# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 03:44:45 2021
#   Inital geometry file: a 151 line input string
#   Ligand name: (3R)-4-amino-3-{[6-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)hexanoyl]amino}-4-oxobutanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[C@@H](CC(O)=O)NC(=O)CCCCCNC(=O)[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
#
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
 6L5  6L5  '(3R)-4-amino-3-{[6-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]carbonyl}amino)hexanoyl]amino}-4-oxobutanoic acid (non-preferred name)'  ligand  64  36  .  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_6L5
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
 6L5  N1   N  N     0  -0.459  30.9514  32.9058   5.0375
 6L5  C2   C  CR6   0   0.453  32.5895  30.7256   5.7081
 6L5  N3   N  NR5   0  -0.537  30.0659  32.5780   7.2689
 6L5  C4   C  CR15  0   0.087  30.3692  31.6744   8.2522
 6L5  C5   C  CR15  0   0.171  29.0851  33.6523   7.2853
 6L5  C6   C  CR15  0  -0.051  27.7798  33.2500   6.5992
 6L5  C8   C  CR15  0  -0.078  27.4223  33.6623   8.8981
 6L5  C11  C  CH2   0  -0.427  26.4040  33.4893  13.3436
 6L5  C12  C  CH2   0  -0.444  25.9502  32.9417  14.6896
 6L5  C14  C  CH2   0  -0.565  26.1310  33.1604  17.2228
 6L5  C15  C  C     0   0.548  24.6366  33.2144  17.4367
 6L5  C16  C  CH1   0  -0.142  22.5858  31.9293  17.6829
 6L5  C17  C  CH2   0  -0.633  22.2228  30.4491  17.7706
 6L5  C18  C  C     0   0.555  20.8047  30.1897  18.2015
 6L5  C7   C  CR15  0  -0.016  26.9805  32.7002   7.7807
 6L5  N2   N  NH2   0  -0.816  33.3843  29.6850   5.9658
 6L5  C9   C  C     0   0.529  27.3142  33.0187  10.2699
 6L5  C10  C  CH2   0  -0.281  25.8048  32.7074  12.1807
 6L5  C13  C  CH2   0  -0.429  26.5264  33.7286  15.8605
 6L5  N4   N  N     0  -0.454  31.3107  30.8430   7.9090
 6L5  O13  O  O     0  -0.496  24.0217  34.2697  17.5100
 6L5  N5   N  NH1   0  -0.628  26.1516  33.2554  10.8859
 6L5  O1   O  O     0  -0.482  28.1908  32.2930  10.7163
 6L5  O    O  O     0  -0.485  28.7704  33.9673   8.6117
 6L5  O14  O  OH1   0  -0.657  25.6094  32.7232   7.5328
 6L5  O15  O  OH1   0  -0.660  27.2051  34.4191   6.0859
 6L5  C1   C  CR56  0  -0.003  31.6482  31.2124   6.6335
 6L5  C    C  CR56  0   0.485  30.8852  32.2914   6.2171
 6L5  C3   C  CR16  0   0.040  31.8695  32.3617   4.2572
 6L5  N    N  N     0  -0.473  32.6712  31.3326   4.5187
 6L5  N6   N  NH1   0  -0.643  24.0153  32.0263  17.5355
 6L5  C52  C  C     0   0.518  21.8856  32.5667  16.4741
 6L5  N21  N  NH2   0  -0.788  20.7972  33.2857  16.7604
 6L5  O12  O  O     0  -0.481  22.2961  32.3753  15.3407
 6L5  O11  O  O     0  -0.436  20.1048  30.9786  18.7848
 6L5  H1   H  HCR5  0   0.308  29.8627  31.6845   9.2057
 6L5  H2   H  HCR5  0   0.286  29.5436  34.5098   6.7854
 6L5  H3   H  HCR5  0   0.270  27.9438  32.4935   5.8232
 6L5  H4   H  HCR5  0   0.266  26.8111  34.5720   8.8538
 6L5  H5   H  HCH2  0   0.227  27.4950  33.4594  13.2782
