# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jun  6 10:53:17 2020
#   Inital geometry file: a 134 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-(3-azidopropyl)amino]-2-azanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCN(CCCN=[N+]=[N-])C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
#
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
 6D5  6D5  '(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(3-azidopropyl)amino]-2-azanyl-butanoic acid'  ligand  57  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6D5
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
 6D5  C1   C  CR16   0   0.045   5.0578   1.1414   1.4999
 6D5  C2   C  CR56   0   0.487   3.3784   0.1147   0.5266
 6D5  C3   C  CR56   0  -0.011   3.6208  -1.0606   1.2172
 6D5  C4   C  CR6    0   0.455   4.7067  -1.0480   2.1109
 6D5  C5   C  CR15   0   0.107   1.9474  -1.4537  -0.0126
 6D5  C6   C  CH2    0  -0.276  -3.4759   1.4997  -0.9822
 6D5  C7   C  CH2    0  -0.453  -3.9019   1.9900   0.3959
 6D5  C8   C  CH2    0  -0.302  -4.9521   3.0859   0.2909
 6D5  N1   N  NH2    0  -0.787  -3.3638  -3.1328   1.3375
 6D5  C9   C  CH1    0  -0.217  -2.2921  -3.1363   0.3530
 6D5  C10  C  C      0   0.399  -1.0565  -4.0070   0.7025
 6D5  O1   O  O      0  -0.606  -1.0524  -4.5963   1.8000
 6D5  C11  C  CH2    0  -0.437  -1.8555  -1.7064   0.0520
 6D5  C12  C  CH2    0  -0.265  -2.9557  -0.8351  -0.5342
 6D5  N2   N  NT     0  -0.416  -2.4537   0.4741  -0.9145
 6D5  C14  C  CH1    0   0.021  -0.4143   1.3716  -1.9542
 6D5  O2   O  O2     0  -0.484   0.3535   1.0042  -0.7998
 6D5  C15  C  CH1    0  -0.044   0.5364   1.2883  -3.1498
 6D5  O3   O  OH1    0  -0.670   1.0787   2.5601  -3.4013
 6D5  C16  C  CH1    0  -0.040   1.6096   0.3289  -2.6229
 6D5  O4   O  OH1    0  -0.654   2.8603   0.4447  -3.2313
 6D5  C17  C  CH1    0   0.222   1.6838   0.7828  -1.1708
 6D5  N3   N  N      0  -0.474   5.4104   0.0840   2.2263
 6D5  N4   N  N      0  -0.459   4.0674   1.2484   0.6315
 6D5  N5   N  NH2    0  -0.817   5.0469  -2.1074   2.8483
 6D5  N6   N  N      0  -0.450   2.7132  -2.0265   0.8671
 6D5  N7   N  NR5    0  -0.550   2.2983  -0.1517  -0.2686
 6D5  N8   N  N      0  -0.363  -5.4394   3.5362   1.6020
 6D5  N9   N  N      1   0.354  -4.6691   4.2008   2.2675
 6D5  N10  N  N     -1  -0.230  -4.0346   4.8241   2.9571
 6D5  H1   H  HCR6   0   0.251   5.6663   2.0279   1.6423
 6D5  H2   H  HCR5   0   0.297   1.1092  -1.9399  -0.4892
 6D5  H4   H  HCH2   0   0.201  -4.3584   1.1626  -1.5525
 6D5  H3   H  HCH2   0   0.233  -3.0720   2.3532  -1.5348
 6D5  H5   H  HCH2   0   0.238  -4.3066   1.1688   0.9917
