# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 17:10:06 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CN(CCO)CC[C@H]([NH3+])C([O-])=O)[C@@H](O)[C@H]3O
#
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
 E7X  E7X  (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate  ligand  54  29  .  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_E7X
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
 E7X  C2   C  CR16   0   0.039   5.6929  -0.6322   1.2612
 E7X  C5   C  CR56   0  -0.002   4.2985  -0.8551  -0.9789
 E7X  C6   C  CR6    0   0.454   5.6732  -1.1572  -0.9804
 E7X  C8   C  CR15   0   0.107   2.2497  -0.4988  -1.3400
 E7X  N    N  NT3    1  -0.800  -5.3127   1.0231   1.9986
 E7X  CA   C  CH1    0  -0.260  -5.5003   0.0864   0.8532
 E7X  C    C  C      0   0.471  -6.3219  -1.1195   1.3890
 E7X  OXT  O  OC     0  -0.569  -6.4023  -2.0995   0.6425
 E7X  CB   C  CH2    0  -0.458  -4.1766  -0.2858   0.2149
 E7X  CG   C  CH2    0  -0.287  -3.4334   0.9094  -0.3739
 E7X  CE   C  CH2    0  -0.318  -2.5719   0.0618  -2.4655
 E7X  C4'  C  CH1    0   0.038  -0.4179   1.3873   0.2541
 E7X  O4'  O  O2     0  -0.487   0.1873   0.1065   0.4293
 E7X  C3'  C  CH1    0  -0.032   0.7413   2.3761   0.3387
 E7X  O3'  O  OH1    0  -0.657   0.2835   3.6328   0.7499
 E7X  C2'  C  CH1    0  -0.046   1.6613   1.6887   1.3535
 E7X  O2'  O  OH1    0  -0.665   1.1830   1.8575   2.6600
 E7X  C1'  C  CH1    0   0.180   1.4637   0.2215   0.9755
 E7X  O    O  O     -1  -0.595  -6.8438  -0.9488   2.5106
 E7X  C01  C  CH2    0  -0.159  -1.6453  -1.0129  -2.9933
 E7X  N1   N  N      0  -0.474   6.3428  -1.0326   0.1710
 E7X  O01  O  OH1    0  -0.663  -1.8175  -2.1900  -2.2422
 E7X  N3   N  N      0  -0.459   4.4158  -0.3165   1.3871
 E7X  C4   C  CR56   0   0.486   3.7634  -0.4453   0.2321
 E7X  N6   N  NH2    0  -0.816   6.3209  -1.5679  -2.0717
 E7X  N7   N  N      0  -0.452   3.3335  -0.8824  -1.9505
 E7X  N9   N  NR5    0  -0.538   2.4436  -0.2121  -0.0176
 E7X  H1   H  HCR6   0   0.252   6.2955  -0.5562   2.1602
 E7X  H2   H  HCR5   0   0.288   1.2790  -0.4228  -1.8028
 E7X  H4   H  HNT3   0   0.454  -6.0368   0.7484   2.6843
 E7X  H6   H  HCH1   0   0.303  -6.1228   0.6197   0.1298
 E7X  H8   H  HCH2   0   0.245  -3.5333  -0.7917   0.9414
 E7X  H9   H  HCH2   0   0.260  -4.3904  -1.0126  -0.5682
 E7X  H10  H  HCH2   0   0.217  -4.1203   1.5090  -0.9946
 E7X  H11  H  HCH2   0   0.230  -3.1169   1.5732   0.4354
 E7X  H12  H  HCH2   0   0.213  -2.5628   0.9053  -3.1733
 E7X  H13  H  HCH2   0   0.239  -3.5900  -0.3343  -2.4860
 E7X  H16  H  HCH1   0   0.237  -1.1048   1.5687   1.0907
 E7X  H17  H  HCH1   0   0.241   1.2520   2.4298  -0.6327
 E7X  H18  H  HOH1   0   0.469   0.9479   4.2940   0.5297
 E7X  H19  H  HCH1   0   0.260   2.7077   2.0028   1.2594
 E7X  H20  H  HOH1   0   0.451   0.8566   2.7624   2.7379
 E7X  H21  H  HCH1   0   0.281   1.5735  -0.4340   1.8444
 E7X  H22  H  HCH2   0   0.200  -1.8850  -1.1674  -4.0538
 E7X  H24  H  HNH2   0   0.411   5.8595  -1.6093  -2.9635
 E7X  H25  H  HNH2   0   0.403   7.3156  -1.7120  -2.0445