 6L5  H6   H  HCH2  0   0.222  26.1126  34.5402  13.2553
 6L5  H7   H  HCH2  0   0.236  24.8568  32.9516  14.7346
 6L5  H8   H  HCH2  0   0.217  26.2465  31.8907  14.7791
 6L5  H9   H  HCH2  0   0.246  26.5045  32.1387  17.3218
 6L5  H10  H  HCH2  0   0.272  26.6015  33.7467  18.0154
 6L5  H11  H  HCH1  0   0.282  22.2797  32.4330  18.6034
 6L5  H12  H  HCH2  0   0.298  22.4315  29.9464  16.8238
 6L5  H13  H  HCH2  0   0.319  22.8661  29.9718  18.5186
 6L5  H15  H  HCR5  0   0.259  27.3361  31.6867   8.0059
 6L5  H16  H  HNH2  0   0.403  34.0944  29.4192   5.3055
 6L5  H17  H  HNH2  0   0.411  33.4077  29.2674   6.8794
 6L5  H18  H  HCH2  0   0.249  24.7164  32.7123  12.2497
 6L5  H19  H  HCH2  0   0.243  26.1203  31.6637  12.2235
 6L5  H20  H  HCH2  0   0.235  27.6176  33.7340  15.7956
 6L5  H21  H  HCH2  0   0.226  26.2112  34.7735  15.7955
 6L5  H22  H  HNH1  0   0.406  25.5226  33.9328  10.4853
 6L5  H23  H  HOH1  0   0.471  25.1884  31.9910   7.9913
 6L5  H24  H  HOH1  0   0.461  26.3096  34.2168   5.7933
 6L5  H25  H  HCR6  0   0.252  31.9881  32.8071   3.2751
 6L5  H26  H  HNH1  0   0.406  24.5479  31.1828  17.3964
 6L5  H27  H  HNH2  0   0.402  20.2310  33.6704  16.0216
 6L5  H28  H  HNH2  0   0.407  20.4660  33.3943  17.7030
 6L5  O2   O  OH1   0  -0.587  20.4256  28.9566  17.9000
 6L5  H14  H  HOH1  0   0.484  19.5299  28.7911  18.2322

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
 6L5  C3   N1   aromatic  1.322  0.020  1.322
 6L5  C3   N    aromatic  1.330  0.020  1.330
 6L5  N1   C    aromatic  1.332  0.020  1.332
 6L5  O15  C6   single    1.400  0.020  1.400
 6L5  N    C2   aromatic  1.338  0.020  1.338
 6L5  C6   C5   single    1.528  0.020  1.528
 6L5  C6   C7   single    1.529  0.020  1.529
 6L5  C    C1   aromatic  1.386  0.020  1.386
 6L5  C    N3   aromatic  1.364  0.020  1.364
 6L5  C2   N2   single    1.335  0.020  1.335
 6L5  C2   C1   aromatic  1.407  0.020  1.407
 6L5  O14  C7   single    1.394  0.020  1.394
 6L5  C5   N3   single    1.455  0.020  1.455
 6L5  C5   O    single    1.399  0.020  1.399
 6L5  C1   N4   aromatic  1.370  0.020  1.370
 6L5  C7   C8   single    1.539  0.020  1.539
 6L5  N3   C4   aromatic  1.369  0.020  1.369
 6L5  O    C8   single    1.411  0.020  1.411
 6L5  C8   C9   single    1.519  0.020  1.519
 6L5  C4   N4   aromatic  1.302  0.020  1.302
 6L5  C9   O1   double    1.222  0.020  1.222
 6L5  C9   N5   single    1.337  0.020  1.337
 6L5  N5   C10  single    1.448  0.020  1.448
 6L5  C10  C11  single    1.524  0.020  1.524
 6L5  C11  C12  single    1.522  0.020  1.522
 6L5  C12  C13  single    1.524  0.020  1.524
 6L5  O12  C52  double    1.221  0.020  1.221
 6L5  C13  C14  single    1.528  0.020  1.528
 6L5  C52  N21  single    1.335  0.020  1.335
 6L5  C52  C16  single    1.535  0.020  1.535
 6L5  C14  C15  single    1.511  0.020  1.511
 6L5  N6   C15  single    1.344  0.020  1.344
 6L5  N6   C16  single    1.440  0.020  1.440
 6L5  C15  O13  double    1.224  0.020  1.224
 6L5  C17  C16  single    1.527  0.020  1.527
