# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 00:58:19 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: methyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-3-O-methyl-beta-D-ribo-hexofuranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1[nH]c2cc3C(=O)NC(=Nc3c(CC[C@H]4O[C@@H](OC)[C@H](O)[C@@H]4OC)c2n1)N
#
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
 1UD  1UD  'methyl 6-[6-amino-2-(methylamino)-8-oxo-7,8-dihydro-1H-imidazo[4,5-g]quinazolin-4-yl]-5,6-dideoxy-3-O-methyl-beta-D-ribo-hexofuranoside'  ligand  53  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1UD
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
 1UD  C1   C  CR66  0  -0.154   3.4343  -0.7979  -0.1034
 1UD  C2   C  CR16  0  -0.374   3.9804   0.4582  -0.4067
 1UD  C3   C  CR56  0   0.363   3.1566   1.5374  -0.2523
 1UD  C4   C  CR56  0   0.135   1.8148   1.4218   0.1909
 1UD  C5   C  CR6   0  -0.062   1.2689   0.1828   0.4991
 1UD  C6   C  CH2   0  -0.492  -0.1559   0.0550   0.9458
 1UD  C7   C  CH2   0  -0.464  -1.0754  -0.3895  -0.1916
 1UD  C8   C  CR66  0   0.220   2.0983  -0.9437   0.3434
 1UD  N9   N  N     0  -0.512   1.5668  -2.1747   0.6424
 1UD  C10  C  CR6   0   0.637   2.3095  -3.2188   0.4906
 1UD  N11  N  NH2   0  -0.836   1.8158  -4.4598   0.7104
 1UD  N12  N  NR16  0  -0.718   3.6063  -3.1571   0.0573
 1UD  C13  C  CR6   0   0.541   4.2541  -1.9825  -0.2563
 1UD  O14  O  O     0  -0.477   5.4181  -2.0009  -0.6304
 1UD  N15  N  NR15  0  -0.750   3.3410   2.8905  -0.4494
 1UD  N16  N  N     0  -0.537   1.2286   2.6562   0.2506
 1UD  C17  C  CR5   0   0.691   2.1657   3.5013  -0.1352
 1UD  N18  N  NH1   0  -0.677   2.0123   4.8261  -0.2112
 1UD  C19  C  CH3   0  -0.544   3.0285   5.7277  -0.6943
 1UD  C20  C  CH1   0   0.291  -4.4626   0.5362   0.5939
 1UD  O21  O  O2    0  -0.492  -5.0824   1.7643   0.5796
 1UD  C22  C  CH3   0  -0.410  -5.0720   2.4453   1.8195
 1UD  O23  O  O2    0  -0.513  -3.0649   0.6912   0.6192
 1UD  C24  C  CH1   0   0.048  -2.5193  -0.5542   0.2257
 1UD  C25  C  CH1   0   0.008  -3.4457  -1.0683  -0.8900
 1UD  O26  O  O2    0  -0.487  -3.6007  -2.4497  -0.7541
 1UD  C26  C  CH3   0  -0.406  -3.9196  -3.1170  -1.9522
 1UD  C27  C  CH1   0  -0.022  -4.7446  -0.2468  -0.6925
 1UD  O28  O  OH1   0  -0.657  -5.8696  -1.0742  -0.6132
 1UD  H1   H  HCR6  0   0.264   5.0033   0.5517  -0.7461
 1UD  H2   H  HCH2  0   0.231  -0.2238  -0.6678   1.7626
 1UD  H3   H  HCH2  0   0.242  -0.4938   1.0162   1.3360
 1UD  H4   H  HCH2  0   0.230  -1.0187   0.3234  -1.0204
 1UD  H5   H  HCH2  0   0.244  -0.7301  -1.3525  -0.5766
 1UD  H6   H  HNH2  0   0.401   0.9421  -4.4981   1.2095
 1UD  H7   H  HNH2  0   0.403   2.4519  -5.2108   0.9232
 1UD  H8   H  HNR6  0   0.419   4.1315  -4.0130  -0.0655
 1UD  H9   H  HNR5  0   0.424   4.1847   3.3335  -0.7750
 1UD  H11  H  HNH1  0   0.407   1.0975   5.1852   0.0010
 1UD  H12  H  HCH3  0   0.244   3.9279   5.6950  -0.0755
 1UD  H13  H  HCH3  0   0.243   3.3111   5.5182  -1.7286
 1UD  H14  H  HCH3  0   0.270   2.6357   6.7389  -0.6525
 1UD  H16  H  HCH3  0   0.213  -5.4711   1.8193   2.6241
 1UD  H17  H  HCH3  0   0.219  -4.0701   2.7773   2.1029
 1UD  H18  H  HCH3  0   0.238  -5.7088   3.3218   1.7149
