# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jun  5 21:01:44 2020
#   Inital geometry file: a 149 line input string
#   Ligand name: (2R)-2-{[6-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)hexanoyl]amino}butanedioic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]([C@@H](O)[C@H]3O)C(=O)NCCCCCC(=O)N[C@H](CC(O)=O)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
 66M  66M  '(2R)-2-{[6-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)hexanoyl]amino}butanedioic acid (non-preferred name)'  ligand  61  36  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_66M
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
 66M  N1   N  N      0  -0.458    8.2484  -0.5176  -0.5069
 66M  C2   C  CR6    0   0.453    8.6596   1.8100   1.0094
 66M  N3   N  NR5    0  -0.540    5.9747   0.3091  -0.6586
 66M  C4   C  CR15   0   0.091    5.3776   1.4391  -0.1673
 66M  C5   C  CH1    0   0.165    5.3935  -0.7529  -1.4738
 66M  C6   C  CH1    0  -0.037    5.2272  -2.0407  -0.6722
 66M  C8   C  CH1    0  -0.071    3.1186  -1.0885  -1.1868
 66M  C11  C  CH2    0  -0.433   -1.4120  -0.5621  -0.1302
 66M  C12  C  CH2    0  -0.425   -2.6275   0.1044   0.4999
 66M  C14  C  CH2    0  -0.592   -5.1419   0.2814   0.5666
 66M  C15  C  C      0   0.569   -6.4793  -0.1681   0.0139
 66M  C16  C  CH1    0  -0.171   -8.8764   0.2776   0.0513
 66M  C17  C  CH2    0  -0.603   -9.7708   1.4953   0.2501
 66M  C18  C  C      0   0.407   -9.5193   2.6333  -0.7575
 66M  C7   C  CH1    0  -0.047    3.8478  -1.8121  -0.0468
 66M  N2   N  NH2    0  -0.816    8.9156   2.9057   1.7280
 66M  C9   C  C      0   0.520    2.0274  -0.1389  -0.7038
 66M  C10  C  CH2    0  -0.270   -0.1151  -0.1055   0.5245
 66M  C13  C  CH2    0  -0.411   -3.9431  -0.3734  -0.1006
 66M  N4   N  N      0  -0.452    6.1903   2.1927   0.5159
 66M  O14  O  O      0  -0.518   -6.6135  -1.2120  -0.6142
 66M  N5   N  NH1    0  -0.631    1.0475  -0.7604  -0.0365
 66M  O1   O  O      0  -0.484    2.0701   1.0629  -0.9163
 66M  O    O  O2     0  -0.483    4.1153  -0.3761  -1.8897
 66M  O15  O  OH1    0  -0.653    3.1714  -2.9919   0.2819
 66M  O16  O  OH1    0  -0.661    5.1976  -3.0978  -1.5883
 66M  C1   C  CR56   0  -0.001    7.3894   1.5327   0.4712
 66M  C    C  CR56   0   0.486    7.2779   0.3604  -0.2592
 66M  C3   C  CR16   0   0.038    9.3917  -0.1466   0.0430
 66M  N    N  N      0  -0.473    9.6453   0.9379   0.7713
 66M  N6   N  NH1    0  -0.629   -7.4997   0.6670   0.2570
 66M  C52  C  C      0   0.406   -9.3167  -0.8748   0.9872
 66M  O13  O  OC    -1  -0.624  -10.3792  -1.4430   0.6593
 66M  O12  O  O      0  -0.602   -8.6135  -1.1191   1.9833
 66M  O11  O  O      0  -0.612   -9.3437   2.3018  -1.9470
 66M  H1   H  HCR5   0   0.302    4.3375   1.6579  -0.3532
 66M  H2   H  HCH1   0   0.293    6.0429  -0.8945  -2.3411
 66M  H3   H  HCH1   0   0.269    6.0137  -2.1667   0.0812
