# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:15:22 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(C)N(C[C@H](O)[C@H](O)[C@H](O)CO)C2=NC(=O)NC(=O)C2=N1
#
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
 DLZ  DLZ  1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol  ligand  41  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DLZ
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
 DLZ  C7    C  CH3   0  -0.772   0.1315   3.3187  -0.1667
 DLZ  C7A   C  CR6   0   0.374   1.0848   2.1787  -0.0800
 DLZ  C5A   C  CR6   0   0.139   2.4015   2.3540   0.3513
 DLZ  C6    C  CH3   0  -0.758   2.9256   3.6940   0.7674
 DLZ  N5    N  N     0  -0.339   3.2377   1.3244   0.3954
 DLZ  C4A   C  CR66  0  -0.026   2.8202   0.1312   0.0598
 DLZ  C4    C  CR6   0   0.547   3.7590  -1.0005   0.1206
 DLZ  O4    O  O     0  -0.437   4.9213  -0.9036   0.4534
 DLZ  N3    N  NR16  0  -0.718   3.1851  -2.1861  -0.2409
 DLZ  C2    C  CR6   0   0.578   1.8580  -2.3981  -0.6201
 DLZ  O2    O  O     0  -0.481   1.4975  -3.5287  -0.8919
 DLZ  N1    N  N     0  -0.606   1.0260  -1.3285  -0.6669
 DLZ  C8    C  CR66  0   0.594   1.5004  -0.1434  -0.3586
 DLZ  N8    N  NR6   0  -0.499   0.6721   0.9472  -0.4496
 DLZ  C1'   C  CH2   0  -0.395  -0.6754   0.7370  -1.0005
 DLZ  C2'   C  CH1   0   0.005  -1.6946   0.3574   0.0846
 DLZ  O2'   O  OH1   0  -0.664  -1.2019  -0.6394   0.9419
 DLZ  C3'   C  CH1   0  -0.034  -3.0053  -0.0917  -0.5919
 DLZ  O3'   O  OH1   0  -0.657  -3.3030   0.6653  -1.7442
 DLZ  C4'   C  CH1   0  -0.009  -4.2168  -0.0877   0.3640
 DLZ  O4'   O  OH1   0  -0.658  -3.9071  -0.4318   1.6902
 DLZ  C5'   C  CH2   0  -0.159  -5.3194  -0.9656  -0.2079
 DLZ  O5'   O  OH1   0  -0.672  -6.4922  -0.7786   0.5478
 DLZ  H7    H  HCH3  0   0.299  -0.0509   3.5955  -1.2075
 DLZ  H7A   H  HCH3  0   0.287  -0.8284   3.0821   0.2893
 DLZ  H7B   H  HCH3  0   0.303   0.5258   4.1927   0.3402
 DLZ  H6    H  HCH3  0   0.264   2.4085   4.0713   1.6506
 DLZ  H6A   H  HCH3  0   0.272   3.9826   3.6079   1.0071
 DLZ  H6B   H  HCH3  0   0.262   2.8146   4.4380  -0.0214
 DLZ  HN3   H  HNR6  0   0.420   3.7781  -3.0067  -0.2171
 DLZ  H1'   H  HCH2  0   0.310  -0.9723   1.6440  -1.5153
 DLZ  H1'A  H  HCH2  0   0.312  -0.5891  -0.0475  -1.7505
 DLZ  H2'   H  HCH1  0   0.248  -1.8871   1.2344   0.7136
 DLZ  HO2'  H  HOH1  0   0.456  -0.7230  -1.2926   0.4083
 DLZ  H3'   H  HCH1  0   0.243  -2.8311  -1.1129  -0.9558
 DLZ  HO3'  H  HOH1  0   0.451  -3.5775   1.5496  -1.4762
 DLZ  H4'   H  HCH1  0   0.228  -4.5867   0.9452   0.4159
 DLZ  HO4'  H  HOH1  0   0.442  -3.3981  -1.2494   1.6932
 DLZ  H5'   H  HCH2  0   0.202  -5.4708  -0.7046  -1.2622
 DLZ  H5'A  H  HCH2  0   0.194  -4.9812  -2.0127  -0.1828
 DLZ  HO5'  H  HOH1  0   0.455  -7.1829  -1.3276   0.1670

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
 DLZ  C7   C7A   single  1.489  0.020  1.489
 DLZ  C7A  C5A   double  1.397  0.020  1.397