 6D5  H6   H  HCH2   0   0.231  -3.0171   2.3616   0.9201
 6D5  H8   H  HCH2   0   0.248  -4.5680   3.9354  -0.2826
 6D5  H7   H  HCH2   0   0.255  -5.8344   2.7184  -0.2302
 6D5  H11  H  HNH2   0   0.322  -2.9881  -2.7868   2.2139
 6D5  H12  H  HCH1   0   0.209  -2.7076  -3.5500  -0.5761
 6D5  H14  H  HCH2   0   0.208  -1.4704  -1.2304   0.9605
 6D5  H13  H  HCH2   0   0.224  -1.0185  -1.7528  -0.6432
 6D5  H15  H  HCH2   0   0.185  -3.4259  -1.3560  -1.3873
 6D5  H16  H  HCH2   0   0.231  -3.7412  -0.7094   0.2110
 6D5  H20  H  HCH1   0   0.243  -0.7627   2.4035  -1.8295
 6D5  H21  H  HCH1   0   0.245   0.0319   0.8855  -4.0381
 6D5  H22  H  HOH1   0   0.448   1.8827   2.4426  -3.9209
 6D5  H23  H  HCH1   0   0.245   1.2251  -0.6986  -2.6723
 6D5  H24  H  HOH1   0   0.469   2.8696  -0.0914  -4.0304
 6D5  H25  H  HCH1   0   0.249   2.2881   1.6958  -1.1049
 6D5  H27  H  HNH2   0   0.402   5.8805  -2.0827   3.4098
 6D5  H28  H  HNH2   0   0.410   4.5899  -2.9928   2.7189
 6D5  O5   O  OC    -1  -0.614  -0.1595  -4.0547  -0.1683
 6D5  C13  C  CH2    0  -0.317  -1.6138   0.4486  -2.0942
 6D5  H9   H  HNH2   0   0.332  -3.6199  -4.0919   1.5394
 6D5  H19  H  HCH2   0   0.240  -1.2627  -0.5695  -2.2790
 6D5  H18  H  HCH2   0   0.228  -2.1644   0.7404  -3.0012

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
 6D5  N5   C4   single    1.335  0.020  1.335
 6D5  C4   N3   aromatic  1.338  0.020  1.338
 6D5  C4   C3   aromatic  1.406  0.020  1.406
 6D5  N6   C3   aromatic  1.371  0.020  1.371
 6D5  N6   C5   aromatic  1.299  0.020  1.299
 6D5  N3   C1   aromatic  1.330  0.020  1.330
 6D5  C3   C2   aromatic  1.385  0.020  1.385
 6D5  C5   N7   aromatic  1.372  0.020  1.372
 6D5  C1   N4   aromatic  1.322  0.020  1.322
 6D5  C2   N7   aromatic  1.367  0.020  1.367
 6D5  C2   N4   aromatic  1.331  0.020  1.331
 6D5  N7   C17  single    1.437  0.020  1.437
 6D5  C17  C16  single    1.523  0.020  1.523
 6D5  C17  O2   single    1.399  0.020  1.399
 6D5  C16  O4   single    1.396  0.020  1.396
 6D5  C16  C15  single    1.533  0.020  1.533
 6D5  N10  N9   double    1.125  0.020  1.125
 6D5  O2   C14  single    1.434  0.020  1.434
 6D5  C8   C7   single    1.522  0.020  1.522
 6D5  C8   N8   single    1.469  0.020  1.469
 6D5  N9   N8   double    1.216  0.020  1.216
 6D5  C13  C14  single    1.520  0.020  1.520
 6D5  C13  N2   single    1.448  0.020  1.448
 6D5  C7   C6   single    1.523  0.020  1.523
 6D5  C14  C15  single    1.530  0.020  1.530
 6D5  C15  O3   single    1.405  0.020  1.405
 6D5  C6   N2   single    1.450  0.020  1.450
 6D5  N2   C12  single    1.453  0.020  1.453
