# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat May 30 19:01:15 2020
#   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  60  39  .  2021-08-04  2021-08-04  
;
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   0.041   6.5398  -2.9442   1.1575
 48H  C2   C  CR56   0   0.487   5.0855  -1.4992   0.3701
 48H  C3   C  CR56   0  -0.011   4.5146  -2.4431  -0.4695
 48H  C4   C  CR6    0   0.449   5.0738  -3.7325  -0.4298
 48H  C5   C  CR15   0   0.066   3.4283  -0.6566  -0.7915
 48H  O1   O  OP    -1  -0.773   1.0325   1.0604  -2.1087
 48H  P1   P  P      0   1.353   0.3413   2.2369  -1.4855
 48H  O2   O  O      0  -0.793  -0.0957   3.3847  -2.3387
 48H  O3   O  O2     0  -0.734  -0.8794   1.7295  -0.5201
 48H  P2   P  P      0   1.341  -2.4466   1.6434  -1.0151
 48H  O4   O  OP    -1  -0.792  -3.1614   2.9148  -0.6833
 48H  O5   O  O      0  -0.797  -2.5174   1.0676  -2.3936
 48H  O6   O  O2     0  -0.613  -2.8303   0.4905   0.0942
 48H  C6   C  CH2    0  -0.164  -4.1916   0.2089   0.3253
 48H  C7   C  CH1    0  -0.085  -4.3233  -0.3819   1.7315
 48H  O7   O  OH1    0  -0.654  -3.8539   0.4857   2.7214
 48H  C8   C  C      0   0.309  -5.7842  -0.7423   1.9647
 48H  O8   O  O      0  -0.383  -6.4775  -0.0403   2.6676
 48H  C9   C  C      0   0.146  -6.3407  -1.9436   1.2641
 48H  C10  C  CH3    0  -0.754  -7.8306  -2.0896   1.1868
 48H  N1   N  N      0  -0.324  -5.4751  -2.7421   0.7947
 48H  C11  C  CH2    0  -0.492  -5.8896  -3.8844   0.0431
 48H  C12  C  C      0   0.417  -6.1496  -3.5496  -1.4644
 48H  O9   O  OC    -1  -0.608  -6.2968  -4.5512  -2.1864
 48H  O10  O  O      0  -0.575  -6.2057  -2.3550  -1.7898
 48H  O11  O  O2     0  -0.615   1.2476   2.7909  -0.2262
 48H  C14  C  CH1    0  -0.043   3.4410   2.9330   0.6970
 48H  C15  C  CH1    0  -0.034   4.9022   3.2496   0.4132
 48H  O12  O  OH1    0  -0.668   5.5432   3.5688   1.6208
 48H  C16  C  CH1    0  -0.047   5.3901   1.9034  -0.1286
 48H  O13  O  OH1    0  -0.652   6.7633   1.6817  -0.0153
 48H  C17  C  CH1    0   0.226   4.6244   0.9289   0.7668
 48H  O14  O  O2     0  -0.490   3.4033   1.5454   1.0470
 48H  N2   N  NR5    0  -0.541   4.3765  -0.3539   0.1511
 48H  N3   N  N      0  -0.454   6.1022  -1.6985   1.2067
 48H  N4   N  N      0  -0.475   6.0972  -3.9481   0.4038
 48H  N5   N  NH2    0  -0.817   4.6347  -4.7329  -1.1991
 48H  N6   N  N      0  -0.459   3.4800  -1.8975  -1.1833
 48H  H1   H  HCR6   0   0.249   7.3687  -3.1861   1.8147
 48H  H2   H  HCR5   0   0.329   2.7034   0.0692  -1.1442
 48H  H5   H  HCH2   0   0.209  -4.8040   1.1166   0.2601
 48H  H6   H  HCH2   0   0.232  -4.5782  -0.5040  -0.4097
 48H  H7   H  HCH1   0   0.262  -3.7192  -1.2902   1.7791
 48H  H8   H  HOH1   0   0.442  -4.4844   1.2081   2.8231
 48H  H9   H  HCH3   0   0.259  -8.3465  -1.3013   1.7275
 48H  H10  H  HCH3   0   0.265  -8.1494  -2.0602   0.1444
 48H  H11  H  HCH3   0   0.258  -8.1528  -3.0487   1.5963
 48H  H12  H  HCH2   0   0.246  -5.1049  -4.6417   0.0903
 48H  H13  H  HCH2   0   0.231  -6.8075  -4.3479   0.4272
 48H  H15  H  HCH2   0   0.206   2.9662   2.7109  -1.3936
 48H  H16  H  HCH2   0   0.229   2.5904   4.2899  -0.7080
 48H  H17  H  HCH1   0   0.262   3.0747   3.5079   1.5531
 48H  H18  H  HCH1   0   0.251   5.0092   4.0524  -0.3287
 48H  H19  H  HOH1   0   0.449   6.4902   3.4328   1.4995
 48H  H20  H  HCH1   0   0.248   5.0459   1.7872  -1.1644
 48H  H21  H  HOH1   0   0.469   7.2064   2.0888  -0.7666
