# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun May 31 05:14:19 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: (3R,5R,8R,10S,11E)-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-11-en-13-oic acid 3,5-dioxide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N=CC(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
 48N  48N  '(3R,5R,8R,10S,11E)-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-11-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_48N
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
 48N  O1   O  O      0  -0.790  -0.6351  -4.4363  -1.7730
 48N  P1   P  P      0   1.357  -1.0034  -3.0810  -1.2603
 48N  O2   O  OP    -1  -0.775  -1.6225  -2.0708  -2.1809
 48N  O3   O  O2     0  -0.733   0.2603  -2.4156  -0.4565
 48N  P2   P  P      0   1.341   1.8238  -2.5717  -0.9327
 48N  O4   O  OP    -1  -0.789   2.4525  -3.7559  -0.2708
 48N  O5   O  O      0  -0.798   1.9474  -2.3695  -2.4096
 48N  O6   O  O2     0  -0.612   2.2916  -1.1989  -0.1458
 48N  C1   C  CH2    0  -0.160   3.6614  -0.8844  -0.1558
 48N  C2   C  CH1    0  -0.106   3.9689  -0.0375   1.0805
 48N  O7   O  OH1    0  -0.648   3.6915  -0.7073   2.2709
 48N  C3   C  C      0   0.373   5.4043   0.4573   1.0226
 48N  O8   O  O      0  -0.378   6.2263   0.0790   1.8203
 48N  C4   C  CH1    0  -0.239   5.7561   1.4385  -0.0890
 48N  C5   C  CH3    0  -0.652   6.6727   0.7540  -1.1032
 48N  N1   N  N      0  -0.301   6.4551   2.5543   0.5075
 48N  C6   C  C1     0  -0.176   5.9730   3.7072   0.3318
 48N  C7   C  C      0   0.365   6.6321   4.9578   0.9051
 48N  O9   O  OC    -1  -0.602   5.9946   6.0079   0.6960
 48N  O10  O  O      0  -0.589   7.7061   4.8162   1.5097
 48N  O11  O  O2     0  -0.615  -1.9272  -3.2265   0.0932
 48N  C8   C  CH2    0  -0.147  -3.3208  -3.3722  -0.0380
 48N  C9   C  CR15   0  -0.042  -4.0027  -2.6703   1.1218
 48N  C10  C  CR15   0  -0.034  -5.5157  -2.6476   0.9586
 48N  O12  O  OH1    0  -0.668  -6.1085  -2.5717   2.2292
 48N  C11  C  CR15   0  -0.049  -5.7045  -1.3389   0.1857
 48N  O13  O  OH1    0  -0.653  -6.9677  -0.7574   0.3059
 48N  C12  C  CR15   0   0.223  -4.6524  -0.4513   0.8508
 48N  O14  O  O      0  -0.489  -3.5975  -1.2997   1.1947
 48N  N2   N  NR5    0  -0.541  -4.1553   0.6045   0.0025
 48N  C13  C  CR5    0   0.487  -4.4711   1.9285   0.1001
 48N  N3   N  N      0  -0.456  -5.2654   2.5278   0.9849
 48N  C14  C  C1     0   0.041  -5.3319   3.8312   0.7788
 48N  N4   N  N      0  -0.475  -4.7289   4.5523  -0.1632
 48N  C15  C  C      0   0.451  -3.9328   3.9356  -1.0439
 48N  N5   N  NH2    0  -0.818  -3.3129   4.6566  -1.9811
 48N  C16  C  CR5    0  -0.012  -3.7753   2.5428  -0.9293
 48N  N6   N  N      0  -0.459  -3.0465   1.6245  -1.6397
 48N  C17  C  CR15   0   0.071  -3.2970   0.4859  -1.0599
 48N  H3   H  HCH2   0   0.219   4.2883  -1.7851  -0.1321
 48N  H4   H  HCH2   0   0.223   3.9230  -0.3325  -1.0657
 48N  H5   H  HCH1   0   0.271   3.3234   0.8495   1.0525
 48N  H6   H  HOH1   0   0.446   4.3676  -1.3791   2.4160
 48N  H7   H  HCH1   0   0.241   4.8322   1.7538  -0.5962
 48N  H8   H  HCH3   0   0.251   6.8771   1.4329  -1.9303
 48N  H9   H  HCH3   0   0.241   7.6180   0.4773  -0.6379
