# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:24:37 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 4-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-2,7-bis(methylamino)pyrido[3',2':4,5]thieno[3,2-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ccc2c(sc3c(nc(NC)nc23)N4CCN(CC4)[C@@H]5O[C@@H]([C@@H](O)[C@H](O)[C@H]5O)C(O)=O)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
 E0V  E0V  4-(4-beta-D-glucopyranuronosylpiperazin-1-yl)-2,7-bis(methylamino)pyrido[3',2':4,5]thieno[3,2-d]pyrimidine  ligand  61  35  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E0V
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
 E0V  C27  C  CH1    0   0.024  -6.1290  -1.1575  -0.1549
 E0V  C19  C  CH2    0  -0.317  -0.2589   0.5146  -1.2936
 E0V  C15  C  CH3    0  -0.507   4.9669   4.7952   0.9284
 E0V  C20  C  CH2    0  -0.291  -1.5897  -0.0837  -0.8813
 E0V  C24  C  CH1    0   0.208  -3.8827   0.6234  -0.3803
 E0V  C31  C  CH1    0   0.009  -4.5128   0.0325  -1.6442
 E0V  C26  C  CH1    0  -0.147  -5.3829  -0.5244   1.0304
 E0V  C23  C  CH2    0  -0.300  -0.6580   2.4158   0.1288
 E0V  C33  C  C      0   0.433  -5.4727  -1.4044   2.2904
 E0V  C29  C  CH1    0  -0.006  -5.9844  -0.2479  -1.3641
 E0V  C01  C  CH3    0  -0.530   8.0139  -4.0917  -0.3242
 E0V  C03  C  CR6    0   0.499   6.0417  -2.6089  -0.3208
 E0V  C04  C  CR16   0  -0.396   6.8259  -1.4488  -0.0760
 E0V  C05  C  CR16   0  -0.179   6.2037  -0.2320   0.0348
 E0V  C06  C  CR56   0   0.070   4.8141  -0.1654  -0.1000
 E0V  C07  C  CR56   0  -0.031   4.1502  -1.3696  -0.3345
 E0V  C10  C  CR56   0  -0.361   2.5911   0.5760  -0.2288
 E0V  C11  C  CR56   0   0.304   3.9176   0.9522  -0.0152
 E0V  C13  C  CR6    0   0.571   3.3069   3.0660   0.3998
 E0V  C17  C  CR6    0   0.548   1.6128   1.5869  -0.1021
 E0V  C22  C  CH2    0  -0.288  -1.9888   1.8034   0.5259
 E0V  N08  N  N      0  -0.489   4.7105  -2.5554  -0.4461
 E0V  N12  N  N      0  -0.509   4.3020   2.1936   0.2793
 E0V  N16  N  N      0  -0.530   2.0022   2.8123   0.2173
 E0V  N18  N  NT     0  -0.506   0.2741   1.3633  -0.2382
 E0V  N21  N  NT     0  -0.464  -2.5163   0.9793  -0.5450
 E0V  O25  O  O2     0  -0.496  -4.0405  -0.2927   0.6906
 E0V  O28  O  OH1    0  -0.709  -7.4919  -1.3314   0.1286
 E0V  O30  O  OH1    0  -0.678  -6.5351  -0.8123  -2.5342
 E0V  O32  O  OH1    0  -0.670  -4.3466   0.9508  -2.6934
 E0V  O34  O  O      0  -0.559  -4.4618  -1.5803   2.9724
 E0V  O35  O  OC    -1  -0.619  -6.6249  -1.8652   2.5187
 E0V  S09  S  S2     0   0.158   2.4207  -1.1540  -0.4681
 E0V  H1   H  HCH1   0   0.189  -5.6427  -2.1218  -0.3861
 E0V  H2   H  HCH2   0   0.255   0.4273  -0.2902  -1.5448
 E0V  H3   H  HCH2   0   0.241  -0.3950   1.1101  -2.2054
 E0V  H4   H  HCH3   0   0.246   4.9284   5.8474   1.1973
 E0V  H5   H  HCH3   0   0.230   5.4685   4.2551   1.7329
 E0V  H6   H  HCH3   0   0.228   5.5765   4.6949   0.0280
 E0V  H7   H  HCH2   0   0.254  -1.9697  -0.6598  -1.7246
 E0V  H8   H  HCH2   0   0.213  -1.4271  -0.7833  -0.0482