 E7X  H7   H  HCH2   0   0.187  -0.6042  -0.6625  -2.9649
 E7X  H23  H  HOH1   0   0.451  -1.2341  -2.8621  -2.6045
 E7X  H5   H  HNT3   0   0.457  -4.4095   0.9085   2.4560
 E7X  C5'  C  CH2    0  -0.299  -1.1721   1.4406  -1.0579
 E7X  N01  N  NT     0  -0.407  -2.2593   0.4861  -1.1120
 E7X  H3   H  HNT3   0   0.464  -5.4177   2.0052   1.7552
 E7X  H14  H  HCH2   0   0.224  -1.5131   2.4773  -1.2156
 E7X  H15  H  HCH2   0   0.232  -0.4683   1.2357  -1.8687

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
 E7X  O    C    deloc     1.249  0.020  1.249
 E7X  C    OXT  deloc     1.235  0.020  1.235
 E7X  C    CA   single    1.554  0.020  1.554
 E7X  N6   C6   single    1.334  0.020  1.334
 E7X  CA   N    single    1.492  0.020  1.492
 E7X  CA   CB   single    1.516  0.020  1.516
 E7X  N1   C6   aromatic  1.338  0.020  1.338
 E7X  N1   C2   aromatic  1.331  0.020  1.331
 E7X  C6   C5   aromatic  1.408  0.020  1.408
 E7X  C2   N3   aromatic  1.322  0.020  1.322
 E7X  C5   N7   aromatic  1.370  0.020  1.370
 E7X  C5   C4   aromatic  1.386  0.020  1.386
 E7X  N7   C8   aromatic  1.302  0.020  1.302
 E7X  N3   C4   aromatic  1.333  0.020  1.333
 E7X  C4   N9   aromatic  1.363  0.020  1.363
 E7X  CB   CG   single    1.526  0.020  1.526
 E7X  C8   N9   aromatic  1.367  0.020  1.367
 E7X  N9   C1'  single    1.461  0.020  1.461
 E7X  CG   N01  single    1.450  0.020  1.450
 E7X  C1'  O4'  single    1.393  0.020  1.393
 E7X  C1'  C2'  single    1.528  0.020  1.528
 E7X  O4'  C4'  single    1.427  0.020  1.427
 E7X  O2'  C2'  single    1.401  0.020  1.401
 E7X  C2'  C3'  single    1.533  0.020  1.533
 E7X  C4'  C5'  single    1.514  0.020  1.514
 E7X  C4'  C3'  single    1.526  0.020  1.526
 E7X  N01  C5'  single    1.448  0.020  1.448
 E7X  N01  CE   single    1.452  0.020  1.452
 E7X  O01  C01  single    1.407  0.020  1.407
 E7X  CE   C01  single    1.514  0.020  1.514
 E7X  C3'  O3'  single    1.399  0.020  1.399
 E7X  C2   H1   single    0.930  0.020  1.080
 E7X  C8   H2   single    0.930  0.020  1.080
 E7X  N    H3   single    0.890  0.020  1.040
 E7X  N    H4   single    0.890  0.020  1.040
 E7X  CA   H6   single    0.970  0.020  1.090
 E7X  CB   H8   single    0.970  0.020  1.090
 E7X  CB   H9   single    0.970  0.020  1.090
 E7X  CG   H10  single    0.970  0.020  1.090
 E7X  CG   H11  single    0.970  0.020  1.090
 E7X  CE   H12  single    0.970  0.020  1.090
 E7X  CE   H13  single    0.970  0.020  1.090
 E7X  C5'  H14  single    0.970  0.020  1.090
 E7X  C5'  H15  single    0.970  0.020  1.090
 E7X  C4'  H16  single    0.970  0.020  1.090
 E7X  C3'  H17  single    0.970  0.020  1.090
 E7X  O3'  H18  single    0.850  0.020  0.980
 E7X  C2'  H19  single    0.970  0.020  1.090
 E7X  O2'  H20  single    0.850  0.020  0.980
 E7X  C1'  H21  single    0.970  0.020  1.090
 E7X  C01  H22  single    0.970  0.020  1.090
 E7X  N6   H24  single    0.860  0.020  1.020
 E7X  N6   H25  single    0.860  0.020  1.020
 E7X  C01  H7   single    0.970  0.020  1.090
 E7X  O01  H23  single    0.850  0.020  0.980
 E7X  N    H5   single    0.890  0.020  1.040

