# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 09:25:40 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: [(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[2-(1~{H}-indol-3-yl)ethyl]phosphonamidic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)NCCc4c[nH]c5ccccc45)[C@@H](O)[C@@H]3O
#
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
 6US  6US  '[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[2-(1~{H}-indol-3-yl)ethyl]phosphonamidic acid'  ligand  58  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6US
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
 6US  C1   C  CH2   0  -0.289  14.6416  11.5694   9.3223
 6US  C5   C  CR56  0   0.007  12.8002  11.9933  16.0201
 6US  C6   C  CR6   0   0.467  13.2944  13.1243  16.6969
 6US  C7   C  CR5   0  -0.011  15.1480  12.1826  11.7112
 6US  C8   C  CR15  0   0.103  12.3846  10.1284  15.1158
 6US  C16  C  CR16  0  -0.371  17.6865  12.3192  11.1186
 6US  C2   C  CR16  0   0.050  11.4779  14.2833  15.8899
 6US  C3   C  CH2   0  -0.535  14.4310  12.5700  10.4599
 6US  C12  C  CR56  0   0.032  16.5643  12.0699  11.9183
 6US  C14  C  CR16  0  -0.284  19.1114  11.6430  12.9607
 6US  P    P  P     0   1.438  13.0026   9.3974   9.0462
 6US  N1P  N  NH1   0  -0.780  14.2715  10.2123   9.6854
 6US  O2P  O  O     0  -0.706  12.6310   9.7935   7.6712
 6US  O5'  O  O2    0  -0.590  11.6855   9.5370   9.9745
 6US  C5'  C  CH2   0  -0.198  11.7694   9.4608  11.3916
 6US  C4'  C  CR15  0  -0.049  10.3483   9.4449  11.9382
 6US  C3'  C  CR15  0   0.003   9.5273  10.6929  11.6504
 6US  O3'  O  OH1   0  -0.668   8.1758  10.3216  11.7612
 6US  C2'  C  CR15  0  -0.072   9.9341  11.6334  12.7915
 6US  O2'  O  OH1   0  -0.655  11.0633  12.3639  12.4087
 6US  C1'  C  CR15  0   0.221  10.1942  10.6196  13.9396
 6US  O4'  O  O     0  -0.501  10.3906   9.3645  13.3597
 6US  N9   N  NR5   0  -0.537  11.3673  10.9580  14.7339
 6US  C4   C  CR56  0   0.488  11.6211  12.1650  15.3151
 6US  N7   N  N     0  -0.469  13.2660  10.7129  15.8794
 6US  N3   N  N     0  -0.480  10.9192  13.2940  15.2113
 6US  N1   N  N     0  -0.471  12.5928  14.2605  16.6124
 6US  C9   C  CR15  0  -0.079  14.5687  11.8039  12.8885
 6US  N10  N  NR15  0  -0.700  15.5217  11.4679  13.8072
 6US  C11  C  CR56  0   0.350  16.7553  11.6129  13.2435
 6US  C13  C  CR16  0  -0.306  18.0245  11.3919  13.7762
 6US  C15  C  CR16  0  -0.266  18.9457  12.1052  11.6446
 6US  H1   H  HCH2  0   0.256  14.0583  11.8736   8.4539
 6US  H2   H  HCH2  0   0.240  15.6882  11.5780   9.0089
 6US  H3   H  HCR5  0   0.303  12.4318   9.0986  14.8005
 6US  H4   H  HCR6  0   0.241  17.5738  12.6774  10.1022
 6US  H5   H  HCR6  0   0.258  10.9641  15.2375  15.8514
 6US  H6   H  HCH2  0   0.244  14.7654  13.5504  10.1071
 6US  H7   H  HCH2  0   0.244  13.3612  12.6575  10.6669
 6US  H8   H  HCR6  0   0.250  20.1105  11.4825  13.3446
 6US  H9   H  HOH1  0   0.495  12.8095   7.2186   9.1484
 6US  H10  H  HNH1  0   0.404  14.7306   9.8475  10.5090