 E0V  H9   H  HCH1   0   0.220  -4.4254   1.5528  -0.1398
 E0V  H10  H  HCH1   0   0.210  -4.0274  -0.9282  -1.8766
 E0V  H11  H  HCH1   0   0.217  -5.8880   0.4319   1.2638
 E0V  H12  H  HCH2   0   0.224  -0.8020   3.1175  -0.7026
 E0V  H13  H  HCH2   0   0.260  -0.2580   2.9775   0.9688
 E0V  H14  H  HCH1   0   0.203  -6.4765   0.7101  -1.1275
 E0V  H15  H  HCH3   0   0.238   8.5972  -3.5685  -1.0855
 E0V  H16  H  HCH3   0   0.238   8.4092  -3.8172   0.6565
 E0V  H17  H  HCH3   0   0.267   8.1690  -5.1579  -0.4607
 E0V  H18  H  HCR6   0   0.281   7.8992  -1.5223   0.0217
 E0V  H19  H  HCR6   0   0.266   6.7798   0.6651   0.2235
 E0V  H20  H  HCH2   0   0.210  -1.8588   1.2407   1.4619
 E0V  H21  H  HCH2   0   0.244  -2.6907   2.6152   0.7293
 E0V  H22  H  HNH1   0   0.394   5.9800  -4.5930  -0.6101
 E0V  H23  H  HNH1   0   0.392   2.8620   4.9905   0.7803
 E0V  H25  H  HOH1   0   0.439  -7.4852  -1.6249   1.0704
 E0V  H26  H  HOH1   0   0.456  -7.4929  -0.8243  -2.4442
 E0V  H27  H  HOH1   0   0.448  -4.8828   0.6472  -3.4339
 E0V  N02  N  NH1    0  -0.646   6.6043  -3.8230  -0.4376
 E0V  N14  N  NH1    0  -0.655   3.6192   4.3320   0.7312

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
 E0V  N02  C01  single    1.439  0.020  1.439
 E0V  N02  C03  single    1.343  0.020  1.343
 E0V  C04  C03  aromatic  1.421  0.020  1.421
 E0V  C04  C05  aromatic  1.371  0.020  1.371
 E0V  C03  N08  aromatic  1.338  0.020  1.338
 E0V  C05  C06  aromatic  1.398  0.020  1.398
 E0V  N08  C07  aromatic  1.316  0.020  1.316
 E0V  C07  C06  aromatic  1.395  0.020  1.395
 E0V  C07  S09  aromatic  1.748  0.020  1.748
 E0V  C06  C11  aromatic  1.435  0.020  1.435
 E0V  C11  N12  aromatic  1.333  0.020  1.333
 E0V  C11  C10  aromatic  1.395  0.020  1.395
 E0V  N12  C13  aromatic  1.329  0.020  1.329
 E0V  S09  C10  aromatic  1.755  0.020  1.755
 E0V  C15  N14  single    1.439  0.020  1.439
 E0V  C10  C17  aromatic  1.412  0.020  1.412
 E0V  C13  N14  single    1.345  0.020  1.345
 E0V  C13  N16  aromatic  1.342  0.020  1.342
 E0V  C17  N16  aromatic  1.325  0.020  1.325
 E0V  C17  N18  single    1.364  0.020  1.364
 E0V  O34  C33  deloc     1.232  0.020  1.232
 E0V  O35  C33  deloc     1.262  0.020  1.262
 E0V  N18  C23  single    1.453  0.020  1.453
 E0V  N18  C19  single    1.455  0.020  1.455
 E0V  C33  C26  single    1.540  0.020  1.540
 E0V  C23  C22  single    1.518  0.020  1.518
 E0V  C22  N21  single    1.451  0.020  1.451
 E0V  O25  C26  single    1.404  0.020  1.404
 E0V  O25  C24  single    1.418  0.020  1.418
 E0V  C19  C20  single    1.516  0.020  1.516
 E0V  C26  C27  single    1.537  0.020  1.537
 E0V  C20  N21  single    1.450  0.020  1.450
 E0V  N21  C24  single    1.422  0.020  1.422
 E0V  C24  C31  single    1.531  0.020  1.531
 E0V  C27  O28  single    1.403  0.020  1.403
 E0V  C27  C29  single    1.520  0.020  1.520
 E0V  C31  C29  single    1.524  0.020  1.524
 E0V  C31  O32  single    1.404  0.020  1.404
 E0V  C29  O30  single    1.411  0.020  1.411
 E0V  C27  H1   single    0.970  0.020  1.090
 E0V  C19  H2   single    0.970  0.020  1.090