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
 E7X  H1   C2   N3   116.17  3.000
 E7X  H1   C2   N1   115.38  3.000
 E7X  N3   C2   N1   128.45  3.000
 E7X  N7   C5   C4   110.72  3.000
 E7X  C4   C5   C6   116.19  3.000
 E7X  N7   C5   C6   133.09  3.000
 E7X  N6   C6   N1   119.33  3.000
 E7X  N1   C6   C5   117.90  3.000
 E7X  N6   C6   C5   122.77  3.000
 E7X  H2   C8   N9   121.89  3.000
 E7X  H2   C8   N7   124.68  3.000
 E7X  N9   C8   N7   113.42  3.000
 E7X  H5   N    H4   107.04  3.000
 E7X  H5   N    H3   107.91  3.000
 E7X  H4   N    H3   110.04  3.000
 E7X  H5   N    CA   112.68  3.000
 E7X  H4   N    CA   104.73  3.000
 E7X  H3   N    CA   114.18  3.000
 E7X  H6   CA   CB   109.78  3.000
 E7X  H6   CA   C    107.79  3.000
 E7X  CB   CA   C    114.60  3.000
 E7X  H6   CA   N    105.86  3.000
 E7X  CB   CA   N    111.57  3.000
 E7X  C    CA   N    106.79  3.000
 E7X  O    C    OXT  128.64  3.000
 E7X  OXT  C    CA   116.21  3.000
 E7X  O    C    CA   115.12  3.000
 E7X  H9   CB   H8   106.50  3.000
 E7X  H9   CB   CG   109.93  3.000
 E7X  H8   CB   CG   109.39  3.000
 E7X  H9   CB   CA   107.16  3.000
 E7X  H8   CB   CA   110.32  3.000
 E7X  CG   CB   CA   113.30  3.000
 E7X  H11  CG   H10  105.47  3.000
 E7X  H11  CG   N01  108.64  3.000
 E7X  H10  CG   N01  112.12  3.000
 E7X  H11  CG   CB   109.33  3.000
 E7X  H10  CG   CB   109.85  3.000
 E7X  N01  CG   CB   111.24  3.000
 E7X  H13  CE   H12  105.86  3.000
 E7X  H13  CE   N01  108.90  3.000
 E7X  H12  CE   N01  111.92  3.000
 E7X  H13  CE   C01  107.85  3.000
 E7X  H12  CE   C01  108.33  3.000
 E7X  N01  CE   C01  113.61  3.000
 E7X  H16  C4'  C3'  109.03  3.000
 E7X  H16  C4'  O4'  108.67  3.000
 E7X  C3'  C4'  O4'  104.63  3.000
 E7X  H16  C4'  C5'  110.05  3.000
 E7X  C3'  C4'  C5'  113.80  3.000
 E7X  O4'  C4'  C5'  110.43  3.000
 E7X  C1'  O4'  C4'  111.25  3.000
 E7X  H17  C3'  C2'  109.17  3.000
 E7X  H17  C3'  O3'  111.59  3.000
 E7X  C2'  C3'  O3'  113.87  3.000
 E7X  H17  C3'  C4'  109.62  3.000
 E7X  O3'  C3'  C4'  110.47  3.000
 E7X  C2'  C3'  C4'  101.66  3.000
 E7X  H18  O3'  C3'  108.89  3.000
 E7X  H19  C2'  C1'  112.16  3.000
 E7X  H19  C2'  O2'  111.79  3.000
 E7X  C1'  C2'  O2'  107.59  3.000
 E7X  H19  C2'  C3'  112.80  3.000
 E7X  O2'  C2'  C3'  111.01  3.000
 E7X  C1'  C2'  C3'  100.91  3.000
 E7X  H20  O2'  C2'  107.67  3.000
 E7X  H21  C1'  N9   107.14  3.000
 E7X  H21  C1'  C2'  111.47  3.000
 E7X  N9   C1'  C2'  111.50  3.000
 E7X  H21  C1'  O4'  110.72  3.000
 E7X  C2'  C1'  O4'  107.14  3.000
 E7X  N9   C1'  O4'  108.87  3.000
 E7X  H7   C01  H22  106.06  3.000
 E7X  H7   C01  O01  111.65  3.000
 E7X  H22  C01  O01  111.78  3.000
 E7X  H7   C01  CE   110.16  3.000
 E7X  H22  C01  CE   107.64  3.000
 E7X  O01  C01  CE   109.44  3.000
 E7X  C6   N1   C2   119.25  3.000
 E7X  H23  O01  C01  108.04  3.000
 E7X  C4   N3   C2   111.56  3.000
 E7X  N9   C4   N3   128.03  3.000
 E7X  N9   C4   C5   105.32  3.000
 E7X  N3   C4   C5   126.65  3.000
 E7X  H25  N6   H24  118.19  3.000
 E7X  H25  N6   C6   120.16  3.000