 48N  H10  H  HCH3   0   0.239   6.2159  -0.1455  -1.5168
 48N  H11  H  H      0   0.206   5.0503   3.8706  -0.2396
 48N  H13  H  HCH2   0   0.210  -3.6788  -2.9656  -0.9900
 48N  H14  H  HCH2   0   0.227  -3.6052  -4.4303  -0.0119
 48N  H15  H  HCR5   0   0.261  -3.7163  -3.1581   2.0585
 48N  H16  H  HCR5   0   0.251  -5.8795  -3.5157   0.3923
 48N  H17  H  HOH1   0   0.449  -7.0053  -2.2346   2.1200
 48N  H18  H  HCR5   0   0.250  -5.4327  -1.4990  -0.8656
 48N  H19  H  HOH1   0   0.469  -7.5545  -1.1555  -0.3450
 48N  H20  H  HCR5   0   0.257  -5.0796   0.0425   1.7314
 48N  H21  H  H      0   0.250  -5.9605   4.3913   1.4628
 48N  H22  H  HNH2   0   0.402  -3.5073   5.6387  -2.0733
 48N  H23  H  HNH2   0   0.410  -2.7735   4.2105  -2.7021
 48N  H24  H  HCR5   0   0.325  -2.8608  -0.4631  -1.3522

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
 48N  O13  C11  single    1.396  0.020  1.396
 48N  O12  C10  single    1.404  0.020  1.404
 48N  C11  C10  single    1.532  0.020  1.532
 48N  C11  C12  single    1.529  0.020  1.529
 48N  C10  C9   single    1.522  0.020  1.522
 48N  C12  N2   single    1.443  0.020  1.443
 48N  C12  O14  single    1.397  0.020  1.397
 48N  N3   C14  aromatic  1.321  0.020  1.321
 48N  N3   C13  aromatic  1.331  0.020  1.331
 48N  C9   O14  single    1.431  0.020  1.431
 48N  C9   C8   single    1.517  0.020  1.517
 48N  C14  N4   aromatic  1.331  0.020  1.331
 48N  O1   P1   deloc     1.495  0.020  1.495
 48N  N2   C13  aromatic  1.365  0.020  1.365
 48N  N2   C17  aromatic  1.371  0.020  1.371
 48N  C13  C16  aromatic  1.386  0.020  1.386
 48N  O11  C8   single    1.407  0.020  1.407
 48N  O11  P1   single    1.645  0.020  1.645
 48N  N4   C15  aromatic  1.338  0.020  1.338
 48N  O7   C2   single    1.394  0.020  1.394
 48N  P1   O2   deloc     1.500  0.020  1.500
 48N  P1   O3   single    1.639  0.020  1.639
 48N  C17  N6   aromatic  1.302  0.020  1.302
 48N  C16  C15  aromatic  1.406  0.020  1.406
 48N  C16  N6   aromatic  1.371  0.020  1.371
 48N  C15  N5   single    1.335  0.020  1.335
 48N  C2   C3   single    1.519  0.020  1.519
 48N  C2   C1   single    1.530  0.020  1.530
 48N  O3   P2   single    1.642  0.020  1.642
 48N  C4   C3   single    1.524  0.020  1.524
 48N  C4   N1   single    1.445  0.020  1.445
 48N  C4   C5   single    1.529  0.020  1.529
 48N  C3   O8   double    1.206  0.020  1.206
 48N  C1   O6   single    1.405  0.020  1.405
 48N  O6   P2   single    1.650  0.020  1.650
 48N  O5   P2   deloc     1.496  0.020  1.496
 48N  N1   C6   double    1.262  0.020  1.262
 48N  P2   O4   deloc     1.495  0.020  1.495
 48N  O10  C7   deloc     1.241  0.020  1.241
 48N  C6   C7   single    1.526  0.020  1.526
 48N  C7   O9   deloc     1.246  0.020  1.246
 48N  C1   H3   single    0.970  0.020  1.090
 48N  C1   H4   single    0.970  0.020  1.090
 48N  C2   H5   single    0.970  0.020  1.090
 48N  O7   H6   single    0.850  0.020  0.980
 48N  C4   H7   single    0.970  0.020  1.090
 48N  C5   H8   single    0.970  0.020  1.090
 48N  C5   H9   single    0.970  0.020  1.090
 48N  C5   H10  single    0.970  0.020  1.090
 48N  C6   H11  single    0.930  0.020  1.080