 66M  H4   H  HCH1   0   0.284    2.6586  -1.8322  -1.8506
 66M  H5   H  HCH2   0   0.222   -1.5027  -1.6492  -0.0374
 66M  H6   H  HCH2   0   0.226   -1.3748  -0.3419  -1.2010
 66M  H7   H  HCH2   0   0.216   -2.6289  -0.0896   1.5782
 66M  H8   H  HCH2   0   0.218   -2.5465   1.1911   0.3889
 66M  H9   H  HCH2   0   0.249   -5.0651   1.3707   0.4990
 66M  H10  H  HCH2   0   0.261   -5.1363   0.0522   1.6385
 66M  H11  H  HCH1   0   0.221   -8.9929  -0.0552  -0.9821
 66M  H12  H  HCH2   0   0.241  -10.8090   1.1673   0.1405
 66M  H13  H  HCH2   0   0.208   -9.6738   1.8659   1.2759
 66M  H15  H  HCH1   0   0.265    3.9455  -1.1520   0.8234
 66M  H16  H  HNH2   0   0.410    8.1722   3.5233   2.0035
 66M  H17  H  HNH2   0   0.403    9.8082   3.0127   2.1788
 66M  H18  H  HCH2   0   0.246    0.0091   0.9701   0.4095
 66M  H19  H  HCH2   0   0.242   -0.1511  -0.3092   1.5980
 66M  H20  H  HCH2   0   0.221   -3.9525  -0.1619  -1.1738
 66M  H21  H  HCH2   0   0.221   -4.0132  -1.4593  -0.0013
 66M  H22  H  HNH1   0   0.401    1.1171  -1.7592   0.0923
 66M  H23  H  HOH1   0   0.475    3.3858  -3.2364   1.1883
 66M  H24  H  HOH1   0   0.455    4.6938  -3.8210  -1.1957
 66M  H25  H  HCR6   0   0.252   10.2358  -0.8089  -0.1156
 66M  H26  H  HNH1   0   0.382   -7.3243   1.4433   0.8762
 66M  O2   O  OC    -1  -0.620   -9.5426   3.7983  -0.3102

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
 66M  C3   N1   aromatic  1.322  0.020  1.322
 66M  C3   N    aromatic  1.331  0.020  1.331
 66M  N1   C    aromatic  1.332  0.020  1.332
 66M  O16  C6   single    1.399  0.020  1.399
 66M  N    C2   aromatic  1.337  0.020  1.337
 66M  C6   C5   single    1.526  0.020  1.526
 66M  C6   C7   single    1.532  0.020  1.532
 66M  C    C1   aromatic  1.386  0.020  1.386
 66M  C    N3   aromatic  1.364  0.020  1.364
 66M  O15  C7   single    1.399  0.020  1.399
 66M  C2   N2   single    1.335  0.020  1.335
 66M  C2   C1   aromatic  1.407  0.020  1.407
 66M  C5   N3   single    1.459  0.020  1.459
 66M  C5   O    single    1.396  0.020  1.396
 66M  C7   C8   single    1.535  0.020  1.535
 66M  C1   N4   aromatic  1.369  0.020  1.369
 66M  N3   C4   aromatic  1.369  0.020  1.369
 66M  O    C8   single    1.412  0.020  1.412
 66M  C8   C9   single    1.525  0.020  1.525
 66M  C4   N4   aromatic  1.302  0.020  1.302
 66M  C9   O1   double    1.221  0.020  1.221
 66M  C9   N5   single    1.339  0.020  1.339
 66M  N5   C10  single    1.448  0.020  1.448
 66M  C10  C11  single    1.523  0.020  1.523
 66M  C11  C12  single    1.523  0.020  1.523
 66M  C12  C13  single    1.523  0.020  1.523
 66M  O12  C52  deloc     1.244  0.020  1.244
 66M  O13  C52  deloc     1.249  0.020  1.249
 66M  C13  C14  single    1.520  0.020  1.520
 66M  C52  C16  single    1.548  0.020  1.548
 66M  C14  C15  single    1.515  0.020  1.515
 66M  N6   C16  single    1.445  0.020  1.445
 66M  N6   C15  single    1.341  0.020  1.341