 DLZ  C7A  N8    single  1.350  0.020  1.350
 DLZ  C5A  C6    single  1.498  0.020  1.498
 DLZ  C5A  N5    single  1.327  0.020  1.327
 DLZ  N5   C4A   double  1.308  0.020  1.308
 DLZ  C4A  C4    single  1.472  0.020  1.472
 DLZ  C4A  C8    single  1.411  0.020  1.411
 DLZ  C4   O4    double  1.213  0.020  1.213
 DLZ  C4   N3    single  1.366  0.020  1.366
 DLZ  N3   C2    single  1.396  0.020  1.396
 DLZ  C2   O2    double  1.217  0.020  1.217
 DLZ  C2   N1    single  1.356  0.020  1.356
 DLZ  N1   C8    double  1.313  0.020  1.313
 DLZ  C8   N8    single  1.372  0.020  1.372
 DLZ  N8   C1'   single  1.471  0.020  1.471
 DLZ  C1'  C2'   single  1.536  0.020  1.536
 DLZ  C2'  O2'   single  1.404  0.020  1.404
 DLZ  C2'  C3'   single  1.542  0.020  1.542
 DLZ  C3'  O3'   single  1.411  0.020  1.411
 DLZ  C3'  C4'   single  1.543  0.020  1.543
 DLZ  C4'  O4'   single  1.405  0.020  1.405
 DLZ  C4'  C5'   single  1.521  0.020  1.521
 DLZ  C5'  O5'   single  1.408  0.020  1.408
 DLZ  C7   H7    single  0.970  0.020  1.090
 DLZ  C7   H7A   single  0.970  0.020  1.090
 DLZ  C7   H7B   single  0.970  0.020  1.090
 DLZ  C6   H6    single  0.970  0.020  1.090
 DLZ  C6   H6A   single  0.970  0.020  1.090
 DLZ  C6   H6B   single  0.970  0.020  1.090
 DLZ  N3   HN3   single  0.860  0.020  1.020
 DLZ  C1'  H1'   single  0.970  0.020  1.090
 DLZ  C1'  H1'A  single  0.970  0.020  1.090
 DLZ  C2'  H2'   single  0.970  0.020  1.090
 DLZ  O2'  HO2'  single  0.850  0.020  0.980
 DLZ  C3'  H3'   single  0.970  0.020  1.090
 DLZ  O3'  HO3'  single  0.850  0.020  0.980
 DLZ  C4'  H4'   single  0.970  0.020  1.090
 DLZ  O4'  HO4'  single  0.850  0.020  0.980
 DLZ  C5'  H5'   single  0.970  0.020  1.090
 DLZ  C5'  H5'A  single  0.970  0.020  1.090
 DLZ  O5'  HO5'  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
 DLZ  H7B   C7   H7A  107.45  3.000
 DLZ  H7B   C7   H7   107.57  3.000
 DLZ  H7A   C7   H7   107.87  3.000
 DLZ  H7B   C7   C7A  110.92  3.000
 DLZ  H7A   C7   C7A  111.95  3.000
 DLZ  H7    C7   C7A  110.88  3.000
 DLZ  N8    C7A  C5A  119.15  3.000
 DLZ  N8    C7A  C7   119.13  3.000
 DLZ  C5A   C7A  C7   121.71  3.000
 DLZ  N5    C5A  C6   117.67  3.000
 DLZ  N5    C5A  C7A  120.46  3.000
 DLZ  C6    C5A  C7A  121.87  3.000
 DLZ  H6B   C6   H6A  108.22  3.000
 DLZ  H6B   C6   H6   107.55  3.000
 DLZ  H6A   C6   H6   108.04  3.000
 DLZ  H6B   C6   C5A  111.96  3.000
 DLZ  H6A   C6   C5A  109.31  3.000
 DLZ  H6    C6   C5A  111.62  3.000
 DLZ  C4A   N5   C5A  119.87  3.000
 DLZ  C8    C4A  C4   117.33  3.000
 DLZ  C8    C4A  N5   123.51  3.000
 DLZ  C4    C4A  N5   119.16  3.000
 DLZ  N3    C4   O4   123.00  3.000
 DLZ  N3    C4   C4A  112.86  3.000
 DLZ  O4    C4   C4A  124.14  3.000
 DLZ  HN3   N3   C2   116.09  3.000
 DLZ  HN3   N3   C4   116.81  3.000
 DLZ  C2    N3   C4   127.09  3.000
 DLZ  N1    C2   O2   122.90  3.000
 DLZ  N1    C2   N3   118.21  3.000
 DLZ  O2    C2   N3   118.89  3.000
 DLZ  C8    N1   C2   118.82  3.000