 E0V  C19  H3   single    0.970  0.020  1.090
 E0V  C15  H4   single    0.970  0.020  1.090
 E0V  C15  H5   single    0.970  0.020  1.090
 E0V  C15  H6   single    0.970  0.020  1.090
 E0V  C20  H7   single    0.970  0.020  1.090
 E0V  C20  H8   single    0.970  0.020  1.090
 E0V  C24  H9   single    0.970  0.020  1.090
 E0V  C31  H10  single    0.970  0.020  1.090
 E0V  C26  H11  single    0.970  0.020  1.090
 E0V  C23  H12  single    0.970  0.020  1.090
 E0V  C23  H13  single    0.970  0.020  1.090
 E0V  C29  H14  single    0.970  0.020  1.090
 E0V  C01  H15  single    0.970  0.020  1.090
 E0V  C01  H16  single    0.970  0.020  1.090
 E0V  C01  H17  single    0.970  0.020  1.090
 E0V  C04  H18  single    0.930  0.020  1.080
 E0V  C05  H19  single    0.930  0.020  1.080
 E0V  C22  H20  single    0.970  0.020  1.090
 E0V  C22  H21  single    0.970  0.020  1.090
 E0V  N02  H22  single    0.860  0.020  1.020
 E0V  N14  H23  single    0.860  0.020  1.020
 E0V  O28  H25  single    0.850  0.020  0.980
 E0V  O30  H26  single    0.850  0.020  0.980
 E0V  O32  H27  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
 E0V  H1   C27  O28  111.21  3.000
 E0V  H1   C27  C29  108.31  3.000
 E0V  O28  C27  C29  109.11  3.000
 E0V  H1   C27  C26  107.89  3.000
 E0V  C29  C27  C26  108.71  3.000
 E0V  O28  C27  C26  111.52  3.000
 E0V  H3   C19  H2   106.74  3.000
 E0V  H3   C19  N18  109.36  3.000
 E0V  H2   C19  N18  111.60  3.000
 E0V  H3   C19  C20  109.34  3.000
 E0V  H2   C19  C20  108.95  3.000
 E0V  N18  C19  C20  110.75  3.000
 E0V  H6   C15  H5   107.81  3.000
 E0V  H6   C15  H4   108.22  3.000
 E0V  H5   C15  H4   108.24  3.000
 E0V  H6   C15  N14  112.36  3.000
 E0V  H5   C15  N14  111.86  3.000
 E0V  H4   C15  N14  108.21  3.000
 E0V  H8   C20  H7   107.54  3.000
 E0V  H8   C20  N21  112.66  3.000
 E0V  H7   C20  N21  110.14  3.000
 E0V  H8   C20  C19  109.09  3.000
 E0V  H7   C20  C19  107.71  3.000
 E0V  N21  C20  C19  109.56  3.000
 E0V  H9   C24  O25  108.96  3.000
 E0V  H9   C24  N21  106.69  3.000
 E0V  O25  C24  N21  110.87  3.000
 E0V  H9   C24  C31  107.63  3.000
 E0V  N21  C24  C31  113.37  3.000
 E0V  O25  C24  C31  109.17  3.000
 E0V  H10  C31  O32  111.14  3.000
 E0V  H10  C31  C29  107.70  3.000
 E0V  O32  C31  C29  111.84  3.000
 E0V  H10  C31  C24  109.24  3.000
 E0V  O32  C31  C24  108.40  3.000
 E0V  C29  C31  C24  108.46  3.000
 E0V  H11  C26  O25  110.17  3.000
 E0V  H11  C26  C33  107.14  3.000
 E0V  O25  C26  C33  110.38  3.000
 E0V  H11  C26  C27  107.29  3.000
 E0V  O25  C26  C27  110.21  3.000
 E0V  C33  C26  C27  111.56  3.000
 E0V  H13  C23  H12  107.67  3.000
 E0V  H13  C23  N18  109.48  3.000
 E0V  H12  C23  N18  110.86  3.000
 E0V  H13  C23  C22  109.21  3.000
 E0V  H12  C23  C22  109.94  3.000
 E0V  N18  C23  C22  109.65  3.000
 E0V  O35  C33  O34  126.65  3.000
 E0V  O35  C33  C26  114.21  3.000
 E0V  O34  C33  C26  119.13  3.000
 E0V  H14  C29  O30  110.56  3.000
 E0V  H14  C29  C31  108.09  3.000
 E0V  O30  C29  C31  107.34  3.000
 E0V  H14  C29  C27  107.86  3.000