 6US  H11  H  HCH2  0   0.249  12.2714   8.5418  11.7096
 6US  H12  H  HCH2  0   0.236  12.3368  10.3091  11.7788
 6US  H13  H  HCR5  0   0.275   9.8389   8.5511  11.5685
 6US  H14  H  HCR5  0   0.261   9.7564  11.1383  10.6768
 6US  H15  H  HOH1  0   0.459   7.6301  11.0989  11.6043
 6US  H16  H  HCR5  0   0.275   9.1089  12.2968  13.0657
 6US  H17  H  HOH1  0   0.467  11.1036  13.1565  12.9572
 6US  H18  H  HCR5  0   0.281   9.3347  10.5758  14.6137
 6US  H19  H  HNH2  0   0.407  14.7076  13.9150  17.9239
 6US  H20  H  HNH2  0   0.413  14.9254  12.2466  17.5537
 6US  H21  H  HCR5  0   0.269  13.5201  11.7697  13.1348
 6US  H22  H  HNR5  0   0.400  15.3155  11.1034  14.7244
 6US  H23  H  HCR6  0   0.259  18.1571  11.0390  14.7912
 6US  H24  H  HCR6  0   0.244  19.8211  12.2951  11.0371
 6US  N6   N  NH2   0  -0.815  14.4295  13.1062  17.3948
 6US  O3P  O  OH1   0  -0.754  13.4929   7.8880   9.2878

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
 6US  C15  C14  aromatic  1.405  0.020  1.405
 6US  C15  C16  aromatic  1.381  0.020  1.381
 6US  C14  C13  aromatic  1.382  0.020  1.382
 6US  C16  C12  aromatic  1.400  0.020  1.400
 6US  O2P  P    double    1.478  0.020  1.478
 6US  C13  C11  aromatic  1.394  0.020  1.394
 6US  C12  C11  aromatic  1.415  0.020  1.415
 6US  C12  C7   aromatic  1.436  0.020  1.436
 6US  C1   C3   single    1.530  0.020  1.530
 6US  C1   N1P  single    1.453  0.020  1.453
 6US  C11  N10  aromatic  1.364  0.020  1.364
 6US  C3   C7   single    1.493  0.020  1.493
 6US  P    N1P  single    1.638  0.020  1.638
 6US  P    O5'  single    1.617  0.020  1.617
 6US  P    O3P  single    1.605  0.020  1.605
 6US  C7   C9   aromatic  1.366  0.020  1.366
 6US  O5'  C5'  single    1.422  0.020  1.422
 6US  N10  C9   aromatic  1.366  0.020  1.366
 6US  O3'  C3'  single    1.406  0.020  1.406
 6US  C5'  C4'  single    1.523  0.020  1.523
 6US  C4'  C3'  single    1.521  0.020  1.521
 6US  C4'  O4'  single    1.424  0.020  1.424
 6US  C3'  C2'  single    1.534  0.020  1.534
 6US  O4'  C1'  single    1.396  0.020  1.396
 6US  C2'  C1'  single    1.554  0.020  1.554
 6US  C2'  O2'  single    1.398  0.020  1.398
 6US  C1'  N9   single    1.457  0.020  1.457
 6US  N3   C4   aromatic  1.333  0.020  1.333
 6US  N3   C2   aromatic  1.323  0.020  1.323
 6US  N9   C4   aromatic  1.363  0.020  1.363
 6US  N9   C8   aromatic  1.367  0.020  1.367
 6US  C4   C5   aromatic  1.384  0.020  1.384
 6US  C2   N1   aromatic  1.329  0.020  1.329
 6US  C8   N7   aromatic  1.304  0.020  1.304
 6US  C5   N7   aromatic  1.370  0.020  1.370
 6US  C5   C6   aromatic  1.408  0.020  1.408
 6US  N1   C6   aromatic  1.338  0.020  1.338
 6US  C6   N6   single    1.333  0.020  1.333
 6US  C1   H1   single    0.970  0.020  1.090
 6US  C1   H2   single    0.970  0.020  1.090
 6US  C8   H3   single    0.930  0.020  1.080
 6US  C16  H4   single    0.930  0.020  1.080
 6US  C2   H5   single    0.930  0.020  1.080