 66M  C16  C17  single    1.524  0.020  1.524
 66M  C15  O14  double    1.226  0.020  1.226
 66M  C17  C18  single    1.541  0.020  1.541
 66M  C18  O11  deloc     1.247  0.020  1.247
 66M  C4   H1   single    0.930  0.020  1.080
 66M  C5   H2   single    0.970  0.020  1.090
 66M  C6   H3   single    0.970  0.020  1.090
 66M  C8   H4   single    0.970  0.020  1.090
 66M  C11  H5   single    0.970  0.020  1.090
 66M  C11  H6   single    0.970  0.020  1.090
 66M  C12  H7   single    0.970  0.020  1.090
 66M  C12  H8   single    0.970  0.020  1.090
 66M  C14  H9   single    0.970  0.020  1.090
 66M  C14  H10  single    0.970  0.020  1.090
 66M  C16  H11  single    0.970  0.020  1.090
 66M  C17  H12  single    0.970  0.020  1.090
 66M  C17  H13  single    0.970  0.020  1.090
 66M  C7   H15  single    0.970  0.020  1.090
 66M  N2   H16  single    0.860  0.020  1.020
 66M  N2   H17  single    0.860  0.020  1.020
 66M  C10  H18  single    0.970  0.020  1.090
 66M  C10  H19  single    0.970  0.020  1.090
 66M  C13  H20  single    0.970  0.020  1.090
 66M  C13  H21  single    0.970  0.020  1.090
 66M  N5   H22  single    0.860  0.020  1.020
 66M  O15  H23  single    0.850  0.020  0.980
 66M  O16  H24  single    0.850  0.020  0.980
 66M  C3   H25  single    0.930  0.020  1.080
 66M  N6   H26  single    0.890  0.020  1.040
 66M  C18  O2   deloc     1.248  0.020  1.248

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
 66M  C3   N1   C    111.58  3.000
 66M  N    C2   C1   117.95  3.000
 66M  C1   C2   N2   122.73  3.000
 66M  N    C2   N2   119.32  3.000
 66M  C    N3   C5   124.84  3.000
 66M  C5   N3   C4   128.85  3.000
 66M  C    N3   C4   106.29  3.000
 66M  H1   C4   N4   125.09  3.000
 66M  H1   C4   N3   121.72  3.000
 66M  N4   C4   N3   113.19  3.000
 66M  H2   C5   O    110.04  3.000
 66M  H2   C5   C6   111.86  3.000
 66M  O    C5   C6   106.52  3.000
 66M  H2   C5   N3   107.52  3.000
 66M  O    C5   N3   109.55  3.000
 66M  C6   C5   N3   111.35  3.000
 66M  H3   C6   O16  112.23  3.000
 66M  H3   C6   C7   112.50  3.000
 66M  O16  C6   C7   111.17  3.000
 66M  H3   C6   C5   112.32  3.000
 66M  C7   C6   C5   100.76  3.000
 66M  O16  C6   C5   107.22  3.000
 66M  H4   C8   O    109.66  3.000
 66M  H4   C8   C9   108.27  3.000
 66M  O    C8   C9   110.40  3.000
 66M  H4   C8   C7   109.20  3.000
 66M  C9   C8   C7   113.48  3.000
 66M  O    C8   C7   105.79  3.000
 66M  H6   C11  H5   106.60  3.000
 66M  H6   C11  C10  109.37  3.000
 66M  H5   C11  C10  109.38  3.000
 66M  H6   C11  C12  110.13  3.000
 66M  H5   C11  C12  109.47  3.000
 66M  C10  C11  C12  111.76  3.000
 66M  H8   C12  H7   105.99  3.000
 66M  H8   C12  C13  109.59  3.000
 66M  H7   C12  C13  109.36  3.000
 66M  H8   C12  C11  109.46  3.000
 66M  H7   C12  C11  109.31  3.000
 66M  C13  C12  C11  112.89  3.000
 66M  H10  C14  H9   105.56  3.000
 66M  H10  C14  C13  109.58  3.000