 6L5  C17  C18  single    1.505  0.020  1.505
 6L5  C18  O11  double    1.205  0.020  1.205
 6L5  C4   H1   single    0.930  0.020  1.080
 6L5  C5   H2   single    0.970  0.020  1.090
 6L5  C6   H3   single    0.970  0.020  1.090
 6L5  C8   H4   single    0.970  0.020  1.090
 6L5  C11  H5   single    0.970  0.020  1.090
 6L5  C11  H6   single    0.970  0.020  1.090
 6L5  C12  H7   single    0.970  0.020  1.090
 6L5  C12  H8   single    0.970  0.020  1.090
 6L5  C14  H9   single    0.970  0.020  1.090
 6L5  C14  H10  single    0.970  0.020  1.090
 6L5  C16  H11  single    0.970  0.020  1.090
 6L5  C17  H12  single    0.970  0.020  1.090
 6L5  C17  H13  single    0.970  0.020  1.090
 6L5  C7   H15  single    0.970  0.020  1.090
 6L5  N2   H16  single    0.860  0.020  1.020
 6L5  N2   H17  single    0.860  0.020  1.020
 6L5  C10  H18  single    0.970  0.020  1.090
 6L5  C10  H19  single    0.970  0.020  1.090
 6L5  C13  H20  single    0.970  0.020  1.090
 6L5  C13  H21  single    0.970  0.020  1.090
 6L5  N5   H22  single    0.860  0.020  1.020
 6L5  O14  H23  single    0.850  0.020  0.980
 6L5  O15  H24  single    0.850  0.020  0.980
 6L5  C3   H25  single    0.930  0.020  1.080
 6L5  N6   H26  single    0.860  0.020  1.020
 6L5  N21  H27  single    0.860  0.020  1.020
 6L5  N21  H28  single    0.860  0.020  1.020
 6L5  C18  O2   single    1.325  0.020  1.325
 6L5  O2   H14  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
 6L5  C3   N1   C    111.56  3.000
 6L5  N    C2   C1   117.95  3.000
 6L5  C1   C2   N2   122.77  3.000
 6L5  N    C2   N2   119.28  3.000
 6L5  C    N3   C5   124.68  3.000
 6L5  C5   N3   C4   128.94  3.000
 6L5  C    N3   C4   106.38  3.000
 6L5  H1   C4   N4   125.31  3.000
 6L5  H1   C4   N3   121.60  3.000
 6L5  N4   C4   N3   113.09  3.000
 6L5  H2   C5   O    110.55  3.000
 6L5  H2   C5   C6   111.05  3.000
 6L5  O    C5   C6   107.02  3.000
 6L5  H2   C5   N3   106.94  3.000
 6L5  O    C5   N3   109.19  3.000
 6L5  C6   C5   N3   112.11  3.000
 6L5  H3   C6   O15  112.22  3.000
 6L5  H3   C6   C7   112.16  3.000
 6L5  O15  C6   C7   111.66  3.000
 6L5  H3   C6   C5   111.82  3.000
 6L5  C7   C6   C5   101.20  3.000
 6L5  O15  C6   C5   107.18  3.000
 6L5  H4   C8   O    110.16  3.000
 6L5  H4   C8   C9   110.37  3.000
 6L5  O    C8   C9   110.04  3.000
 6L5  H4   C8   C7   109.22  3.000
 6L5  C9   C8   C7   111.74  3.000
 6L5  O    C8   C7   105.19  3.000
 6L5  H6   C11  H5   106.69  3.000
 6L5  H6   C11  C10  109.06  3.000
 6L5  H5   C11  C10  109.42  3.000
 6L5  H6   C11  C12  109.73  3.000
 6L5  H5   C11  C12  109.91  3.000
 6L5  C10  C11  C12  111.90  3.000
 6L5  H8   C12  H7   105.99  3.000
 6L5  H8   C12  C13  109.29  3.000
 6L5  H7   C12  C13  109.97  3.000
 6L5  H8   C12  C11  109.68  3.000
 6L5  H7   C12  C11  109.33  3.000
 6L5  C13  C12  C11  112.39  3.000
 6L5  H10  C14  H9   106.80  3.000
 6L5  H10  C14  C13  109.62  3.000
 6L5  H9   C14  C13  109.89  3.000
 6L5  H10  C14  C15  107.71  3.000
 6L5  H9   C14  C15  111.03  3.000
 6L5  C13  C14  C15  111.65  3.000
