# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 10:22:52 2021
#   Inital geometry file: a 153 line input string
#   Ligand name: (3R,5R,8R,10E)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-3,5,8-trihydroxy-10-methyl-9-oxo-2,4,6-trioxa-11-aza-3,5-diphosphatridec-10-en-13-oic acid 3,5-dioxide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=NCC(O)=O)C(=O)[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[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
 48H  48H  '(3R,5R,8R,10E)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-3,5,8-trihydroxy-10-methyl-9-oxo-2,4,6-trioxa-11-aza-3,5-diphosphatridec-10-en-13-oic acid 3,5-dioxide (non-preferred name)'  ligand  63  39  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_48H
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
 48H  C1   C  CR16  0   0.047  -57.0380  -18.7166  -16.9285
 48H  C2   C  CR56  0   0.490  -54.9364  -19.1983  -16.5210
 48H  C3   C  CR56  0  -0.011  -54.8642  -18.2831  -15.4839
 48H  C4   C  CR6   0   0.463  -56.0375  -17.5547  -15.2126
 48H  C5   C  CR15  0   0.111  -52.9506  -19.1670  -15.6005
 48H  O1   O  OH1   0  -0.717  -47.8132  -21.0723  -17.6882
 48H  P1   P  P     0   1.503  -47.8650  -22.4793  -16.9636
 48H  O2   O  O     0  -0.681  -46.9178  -23.5264  -17.3921
 48H  O3   O  O2    0  -0.701  -47.6481  -21.9413  -15.4551
 48H  P2   P  P     0   1.492  -47.3869  -22.9101  -14.1642
 48H  O4   O  OH1   0  -0.718  -47.3680  -21.8581  -12.9858
 48H  O5   O  O     0  -0.667  -48.3154  -24.0457  -14.1118
 48H  O6   O  O2    0  -0.573  -45.8745  -23.3455  -14.2937
 48H  C6   C  CH2   0  -0.208  -44.7585  -22.4437  -14.3077
 48H  C7   C  CH1   0  -0.107  -43.8237  -22.8561  -15.4441
 48H  O7   O  OH1   0  -0.672  -44.3268  -22.5493  -16.7011
 48H  C8   C  C     0   0.352  -42.5111  -22.1094  -15.2649
 48H  O8   O  O     0  -0.347  -42.1232  -21.2979  -16.0623
 48H  C9   C  C     0   0.114  -41.7305  -22.4071  -14.0058
 48H  C10  C  CH3   0  -0.774  -41.5177  -23.8371  -13.6096
 48H  N1   N  N     0  -0.316  -41.3336  -21.3815  -13.3821
 48H  C11  C  CH2   0  -0.456  -40.6069  -21.5621  -12.1578
 48H  C12  C  C     0   0.535  -40.3720  -20.2378  -11.4719
 48H  O9   O  OH1   0  -0.595  -39.6932  -20.4108  -10.3442
 48H  O10  O  O     0  -0.430  -40.7441  -19.1685  -11.8749
 48H  O11  O  O2    0  -0.568  -49.3578  -23.0025  -17.0211
 48H  C14  C  CR15  0  -0.033  -51.6435  -22.4435  -17.4306
 48H  C15  C  CR15  0  -0.029  -51.4966  -21.7047  -18.7653
 48H  O12  O  OH1   0  -0.665  -52.2866  -22.2751  -19.7722
 48H  C16  C  CR15  0  -0.017  -52.0984  -20.3526  -18.4133
 48H  O13  O  OH1   0  -0.648  -52.4795  -19.6254  -19.5349
 48H  C17  C  CR15  0   0.184  -53.2650  -20.7781  -17.5116
 48H  O14  O  O     0  -0.491  -52.7932  -21.8890  -16.7927
 48H  N2   N  NR5   0  -0.543  -53.6917  -19.7595  -16.5900
 48H  N3   N  N     0  -0.457  -55.9995  -19.4564  -17.2776