 E0V  O30  C29  C27  112.53  3.000
 E0V  C31  C29  C27  110.37  3.000
 E0V  H17  C01  H16  107.92  3.000
 E0V  H17  C01  H15  107.84  3.000
 E0V  H16  C01  H15  108.18  3.000
 E0V  H17  C01  N02  108.26  3.000
 E0V  H16  C01  N02  112.22  3.000
 E0V  H15  C01  N02  112.24  3.000
 E0V  N08  C03  N02  116.40  3.000
 E0V  N08  C03  C04  122.16  3.000
 E0V  N02  C03  C04  121.44  3.000
 E0V  H18  C04  C05  120.26  3.000
 E0V  H18  C04  C03  120.54  3.000
 E0V  C05  C04  C03  119.20  3.000
 E0V  H19  C05  C06  120.42  3.000
 E0V  H19  C05  C04  120.52  3.000
 E0V  C06  C05  C04  119.06  3.000
 E0V  C11  C06  C07  112.63  3.000
 E0V  C11  C06  C05  130.73  3.000
 E0V  C07  C06  C05  116.63  3.000
 E0V  S09  C07  N08  121.73  3.000
 E0V  S09  C07  C06  112.16  3.000
 E0V  N08  C07  C06  126.11  3.000
 E0V  S09  C10  C17  130.59  3.000
 E0V  C17  C10  C11  116.85  3.000
 E0V  S09  C10  C11  112.27  3.000
 E0V  N12  C11  C10  124.01  3.000
 E0V  C10  C11  C06  112.01  3.000
 E0V  N12  C11  C06  123.94  3.000
 E0V  N16  C13  N14  115.92  3.000
 E0V  N16  C13  N12  126.28  3.000
 E0V  N14  C13  N12  117.80  3.000
 E0V  N18  C17  N16  117.65  3.000
 E0V  N18  C17  C10  123.61  3.000
 E0V  N16  C17  C10  118.69  3.000
 E0V  H21  C22  H20  107.32  3.000
 E0V  H21  C22  N21  109.03  3.000
 E0V  H20  C22  N21  112.37  3.000
 E0V  H21  C22  C23  108.20  3.000
 E0V  H20  C22  C23  108.99  3.000
 E0V  N21  C22  C23  110.79  3.000
 E0V  C07  N08  C03  116.84  3.000
 E0V  C13  N12  C11  114.56  3.000
 E0V  C17  N16  C13  119.57  3.000
 E0V  C17  N18  C23  119.05  3.000
 E0V  C23  N18  C19  111.76  3.000
 E0V  C17  N18  C19  121.82  3.000
 E0V  C22  N21  C24  113.97  3.000
 E0V  C24  N21  C20  117.23  3.000
 E0V  C22  N21  C20  110.82  3.000
 E0V  C26  O25  C24  113.32  3.000
 E0V  H25  O28  C27  102.90  3.000
 E0V  H26  O30  C29  108.42  3.000
 E0V  H27  O32  C31  107.60  3.000
 E0V  C10  S09  C07   90.87  3.000
 E0V  H22  N02  C03  116.53  3.000
 E0V  H22  N02  C01  118.57  3.000
 E0V  C03  N02  C01  124.89  3.000
 E0V  H23  N14  C13  116.99  3.000
 E0V  H23  N14  C15  119.23  3.000
 E0V  C13  N14  C15  123.65  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
 E0V  CONST_01  C06  C05  C04  C03     0.00   0.0  0
 E0V  CONST_02  C06  C07  N08  C03     0.00   0.0  0
 E0V  CONST_03  S09  C07  N08  C03   180.00   0.0  0
 E0V  CONST_04  C07  N08  C03  C04     0.00   0.0  0
 E0V  CONST_05  C07  C06  C05  C04     0.00   0.0  0
 E0V  CONST_06  C11  C06  C05  C04   180.00   0.0  0
 E0V  CONST_07  N08  C03  C04  C05     0.00   0.0  0
 E0V  CONST_08  N08  C07  C06  C05     0.00   0.0  0
 E0V  CONST_09  S09  C07  C06  C05   180.00   0.0  0
 E0V  CONST_10  N12  C11  C06  C05     0.00   0.0  0
 E0V  CONST_11  C10  C11  C06  C05   180.00   0.0  0
 E0V  CONST_12  C10  S09  C07  C06     0.00   0.0  0
 E0V  CONST_13  C13  N12  C11  C06   180.00   0.0  0
 E0V  CONST_14  S09  C10  C11  C06     0.00   0.0  0
 E0V  CONST_15  C17  C10  C11  C06   180.00   0.0  0
 E0V  CONST_16  N12  C11  C06  C07   180.00   0.0  0
