# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 16:56:06 2021
#   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  58  32  .  2021-08-05  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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   0.044  49.2969  42.1574  126.5883
 6D5  C2   C  CR56   0   0.490  50.0560  40.1829  127.1747
 6D5  C3   C  CR56   0  -0.012  50.4435  39.8823  125.8783
 6D5  C4   C  CR6    0   0.459  50.1904  40.8674  124.9063
 6D5  C5   C  CR15   0   0.109  50.9662  38.1989  127.0381
 6D5  C6   C  CH2    0  -0.307  51.1960  33.7184  130.9722
 6D5  C7   C  CH2    0  -0.481  52.2966  33.0934  130.1136
 6D5  C8   C  CH2    0  -0.290  51.9582  31.6847  129.6707
 6D5  N1   N  NH2    0  -0.783  53.4259  36.2819  135.1558
 6D5  C9   C  CH1    0  -0.226  52.7177  35.0267  135.0662
 6D5  C10  C  C      0   0.515  53.6311  33.8079  135.0180
 6D5  O1   O  O      0  -0.441  54.8267  33.8480  134.8669
 6D5  C11  C  CH2    0  -0.423  51.7505  35.0190  133.8754
 6D5  C12  C  CH2    0  -0.313  52.4275  35.1464  132.5144
 6D5  N2   N  NT     0  -0.416  51.4519  35.0645  131.4417
 6D5  C14  C  CH1    0  -0.002  51.0344  37.3949  130.8775
 6D5  O2   O  O2     0  -0.499  51.3356  38.4192  129.9220
 6D5  C15  C  CH1    0  -0.037  49.5120  37.3900  131.0231
 6D5  O3   O  OH1    0  -0.669  49.0514  38.3422  131.9472
 6D5  C16  C  CH1    0  -0.009  49.0907  37.8493  129.6288
 6D5  O4   O  OH1    0  -0.653  47.8304  38.4249  129.5060
 6D5  C17  C  CH1    0   0.206  50.1649  38.8924  129.3224
 6D5  N3   N  N      0  -0.475  49.6091  42.0047  125.3040
 6D5  N4   N  N      0  -0.455  49.4781  41.3093  127.5856
 6D5  N5   N  NH2    0  -0.817  50.5039  40.7080  123.6200
 6D5  N6   N  N      0  -0.450  51.0139  38.6372  125.8159
 6D5  N7   N  NR5    0  -0.536  50.3994  39.0868  127.9126
 6D5  N8   N  N      0  -0.380  51.8829  30.8168  130.8571
 6D5  N9   N  N      1   0.376  51.4527  29.6947  130.6866
 6D5  N10  N  N     -1  -0.233  51.0665  28.6390  130.6286
 6D5  H1   H  HCR6   0   0.252  48.8310  43.1030  126.8443
 6D5  H2   H  HCR5   0   0.295  51.3421  37.2408  127.3638
 6D5  H4   H  HCH2   0   0.233  50.2620  33.7243  130.4000
 6D5  H3   H  HCH2   0   0.240  51.0084  33.0833  131.8420
 6D5  H5   H  HCH2   0   0.237  53.2502  33.0817  130.6486
 6D5  H6   H  HCH2   0   0.246  52.4525  33.6917  129.2122
 6D5  H8   H  HCH2   0   0.247  51.0057  31.6746  129.1309
 6D5  H7   H  HCH2   0   0.262  52.7260  31.3101  128.9889
 6D5  H9   H  HNH2   0   0.356  53.9516  36.3244  136.0193
 6D5  H11  H  HNH2   0   0.347  54.1086  36.3686  134.4138
 6D5  H12  H  HCH1   0   0.285  52.1082  34.9246  135.9698
 6D5  H14  H  HCH2   0   0.240  51.0610  35.8568  134.0016
 6D5  H13  H  HCH2   0   0.240  51.1450  34.1111  133.9043
 6D5  H15  H  HCH2   0   0.225  53.2143  34.3873  132.3982
 6D5  H16  H  HCH2   0   0.239  52.9446  36.1075  132.4560
 6D5  H20  H  HCH1   0   0.250  51.5099  37.6689  131.8258
 6D5  H21  H  HCH1   0   0.253  49.1493  36.3834  131.2613
 6D5  H22  H  HOH1   0   0.452  49.3352  38.0744  132.8269
 6D5  H23  H  HCH1   0   0.240  49.2134  37.0001  128.9412
 6D5  H24  H  HOH1   0   0.463  47.1650  37.7347  129.5887