 48H  N4   N  N     0  -0.474  -57.1156  -17.8027  -15.9654
 48H  N5   N  NH2   0  -0.816  -56.1131  -16.6426  -14.2437
 48H  N6   N  N     0  -0.446  -53.6138  -18.2826  -14.9198
 48H  H1   H  HCR6  0   0.254  -57.9474  -18.8707  -17.4992
 48H  H2   H  HCR5  0   0.296  -51.9202  -19.4351  -15.4195
 48H  H3   H  HOH1  0   0.517  -47.6002  -21.1124  -18.6318
 48H  H4   H  HOH1  0   0.516  -48.2306  -21.6150  -12.6198
 48H  H5   H  HCH2  0   0.267  -44.2716  -22.5132  -13.3343
 48H  H6   H  HCH2  0   0.269  -45.0736  -21.4080  -14.4548
 48H  H7   H  HCH1  0   0.267  -43.6138  -23.9309  -15.3295
 48H  H8   H  HOH1  0   0.464  -45.0900  -23.1112  -16.9053
 48H  H9   H  HCH3  0   0.286  -40.5006  -23.9887  -13.2473
 48H  H10  H  HCH3  0   0.282  -42.1920  -24.1224  -12.7971
 48H  H11  H  HCH3  0   0.275  -41.6825  -24.5251  -14.4360
 48H  H12  H  HCH2  0   0.292  -41.1240  -22.2257  -11.4544
 48H  H13  H  HCH2  0   0.300  -39.6327  -22.0333  -12.3404
 48H  H14  H  HOH1  0   0.485  -39.5530  -19.5585   -9.9055
 48H  H15  H  HCH2  0   0.241  -50.2180  -21.2029  -16.3705
 48H  H16  H  HCH2  0   0.281  -50.7033  -22.6639  -15.5031
 48H  H17  H  HCR5  0   0.278  -51.8061  -23.5140  -17.5919
 48H  H18  H  HCR5  0   0.255  -50.4474  -21.6191  -19.0719
 48H  H19  H  HOH1  0   0.461  -51.9282  -23.1418  -19.9891
 48H  H20  H  HCR5  0   0.249  -51.3659  -19.8003  -17.8080
 48H  H21  H  HOH1  0   0.465  -52.5692  -18.6997  -19.2893
 48H  H22  H  HCR5  0   0.269  -54.1415  -21.0313  -18.1165
 48H  H23  H  HNH2  0   0.405  -56.9621  -16.1235  -14.1004
 48H  H24  H  HNH2  0   0.412  -55.3136  -16.4148  -13.6795
 48H  C13  C  CH2   0  -0.215  -50.4640  -22.2622  -16.4884

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
 48H  O13  C16  single    1.390  0.020  1.390
 48H  O12  C15  single    1.401  0.020  1.401
 48H  C16  C15  single    1.521  0.020  1.521
 48H  C16  C17  single    1.535  0.020  1.535
 48H  C15  C14  single    1.533  0.020  1.533
 48H  C17  N2   single    1.438  0.020  1.438
 48H  C17  O14  single    1.405  0.020  1.405
 48H  N3   C1   aromatic  1.322  0.020  1.322
 48H  N3   C2   aromatic  1.330  0.020  1.330
 48H  C1   N4   aromatic  1.330  0.020  1.330
 48H  C14  O14  single    1.427  0.020  1.427
 48H  C14  C13  single    1.520  0.020  1.520
 48H  C2   N2   aromatic  1.367  0.020  1.367
 48H  C2   C3   aromatic  1.385  0.020  1.385
 48H  N2   C5   aromatic  1.371  0.020  1.371
 48H  O2   P1   double    1.476  0.020  1.476
 48H  N4   C4   aromatic  1.338  0.020  1.338
 48H  O11  C13  single    1.434  0.020  1.434
 48H  O11  P1   single    1.583  0.020  1.583
 48H  O7   C7   single    1.388  0.020  1.388
 48H  O1   P1   single    1.583  0.020  1.583
 48H  P1   O3   single    1.616  0.020  1.616
 48H  C5   N6   aromatic  1.298  0.020  1.298
 48H  C3   C4   aromatic  1.407  0.020  1.407
 48H  C3   N6   aromatic  1.372  0.020  1.372
 48H  C4   N5   single    1.333  0.020  1.333