 48N  C8   H13  single    0.970  0.020  1.090
 48N  C8   H14  single    0.970  0.020  1.090
 48N  C9   H15  single    0.970  0.020  1.090
 48N  C10  H16  single    0.970  0.020  1.090
 48N  O12  H17  single    0.850  0.020  0.980
 48N  C11  H18  single    0.970  0.020  1.090
 48N  O13  H19  single    0.850  0.020  0.980
 48N  C12  H20  single    0.970  0.020  1.090
 48N  C14  H21  single    0.930  0.020  1.080
 48N  N5   H22  single    0.860  0.020  1.020
 48N  N5   H23  single    0.860  0.020  1.020
 48N  C17  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
 48N  O11  P1   O3    93.75  3.000
 48N  O3   P1   O2   110.22  3.000
 48N  O11  P1   O2   109.43  3.000
 48N  O3   P1   O1   110.26  3.000
 48N  O2   P1   O1   120.10  3.000
 48N  O11  P1   O1   109.90  3.000
 48N  P2   O3   P1   123.60  3.000
 48N  O6   P2   O5   109.57  3.000
 48N  O5   P2   O4   120.63  3.000
 48N  O6   P2   O4   109.18  3.000
 48N  O4   P2   O3   110.32  3.000
 48N  O5   P2   O3   110.62  3.000
 48N  O6   P2   O3    93.01  3.000
 48N  C1   O6   P2   117.33  3.000
 48N  H4   C1   H3   107.15  3.000
 48N  H4   C1   C2   110.14  3.000
 48N  H3   C1   C2   108.78  3.000
 48N  H4   C1   O6   110.56  3.000
 48N  H3   C1   O6   111.89  3.000
 48N  C2   C1   O6   108.30  3.000
 48N  H5   C2   C3   106.95  3.000
 48N  H5   C2   O7   107.05  3.000
 48N  C3   C2   O7   112.15  3.000
 48N  H5   C2   C1   107.97  3.000
 48N  C3   C2   C1   109.84  3.000
 48N  O7   C2   C1   112.60  3.000
 48N  H6   O7   C2   108.90  3.000
 48N  C4   C3   O8   121.81  3.000
 48N  O8   C3   C2   121.09  3.000
 48N  C4   C3   C2   117.10  3.000
 48N  H7   C4   N1   112.03  3.000
 48N  H7   C4   C5   109.03  3.000
 48N  N1   C4   C5   109.23  3.000
 48N  H7   C4   C3   109.08  3.000
 48N  C5   C4   C3   109.52  3.000
 48N  N1   C4   C3   107.92  3.000
 48N  H10  C5   H9   108.42  3.000
 48N  H10  C5   H8   107.74  3.000
 48N  H9   C5   H8   108.65  3.000
 48N  H10  C5   C4   111.70  3.000
 48N  H9   C5   C4   110.52  3.000
 48N  H8   C5   C4   109.70  3.000
 48N  C6   N1   C4   117.59  3.000
 48N  H11  C6   C7   115.90  3.000
 48N  H11  C6   N1   121.98  3.000
 48N  C7   C6   N1   122.11  3.000
 48N  O10  C7   O9   128.38  3.000
 48N  O9   C7   C6   114.00  3.000
 48N  O10  C7   C6   117.62  3.000
 48N  C8   O11  P1   119.24  3.000
 48N  H14  C8   H13  107.11  3.000
 48N  H14  C8   C9   108.16  3.000
 48N  H13  C8   C9   110.23  3.000
 48N  H14  C8   O11  110.77  3.000
 48N  H13  C8   O11  111.49  3.000
 48N  C9   C8   O11  109.01  3.000
 48N  H15  C9   O14  108.01  3.000
 48N  H15  C9   C10  111.02  3.000
 48N  O14  C9   C10  105.82  3.000
 48N  H15  C9   C8   109.30  3.000
 48N  O14  C9   C8   110.77  3.000
 48N  C10  C9   C8   111.81  3.000
 48N  H16  C10  C11  111.98  3.000
 48N  H16  C10  O12  111.68  3.000
 48N  C11  C10  O12  111.00  3.000
 48N  H16  C10  C9   111.89  3.000
 48N  C11  C10  C9   100.92  3.000
 48N  O12  C10  C9   108.87  3.000
 48N  H17  O12  C10  108.00  3.000
 48N  H18  C11  C12  109.33  3.000
 48N  H18  C11  O13  111.55  3.000
 48N  C12  C11  O13  110.09  3.000
 48N  H18  C11  C10  109.15  3.000
 48N  C12  C11  C10  101.06  3.000