 1UD  H19  H  HCH1  0   0.218  -2.5797  -1.2681   1.0631
 1UD  H20  H  HCH1  0   0.226  -3.0131  -0.8292  -1.8716
 1UD  H21  H  HCH3  0   0.212  -4.8851  -2.8123  -2.3639
 1UD  H22  H  HCH3  0   0.205  -3.1536  -2.9542  -2.7192
 1UD  H23  H  HCH3  0   0.231  -3.9618  -4.1835  -1.7326
 1UD  H24  H  HCH1  0   0.228  -4.8324   0.4781  -1.5119
 1UD  H25  H  HOH1  0   0.456  -6.6529  -0.5223  -0.6965
 1UD  H15  H  HCH1  0   0.181  -4.7907  -0.0570   1.4688

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
 1UD  C19  N18  single    1.442  0.020  1.442
 1UD  C22  O21  single    1.415  0.020  1.415
 1UD  O21  C20  single    1.376  0.020  1.376
 1UD  N18  C17  single    1.336  0.020  1.336
 1UD  C20  C27  single    1.532  0.020  1.532
 1UD  C20  O23  single    1.407  0.020  1.407
 1UD  C27  O28  single    1.399  0.020  1.399
 1UD  C27  C25  single    1.549  0.020  1.549
 1UD  C17  N16  aromatic  1.319  0.020  1.319
 1UD  C17  N15  aromatic  1.361  0.020  1.361
 1UD  O23  C24  single    1.415  0.020  1.415
 1UD  N16  C4   aromatic  1.368  0.020  1.368
 1UD  C25  C24  single    1.539  0.020  1.539
 1UD  C25  O26  single    1.397  0.020  1.397
 1UD  N15  C3   aromatic  1.380  0.020  1.380
 1UD  C24  C7   single    1.512  0.020  1.512
 1UD  C7   C6   single    1.529  0.020  1.529
 1UD  C4   C3   aromatic  1.418  0.020  1.418
 1UD  C4   C5   aromatic  1.389  0.020  1.389
 1UD  O26  C26  single    1.408  0.020  1.408
 1UD  C6   C5   single    1.499  0.020  1.499
 1UD  C3   C2   aromatic  1.366  0.020  1.366
 1UD  C5   C8   aromatic  1.408  0.020  1.408
 1UD  C2   C1   aromatic  1.403  0.020  1.403
 1UD  C8   C1   aromatic  1.416  0.020  1.416
 1UD  C8   N9   single    1.374  0.020  1.374
 1UD  C1   C13  single    1.449  0.020  1.449
 1UD  N9   C10  double    1.290  0.020  1.290
 1UD  C13  O14  double    1.223  0.020  1.223
 1UD  C13  N12  single    1.378  0.020  1.378
 1UD  C10  N12  single    1.369  0.020  1.369
 1UD  C10  N11  single    1.354  0.020  1.354
 1UD  C2   H1   single    0.930  0.020  1.080
 1UD  C6   H2   single    0.970  0.020  1.090
 1UD  C6   H3   single    0.970  0.020  1.090
 1UD  C7   H4   single    0.970  0.020  1.090
 1UD  C7   H5   single    0.970  0.020  1.090
 1UD  N11  H6   single    0.890  0.020  1.040
 1UD  N11  H7   single    0.890  0.020  1.040
 1UD  N12  H8   single    0.860  0.020  1.020
 1UD  N15  H9   single    0.860  0.020  1.020
 1UD  N18  H11  single    0.860  0.020  1.020
 1UD  C19  H12  single    0.970  0.020  1.090
 1UD  C19  H13  single    0.970  0.020  1.090
 1UD  C19  H14  single    0.970  0.020  1.090
 1UD  C20  H15  single    0.970  0.020  1.090
 1UD  C22  H16  single    0.970  0.020  1.090
 1UD  C22  H17  single    0.970  0.020  1.090
 1UD  C22  H18  single    0.970  0.020  1.090
 1UD  C24  H19  single    0.970  0.020  1.090
 1UD  C25  H20  single    0.970  0.020  1.090
 1UD  C26  H21  single    0.970  0.020  1.090
 1UD  C26  H22  single    0.970  0.020  1.090
 1UD  C26  H23  single    0.970  0.020  1.090
 1UD  C27  H24  single    0.970  0.020  1.090
 1UD  O28  H25  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
 1UD  C13  C1   C8   118.87  3.000
 1UD  C13  C1   C2   119.28  3.000
 1UD  C8   C1   C2   121.84  3.000