 48H  O8   C8   double    1.202  0.020  1.202
 48H  C7   C8   single    1.521  0.020  1.521
 48H  C7   C6   single    1.528  0.020  1.528
 48H  C8   C9   single    1.511  0.020  1.511
 48H  O3   P2   single    1.635  0.020  1.635
 48H  O6   C6   single    1.435  0.020  1.435
 48H  O6   P2   single    1.579  0.020  1.579
 48H  O5   P2   double    1.468  0.020  1.468
 48H  C9   N1   double    1.264  0.020  1.264
 48H  C9   C10  single    1.499  0.020  1.499
 48H  P2   O4   single    1.580  0.020  1.580
 48H  O10  C12  double    1.202  0.020  1.202
 48H  N1   C11  single    1.435  0.020  1.435
 48H  C12  C11  single    1.510  0.020  1.510
 48H  C12  O9   single    1.328  0.020  1.328
 48H  C1   H1   single    0.930  0.020  1.080
 48H  C5   H2   single    0.930  0.020  1.080
 48H  O1   H3   single    0.850  0.020  0.980
 48H  O4   H4   single    0.850  0.020  0.980
 48H  C6   H5   single    0.970  0.020  1.090
 48H  C6   H6   single    0.970  0.020  1.090
 48H  C7   H7   single    0.970  0.020  1.090
 48H  O7   H8   single    0.850  0.020  0.980
 48H  C10  H9   single    0.970  0.020  1.090
 48H  C10  H10  single    0.970  0.020  1.090
 48H  C10  H11  single    0.970  0.020  1.090
 48H  C11  H12  single    0.970  0.020  1.090
 48H  C11  H13  single    0.970  0.020  1.090
 48H  O9   H14  single    0.850  0.020  0.980
 48H  C13  H15  single    0.970  0.020  1.090
 48H  C13  H16  single    0.970  0.020  1.090
 48H  C14  H17  single    0.970  0.020  1.090
 48H  C15  H18  single    0.970  0.020  1.090
 48H  O12  H19  single    0.850  0.020  0.980
 48H  C16  H20  single    0.970  0.020  1.090
 48H  O13  H21  single    0.850  0.020  0.980
 48H  C17  H22  single    0.970  0.020  1.090
 48H  N5   H23  single    0.860  0.020  1.020
 48H  N5   H24  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
 48H  H1   C1   N4   115.45  3.000
 48H  H1   C1   N3   116.11  3.000
 48H  N4   C1   N3   128.43  3.000
 48H  N3   C2   N2   128.26  3.000
 48H  N2   C2   C3   105.16  3.000
 48H  N3   C2   C3   126.57  3.000
 48H  N6   C3   C4   132.88  3.000
 48H  N6   C3   C2   110.84  3.000
 48H  C4   C3   C2   116.28  3.000
 48H  N5   C4   N4   119.35  3.000
 48H  N5   C4   C3   122.79  3.000
 48H  N4   C4   C3   117.86  3.000
 48H  H2   C5   N6   124.65  3.000
 48H  H2   C5   N2   121.97  3.000
 48H  N6   C5   N2   113.37  3.000
 48H  H3   O1   P1   114.60  3.000
 48H  O11  P1   O3   105.69  3.000
 48H  O3   P1   O2   114.90  3.000
 48H  O11  P1   O2   111.12  3.000
 48H  O3   P1   O1    97.29  3.000
 48H  O11  P1   O1   107.94  3.000
 48H  O2   P1   O1   118.47  3.000
 48H  P2   O3   P1   124.14  3.000
 48H  O6   P2   O5   113.30  3.000
 48H  O5   P2   O4   119.74  3.000
 48H  O6   P2   O4   103.49  3.000
 48H  O4   P2   O3   101.32  3.000
 48H  O5   P2   O3   112.67  3.000
 48H  O6   P2   O3   104.57  3.000
 48H  H4   O4   P2   116.02  3.000
 48H  C6   O6   P2   124.92  3.000
 48H  H6   C6   H5   108.01  3.000
