  3.000
 1XL  C6   C7   N8   121.26  3.000
 1XL  C4A  C8A  N1   125.77  3.000
 1XL  C4A  C8A  N8   115.06  3.000
 1XL  N1   C8A  N8   119.17  3.000
 1XL  C2   N1   C8A  118.90  3.000
 1XL  N3   C2   O2   119.03  3.000
 1XL  N3   C2   N1   118.21  3.000
 1XL  O2   C2   N1   122.76  3.000
 1XL  H14  N3   C4   116.78  3.000
 1XL  H14  N3   C2   115.90  3.000
 1XL  C4   N3   C2   127.29  3.000
 1XL  C4A  C4   O4   123.80  3.000
 1XL  C4A  C4   N3   112.96  3.000
 1XL  O4   C4   N3   123.23  3.000
 1XL  N5   C4A  C4   119.11  3.000
 1XL  N5   C4A  C8A  124.07  3.000
 1XL  C4   C4A  C8A  116.81  3.000
 1XL  C6   N5   C4A  118.98  3.000
 1XL  CAI  C6   N5   118.20  3.000
 1XL  CAI  C6   C7   121.83  3.000
 1XL  N5   C6   C7   119.96  3.000
 1XL  H16  CAI  H15  106.84  3.000
 1XL  H16  CAI  OAC  112.38  3.000
 1XL  H15  CAI  OAC  111.70  3.000
 1XL  H16  CAI  C6   109.18  3.000
 1XL  H15  CAI  C6   108.31  3.000
 1XL  OAC  CAI  C6   108.33  3.000
 1XL  H17  OAC  CAI  107.84  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
 1XL  CONST_01  C2   N1   C8A  N8   180.00   0.0  0
 1XL  CONST_02  N1   C8A  N8   C7   180.00   0.0  0
 1XL  CONST_03  C4A  C8A  N8   C7     0.00   0.0  0
 1XL  CONST_04  N3   C2   N1   C8A    0.00   0.0  0
 1XL  CONST_05  C4   N3   C2   N1     0.00   0.0  0
 1XL  CONST_06  C4A  C8A  N1   C2     0.00   0.0  0
 1XL  CONST_07  N1   C8A  N8   CAK    0.00   0.0  0
 1XL  CONST_08  C4A  C8A  N8   CAK  180.00   0.0  0
 1XL  CONST_09  O2   C2   N1   C8A  180.00   0.0  0
 1XL  CONST_10  C4   N3   C2   O2   180.00   0.0  0
 1XL  CONST_11  H14  N3   C2   N1   180.00   0.0  0
 1XL  Var_01    C8A  N8   CAK  CAU  -87.02  30.0  3
 1XL  Var_02    OAC  CAI  C6   C7   117.62  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
 1XL  chir_01  CAT  CAV  OAE  CAJ  positiv
 1XL  chir_02  CAV  OAG  CAT  CAU  positiv
 1XL  chir_03  CAU  OAF  CAV  CAK  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
 1XL  plan-1  CAK  0.020
 1XL  plan-1  N8   0.020
 1XL  plan-1  C7   0.020
 1XL  plan-1  C8A  0.020
 1XL  plan-1  N1   0.020
 1XL  plan-1  C2   0.020
 1XL  plan-1  O2   0.020
 1XL  plan-1  N3   0.020
 1XL  plan-1  C4   0.020
 1XL  plan-1  O4   0.020
 1XL  plan-1  C4A  0.020
 1XL  plan-1  N5   0.020
 1XL  plan-1  C6   0.020
 1XL  plan-1  CAI  0.020
 1XL  plan-1  H12  0.020
 1XL  plan-1  H14  0.020