 48H  H22  H  HCH1   0   0.257   5.1961   0.7247   1.6796
 48H  H23  H  HNH2   0   0.409   3.7988  -4.6279  -1.7468
 48H  H24  H  HNH2   0   0.401   4.9978  -5.6613  -1.0684
 48H  C13  C  CH2    0  -0.148   2.5609   3.2130  -0.5066

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    1.396  0.020  1.396
 48H  O12  C15  single    1.404  0.020  1.404
 48H  C16  C15  single    1.531  0.020  1.531
 48H  C16  C17  single    1.529  0.020  1.529
 48H  C15  C14  single    1.522  0.020  1.522
 48H  C17  N2   single    1.444  0.020  1.444
 48H  C17  O14  single    1.396  0.020  1.396
 48H  N3   C1   aromatic  1.321  0.020  1.321
 48H  N3   C2   aromatic  1.332  0.020  1.332
 48H  C1   N4   aromatic  1.331  0.020  1.331
 48H  C14  O14  single    1.432  0.020  1.432
 48H  C14  C13  single    1.517  0.020  1.517
 48H  C2   N2   aromatic  1.365  0.020  1.365
 48H  C2   C3   aromatic  1.386  0.020  1.386
 48H  N2   C5   aromatic  1.371  0.020  1.371
 48H  O2   P1   deloc     1.495  0.020  1.495
 48H  N4   C4   aromatic  1.337  0.020  1.337
 48H  O11  C13  single    1.408  0.020  1.408
 48H  O11  P1   single    1.647  0.020  1.647
 48H  O7   C7   single    1.398  0.020  1.398
 48H  O1   P1   deloc     1.500  0.020  1.500
 48H  P1   O3   single    1.637  0.020  1.637
 48H  C5   N6   aromatic  1.302  0.020  1.302
 48H  C3   C4   aromatic  1.406  0.020  1.406
 48H  C3   N6   aromatic  1.370  0.020  1.370
 48H  C4   N5   single    1.336  0.020  1.336
 48H  O8   C8   double    1.211  0.020  1.211
 48H  C7   C8   single    1.523  0.020  1.523
 48H  C7   C6   single    1.531  0.020  1.531
 48H  C8   C9   single    1.498  0.020  1.498
 48H  O3   P2   single    1.646  0.020  1.646
 48H  O6   C6   single    1.409  0.020  1.409
 48H  O6   P2   single    1.645  0.020  1.645
 48H  O5   P2   deloc     1.496  0.020  1.496
 48H  C9   N1   double    1.268  0.020  1.268
 48H  C9   C10  single    1.499  0.020  1.499
 48H  P2   O4   deloc     1.496  0.020  1.496
 48H  O10  C12  deloc     1.239  0.020  1.239
 48H  N1   C11  single    1.429  0.020  1.429
 48H  C12  C11  single    1.566  0.020  1.566
 48H  C12  O9   deloc     1.243  0.020  1.243
 48H  C1   H1   single    0.930  0.020  1.080
 48H  C5   H2   single    0.930  0.020  1.080
 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  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   115.39  3.000
 48H  H1   C1   N3   116.14  3.000
 48H  N4   C1   N3   128.47  3.000
 48H  N3   C2   N2   128.54  3.000
 48H  N2   C2   C3   105.09  3.000
 48H  N3   C2   C3   126.37  3.000
 48H  N6   C3   C4   132.86  3.000
 48H  N6   C3   C2   110.81  3.000
 48H  C4   C3   C2   116.33  3.000
 48H  N5   C4   N4   119.31  3.000
 48H  N5   C4   C3   122.66  3.000
 48H  N4   C4   C3   118.02  3.000
 48H  H2   C5   N6   124.49  3.000
 48H  H2   C5   N2   122.55  3.000
 48H  N6   C5   N2   112.94  3.000
 48H  O11  P1   O3    93.65  3.000
 48H  O3   P1   O2   110.88  3.000
 48H  O11  P1   O2   109.80  3.000
 48H  O3   P1   O1   110.21  3.000
 48H  O11  P1   O1   109.13  3.000
 48H  O2   P1   O1   119.97  3.000
 48H  P2   O3   P1   123.30  3.000
 48H  O6   P2   O5   109.91  3.000
 48H  O5   P2   O4   120.60  3.000
 48H  O6   P2   O4   109.55  3.000
 48H  O4   P2   O3   110.11  3.000
 48H  O5   P2   O3   110.02  3.000
 48H  O6   P2   O3    93.21  3.000
 48H  C6   O6   P2   118.41  3.000
 48H  H6   C6   H5   107.57  3.000
 48H  H6   C6   C7   109.58  3.000