 48H  H6   C6   C7   109.40  3.000
 48H  H5   C6   C7   111.93  3.000
 48H  H6   C6   O6   111.88  3.000
 48H  H5   C6   O6   107.37  3.000
 48H  C7   C6   O6   108.27  3.000
 48H  H7   C7   C8   107.61  3.000
 48H  H7   C7   O7   112.27  3.000
 48H  C8   C7   O7   108.12  3.000
 48H  H7   C7   C6   107.62  3.000
 48H  C8   C7   C6   107.93  3.000
 48H  O7   C7   C6   113.08  3.000
 48H  H8   O7   C7   110.36  3.000
 48H  C9   C8   O8   121.27  3.000
 48H  C9   C8   C7   116.57  3.000
 48H  O8   C8   C7   122.14  3.000
 48H  N1   C9   C10  126.79  3.000
 48H  C10  C9   C8   118.79  3.000
 48H  N1   C9   C8   114.42  3.000
 48H  H11  C10  H10  107.82  3.000
 48H  H11  C10  H9   107.81  3.000
 48H  H10  C10  H9   106.98  3.000
 48H  H11  C10  C9   112.39  3.000
 48H  H10  C10  C9   110.96  3.000
 48H  H9   C10  C9   110.67  3.000
 48H  C11  N1   C9   118.54  3.000
 48H  H13  C11  H12  105.40  3.000
 48H  H13  C11  C12  108.30  3.000
 48H  H12  C11  C12  108.22  3.000
 48H  H13  C11  N1   111.20  3.000
 48H  H12  C11  N1   112.62  3.000
 48H  C12  C11  N1   110.85  3.000
 48H  O10  C12  O9   123.99  3.000
 48H  O9   C12  C11  110.56  3.000
 48H  O10  C12  C11  125.45  3.000
 48H  H14  O9   C12  110.12  3.000
 48H  C13  O11  P1   122.92  3.000
 48H  H17  C14  O14  109.04  3.000
 48H  H17  C14  C15  110.93  3.000
 48H  O14  C14  C15  106.21  3.000
 48H  H17  C14  C13  108.85  3.000
 48H  O14  C14  C13  107.56  3.000
 48H  C15  C14  C13  114.07  3.000
 48H  H18  C15  C16  111.96  3.000
 48H  H18  C15  O12  111.73  3.000
 48H  C16  C15  O12  107.76  3.000
 48H  H18  C15  C14  111.90  3.000
 48H  C16  C15  C14  100.90  3.000
 48H  O12  C15  C14  112.06  3.000
 48H  H19  O12  C15  108.57  3.000
 48H  H20  C16  C17  108.81  3.000
 48H  H20  C16  O13  111.36  3.000
 48H  C17  C16  O13  114.26  3.000
 48H  H20  C16  C15  108.08  3.000
 48H  C17  C16  C15  100.96  3.000
 48H  O13  C16  C15  112.76  3.000
 48H  H21  O13  C16  108.85  3.000
 48H  H22  C17  N2   106.28  3.000
 48H  H22  C17  O14  111.64  3.000
 48H  N2   C17  O14  109.37  3.000
 48H  H22  C17  C16  110.37  3.000
 48H  O14  C17  C16  105.35  3.000
 48H  N2   C17  C16  113.93  3.000
 48H  C17  O14  C14  110.43  3.000
 48H  C17  N2   C5   127.45  3.000
 48H  C5   N2   C2   106.16  3.000
 48H  C17  N2   C2   126.38  3.000
 48H  C2   N3   C1   111.65  3.000
 48H  C4   N4   C1   119.19  3.000
 48H  H24  N5   H23  118.35  3.000
 48H  H24  N5   C4   121.22  3.000
 48H  H23  N5   C4   120.32  3.000
 48H  C5   N6   C3   104.46  3.000
 48H  H16  C13  H15  107.98  3.000
 48H  H16  C13  C14  110.23  3.000
 48H  H15  C13  C14  110.90  3.000
 48H  H16  C13  O11  108.35  3.000
 48H  H15  C13  O11  111.50  3.000
 48H  C14  C13  O11  107.86  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
 48H  CONST_01  N2   C2   N3   C1    180.00   0.0  0
 48H  CONST_02  C3   C2   N3   C1      0.00   0.0  0
 48H  CONST_03  C3   C4   N4   C1      0.00   0.0  0