 1UD  H1   C2   C3   122.50  3.000
 1UD  H1   C2   C1   120.88  3.000
 1UD  C3   C2   C1   116.62  3.000
 1UD  N15  C3   C4   104.54  3.000
 1UD  C4   C3   C2   122.78  3.000
 1UD  N15  C3   C2   132.68  3.000
 1UD  N16  C4   C5   128.84  3.000
 1UD  C5   C4   C3   120.94  3.000
 1UD  N16  C4   C3   110.22  3.000
 1UD  C8   C5   C6   121.67  3.000
 1UD  C8   C5   C4   117.25  3.000
 1UD  C6   C5   C4   121.06  3.000
 1UD  H3   C6   H2   107.23  3.000
 1UD  H3   C6   C7   109.64  3.000
 1UD  H2   C6   C7   109.05  3.000
 1UD  H3   C6   C5   109.02  3.000
 1UD  H2   C6   C5   109.77  3.000
 1UD  C7   C6   C5   112.01  3.000
 1UD  H5   C7   H4   106.90  3.000
 1UD  H5   C7   C24  107.63  3.000
 1UD  H4   C7   C24  109.23  3.000
 1UD  H5   C7   C6   109.16  3.000
 1UD  H4   C7   C6   110.05  3.000
 1UD  C24  C7   C6   113.63  3.000
 1UD  N9   C8   C5   117.72  3.000
 1UD  N9   C8   C1   121.73  3.000
 1UD  C5   C8   C1   120.55  3.000
 1UD  C10  N9   C8   118.48  3.000
 1UD  N12  C10  N11  116.00  3.000
 1UD  N11  C10  N9   120.85  3.000
 1UD  N12  C10  N9   123.10  3.000
 1UD  H7   N11  H6   114.53  3.000
 1UD  H7   N11  C10  119.18  3.000
 1UD  H6   N11  C10  115.58  3.000
 1UD  H8   N12  C13  116.72  3.000
 1UD  H8   N12  C10  119.48  3.000
 1UD  C13  N12  C10  123.79  3.000
 1UD  O14  C13  N12  120.29  3.000
 1UD  N12  C13  C1   114.02  3.000
 1UD  O14  C13  C1   125.68  3.000
 1UD  H9   N15  C17  126.91  3.000
 1UD  H9   N15  C3   126.12  3.000
 1UD  C17  N15  C3   106.96  3.000
 1UD  C17  N16  C4   105.12  3.000
 1UD  N18  C17  N16  124.77  3.000
 1UD  N16  C17  N15  113.16  3.000
 1UD  N18  C17  N15  122.07  3.000
 1UD  H11  N18  C19  119.25  3.000
 1UD  H11  N18  C17  116.53  3.000
 1UD  C19  N18  C17  123.94  3.000
 1UD  H14  C19  H13  107.97  3.000
 1UD  H14  C19  H12  107.70  3.000
 1UD  H13  C19  H12  108.52  3.000
 1UD  H14  C19  N18  108.34  3.000
 1UD  H13  C19  N18  112.31  3.000
 1UD  H12  C19  N18  111.83  3.000
 1UD  H15  C20  C27  109.59  3.000
 1UD  H15  C20  O23  109.85  3.000
 1UD  C27  C20  O23  104.73  3.000
 1UD  H15  C20  O21  110.68  3.000
 1UD  O23  C20  O21  110.45  3.000
 1UD  C27  C20  O21  111.38  3.000
 1UD  C22  O21  C20  114.67  3.000
 1UD  H18  C22  H17  108.47  3.000
 1UD  H18  C22  H16  108.52  3.000
 1UD  H17  C22  H16  108.50  3.000
 1UD  H18  C22  O21  107.41  3.000
 1UD  H17  C22  O21  112.35  3.000
 1UD  H16  C22  O21  111.48  3.000
 1UD  C24  O23  C20  106.32  3.000
 1UD  H19  C24  C25  107.55  3.000
 1UD  H19  C24  O23  109.73  3.000
 1UD  C25  C24  O23  105.28  3.000
 1UD  H19  C24  C7   109.42  3.000
 1UD  C25  C24  C7   114.29  3.000
 1UD  O23  C24  C7   110.42  3.000
 1UD  H20  C25  C27  109.18  3.000
 1UD  H20  C25  O26  110.22  3.000
 1UD  C27  C25  O26  114.77  3.000
 1UD  H20  C25  C24  109.75  3.000
 1UD  O26  C25  C24  109.07  3.000
 1UD  C27  C25  C24  103.60  3.000
 1UD  C26  O26  C25  114.27  3.000
 1UD  H23  C26  H22  108.27  3.000
 1UD  H23  C26  H21  108.33  3.000
 1UD  H22  C26  H21  108.20  3.000
 1UD  H23  C26  O26  107.52  3.000
 1UD  H22  C26  O26  111.52  3.000
 1UD  H21  C26  O26  112.86  3.000
 1UD  H24  C27  O28  111.64  3.000
 1UD  H24  C27  C25  108.79  3.000
 1UD  O28  C27  C25  111.58  3.000