 E0V  CONST_17  C10  C11  C06  C07     0.00   0.0  0
 E0V  CONST_18  C11  C10  S09  C07     0.00   0.0  0
 E0V  CONST_19  C17  C10  S09  C07   180.00   0.0  0
 E0V  CONST_20  C13  N12  C11  C10     0.00   0.0  0
 E0V  CONST_21  N08  C07  S09  C10   180.00   0.0  0
 E0V  CONST_22  C13  N16  C17  C10     0.00   0.0  0
 E0V  CONST_23  N08  C07  C06  C11   180.00   0.0  0
 E0V  CONST_24  S09  C07  C06  C11     0.00   0.0  0
 E0V  CONST_25  N16  C13  N12  C11     0.00   0.0  0
 E0V  CONST_26  N16  C17  C10  C11     0.00   0.0  0
 E0V  CONST_27  N12  C11  C10  C17     0.00   0.0  0
 E0V  CONST_28  N12  C13  N16  C17     0.00   0.0  0
 E0V  CONST_29  S09  C10  C11  N12   180.00   0.0  0
 E0V  CONST_30  S09  C10  C17  N16   180.00   0.0  0
 E0V  CONST_31  N18  C17  C10  C11   180.00   0.0  0
 E0V  CONST_32  N18  C17  N16  C13   180.00   0.0  0
 E0V  CONST_33  S09  C10  C17  N18     0.00   0.0  0
 E0V  CONST_34  N02  C03  C04  C05   180.00   0.0  0
 E0V  CONST_35  N02  C03  N08  C07   180.00   0.0  0
 E0V  CONST_36  N14  C13  N12  C11   180.00   0.0  0
 E0V  CONST_37  N14  C13  N16  C17   180.00   0.0  0
 E0V  CONST_38  H19  C05  C04  C03   180.00   0.0  0
 E0V  CONST_39  H18  C04  C05  C06   180.00   0.0  0
 E0V  CONST_40  N12  C13  N14  C15     0.00   0.0  0
 E0V  CONST_41  N16  C13  N14  C15   180.00   0.0  0
 E0V  CONST_42  C04  C03  N02  C01     0.00   0.0  0
 E0V  CONST_43  N08  C03  N02  C01   180.00   0.0  0
 E0V  CONST_44  H22  N02  C03  C04   180.00   0.0  0
 E0V  CONST_45  H23  N14  C13  N12   180.00   0.0  0
 E0V  Var_01    C10  C17  N18  C19   -42.64  30.0  1
 E0V  Var_02    C22  C23  N18  C19    55.83  30.0  1
 E0V  Var_03    C22  N21  C20  C19   -58.40  30.0  1
 E0V  Var_04    C17  N18  C19  C20   153.67  30.0  1
 E0V  Var_05    C23  C22  N21  C20    58.90  30.0  1
 E0V  Var_06    N21  C22  C23  N18   -56.65  30.0  1
 E0V  Var_07    N21  C20  C19  N18    56.97  30.0  1
 E0V  Var_08    H15  C01  N02  C03   -61.24  30.0  3
 E0V  Var_09    H4   C15  N14  C13  -179.37  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
 E0V  chir_01  C27  C26  O28  C29  negativ
 E0V  chir_02  C24  O25  N21  C31  negativ
 E0V  chir_03  C31  O32  C24  C29  negativ
 E0V  chir_04  C26  O25  C27  C33  negativ
 E0V  chir_05  C29  O30  C27  C31  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
 E0V  plan-1  C01  0.020
 E0V  plan-1  C03  0.020
 E0V  plan-1  H22  0.020
 E0V  plan-1  N02  0.020
 E0V  plan-2  C03  0.020
 E0V  plan-2  C04  0.020
 E0V  plan-2  C05  0.020
 E0V  plan-2  C06  0.020
 E0V  plan-2  C07  0.020
 E0V  plan-2  C10  0.020
 E0V  plan-2  C11  0.020
 E0V  plan-2  C13  0.020
 E0V  plan-2  C17  0.020
 E0V  plan-2  N08  0.020
 E0V  plan-2  N12  0.020
 E0V  plan-2  N16  0.020
 E0V  plan-2  N18  0.020
 E0V  plan-2  S09  0.020
 E0V  plan-2  H18  0.020
 E0V  plan-2  H19  0.020
 E0V  plan-2  N02  0.020
 E0V  plan-2  N14  0.020
 E0V  plan-3  C15  0.020
 E0V  plan-3  C13  0.020
 E0V  plan-3  H23  0.020
 E0V  plan-3  N14  0.020
 E0V  plan-4  C26  0.020
 E0V  plan-4  C33  0.020
 E0V  plan-4  O34  0.020
 E0V  plan-4  O35  0.020