 48H  H5   C6   C7   109.02  3.000
 48H  H6   C6   O6   111.18  3.000
 48H  H5   C6   O6   111.36  3.000
 48H  C7   C6   O6   108.11  3.000
 48H  H7   C7   C8   109.11  3.000
 48H  H7   C7   O7   107.44  3.000
 48H  C8   C7   O7   111.14  3.000
 48H  H7   C7   C6   108.27  3.000
 48H  C8   C7   C6   108.34  3.000
 48H  O7   C7   C6   112.46  3.000
 48H  H8   O7   C7   108.67  3.000
 48H  C9   C8   O8   121.56  3.000
 48H  C9   C8   C7   118.33  3.000
 48H  O8   C8   C7   120.06  3.000
 48H  N1   C9   C10  126.74  3.000
 48H  C10  C9   C8   118.13  3.000
 48H  N1   C9   C8   115.13  3.000
 48H  H11  C10  H10  107.22  3.000
 48H  H11  C10  H9   108.11  3.000
 48H  H10  C10  H9   108.51  3.000
 48H  H11  C10  C9   111.08  3.000
 48H  H10  C10  C9   109.70  3.000
 48H  H9   C10  C9   112.07  3.000
 48H  C11  N1   C9   120.01  3.000
 48H  H13  C11  H12  107.04  3.000
 48H  H13  C11  C12  106.76  3.000
 48H  H12  C11  C12  108.02  3.000
 48H  H13  C11  N1   113.34  3.000
 48H  H12  C11  N1   108.86  3.000
 48H  C12  C11  N1   112.56  3.000
 48H  O10  C12  O9   128.21  3.000
 48H  O9   C12  C11  113.98  3.000
 48H  O10  C12  C11  117.80  3.000
 48H  C13  O11  P1   117.50  3.000
 48H  H17  C14  O14  108.01  3.000
 48H  H17  C14  C15  110.98  3.000
 48H  O14  C14  C15  105.81  3.000
 48H  H17  C14  C13  109.24  3.000
 48H  O14  C14  C13  110.95  3.000
 48H  C15  C14  C13  111.76  3.000
 48H  H18  C15  C16  111.88  3.000
 48H  H18  C15  O12  111.73  3.000
 48H  C16  C15  O12  111.03  3.000
 48H  H18  C15  C14  111.82  3.000
 48H  C16  C15  C14  100.90  3.000
 48H  O12  C15  C14  108.98  3.000
 48H  H19  O12  C15  107.94  3.000
 48H  H20  C16  C17  109.16  3.000
 48H  H20  C16  O13  111.61  3.000
 48H  C17  C16  O13  110.12  3.000
 48H  H20  C16  C15  109.09  3.000
 48H  C17  C16  C15  101.16  3.000
 48H  O13  C16  C15  115.12  3.000
 48H  H21  O13  C16  108.81  3.000
 48H  H22  C17  N2   106.20  3.000
 48H  H22  C17  O14  111.79  3.000
 48H  N2   C17  O14  109.12  3.000
 48H  H22  C17  C16  110.20  3.000
 48H  O14  C17  C16  105.91  3.000
 48H  N2   C17  C16  113.73  3.000
 48H  C17  O14  C14  110.85  3.000
 48H  C17  N2   C5   127.44  3.000
 48H  C5   N2   C2   106.53  3.000
 48H  C17  N2   C2   126.00  3.000
 48H  C2   N3   C1   111.75  3.000
 48H  C4   N4   C1   119.06  3.000
 48H  H24  N5   H23  117.88  3.000
 48H  H24  N5   C4   119.86  3.000
 48H  H23  N5   C4   120.59  3.000
 48H  C5   N6   C3   104.64  3.000
 48H  H16  C13  H15  106.93  3.000
 48H  H16  C13  C14  108.15  3.000
 48H  H15  C13  C14  110.04  3.000
 48H  H16  C13  O11  110.87  3.000
 48H  H15  C13  O11  111.63  3.000
 48H  C14  C13  O11  109.14  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      0.00   0.0  0
 48H  CONST_27  H24  N5   C4   C3    180.00   0.0  0
 48H  Var_01    C14  C13  O11  P1   -148.19  30.0  3
 48H  Var_02    O6   P2   O3   P1    155.27  30.0  3
 48H  Var_03    O11  P1   O3   P2    151.98  30.0  2
 48H  Var_04    C7   C6   O6   P2   -155.69  30.0  3
 48H  Var_05    N1   C9   C8   C7     16.45  30.0  2
 48H  Var_06    C12  C11  N1   C9     84.01  30.0  3
 48H  Var_07    O10  C12  C11  N1    -12.29  30.0  2
 48H  Var_08    H9   C10  C9   C8     -3.73  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
 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

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-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