 6D5  C12  C11  single    1.521  0.020  1.521
 6D5  C11  C9   single    1.525  0.020  1.525
 6D5  N1   C9   single    1.455  0.020  1.455
 6D5  C9   C10  single    1.551  0.020  1.551
 6D5  O1   C10  deloc     1.246  0.020  1.246
 6D5  C10  O5   deloc     1.251  0.020  1.251
 6D5  C1   H1   single    0.930  0.020  1.080
 6D5  C5   H2   single    0.930  0.020  1.080
 6D5  C6   H4   single    0.970  0.020  1.090
 6D5  C6   H3   single    0.970  0.020  1.090
 6D5  C7   H5   single    0.970  0.020  1.090
 6D5  C7   H6   single    0.970  0.020  1.090
 6D5  C8   H8   single    0.970  0.020  1.090
 6D5  C8   H7   single    0.970  0.020  1.090
 6D5  N1   H9   single    0.890  0.020  1.040
 6D5  N1   H11  single    0.890  0.020  1.040
 6D5  C9   H12  single    0.970  0.020  1.090
 6D5  C11  H14  single    0.970  0.020  1.090
 6D5  C11  H13  single    0.970  0.020  1.090
 6D5  C12  H15  single    0.970  0.020  1.090
 6D5  C12  H16  single    0.970  0.020  1.090
 6D5  C13  H19  single    0.970  0.020  1.090
 6D5  C13  H18  single    0.970  0.020  1.090
 6D5  C14  H20  single    0.970  0.020  1.090
 6D5  C15  H21  single    0.970  0.020  1.090
 6D5  O3   H22  single    0.850  0.020  0.980
 6D5  C16  H23  single    0.970  0.020  1.090
 6D5  O4   H24  single    0.850  0.020  0.980
 6D5  C17  H25  single    0.970  0.020  1.090
 6D5  N5   H27  single    0.860  0.020  1.020
 6D5  N5   H28  single    0.860  0.020  1.020

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
 6D5  H1   C1   N4   116.13  3.000
 6D5  H1   C1   N3   115.42  3.000
 6D5  N4   C1   N3   128.44  3.000
 6D5  N7   C2   N4   128.37  3.000
 6D5  N4   C2   C3   126.39  3.000
 6D5  N7   C2   C3   105.24  3.000
 6D5  N6   C3   C4   132.82  3.000
 6D5  N6   C3   C2   110.79  3.000
 6D5  C4   C3   C2   116.39  3.000
 6D5  N5   C4   N3   119.33  3.000
 6D5  N3   C4   C3   117.94  3.000
 6D5  N5   C4   C3   122.73  3.000
 6D5  H2   C5   N7   122.91  3.000
 6D5  H2   C5   N6   123.90  3.000
 6D5  N7   C5   N6   113.19  3.000
 6D5  H3   C6   H4   105.81  3.000
 6D5  H3   C6   N2   108.37  3.000
 6D5  H4   C6   N2   111.83  3.000
 6D5  H3   C6   C7   108.01  3.000
 6D5  H4   C6   C7   110.01  3.000
 6D5  N2   C6   C7   112.50  3.000
 6D5  H6   C7   H5   107.09  3.000
 6D5  H6   C7   C8   110.29  3.000
 6D5  H5   C7   C8   108.87  3.000
 6D5  H6   C7   C6   108.46  3.000
 6D5  H5   C7   C6   110.80  3.000
 6D5  C8   C7   C6   111.25  3.000
 6D5  H7   C8   H8   107.19  3.000
 6D5  H7   C8   N8   105.18  3.000
 6D5  H8   C8   N8   110.25  3.000
 6D5  H7   C8   C7   110.44  3.000
 6D5  H8   C8   C7   110.67  3.000