 48H  CONST_04  N4   C1   N3   C2      0.00   0.0  0
 48H  CONST_05  N6   C5   N2   C2      0.00   0.0  0
 48H  CONST_06  N4   C4   C3   C2      0.00   0.0  0
 48H  CONST_07  C5   N6   C3   C2      0.00   0.0  0
 48H  CONST_08  C5   N2   C2   C3      0.00   0.0  0
 48H  CONST_09  N2   C5   N6   C3      0.00   0.0  0
 48H  CONST_10  N3   C1   N4   C4      0.00   0.0  0
 48H  CONST_11  N3   C2   C3   C4      0.00   0.0  0
 48H  CONST_12  N2   C2   C3   C4    180.00   0.0  0
 48H  CONST_13  C5   N6   C3   C4    180.00   0.0  0
 48H  CONST_14  N3   C2   N2   C5    180.00   0.0  0
 48H  CONST_15  N6   C3   C2   N2      0.00   0.0  0
 48H  CONST_16  N6   C3   C2   N3    180.00   0.0  0
 48H  CONST_17  N6   C3   C4   N4    180.00   0.0  0
 48H  CONST_18  C17  N2   C2   C3    180.00   0.0  0
 48H  CONST_19  N3   C2   N2   C17     0.00   0.0  0
 48H  CONST_20  N6   C5   N2   C17   180.00   0.0  0
 48H  CONST_21  N5   C4   N4   C1    180.00   0.0  0
 48H  CONST_22  N5   C4   C3   C2    180.00   0.0  0
 48H  CONST_23  N6   C3   C4   N5      0.00   0.0  0
 48H  CONST_24  H1   C1   N3   C2    180.00   0.0  0
 48H  CONST_25  H2   C5   N2   C2    180.00   0.0  0
 48H  CONST_26  H23  N5   C4   C3    180.00   0.0  0
 48H  CONST_27  H24  N5   C4   C3      0.00   0.0  0
 48H  CONST_28  H14  O9   C12  C11   180.00   0.0  0
 48H  Var_01    C14  C13  O11  P1    141.68  30.0  3
 48H  Var_02    O6   P2   O3   P1     76.94  30.0  3
 48H  Var_03    O11  P1   O3   P2     77.81  30.0  2
 48H  Var_04    C7   C6   O6   P2   -134.10  30.0  3
 48H  Var_05    N1   C9   C8   C7   -131.77  30.0  2
 48H  Var_06    C12  C11  N1   C9   -172.79  30.0  3
 48H  Var_07    O10  C12  C11  N1      0.55  30.0  1
 48H  Var_08    H9   C10  C9   C8    138.72  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
 48H  chir_03  C7   O7   C8   C6   negativ
 48H  chir_04  C14  C15  O14  C13  positiv
 48H  chir_05  C15  O12  C14  C16  positiv
 48H  chir_06  C16  O13  C15  C17  positiv
 48H  chir_07  C17  O14  N2   C16  negativ
 48H  chir_08  P1   O11  O1   O3   both
 48H  chir_09  P2   O6   O5   O4   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
 48H  plan-1  C1   0.020
 48H  plan-1  C2   0.020
 48H  plan-1  C3   0.020
 48H  plan-1  C4   0.020
 48H  plan-1  C5   0.020
 48H  plan-1  C17  0.020
 48H  plan-1  N2   0.020
 48H  plan-1  N3   0.020
 48H  plan-1  N4   0.020
 48H  plan-1  N5   0.020
 48H  plan-1  N6   0.020
 48H  plan-1  H1   0.020
 48H  plan-1  H2   0.020
 48H  plan-2  C4   0.020
 48H  plan-2  N5   0.020
 48H  plan-2  H23  0.020
 48H  plan-2  H24  0.020
 48H  plan-3  C7   0.020
 48H  plan-3  C8   0.020
 48H  plan-3  O8   0.020
 48H  plan-3  C9   0.020
 48H  plan-4  C11  0.020
 48H  plan-4  C12  0.020
 48H  plan-4  O9   0.020
 48H  plan-4  O10  0.020
 48H  plan-4  H14  0.020
 48H  plan-5  C8   0.020
 48H  plan-5  C9   0.020
 48H  plan-5  C10  0.020
 48H  plan-5  N1   0.020
 48H  plan-5  C11  0.020