 66M  H9   C14  C13  110.27  3.000
 66M  H10  C14  C15  107.40  3.000
 66M  H9   C14  C15  109.56  3.000
 66M  C13  C14  C15  114.09  3.000
 66M  N6   C15  O14  122.69  3.000
 66M  O14  C15  C14  122.42  3.000
 66M  N6   C15  C14  114.88  3.000
 66M  H11  C16  C52  108.35  3.000
 66M  H11  C16  N6   108.57  3.000
 66M  C52  C16  N6   112.66  3.000
 66M  H11  C16  C17  107.72  3.000
 66M  N6   C16  C17  108.97  3.000
 66M  C52  C16  C17  110.42  3.000
 66M  H13  C17  H12  106.22  3.000
 66M  H13  C17  C18  110.38  3.000
 66M  H12  C17  C18  108.10  3.000
 66M  H13  C17  C16  109.92  3.000
 66M  H12  C17  C16  107.71  3.000
 66M  C18  C17  C16  114.15  3.000
 66M  O2   C18  O11  126.33  3.000
 66M  O2   C18  C17  116.87  3.000
 66M  O11  C18  C17  116.77  3.000
 66M  H15  C7   O15  111.36  3.000
 66M  H15  C7   C8   110.36  3.000
 66M  O15  C7   C8   110.02  3.000
 66M  H15  C7   C6   109.49  3.000
 66M  C8   C7   C6   101.25  3.000
 66M  O15  C7   C6   113.92  3.000
 66M  H17  N2   H16  117.93  3.000
 66M  H17  N2   C2   119.92  3.000
 66M  H16  N2   C2   120.67  3.000
 66M  O1   C9   N5   124.70  3.000
 66M  N5   C9   C8   113.12  3.000
 66M  O1   C9   C8   122.18  3.000
 66M  H19  C10  H18  106.95  3.000
 66M  H19  C10  N5   108.83  3.000
 66M  H18  C10  N5   108.32  3.000
 66M  H19  C10  C11  109.78  3.000
 66M  H18  C10  C11  110.36  3.000
 66M  N5   C10  C11  112.44  3.000
 66M  H21  C13  H20  106.31  3.000
 66M  H21  C13  C14  109.73  3.000
 66M  H20  C13  C14  109.91  3.000
 66M  H21  C13  C12  109.35  3.000
 66M  H20  C13  C12  109.48  3.000
 66M  C14  C13  C12  111.90  3.000
 66M  C1   N4   C4   104.50  3.000
 66M  H22  N5   C10  116.97  3.000
 66M  H22  N5   C9   118.20  3.000
 66M  C10  N5   C9   124.83  3.000
 66M  C8   O    C5   111.21  3.000
 66M  H23  O15  C7   109.12  3.000
 66M  H24  O16  C6   108.11  3.000
 66M  C    C1   N4   110.76  3.000
 66M  N4   C1   C2   133.07  3.000
 66M  C    C1   C2   116.17  3.000
 66M  C1   C    N3   105.25  3.000
 66M  N3   C    N1   128.09  3.000
 66M  C1   C    N1   126.65  3.000
 66M  H25  C3   N    115.43  3.000
 66M  H25  C3   N1   116.16  3.000
 66M  N    C3   N1   128.41  3.000
 66M  C3   N    C2   119.23  3.000
 66M  H26  N6   C16  117.42  3.000
 66M  H26  N6   C15  117.29  3.000
 66M  C16  N6   C15  122.09  3.000
 66M  O12  C52  O13  127.02  3.000
 66M  O13  C52  C16  114.96  3.000
 66M  O12  C52  C16  118.01  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
 66M  CONST_01  C2   N    C3   N1      0.00   0.0  0
 66M  CONST_02  C2   C1   C    N1      0.00   0.0  0
 66M  CONST_03  N4   C1   C    N1    180.00   0.0  0
 66M  CONST_04  C4   N3   C    N1    180.00   0.0  0
 66M  CONST_05  N3   C    C1   C2    180.00   0.0  0
 66M  CONST_06  C4   N4   C1   C2    180.00   0.0  0
 66M  CONST_07  C3   N1   C    N3    180.00   0.0  0
 66M  CONST_08  N4   C1   C    N3      0.00   0.0  0
 66M  CONST_09  C1   N4   C4   N3      0.00   0.0  0