 6D5  H25  H  HCH1   0   0.261  49.8668  39.8696  129.7195
 6D5  H26  H  HOH1   0   0.480  53.5560  31.9163  135.1059
 6D5  H27  H  HNH2   0   0.404  50.2925  41.4283  122.9517
 6D5  H28  H  HNH2   0   0.411  50.9376  39.8636  123.2914
 6D5  C13  C  CH2    0  -0.332  51.5949  36.0570  130.4017
 6D5  O5   O  OH1    0  -0.592  52.9542  32.6736  135.1609
 6D5  H19  H  HCH2   0   0.237  51.0349  35.7212  129.5232
 6D5  H18  H  HCH2   0   0.234  52.6333  36.2007  130.0689

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    1.333  0.020  1.333
 6D5  C4   N3   aromatic  1.338  0.020  1.338
 6D5  C4   C3   aromatic  1.407  0.020  1.407
 6D5  N6   C3   aromatic  1.371  0.020  1.371
 6D5  N6   C5   aromatic  1.299  0.020  1.299
 6D5  N3   C1   aromatic  1.331  0.020  1.331
 6D5  C3   C2   aromatic  1.386  0.020  1.386
 6D5  C5   N7   aromatic  1.369  0.020  1.369
 6D5  C1   N4   aromatic  1.322  0.020  1.322
 6D5  C2   N7   aromatic  1.365  0.020  1.365
 6D5  C2   N4   aromatic  1.331  0.020  1.331
 6D5  N7   C17  single    1.442  0.020  1.442
 6D5  C17  C16  single    1.528  0.020  1.528
 6D5  C17  O2   single    1.398  0.020  1.398
 6D5  C16  O4   single    1.391  0.020  1.391
 6D5  C16  C15  single    1.527  0.020  1.527
 6D5  N10  N9   double    1.126  0.020  1.126
 6D5  O2   C14  single    1.433  0.020  1.433
 6D5  C8   C7   single    1.515  0.020  1.515
 6D5  C8   N8   single    1.472  0.020  1.472
 6D5  N9   N8   double    1.214  0.020  1.214
 6D5  C13  C14  single    1.527  0.020  1.527
 6D5  C13  N2   single    1.445  0.020  1.445
 6D5  C7   C6   single    1.529  0.020  1.529
 6D5  C14  C15  single    1.529  0.020  1.529
 6D5  C15  O3   single    1.405  0.020  1.405
 6D5  C6   N2   single    1.448  0.020  1.448
 6D5  N2   C12  single    1.452  0.020  1.452
 6D5  C12  C11  single    1.525  0.020  1.525
 6D5  C11  C9   single    1.534  0.020  1.534
 6D5  N1   C9   single    1.444  0.020  1.444
 6D5  C9   C10  single    1.524  0.020  1.524
 6D5  O1   C10  double    1.206  0.020  1.206
 6D5  C10  O5   single    1.329  0.020  1.329
 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  O5   H26  single    0.850  0.020  0.980
 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   116.12  3.000
 6D5  H1   C1   N3   115.38  3.000
 6D5  N4   C1   N3   128.51  3.000
 6D5  N7   C2   N4   128.45  3.000
 6D5  N4   C2   C3   126.41  3.000
 6D5  N7   C2   C3   105.13  3.000
 6D5  N6   C3   C4   132.79  3.000
 6D5  N6   C3   C2   110.85  3.000
 6D5  C4   C3   C2   116.37  3.000
 6D5  N5   C4   N3   119.38  3.000
 6D5  N3   C4   C3   117.91  3.000
 6D5  N5   C4   C3   122.71  3.000
 6D5  H2   C5   N7   121.81  3.000
 6D5  H2   C5   N6   124.77  3.000
 6D5  N7   C5   N6   113.41  3.000
 6D5  H3   C6   H4   105.81  3.000
 6D5  H3   C6   N2   108.20  3.000
 6D5  H4   C6   N2   108.36  3.000
 6D5  H3   C6   C7   109.44  3.000
 6D5  H4   C6   C7   108.82  3.000
 6D5  N2   C6   C7   115.76  3.000
 6D5  H6   C7   H5   106.56  3.000
 6D5  H6   C7   C8   107.44  3.000
 6D5  H5   C7   C8   109.14  3.000
 6D5  H6   C7   C6   110.00  3.000
 6D5  H5   C7   C6   110.93  3.000
 6D5  C8   C7   C6   112.54  3.000
 6D5  H7   C8   H8   107.48  3.000
 6D5  H7   C8   N8   109.67  3.000