 1UD  H24  C27  C20  107.70  3.000
 1UD  C25  C27  C20  102.92  3.000
 1UD  O28  C27  C20  113.75  3.000
 1UD  H25  O28  C27  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
 1UD  CONST_01  N15  C3   C2   C1   180.00   0.0  0
 1UD  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 1UD  CONST_03  C4   C5   C8   C1     0.00   0.0  0
 1UD  CONST_04  C17  N15  C3   C2   180.00   0.0  0
 1UD  CONST_05  N16  C4   C3   C2   180.00   0.0  0
 1UD  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 1UD  CONST_07  C5   C8   C1   C2     0.00   0.0  0
 1UD  CONST_08  N16  C17  N15  C3     0.00   0.0  0
 1UD  CONST_09  C17  N16  C4   C3     0.00   0.0  0
 1UD  CONST_10  C8   C5   C4   C3     0.00   0.0  0
 1UD  CONST_11  C8   C1   C2   C3     0.00   0.0  0
 1UD  CONST_12  N15  C17  N16  C4     0.00   0.0  0
 1UD  CONST_13  C17  N15  C3   C4     0.00   0.0  0
 1UD  CONST_14  C17  N16  C4   C5   180.00   0.0  0
 1UD  CONST_15  N15  C3   C4   C5   180.00   0.0  0
 1UD  CONST_16  N16  C4   C5   C8   180.00   0.0  0
 1UD  CONST_17  N16  C4   C3   N15    0.00   0.0  0
 1UD  CONST_18  C10  N12  C13  C1     0.00   0.0  0
 1UD  CONST_19  N12  C10  N9   C8     0.00   0.0  0
 1UD  CONST_20  C13  N12  C10  N9     0.00   0.0  0
 1UD  CONST_21  C6   C5   C8   C1   180.00   0.0  0
 1UD  CONST_22  N18  C17  N15  C3   180.00   0.0  0
 1UD  CONST_23  C6   C5   C4   C3   180.00   0.0  0
 1UD  CONST_24  N18  C17  N16  C4   180.00   0.0  0
 1UD  CONST_25  N16  C4   C5   C6     0.00   0.0  0
 1UD  CONST_26  N9   C8   C5   C6     0.00   0.0  0
 1UD  CONST_27  N11  C10  N9   C8   180.00   0.0  0
 1UD  CONST_28  O14  C13  N12  C10  180.00   0.0  0
 1UD  CONST_29  C13  N12  C10  N11  180.00   0.0  0
 1UD  CONST_30  H9   N15  C3   C2     0.00   0.0  0
 1UD  CONST_31  H1   C2   C3   C4   180.00   0.0  0
 1UD  CONST_32  H8   N12  C13  C1   180.00   0.0  0
 1UD  CONST_33  C19  N18  C17  N15    0.00   0.0  0
 1UD  CONST_34  C19  N18  C17  N16  180.00   0.0  0
 1UD  CONST_35  H11  N18  C17  N15  180.00   0.0  0
 1UD  CONST_36  H6   N11  C10  N9     0.00   0.0  0
 1UD  Var_01    C7   C6   C5   C4    99.96  30.0  2
 1UD  Var_02    C24  C7   C6   C5   178.96  30.0  1
 1UD  Var_03    H12  C19  N18  C17  -61.78  30.0  3
 1UD  Var_04    H16  C22  O21  C20  -53.19  30.0  3
 1UD  Var_05    H21  C26  O26  C25  -63.56  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
 1UD  chir_01  C20  O21  C27  O23  negativ
 1UD  chir_02  C24  O23  C25  C7   negativ
 1UD  chir_03  C25  O26  C27  C24  negativ
 1UD  chir_04  C27  O28  C20  C25  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
 1UD  plan-1  C1   0.020
 1UD  plan-1  C2   0.020
 1UD  plan-1  C3   0.020
 1UD  plan-1  C4   0.020
 1UD  plan-1  C5   0.020
 1UD  plan-1  C6   0.020
 1UD  plan-1  C8   0.020
 1UD  plan-1  N9   0.020
 1UD  plan-1  C10  0.020
 1UD  plan-1  N11  0.020
 1UD  plan-1  N12  0.020
 1UD  plan-1  C13  0.020
 1UD  plan-1  O14  0.020
 1UD  plan-1  N15  0.020
 1UD  plan-1  N16  0.020
 1UD  plan-1  C17  0.020
 1UD  plan-1  N18  0.020
 1UD  plan-1  H1   0.020
 1UD  plan-1  H6   0.020
 1UD  plan-1  H7   0.020
 1UD  plan-1  H8   0.020
 1UD  plan-1  H9   0.020
 1UD  plan-2  C17  0.020
 1UD  plan-2  N18  0.020
 1UD  plan-2  C19  0.020
 1UD  plan-2  H11  0.020