 E7X  H24  N6   C6   121.05  3.000
 E7X  C8   N7   C5   104.36  3.000
 E7X  C4   N9   C1'  125.14  3.000
 E7X  C1'  N9   C8   128.66  3.000
 E7X  C4   N9   C8   106.18  3.000
 E7X  H15  C5'  H14  105.62  3.000
 E7X  H15  C5'  N01  109.40  3.000
 E7X  H14  C5'  N01  112.48  3.000
 E7X  H15  C5'  C4'  108.38  3.000
 E7X  H14  C5'  C4'  108.13  3.000
 E7X  N01  C5'  C4'  112.53  3.000
 E7X  C5'  N01  CE   112.90  3.000
 E7X  CE   N01  CG   112.66  3.000
 E7X  C5'  N01  CG   113.36  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
 E7X  CONST_01  C5   C6   N1   C2      0.00   0.0  0
 E7X  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 E7X  CONST_03  N9   C4   N3   C2    180.00   0.0  0
 E7X  CONST_04  N9   C8   N7   C5      0.00   0.0  0
 E7X  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 E7X  CONST_06  N3   C2   N1   C6      0.00   0.0  0
 E7X  CONST_07  C8   N7   C5   C6    180.00   0.0  0
 E7X  CONST_08  N3   C4   C5   C6      0.00   0.0  0
 E7X  CONST_09  N9   C4   C5   C6    180.00   0.0  0
 E7X  CONST_10  C4   C5   N7   C8      0.00   0.0  0
 E7X  CONST_11  N3   C4   N9   C8    180.00   0.0  0
 E7X  CONST_12  N7   C5   C6   N1    180.00   0.0  0
 E7X  CONST_13  C4   C5   C6   N1      0.00   0.0  0
 E7X  CONST_14  C4   N3   C2   N1      0.00   0.0  0
 E7X  CONST_15  N7   C5   C4   N3    180.00   0.0  0
 E7X  CONST_16  N7   C8   N9   C4      0.00   0.0  0
 E7X  CONST_17  N9   C4   C5   N7      0.00   0.0  0
 E7X  CONST_18  C1'  N9   C4   C5    180.00   0.0  0
 E7X  CONST_19  N3   C4   N9   C1'     0.00   0.0  0
 E7X  CONST_20  N7   C8   N9   C1'   180.00   0.0  0
 E7X  CONST_21  N6   C6   N1   C2    180.00   0.0  0
 E7X  CONST_22  N6   C6   C5   C4    180.00   0.0  0
 E7X  CONST_23  N7   C5   C6   N6      0.00   0.0  0
 E7X  CONST_24  H2   C8   N7   C5    180.00   0.0  0
 E7X  CONST_25  H1   C2   N1   C6    180.00   0.0  0
 E7X  CONST_26  H24  N6   C6   C5      0.00   0.0  0
 E7X  CONST_27  H25  N6   C6   C5    180.00   0.0  0
 E7X  Var_01    C4'  C5'  N01  CG     77.79  30.0  3
 E7X  Var_02    N01  CG   CB   CA   -173.04  30.0  3
 E7X  Var_03    C5'  N01  CG   CB   -147.83  30.0  3
 E7X  Var_04    C01  CE   N01  CG   -149.16  30.0  3
 E7X  Var_05    O01  C01  CE   N01    65.38  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
 E7X  chir_01  CA   C    N    CB   negativ
 E7X  chir_02  C4'  O4'  C5'  C3'  positiv
 E7X  chir_03  C3'  O3'  C4'  C2'  positiv
 E7X  chir_04  C2'  O2'  C3'  C1'  positiv
 E7X  chir_05  C1'  O4'  N9   C2'  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
 E7X  plan-1  C2   0.020
 E7X  plan-1  C5   0.020
 E7X  plan-1  C6   0.020
 E7X  plan-1  C8   0.020
 E7X  plan-1  C1'  0.020
 E7X  plan-1  N1   0.020
 E7X  plan-1  N3   0.020
 E7X  plan-1  C4   0.020
 E7X  plan-1  N6   0.020
 E7X  plan-1  N7   0.020
 E7X  plan-1  N9   0.020
 E7X  plan-1  H1   0.020
 E7X  plan-1  H2   0.020
 E7X  plan-2  C6   0.020
 E7X  plan-2  N6   0.020
 E7X  plan-2  H24  0.020
 E7X  plan-2  H25  0.020
 E7X  plan-3  CA   0.020
 E7X  plan-3  C    0.020
 E7X  plan-3  OXT  0.020
 E7X  plan-3  O    0.020