 6US  C3   H6   single    0.970  0.020  1.090
 6US  C3   H7   single    0.970  0.020  1.090
 6US  C14  H8   single    0.930  0.020  1.080
 6US  O3P  H9   single    0.850  0.020  0.980
 6US  N1P  H10  single    0.860  0.020  1.020
 6US  C5'  H11  single    0.970  0.020  1.090
 6US  C5'  H12  single    0.970  0.020  1.090
 6US  C4'  H13  single    0.970  0.020  1.090
 6US  C3'  H14  single    0.970  0.020  1.090
 6US  O3'  H15  single    0.850  0.020  0.980
 6US  C2'  H16  single    0.970  0.020  1.090
 6US  O2'  H17  single    0.850  0.020  0.980
 6US  C1'  H18  single    0.970  0.020  1.090
 6US  N6   H19  single    0.860  0.020  1.020
 6US  N6   H20  single    0.860  0.020  1.020
 6US  C9   H21  single    0.930  0.020  1.080
 6US  N10  H22  single    0.860  0.020  1.020
 6US  C13  H23  single    0.930  0.020  1.080
 6US  C15  H24  single    0.930  0.020  1.080

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
 6US  H2   C1   H1   106.38  3.000
 6US  H2   C1   N1P  108.85  3.000
 6US  H1   C1   N1P  108.89  3.000
 6US  H2   C1   C3   109.88  3.000
 6US  H1   C1   C3   109.66  3.000
 6US  N1P  C1   C3   112.96  3.000
 6US  N7   C5   C4   110.69  3.000
 6US  N7   C5   C6   132.92  3.000
 6US  C4   C5   C6   116.37  3.000
 6US  N6   C6   N1   119.42  3.000
 6US  N6   C6   C5   122.68  3.000
 6US  N1   C6   C5   117.89  3.000
 6US  C9   C7   C12  105.80  3.000
 6US  C9   C7   C3   126.20  3.000
 6US  C12  C7   C3   127.94  3.000
 6US  H3   C8   N7   124.74  3.000
 6US  H3   C8   N9   122.04  3.000
 6US  N7   C8   N9   113.22  3.000
 6US  H4   C16  C15  120.22  3.000
 6US  H4   C16  C12  120.74  3.000
 6US  C15  C16  C12  119.04  3.000
 6US  H5   C2   N1   115.59  3.000
 6US  H5   C2   N3   116.07  3.000
 6US  N1   C2   N3   128.33  3.000
 6US  H7   C3   H6   106.76  3.000
 6US  H7   C3   C7   109.39  3.000
 6US  H6   C3   C7   110.84  3.000
 6US  H7   C3   C1   109.14  3.000
 6US  H6   C3   C1   107.71  3.000
 6US  C7   C3   C1   112.79  3.000
 6US  C11  C12  C16  118.96  3.000
 6US  C11  C12  C7   107.07  3.000
 6US  C16  C12  C7   133.96  3.000
 6US  H8   C14  C15  119.35  3.000
 6US  H8   C14  C13  119.33  3.000
 6US  C15  C14  C13  121.32  3.000
 6US  O5'  P    O2P  107.82  3.000
 6US  O5'  P    N1P  111.34  3.000
 6US  O2P  P    N1P  115.11  3.000
 6US  O5'  P    O3P  104.09  3.000
 6US  N1P  P    O3P   99.93  3.000
 6US  O2P  P    O3P  117.95  3.000
 6US  H10  N1P  P    119.35  3.000
 6US  H10  N1P  C1   115.15  3.000
 6US  P    N1P  C1   124.37  3.000
 6US  C5'  O5'  P    121.29  3.000
 6US  H12  C5'  H11  108.12  3.000
 6US  H12  C5'  C4'  111.46  3.000
 6US  H11  C5'  C4'  108.36  3.000
 6US  H12  C5'  O5'  110.04  3.000
 6US  H11  C5'  O5'  111.21  3.000
 6US  C4'  C5'  O5'  107.66  3.000
 6US  H13  C4'  O4'  107.77  3.000
 6US  H13  C4'  C3'  110.81  3.000
 6US  O4'  C4'  C3'  104.54  3.000
 6US  H13  C4'  C5'  108.79  3.000
 6US  O4'  C4'  C5'  109.34  3.000
 6US  C3'  C4'  C5'  115.29  3.000
 6US  H14  C3'  C2'  110.89  3.000
