# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun  7 22:38:59 2020
#   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  63  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_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    7.9676  -0.1977  -1.1125
 6L5  C2   C  CR6    0   0.454    8.1281   2.5344  -0.4816
 6L5  N3   N  NR5    0  -0.539    5.5888   0.1496  -0.8052
 6L5  C4   C  CR15   0   0.088    4.8599   1.2625  -0.4801
 6L5  C5   C  CR15   0   0.172    5.1198  -1.1995  -1.0923
 6L5  C6   C  CR15   0  -0.047    5.3716  -2.1492   0.0762
 6L5  C8   C  CR15   0  -0.068    3.0520  -1.8328  -0.2589
 6L5  C11  C  CH2    0  -0.428   -1.3890  -1.0528   0.5061
 6L5  C12  C  CH2    0  -0.425   -2.6202  -0.4036   1.1245
 6L5  C14  C  CH2    0  -0.583   -5.0030   0.3511   0.7691
 6L5  C15  C  C      0   0.571   -6.1783   0.4670  -0.1777
 6L5  C16  C  CH1    0  -0.173   -8.5819   0.7879  -0.3570
 6L5  C17  C  CH2    0  -0.615   -9.7400   1.1317   0.5720
 6L5  C18  C  C      0   0.419   -9.6271   2.5222   1.2372
 6L5  C7   C  CR15   0  -0.032    4.0742  -1.9828   0.8758
 6L5  N2   N  NH2    0  -0.816    8.2629   3.8315  -0.1982
 6L5  C9   C  C      0   0.523    1.8346  -1.0226   0.1632
 6L5  C10  C  CH2    0  -0.280   -0.2247  -1.1149   1.4876
 6L5  C13  C  CH2    0  -0.412   -3.7890  -0.3255   0.1506
 6L5  N4   N  N      0  -0.453    5.5962   2.3212  -0.3000
 6L5  O13  O  O      0  -0.505   -6.0550   0.4452  -1.3957
 6L5  N5   N  NH1    0  -0.624    0.9709  -1.7056   0.9213
 6L5  O1   O  O      0  -0.482    1.6953   0.1527  -0.1400
 6L5  O    O  O      0  -0.485    3.7380  -1.1725  -1.2999
 6L5  O14  O  OH1    0  -0.653    3.7552  -3.0800   1.6781
 6L5  O15  O  OH1    0  -0.661    5.4702  -3.4395  -0.4570
 6L5  C1   C  CR56   0  -0.002    6.8776   1.8904  -0.5195
 6L5  C    C  CR56   0   0.485    6.8945   0.5420  -0.8379
 6L5  C3   C  CR16   0   0.039    9.0785   0.5159  -1.0488
 6L5  N    N  N      0  -0.473    9.2167   1.8061  -0.7545
 6L5  N6   N  NH1    0  -0.635   -7.3742   0.6305   0.4086
 6L5  C52  C  C      0   0.520   -8.8985  -0.4967  -1.1217
 6L5  N21  N  NH2    0  -0.803   -9.5615  -0.3031  -2.2710
 6L5  O12  O  O      0  -0.491   -8.6098  -1.6012  -0.6901
 6L5  O11  O  O      0  -0.599   -8.9928   3.3969   0.6195
 6L5  H1   H  HCR5   0   0.306    3.7843   1.2307  -0.3965
 6L5  H2   H  HCR5   0   0.288    5.6327  -1.5354  -1.9973
 6L5  H3   H  HCR5   0   0.268    6.2607  -1.8694   0.6533
 6L5  H4   H  HCR5   0   0.276    2.7343  -2.8279  -0.5948
 6L5  H5   H  HCH2   0   0.222   -1.6327  -2.0653   0.1714
 6L5  H6   H  HCH2   0   0.227   -1.0854  -0.4905  -0.3810
 6L5  H7   H  HCH2   0   0.216   -2.9216  -0.9626   2.0170
 6L5  H8   H  HCH2   0   0.217   -2.3660   0.6050   1.4676
 6L5  H9   H  HCH2   0   0.268   -4.7387   1.3643   1.0918
 6L5  H10  H  HCH2   0   0.252   -5.3081  -0.1788   1.6760
 6L5  H11  H  HCH1   0   0.258   -8.4548   1.6080  -1.0684
 6L5  H12  H  HCH2   0   0.260  -10.6698   1.1235  -0.0061
 6L5  H13  H  HCH2   0   0.235   -9.8519   0.3518   1.3308
 6L5  H15  H  HCR5   0   0.261    4.1258  -1.0562   1.4609
 6L5  H16  H  HNH2   0   0.411    7.4709   4.3817   0.0844
 6L5  H17  H  HNH2   0   0.403    9.1791   4.2323  -0.0941
 6L5  H18  H  HCH2   0   0.238    0.0107  -0.1147   1.8563
 6L5  H19  H  HCH2   0   0.251   -0.5009  -1.7140   2.3559