 DLZ  N8    C8   N1   118.92  3.000
 DLZ  N8    C8   C4A  115.43  3.000
 DLZ  N1    C8   C4A  125.66  3.000
 DLZ  C1'   N8   C8   117.66  3.000
 DLZ  C1'   N8   C7A  120.85  3.000
 DLZ  C8    N8   C7A  121.47  3.000
 DLZ  H1'A  C1'  H1'  107.30  3.000
 DLZ  H1'A  C1'  C2'  111.17  3.000
 DLZ  H1'   C1'  C2'  111.12  3.000
 DLZ  H1'A  C1'  N8   106.76  3.000
 DLZ  H1'   C1'  N8   108.00  3.000
 DLZ  C2'   C1'  N8   112.24  3.000
 DLZ  H2'   C2'  C3'  109.60  3.000
 DLZ  H2'   C2'  O2'  106.22  3.000
 DLZ  C3'   C2'  O2'  111.06  3.000
 DLZ  H2'   C2'  C1'  108.91  3.000
 DLZ  C3'   C2'  C1'  109.03  3.000
 DLZ  O2'   C2'  C1'  111.95  3.000
 DLZ  HO2'  O2'  C2'  108.39  3.000
 DLZ  H3'   C3'  C4'  109.40  3.000
 DLZ  H3'   C3'  O3'  105.18  3.000
 DLZ  C4'   C3'  O3'  109.81  3.000
 DLZ  H3'   C3'  C2'  106.35  3.000
 DLZ  C4'   C3'  C2'  113.26  3.000
 DLZ  O3'   C3'  C2'  112.43  3.000
 DLZ  HO3'  O3'  C3'  108.98  3.000
 DLZ  H4'   C4'  C5'  108.45  3.000
 DLZ  H4'   C4'  O4'  105.07  3.000
 DLZ  C5'   C4'  O4'  111.93  3.000
 DLZ  H4'   C4'  C3'  107.22  3.000
 DLZ  C5'   C4'  C3'  109.56  3.000
 DLZ  O4'   C4'  C3'  114.27  3.000
 DLZ  HO4'  O4'  C4'  109.12  3.000
 DLZ  H5'A  C5'  H5'  106.90  3.000
 DLZ  H5'A  C5'  O5'  111.72  3.000
 DLZ  H5'   C5'  O5'  111.69  3.000
 DLZ  H5'A  C5'  C4'  108.53  3.000
 DLZ  H5'   C5'  C4'  108.91  3.000
 DLZ  O5'   C5'  C4'  108.99  3.000
 DLZ  HO5'  O5'  C5'  108.07  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
 DLZ  CONST_01  C4A  C8   N8   C7A    0.00   0.0  0
 DLZ  CONST_02  N1   C8   N8   C7A  180.00   0.0  0
 DLZ  CONST_03  C2   N3   C4   C4A    0.00   0.0  0
 DLZ  CONST_04  C2   N1   C8   C4A    0.00   0.0  0
 DLZ  CONST_05  N1   C2   N3   C4     0.00   0.0  0
 DLZ  CONST_06  C8   N1   C2   N3     0.00   0.0  0
 DLZ  CONST_07  N8   C8   N1   C2   180.00   0.0  0
 DLZ  CONST_08  C1'  N8   C8   C4A  180.00   0.0  0
 DLZ  CONST_09  O2   C2   N3   C4   180.00   0.0  0
 DLZ  CONST_10  C2   N3   C4   O4   180.00   0.0  0
 DLZ  CONST_11  C8   N1   C2   O2   180.00   0.0  0
 DLZ  CONST_12  C1'  N8   C8   N1     0.00   0.0  0
 DLZ  CONST_13  HN3  N3   C4   C4A  180.00   0.0  0
 DLZ  Var_01    C2'  C1'  N8   C7A  -92.93  30.0  3
 DLZ  Var_02    H6   C6   C5A  C7A   63.84  30.0  3
 DLZ  Var_03    H7   C7   C7A  C5A  107.01  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
 DLZ  chir_01  C2'  C1'  O2'  C3'  positiv
 DLZ  chir_02  C3'  O3'  C2'  C4'  negativ
 DLZ  chir_03  C4'  O4'  C3'  C5'  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
 DLZ  plan-1  C7   0.020
 DLZ  plan-1  C7A  0.020
 DLZ  plan-1  C5A  0.020
 DLZ  plan-1  C6   0.020
 DLZ  plan-1  N5   0.020
 DLZ  plan-1  C4A  0.020
 DLZ  plan-1  C4   0.020
 DLZ  plan-1  O4   0.020
 DLZ  plan-1  N3   0.020
 DLZ  plan-1  C2   0.020
 DLZ  plan-1  O2   0.020
 DLZ  plan-1  N1   0.020
 DLZ  plan-1  C8   0.020
 DLZ  plan-1  N8   0.020
 DLZ  plan-1  C1'  0.020
 DLZ  plan-1  HN3  0.020