 6US  H14  C3'  O3'  112.25  3.000
 6US  C2'  C3'  O3'  111.00  3.000
 6US  H14  C3'  C4'  112.89  3.000
 6US  C2'  C3'  C4'  102.66  3.000
 6US  O3'  C3'  C4'  106.69  3.000
 6US  H15  O3'  C3'  108.59  3.000
 6US  H16  C2'  C1'  109.68  3.000
 6US  H16  C2'  O2'  111.16  3.000
 6US  C1'  C2'  O2'  114.08  3.000
 6US  H16  C2'  C3'  111.00  3.000
 6US  O2'  C2'  C3'  109.33  3.000
 6US  C1'  C2'  C3'  101.19  3.000
 6US  H17  O2'  C2'  107.90  3.000
 6US  H18  C1'  N9   107.83  3.000
 6US  H18  C1'  O4'  109.31  3.000
 6US  N9   C1'  O4'  108.78  3.000
 6US  H18  C1'  C2'  110.50  3.000
 6US  N9   C1'  C2'  112.72  3.000
 6US  O4'  C1'  C2'  107.65  3.000
 6US  C1'  O4'  C4'  111.07  3.000
 6US  C4   N9   C1'  126.01  3.000
 6US  C4   N9   C8   106.24  3.000
 6US  C1'  N9   C8   127.64  3.000
 6US  N3   C4   N9   128.20  3.000
 6US  N9   C4   C5   105.41  3.000
 6US  N3   C4   C5   126.37  3.000
 6US  C8   N7   C5   104.44  3.000
 6US  C4   N3   C2   111.76  3.000
 6US  C2   N1   C6   119.27  3.000
 6US  H21  C9   N10  121.16  3.000
 6US  H21  C9   C7   128.21  3.000
 6US  N10  C9   C7   110.62  3.000
 6US  H22  N10  C11  126.83  3.000
 6US  H22  N10  C9   123.93  3.000
 6US  C11  N10  C9   109.08  3.000
 6US  C13  C11  N10  130.43  3.000
 6US  N10  C11  C12  107.42  3.000
 6US  C13  C11  C12  122.14  3.000
 6US  H23  C13  C11  121.42  3.000
 6US  H23  C13  C14  121.07  3.000
 6US  C11  C13  C14  117.51  3.000
 6US  H24  C15  C14  119.22  3.000
 6US  H24  C15  C16  119.76  3.000
 6US  C14  C15  C16  121.02  3.000
 6US  H20  N6   H19  117.92  3.000
 6US  H20  N6   C6   120.98  3.000
 6US  H19  N6   C6   120.01  3.000
 6US  H9   O3P  P    114.42  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
 6US  CONST_01  C2   N3   C4   C5      0.00   0.0  0
 6US  CONST_02  C8   N9   C4   C5      0.00   0.0  0
 6US  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 6US  CONST_04  C2   N1   C6   C5      0.00   0.0  0
 6US  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 6US  CONST_06  N9   C4   C5   C6    180.00   0.0  0
 6US  CONST_07  C8   N7   C5   C6    180.00   0.0  0
 6US  CONST_08  N3   C2   N1   C6      0.00   0.0  0
 6US  CONST_09  C15  C16  C12  C7    180.00   0.0  0
 6US  CONST_10  C13  C11  C12  C7    180.00   0.0  0
 6US  CONST_11  N10  C11  C12  C7      0.00   0.0  0
 6US  CONST_12  C11  N10  C9   C7      0.00   0.0  0
 6US  CONST_13  N3   C4   N9   C8    180.00   0.0  0
 6US  CONST_14  C4   C5   N7   C8      0.00   0.0  0
 6US  CONST_15  C13  C14  C15  C16     0.00   0.0  0
 6US  CONST_16  C13  C11  C12  C16     0.00   0.0  0
 6US  CONST_17  N10  C11  C12  C16   180.00   0.0  0
 6US  CONST_18  C9   C7   C12  C16   180.00   0.0  0
 6US  CONST_19  N9   C4   N3   C2    180.00   0.0  0
 6US  CONST_20  C14  C15  C16  C12     0.00   0.0  0
 6US  CONST_21  C14  C13  C11  C12     0.00   0.0  0
 6US  CONST_22  C9   N10  C11  C12     0.00   0.0  0
 6US  CONST_23  N10  C9   C7   C12     0.00   0.0  0