 6L5  H20  H  HCH2   0   0.224   -3.4780   0.2187  -0.7441
 6L5  H21  H  HCH2   0   0.222   -4.0573  -1.3337  -0.1777
 6L5  H22  H  HNH1   0   0.403    1.1626  -2.6733   1.1255
 6L5  H23  H  HOH1   0   0.473    4.0554  -2.9118   2.5763
 6L5  H24  H  HOH1   0   0.456    5.3248  -4.0712   0.2572
 6L5  H25  H  HCR6   0   0.252   10.0004  -0.0144  -1.2626
 6L5  H26  H  HNH1   0   0.397   -7.4404   0.5893   1.4128
 6L5  H27  H  HNH2   0   0.405   -9.7581   0.6181  -2.6221
 6L5  H28  H  HNH2   0   0.399   -9.8817  -1.0848  -2.8190
 6L5  O2   O  OC    -1  -0.614  -10.2236   2.6538   2.3230

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  1.331  0.020  1.331
 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    1.527  0.020  1.527
 6L5  C6   C7   single    1.533  0.020  1.533
 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    1.396  0.020  1.396
 6L5  C5   N3   single    1.457  0.020  1.457
 6L5  C5   O    single    1.398  0.020  1.398
 6L5  C1   N4   aromatic  1.370  0.020  1.370
 6L5  C7   C8   single    1.535  0.020  1.535
 6L5  N3   C4   aromatic  1.369  0.020  1.369
 6L5  O    C8   single    1.411  0.020  1.411
 6L5  C8   C9   single    1.522  0.020  1.522
 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    1.449  0.020  1.449
 6L5  C10  C11  single    1.524  0.020  1.524
 6L5  C11  C12  single    1.523  0.020  1.523
 6L5  C12  C13  single    1.523  0.020  1.523
 6L5  O12  C52  double    1.221  0.020  1.221
 6L5  C13  C14  single    1.521  0.020  1.521
 6L5  C52  N21  single    1.341  0.020  1.341
 6L5  C52  C16  single    1.528  0.020  1.528
 6L5  C14  C15  single    1.514  0.020  1.514
 6L5  N6   C15  single    1.342  0.020  1.342
 6L5  N6   C16  single    1.439  0.020  1.439
 6L5  C15  O13  double    1.224  0.020  1.224
 6L5  C17  C16  single    1.524  0.020  1.524
 6L5  C17  C18  single    1.546  0.020  1.546
 6L5  C18  O11  deloc     1.245  0.020  1.245
 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   deloc     1.246  0.020  1.246

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    111.55  3.000
 6L5  N    C2   C1   117.94  3.000
 6L5  C1   C2   N2   122.71  3.000
 6L5  N    C2   N2   119.35  3.000
 6L5  C    N3   C5   124.74  3.000
 6L5  C5   N3   C4   128.90  3.000
 6L5  C    N3   C4   106.35  3.000
 6L5  H1   C4   N4   125.22  3.000
 6L5  H1   C4   N3   121.66  3.000
 6L5  N4   C4   N3   113.12  3.000
 6L5  H2   C5   O    110.29  3.000
 6L5  H2   C5   C6   111.41  3.000
 6L5  O    C5   C6   106.79  3.000
 6L5  H2   C5   N3   107.26  3.000
 6L5  O    C5   N3   109.25  3.000
 6L5  C6   C5   N3   111.84  3.000
 6L5  H3   C6   O15  112.25  3.000
 6L5  H3   C6   C7   112.59  3.000
 6L5  O15  C6   C7   111.00  3.000
 6L5  H3   C6   C5   112.21  3.000
 6L5  C7   C6   C5   101.08  3.000
 6L5  O15  C6   C5   107.07  3.000
 6L5  H4   C8   O    109.84  3.000
 6L5  H4   C8   C9   109.64  3.000
 6L5  O    C8   C9   110.15  3.000
 6L5  H4   C8   C7   109.30  3.000
 6L5  C9   C8   C7   112.32  3.000
 6L5  O    C8   C7   105.51  3.000
 6L5  H6   C11  H5   106.83  3.000
 6L5  H6   C11  C10  109.35  3.000
 6L5  H5   C11  C10  109.23  3.000
 6L5  H6   C11  C12  109.56  3.000
 6L5  H5   C11  C12  109.80  3.000
 6L5  C10  C11  C12  111.93  3.000
 6L5  H8   C12  H7   106.17  3.000
 6L5  H8   C12  C13  109.33  3.000
 6L5  H7   C12  C13  109.63  3.000
 6L5  H8   C12  C11  109.39  3.000