 6D5  N8   C8   C7   112.83  3.000
 6D5  H11  N1   H9   104.15  3.000
 6D5  H11  N1   C9   108.21  3.000
 6D5  H9   N1   C9   108.59  3.000
 6D5  H12  C9   C11  107.12  3.000
 6D5  H12  C9   C10  106.28  3.000
 6D5  C11  C9   C10  110.04  3.000
 6D5  H12  C9   N1   107.13  3.000
 6D5  C10  C9   N1   115.81  3.000
 6D5  C11  C9   N1   110.01  3.000
 6D5  O5   C10  O1   126.36  3.000
 6D5  O5   C10  C9   115.83  3.000
 6D5  O1   C10  C9   117.81  3.000
 6D5  H13  C11  H14  106.12  3.000
 6D5  H13  C11  C12  109.53  3.000
 6D5  H14  C11  C12  108.96  3.000
 6D5  H13  C11  C9   107.83  3.000
 6D5  H14  C11  C9   110.14  3.000
 6D5  C12  C11  C9   113.96  3.000
 6D5  H16  C12  H15  106.00  3.000
 6D5  H16  C12  N2   108.90  3.000
 6D5  H15  C12  N2   111.71  3.000
 6D5  H16  C12  C11  108.90  3.000
 6D5  H15  C12  C11  109.60  3.000
 6D5  N2   C12  C11  111.54  3.000
 6D5  C13  N2   C12  113.43  3.000
 6D5  C12  N2   C6   113.96  3.000
 6D5  C13  N2   C6   112.54  3.000
 6D5  H20  C14  C15  109.74  3.000
 6D5  H20  C14  O2   108.65  3.000
 6D5  C15  C14  O2   106.41  3.000
 6D5  H20  C14  C13  109.34  3.000
 6D5  C15  C14  C13  112.66  3.000
 6D5  O2   C14  C13  109.94  3.000
 6D5  C17  O2   C14  109.64  3.000
 6D5  H21  C15  C16  111.72  3.000
 6D5  H21  C15  O3   111.38  3.000
 6D5  C16  C15  O3   110.96  3.000
 6D5  H21  C15  C14  111.52  3.000
 6D5  O3   C15  C14  109.29  3.000
 6D5  C16  C15  C14  101.57  3.000
 6D5  H22  O3   C15  107.93  3.000
 6D5  H23  C16  C17  109.80  3.000
 6D5  H23  C16  O4   111.82  3.000
 6D5  C17  C16  O4   110.32  3.000
 6D5  H23  C16  C15  108.96  3.000
 6D5  O4   C16  C15  115.19  3.000
 6D5  C17  C16  C15  100.10  3.000
 6D5  H24  O4   C16  108.93  3.000
 6D5  H25  C17  N7   105.54  3.000
 6D5  H25  C17  C16  109.40  3.000
 6D5  N7   C17  C16  115.19  3.000
 6D5  H25  C17  O2   112.10  3.000
 6D5  C16  C17  O2   104.70  3.000
 6D5  N7   C17  O2   110.07  3.000
 6D5  C4   N3   C1   119.08  3.000
 6D5  C2   N4   C1   111.76  3.000
 6D5  H28  N5   H27  118.08  3.000
 6D5  H28  N5   C4   120.82  3.000
 6D5  H27  N5   C4   120.02  3.000
 6D5  C5   N6   C3   104.62  3.000
 6D5  C17  N7   C5   128.66  3.000
 6D5  C17  N7   C2   125.18  3.000
 6D5  C5   N7   C2   106.16  3.000
 6D5  N9   N8   C8   116.48  3.000
 6D5  N10  N9   N8   174.50  3.000
 6D5  H18  C13  H19  105.58  3.000
 6D5  H18  C13  C14  108.05  3.000
 6D5  H19  C13  C14  109.14  3.000
 6D5  H18  C13  N2   112.11  3.000
 6D5  H19  C13  N2   109.90  3.000
 6D5  C14  C13  N2   111.83  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
 6D5  CONST_01  C3   C4   N3   C1      0.00   0.0  0