 66M  CONST_10  C1   C    N3   C4      0.00   0.0  0
 66M  CONST_11  C    C1   N4   C4      0.00   0.0  0
 66M  CONST_12  N    C2   C1   N4    180.00   0.0  0
 66M  CONST_13  C    N3   C4   N4      0.00   0.0  0
 66M  CONST_14  C3   N1   C    C1      0.00   0.0  0
 66M  CONST_15  C3   N    C2   C1      0.00   0.0  0
 66M  CONST_16  N    C3   N1   C       0.00   0.0  0
 66M  CONST_17  N    C2   C1   C       0.00   0.0  0
 66M  CONST_18  C5   N3   C    N1      0.00   0.0  0
 66M  CONST_19  C1   C    N3   C5    180.00   0.0  0
 66M  CONST_20  N4   C4   N3   C5    180.00   0.0  0
 66M  CONST_21  C3   N    C2   N2    180.00   0.0  0
 66M  CONST_22  C    C1   C2   N2    180.00   0.0  0
 66M  CONST_23  N4   C1   C2   N2      0.00   0.0  0
 66M  CONST_24  H25  C3   N    C2    180.00   0.0  0
 66M  CONST_25  H1   C4   N3   C5      0.00   0.0  0
 66M  CONST_26  H16  N2   C2   C1      0.00   0.0  0
 66M  CONST_27  H17  N2   C2   C1    180.00   0.0  0
 66M  CONST_28  C10  N5   C9   C8    180.00   0.0  0
 66M  CONST_29  H22  N5   C9   C8      0.00   0.0  0
 66M  CONST_30  C16  N6   C15  C14   180.00   0.0  0
 66M  CONST_31  O14  C15  N6   C16     0.00   0.0  0
 66M  CONST_32  O1   C9   N5   C10     0.00   0.0  0
 66M  CONST_33  H26  N6   C15  C14     0.00   0.0  0
 66M  Var_01    C9   N5   C10  C11   115.80  30.0  2
 66M  Var_02    C14  C13  C12  C11   178.66  30.0  3
 66M  Var_03    N5   C10  C11  C12   178.27  30.0  1
 66M  Var_04    C15  C14  C13  C12  -179.52  30.0  3
 66M  Var_05    O11  C18  C17  C16    42.18  30.0  3
 66M  Var_06    C13  C12  C11  C10  -177.83  30.0  3
 66M  Var_07    N6   C15  C14  C13  -159.61  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
 66M  chir_01  C5   C6   N3   O    positiv
 66M  chir_02  C6   O16  C7   C5   positiv
 66M  chir_03  C8   O    C9   C7   positiv
 66M  chir_04  C16  C52  N6   C17  positiv
 66M  chir_05  C7   C6   O15  C8   positiv

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
 66M  plan-1  N1   0.020
 66M  plan-1  C2   0.020
 66M  plan-1  N3   0.020
 66M  plan-1  C4   0.020
 66M  plan-1  C5   0.020
 66M  plan-1  N2   0.020
 66M  plan-1  N4   0.020
 66M  plan-1  C1   0.020
 66M  plan-1  C    0.020
 66M  plan-1  C3   0.020
 66M  plan-1  N    0.020
 66M  plan-1  H1   0.020
 66M  plan-1  H25  0.020
 66M  plan-2  C8   0.020
 66M  plan-2  C9   0.020
 66M  plan-2  C10  0.020
 66M  plan-2  N5   0.020
 66M  plan-2  O1   0.020
 66M  plan-2  H22  0.020
 66M  plan-3  C2   0.020
 66M  plan-3  N2   0.020
 66M  plan-3  H16  0.020
 66M  plan-3  H17  0.020
 66M  plan-4  C14  0.020
 66M  plan-4  C15  0.020
 66M  plan-4  C16  0.020
 66M  plan-4  O14  0.020
 66M  plan-4  N6   0.020
 66M  plan-4  H26  0.020
 66M  plan-5  C17  0.020
 66M  plan-5  C18  0.020
 66M  plan-5  O11  0.020
 66M  plan-5  O2   0.020
 66M  plan-6  C16  0.020
 66M  plan-6  C52  0.020
 66M  plan-6  O13  0.020
 66M  plan-6  O12  0.020