 6L5  H7   C12  C11  109.62  3.000
 6L5  C13  C12  C11  112.49  3.000
 6L5  H10  C14  H9   105.73  3.000
 6L5  H10  C14  C13  110.14  3.000
 6L5  H9   C14  C13  109.78  3.000
 6L5  H10  C14  C15  109.83  3.000
 6L5  H9   C14  C15  107.50  3.000
 6L5  C13  C14  C15  113.54  3.000
 6L5  N6   C15  O13  121.77  3.000
 6L5  O13  C15  C14  122.87  3.000
 6L5  N6   C15  C14  115.34  3.000
 6L5  H11  C16  C52  109.22  3.000
 6L5  H11  C16  N6   109.32  3.000
 6L5  C52  C16  N6   110.38  3.000
 6L5  H11  C16  C17  108.42  3.000
 6L5  N6   C16  C17  109.77  3.000
 6L5  C52  C16  C17  109.71  3.000
 6L5  H13  C17  H12  105.90  3.000
 6L5  H13  C17  C18  110.51  3.000
 6L5  H12  C17  C18  107.22  3.000
 6L5  H13  C17  C16  109.86  3.000
 6L5  H12  C17  C16  108.77  3.000
 6L5  C18  C17  C16  114.20  3.000
 6L5  O2   C18  O11  127.04  3.000
 6L5  O2   C18  C17  115.80  3.000
 6L5  O11  C18  C17  117.12  3.000
 6L5  H15  C7   O14  111.59  3.000
 6L5  H15  C7   C8   110.06  3.000
 6L5  O14  C7   C8   110.46  3.000
 6L5  H15  C7   C6   109.27  3.000
 6L5  C8   C7   C6   100.87  3.000
 6L5  O14  C7   C6   114.07  3.000
 6L5  H17  N2   H16  118.08  3.000
 6L5  H17  N2   C2   120.10  3.000
 6L5  H16  N2   C2   120.81  3.000
 6L5  O1   C9   N5   123.95  3.000
 6L5  N5   C9   C8   113.71  3.000
 6L5  O1   C9   C8   122.31  3.000
 6L5  H19  C10  H18  106.81  3.000
 6L5  H19  C10  N5   107.24  3.000
 6L5  H18  C10  N5   109.12  3.000
 6L5  H19  C10  C11  109.98  3.000
 6L5  H18  C10  C11  110.17  3.000
 6L5  N5   C10  C11  113.28  3.000
 6L5  H21  C13  H20  106.45  3.000
 6L5  H21  C13  C14  109.65  3.000
 6L5  H20  C13  C14  109.80  3.000
 6L5  H21  C13  C12  109.44  3.000
 6L5  H20  C13  C12  109.31  3.000
 6L5  C14  C13  C12  112.04  3.000
 6L5  C1   N4   C4   104.54  3.000
 6L5  H22  N5   C10  117.99  3.000
 6L5  H22  N5   C9   118.86  3.000
 6L5  C10  N5   C9   123.13  3.000
 6L5  C8   O    C5   111.23  3.000
 6L5  H23  O14  C7   109.14  3.000
 6L5  H24  O15  C6   108.12  3.000
 6L5  C    C1   N4   110.75  3.000
 6L5  N4   C1   C2   133.09  3.000
 6L5  C    C1   C2   116.15  3.000
 6L5  C1   C    N3   105.24  3.000
 6L5  N3   C    N1   128.07  3.000
 6L5  C1   C    N1   126.70  3.000
 6L5  H25  C3   N    115.43  3.000
 6L5  H25  C3   N1   116.15  3.000
 6L5  N    C3   N1   128.42  3.000
 6L5  C3   N    C2   119.24  3.000
 6L5  H26  N6   C16  118.67  3.000
 6L5  H26  N6   C15  119.29  3.000
 6L5  C16  N6   C15  121.94  3.000
 6L5  O12  C52  N21  123.42  3.000
 6L5  N21  C52  C16  114.21  3.000
 6L5  O12  C52  C16  122.33  3.000
 6L5  H28  N21  H27  117.33  3.000
 6L5  H28  N21  C52  120.77  3.000
 6L5  H27  N21  C52  121.89  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      0.00   0.0  0
 6L5  CONST_27  H17  N2   C2   C1    180.00   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     0.00   0.0  0
 6L5  CONST_35  H28  N21  C52  C16   180.00   0.0  0
 6L5  Var_01    C9   N5   C10  C11    81.89  30.0  1
 6L5  Var_02    C14  C13  C12  C11  -178.78  30.0  3
 6L5  Var_03    N5   C10  C11  C12  -178.93  30.0  1
 6L5  Var_04    C15  C14  C13  C12   179.07  30.0  3
 6L5  Var_05    O11  C18  C17  C16    27.80  30.0  3
 6L5  Var_06    C13  C12  C11  C10   179.57  30.0  3
 6L5  Var_07    N6   C15  C14  C13   158.73  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-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