 6L5  N6   C15  O13  121.70  3.000
 6L5  O13  C15  C14  122.45  3.000
 6L5  N6   C15  C14  115.85  3.000
 6L5  H11  C16  C52  110.12  3.000
 6L5  H11  C16  N6   109.45  3.000
 6L5  C52  C16  N6   110.12  3.000
 6L5  H11  C16  C17  109.38  3.000
 6L5  N6   C16  C17  107.89  3.000
 6L5  C52  C16  C17  109.83  3.000
 6L5  H13  C17  H12  106.21  3.000
 6L5  H13  C17  C18  106.42  3.000
 6L5  H12  C17  C18  110.43  3.000
 6L5  H13  C17  C16  108.78  3.000
 6L5  H12  C17  C16  110.55  3.000
 6L5  C18  C17  C16  114.06  3.000
 6L5  O2   C18  O11  123.58  3.000
 6L5  O2   C18  C17  111.41  3.000
 6L5  O11  C18  C17  124.97  3.000
 6L5  H15  C7   O14  111.75  3.000
 6L5  H15  C7   C8   109.59  3.000
 6L5  O14  C7   C8   113.65  3.000
 6L5  H15  C7   C6   108.74  3.000
 6L5  C8   C7   C6   100.73  3.000
 6L5  O14  C7   C6   111.77  3.000
 6L5  H17  N2   H16  118.09  3.000
 6L5  H17  N2   C2   120.90  3.000
 6L5  H16  N2   C2   120.00  3.000
 6L5  O1   C9   N5   124.09  3.000
 6L5  N5   C9   C8   113.77  3.000
 6L5  O1   C9   C8   122.02  3.000
 6L5  H19  C10  H18  106.88  3.000
 6L5  H19  C10  N5   109.14  3.000
 6L5  H18  C10  N5   107.09  3.000
 6L5  H19  C10  C11  110.31  3.000
 6L5  H18  C10  C11  109.98  3.000
 6L5  N5   C10  C11  113.20  3.000
 6L5  H21  C13  H20  106.24  3.000
 6L5  H21  C13  C14  109.50  3.000
 6L5  H20  C13  C14  108.24  3.000
 6L5  H21  C13  C12  109.81  3.000
 6L5  H20  C13  C12  109.53  3.000
 6L5  C14  C13  C12  113.27  3.000
 6L5  C1   N4   C4   104.56  3.000
 6L5  H22  N5   C10  117.41  3.000
 6L5  H22  N5   C9   118.61  3.000
 6L5  C10  N5   C9   123.59  3.000
 6L5  C8   O    C5   111.01  3.000
 6L5  H23  O14  C7   109.48  3.000
 6L5  H24  O15  C6   108.51  3.000
 6L5  C    C1   N4   110.74  3.000
 6L5  N4   C1   C2   133.15  3.000
 6L5  C    C1   C2   116.12  3.000
 6L5  C1   C    N3   105.23  3.000
 6L5  N3   C    N1   128.03  3.000
 6L5  C1   C    N1   126.74  3.000
 6L5  H25  C3   N    115.44  3.000
 6L5  H25  C3   N1   116.19  3.000
 6L5  N    C3   N1   128.38  3.000
 6L5  C3   N    C2   119.26  3.000
 6L5  H26  N6   C16  118.85  3.000
 6L5  H26  N6   C15  119.05  3.000
 6L5  C16  N6   C15  121.72  3.000
 6L5  O12  C52  N21  123.89  3.000
 6L5  N21  C52  C16  115.24  3.000
 6L5  O12  C52  C16  120.84  3.000
 6L5  H28  N21  H27  117.48  3.000
 6L5  H28  N21  C52  121.86  3.000
 6L5  H27  N21  C52  120.44  3.000
 6L5  H14  O2   C18  110.20  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
 6L5  CONST_01  C2   N    C3   N1      0.00   0.0  0
 6L5  CONST_02  C2   C1   C    N1      0.00   0.0  0
 6L5  CONST_03  N4   C1   C    N1    180.00   0.0  0
 6L5  CONST_04  C4   N3   C    N1    180.00   0.0  0
 6L5  CONST_05  N3   C    C1   C2    180.00   0.0  0
 6L5  CONST_06  C4   N4   C1   C2    180.00   0.0  0
 6L5  CONST_07  C3   N1   C    N3    180.00   0.0  0
 6L5  CONST_08  N4   C1   C    N3      0.00   0.0  0
 6L5  CONST_09  C1   N4   C4   N3      0.00   0.0  0
 6L5  CONST_10  C1   C    N3   C4      0.00   0.0  0