 6US  CONST_24  N10  C11  C13  C14   180.00   0.0  0
 6US  CONST_25  N7   C5   C4   N9      0.00   0.0  0
 6US  CONST_26  N1   C2   N3   C4      0.00   0.0  0
 6US  CONST_27  N7   C8   N9   C4      0.00   0.0  0
 6US  CONST_28  N1   C6   C5   C4      0.00   0.0  0
 6US  CONST_29  N3   C4   C5   N7    180.00   0.0  0
 6US  CONST_30  N1   C6   C5   N7    180.00   0.0  0
 6US  CONST_31  C11  C12  C7   C9      0.00   0.0  0
 6US  CONST_32  C13  C11  N10  C9    180.00   0.0  0
 6US  CONST_33  C15  C14  C13  C11     0.00   0.0  0
 6US  CONST_34  C15  C16  C12  C11     0.00   0.0  0
 6US  CONST_35  C1'  N9   C4   C5    180.00   0.0  0
 6US  CONST_36  N3   C4   N9   C1'     0.00   0.0  0
 6US  CONST_37  N7   C8   N9   C1'   180.00   0.0  0
 6US  CONST_38  C3   C7   C12  C16     0.00   0.0  0
 6US  CONST_39  N6   C6   N1   C2    180.00   0.0  0
 6US  CONST_40  C11  C12  C7   C3    180.00   0.0  0
 6US  CONST_41  N10  C9   C7   C3    180.00   0.0  0
 6US  CONST_42  N6   C6   C5   C4    180.00   0.0  0
 6US  CONST_43  N6   C6   C5   N7      0.00   0.0  0
 6US  CONST_44  H3   C8   N7   C5    180.00   0.0  0
 6US  CONST_45  H5   C2   N1   C6    180.00   0.0  0
 6US  CONST_46  H4   C16  C12  C7      0.00   0.0  0
 6US  CONST_47  H22  N10  C9   C7    180.00   0.0  0
 6US  CONST_48  H8   C14  C15  C16   180.00   0.0  0
 6US  CONST_49  H24  C15  C16  C12   180.00   0.0  0
 6US  CONST_50  H23  C13  C11  C12   180.00   0.0  0
 6US  CONST_51  H21  C9   C7   C12   180.00   0.0  0
 6US  CONST_52  H19  N6   C6   C5    180.00   0.0  0
 6US  CONST_53  H20  N6   C6   C5      0.00   0.0  0
 6US  Var_01    C12  C7   C3   C1     64.05  30.0  2
 6US  Var_02    N1P  C1   C3   C7     55.52  30.0  1
 6US  Var_03    C4'  C5'  O5'  P    -172.67  30.0  3
 6US  Var_04    O2P  P    N1P  C1     28.26  30.0  2
 6US  Var_05    P    N1P  C1   C3    112.33  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
 6US  chir_02  C4'  C5'  C3'  O4'  positiv
 6US  chir_03  C3'  O3'  C2'  C4'  negativ
 6US  chir_04  C2'  O2'  C1'  C3'  positiv
 6US  chir_05  C1'  O4'  N9   C2'  negativ
 6US  chir_06  P    N1P  O5'  O3P  both

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
 6US  plan-1  C7   0.020
 6US  plan-1  C16  0.020
 6US  plan-1  C3   0.020
 6US  plan-1  C12  0.020
 6US  plan-1  C14  0.020
 6US  plan-1  C9   0.020
 6US  plan-1  N10  0.020
 6US  plan-1  C11  0.020
 6US  plan-1  C13  0.020
 6US  plan-1  C15  0.020
 6US  plan-1  H4   0.020
 6US  plan-1  H8   0.020
 6US  plan-1  H21  0.020
 6US  plan-1  H22  0.020
 6US  plan-1  H23  0.020
 6US  plan-1  H24  0.020
 6US  plan-2  C5   0.020
 6US  plan-2  C6   0.020
 6US  plan-2  C8   0.020
 6US  plan-2  C2   0.020
 6US  plan-2  C1'  0.020
 6US  plan-2  N9   0.020
 6US  plan-2  C4   0.020
 6US  plan-2  N7   0.020
 6US  plan-2  N3   0.020
 6US  plan-2  N1   0.020
 6US  plan-2  H3   0.020
 6US  plan-2  H5   0.020
 6US  plan-2  N6   0.020
 6US  plan-3  C6   0.020
 6US  plan-3  H19  0.020
 6US  plan-3  H20  0.020
 6US  plan-3  N6   0.020