 6D5  H8   C8   N8   110.33  3.000
 6D5  H7   C8   C7   110.13  3.000
 6D5  H8   C8   C7   110.31  3.000
 6D5  N8   C8   C7   108.91  3.000
 6D5  H11  N1   H9   105.75  3.000
 6D5  H11  N1   C9   111.10  3.000
 6D5  H9   N1   C9   110.14  3.000
 6D5  H12  C9   C11  106.81  3.000
 6D5  H12  C9   C10  106.57  3.000
 6D5  C11  C9   C10  110.44  3.000
 6D5  H12  C9   N1   107.64  3.000
 6D5  C10  C9   N1   113.78  3.000
 6D5  C11  C9   N1   111.21  3.000
 6D5  O5   C10  O1   123.16  3.000
 6D5  O5   C10  C9   111.97  3.000
 6D5  O1   C10  C9   124.87  3.000
 6D5  H13  C11  H14  106.54  3.000
 6D5  H13  C11  C12  109.83  3.000
 6D5  H14  C11  C12  108.61  3.000
 6D5  H13  C11  C9   109.48  3.000
 6D5  H14  C11  C9   107.72  3.000
 6D5  C12  C11  C9   114.35  3.000
 6D5  H16  C12  H15  105.25  3.000
 6D5  H16  C12  N2   109.14  3.000
 6D5  H15  C12  N2   111.33  3.000
 6D5  H16  C12  C11  109.34  3.000
 6D5  H15  C12  C11  110.74  3.000
 6D5  N2   C12  C11  110.86  3.000
 6D5  C13  N2   C12  115.24  3.000
 6D5  C12  N2   C6   114.24  3.000
 6D5  C13  N2   C6   115.00  3.000
 6D5  H20  C14  C15  110.51  3.000
 6D5  H20  C14  O2   107.89  3.000
 6D5  C15  C14  O2   105.97  3.000
 6D5  H20  C14  C13  109.24  3.000
 6D5  C15  C14  C13  113.10  3.000
 6D5  O2   C14  C13  109.97  3.000
 6D5  C17  O2   C14  110.61  3.000
 6D5  H21  C15  C16  112.54  3.000
 6D5  H21  C15  O3   111.78  3.000
 6D5  C16  C15  O3   107.84  3.000
 6D5  H21  C15  C14  110.67  3.000
 6D5  O3   C15  C14  112.76  3.000
 6D5  C16  C15  C14  100.76  3.000
 6D5  H22  O3   C15  108.43  3.000
 6D5  H23  C16  C17  108.87  3.000
 6D5  H23  C16  O4   111.44  3.000
 6D5  C17  C16  O4   109.68  3.000
 6D5  H23  C16  C15  107.93  3.000
 6D5  O4   C16  C15  117.06  3.000
 6D5  C17  C16  C15  101.21  3.000
 6D5  H24  O4   C16  108.80  3.000
 6D5  H25  C17  N7   106.15  3.000
 6D5  H25  C17  C16  110.16  3.000
 6D5  N7   C17  C16  113.71  3.000
 6D5  H25  C17  O2   111.98  3.000
 6D5  C16  C17  O2   105.76  3.000
 6D5  N7   C17  O2   109.19  3.000
 6D5  C4   N3   C1   119.11  3.000
 6D5  C2   N4   C1   111.70  3.000
 6D5  H28  N5   H27  118.40  3.000
 6D5  H28  N5   C4   121.17  3.000
 6D5  H27  N5   C4   120.42  3.000
 6D5  C5   N6   C3   104.37  3.000
 6D5  C17  N7   C5   127.18  3.000
 6D5  C17  N7   C2   126.55  3.000
 6D5  C5   N7   C2   106.24  3.000
 6D5  N9   N8   C8   116.74  3.000
 6D5  N10  N9   N8   174.80  3.000
 6D5  H18  C13  H19  106.27  3.000
 6D5  H18  C13  C14  109.05  3.000
 6D5  H19  C13  C14  109.34  3.000
 6D5  H18  C13  N2   113.64  3.000
 6D5  H19  C13  N2   108.44  3.000
 6D5  C14  C13  N2   109.97  3.000
 6D5  H26  O5   C10  110.17  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  CONST_28  H26  O5   C10  C9   180.00   0.0  0
 6D5  Var_01    C14  C13  N2   C6   146.02  30.0  2
 6D5  Var_02    N8   C8   C7   C6   -64.76  30.0  1
 6D5  Var_03    C11  C12  N2   C6   -89.12  30.0  3
 6D5  Var_04    C13  N2   C6   C7    62.39  30.0  3
 6D5  Var_05    N2   C6   C7   C8   179.62  30.0  3
 6D5  Var_06    N2   C12  C11  C9   177.18  30.0  2

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  H26  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