 6L5  CONST_11  C    C1   N4   C4      0.00   0.0  0
 6L5  CONST_12  N    C2   C1   N4    180.00   0.0  0
 6L5  CONST_13  C    N3   C4   N4      0.00   0.0  0
 6L5  CONST_14  C3   N1   C    C1      0.00   0.0  0
 6L5  CONST_15  C3   N    C2   C1      0.00   0.0  0
 6L5  CONST_16  N    C3   N1   C       0.00   0.0  0
 6L5  CONST_17  N    C2   C1   C       0.00   0.0  0
 6L5  CONST_18  C5   N3   C    N1      0.00   0.0  0
 6L5  CONST_19  C1   C    N3   C5    180.00   0.0  0
 6L5  CONST_20  N4   C4   N3   C5    180.00   0.0  0
 6L5  CONST_21  C3   N    C2   N2    180.00   0.0  0
 6L5  CONST_22  C    C1   C2   N2    180.00   0.0  0
 6L5  CONST_23  N4   C1   C2   N2      0.00   0.0  0
 6L5  CONST_24  H25  C3   N    C2    180.00   0.0  0
 6L5  CONST_25  H1   C4   N3   C5      0.00   0.0  0
 6L5  CONST_26  H16  N2   C2   C1    180.00   0.0  0
 6L5  CONST_27  H17  N2   C2   C1      0.00   0.0  0
 6L5  CONST_28  C10  N5   C9   C8    180.00   0.0  0
 6L5  CONST_29  H22  N5   C9   C8      0.00   0.0  0
 6L5  CONST_30  C16  N6   C15  C14   180.00   0.0  0
 6L5  CONST_31  O13  C15  N6   C16     0.00   0.0  0
 6L5  CONST_32  O1   C9   N5   C10     0.00   0.0  0
 6L5  CONST_33  H26  N6   C15  C14     0.00   0.0  0
 6L5  CONST_34  H27  N21  C52  C16   180.00   0.0  0
 6L5  CONST_35  H28  N21  C52  C16     0.00   0.0  0
 6L5  CONST_36  H14  O2   C18  C17   180.00   0.0  0
 6L5  Var_01    C9   N5   C10  C11    81.18  30.0  2
 6L5  Var_02    C14  C13  C12  C11  -177.58  30.0  3
 6L5  Var_03    N5   C10  C11  C12   176.40  30.0  2
 6L5  Var_04    C15  C14  C13  C12   -62.63  30.0  3
 6L5  Var_05    O11  C18  C17  C16   -20.16  30.0  3
 6L5  Var_06    C13  C12  C11  C10  -179.14  30.0  3
 6L5  Var_07    N6   C15  C14  C13   114.95  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
 6L5  chir_01  C5   C6   N3   O    positiv
 6L5  chir_02  C6   O15  C7   C5   positiv
 6L5  chir_03  C8   O    C9   C7   positiv
 6L5  chir_04  C16  C52  N6   C17  positiv
 6L5  chir_05  C7   C6   O14  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
 6L5  plan-1  C17  0.020
 6L5  plan-1  C18  0.020
 6L5  plan-1  O11  0.020
 6L5  plan-1  O2   0.020
 6L5  plan-1  H14  0.020
 6L5  plan-2  N1   0.020
 6L5  plan-2  C2   0.020
 6L5  plan-2  N3   0.020
 6L5  plan-2  C4   0.020
 6L5  plan-2  C5   0.020
 6L5  plan-2  N2   0.020
 6L5  plan-2  N4   0.020
 6L5  plan-2  C1   0.020
 6L5  plan-2  C    0.020
 6L5  plan-2  C3   0.020
 6L5  plan-2  N    0.020
 6L5  plan-2  H1   0.020
 6L5  plan-2  H25  0.020
 6L5  plan-3  C8   0.020
 6L5  plan-3  C9   0.020
 6L5  plan-3  C10  0.020
 6L5  plan-3  N5   0.020
 6L5  plan-3  O1   0.020
 6L5  plan-3  H22  0.020
 6L5  plan-4  C16  0.020
 6L5  plan-4  C52  0.020
 6L5  plan-4  N21  0.020
 6L5  plan-4  O12  0.020
 6L5  plan-4  H27  0.020
 6L5  plan-4  H28  0.020
 6L5  plan-5  C2   0.020
 6L5  plan-5  N2   0.020
 6L5  plan-5  H16  0.020
 6L5  plan-5  H17  0.020
 6L5  plan-6  C14  0.020
 6L5  plan-6  C15  0.020
 6L5  plan-6  C16  0.020
 6L5  plan-6  O13  0.020
 6L5  plan-6  N6   0.020
 6L5  plan-6  H26  0.020