 6D5  CONST_02  C3   C2   N4   C1      0.00   0.0  0
 6D5  CONST_03  N7   C2   N4   C1    180.00   0.0  0
 6D5  CONST_04  N3   C4   C3   C2      0.00   0.0  0
 6D5  CONST_05  C5   N6   C3   C2      0.00   0.0  0
 6D5  CONST_06  N6   C5   N7   C2      0.00   0.0  0
 6D5  CONST_07  N3   C1   N4   C2      0.00   0.0  0
 6D5  CONST_08  N7   C5   N6   C3      0.00   0.0  0
 6D5  CONST_09  C5   N7   C2   C3      0.00   0.0  0
 6D5  CONST_10  N4   C1   N3   C4      0.00   0.0  0
 6D5  CONST_11  C5   N6   C3   C4    180.00   0.0  0
 6D5  CONST_12  N7   C2   C3   C4    180.00   0.0  0
 6D5  CONST_13  N4   C2   C3   C4      0.00   0.0  0
 6D5  CONST_14  N4   C2   N7   C5    180.00   0.0  0
 6D5  CONST_15  N6   C3   C4   N3    180.00   0.0  0
 6D5  CONST_16  N6   C3   C2   N4    180.00   0.0  0
 6D5  CONST_17  N7   C2   C3   N6      0.00   0.0  0
 6D5  CONST_18  C17  N7   C2   C3    180.00   0.0  0
 6D5  CONST_19  N6   C5   N7   C17   180.00   0.0  0
 6D5  CONST_20  N4   C2   N7   C17     0.00   0.0  0
 6D5  CONST_21  N5   C4   N3   C1    180.00   0.0  0
 6D5  CONST_22  N5   C4   C3   C2    180.00   0.0  0
 6D5  CONST_23  N6   C3   C4   N5      0.00   0.0  0
 6D5  CONST_24  H2   C5   N7   C2    180.00   0.0  0
 6D5  CONST_25  H1   C1   N4   C2    180.00   0.0  0
 6D5  CONST_26  H27  N5   C4   C3    180.00   0.0  0
 6D5  CONST_27  H28  N5   C4   C3      0.00   0.0  0
 6D5  Var_01    C14  C13  N2   C6     89.23  30.0  1
 6D5  Var_02    N8   C8   C7   C6    177.02  30.0  1
 6D5  Var_03    C11  C12  N2   C6   -157.32  30.0  3
 6D5  Var_04    C13  N2   C6   C7   -152.65  30.0  3
 6D5  Var_05    N2   C6   C7   C8    178.75  30.0  3
 6D5  Var_06    N2   C12  C11  C9   -174.73  30.0  1

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
 6D5  chir_01  C9   C11  N1   C10  positiv
 6D5  chir_02  C14  O2   C13  C15  positiv
 6D5  chir_03  C15  O3   C14  C16  positiv
 6D5  chir_04  C16  O4   C15  C17  positiv
 6D5  chir_05  C17  O2   N7   C16  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
 6D5  plan-1  C1   0.020
 6D5  plan-1  C2   0.020
 6D5  plan-1  C3   0.020
 6D5  plan-1  C4   0.020
 6D5  plan-1  C5   0.020
 6D5  plan-1  C17  0.020
 6D5  plan-1  N3   0.020
 6D5  plan-1  N4   0.020
 6D5  plan-1  N5   0.020
 6D5  plan-1  N6   0.020
 6D5  plan-1  N7   0.020
 6D5  plan-1  H1   0.020
 6D5  plan-1  H2   0.020
 6D5  plan-2  C4   0.020
 6D5  plan-2  N5   0.020
 6D5  plan-2  H27  0.020
 6D5  plan-2  H28  0.020
 6D5  plan-3  C9   0.020
 6D5  plan-3  C10  0.020
 6D5  plan-3  O1   0.020
 6D5  plan-3  O5   0.020
 6D5  plan-4  C8   0.020
 6D5  plan-4  N8   0.020
 6D5  plan-4  N9   0.020
 6D5  plan-4  N10  0.020