 48N  O13  C11  C10  115.09  3.000
 48N  H19  O13  C11  108.74  3.000
 48N  H20  C12  N2   106.08  3.000
 48N  H20  C12  O14  111.72  3.000
 48N  N2   C12  O14  109.21  3.000
 48N  H20  C12  C11  110.05  3.000
 48N  O14  C12  C11  105.91  3.000
 48N  N2   C12  C11  113.97  3.000
 48N  C12  O14  C9   110.82  3.000
 48N  C17  N2   C13  106.51  3.000
 48N  C17  N2   C12  127.45  3.000
 48N  C13  N2   C12  126.03  3.000
 48N  C16  C13  N3   126.41  3.000
 48N  C16  C13  N2   105.11  3.000
 48N  N3   C13  N2   128.48  3.000
 48N  C14  N3   C13  111.74  3.000
 48N  H21  C14  N4   115.41  3.000
 48N  H21  C14  N3   116.12  3.000
 48N  N4   C14  N3   128.47  3.000
 48N  C15  N4   C14  119.07  3.000
 48N  C16  C15  N5   122.69  3.000
 48N  N5   C15  N4   119.31  3.000
 48N  C16  C15  N4   118.00  3.000
 48N  H23  N5   H22  118.14  3.000
 48N  H23  N5   C15  120.87  3.000
 48N  H22  N5   C15  120.14  3.000
 48N  N6   C16  C15  132.90  3.000
 48N  N6   C16  C13  110.79  3.000
 48N  C15  C16  C13  116.31  3.000
 48N  C17  N6   C16  104.64  3.000
 48N  H24  C17  N6   124.59  3.000
 48N  H24  C17  N2   122.43  3.000
 48N  N6   C17  N2   112.95  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
 48N  CONST_01  C14  N3   C13  N2    180.00   0.0  0
 48N  CONST_02  C15  C16  C13  N2    180.00   0.0  0
 48N  CONST_03  N6   C16  C13  N2      0.00   0.0  0
 48N  CONST_04  C16  N6   C17  N2      0.00   0.0  0
 48N  CONST_05  N4   C14  N3   C13     0.00   0.0  0
 48N  CONST_06  N6   C17  N2   C13     0.00   0.0  0
 48N  CONST_07  N4   C15  C16  C13     0.00   0.0  0
 48N  CONST_08  C17  N6   C16  C13     0.00   0.0  0
 48N  CONST_09  C15  N4   C14  N3      0.00   0.0  0
 48N  CONST_10  C17  N2   C13  N3    180.00   0.0  0
 48N  CONST_11  C15  C16  C13  N3      0.00   0.0  0
 48N  CONST_12  N6   C16  C13  N3    180.00   0.0  0
 48N  CONST_13  C16  C13  N3   C14     0.00   0.0  0
 48N  CONST_14  C16  C15  N4   C14     0.00   0.0  0
 48N  CONST_15  N6   C16  C15  N4    180.00   0.0  0
 48N  CONST_16  C17  N6   C16  C15   180.00   0.0  0
 48N  CONST_17  C17  N2   C13  C16     0.00   0.0  0
 48N  CONST_18  N3   C13  N2   C12     0.00   0.0  0
 48N  CONST_19  C16  C13  N2   C12   180.00   0.0  0
 48N  CONST_20  N6   C17  N2   C12   180.00   0.0  0
 48N  CONST_21  N5   C15  C16  C13   180.00   0.0  0
 48N  CONST_22  N5   C15  N4   C14   180.00   0.0  0
 48N  CONST_23  N6   C16  C15  N5      0.00   0.0  0
 48N  CONST_24  H24  C17  N2   C12     0.00   0.0  0
 48N  CONST_25  H21  C14  N3   C13   180.00   0.0  0
 48N  CONST_26  H22  N5   C15  N4      0.00   0.0  0
 48N  CONST_27  H23  N5   C15  N4    180.00   0.0  0
 48N  Var_01    C9   C8   O11  P1   -145.65  30.0  3
 48N  Var_02    C7   C6   N1   C4   -179.51   0.0  2
 48N  Var_03    O6   P2   O3   P1    156.24  30.0  3
 48N  Var_04    O11  P1   O3   P2    151.26  30.0  2
 48N  Var_05    C2   C1   O6   P2   -154.11  30.0  2
 48N  Var_06    O10  C7   C6   N1      3.18  30.0  2

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
 48N  chir_03  C2   O7   C3   C1   negativ
 48N  chir_04  C4   N1   C3   C5   positiv
 48N  chir_05  C9   C10  O14  C8   positiv
 48N  chir_06  C10  O12  C9   C11  positiv
 48N  chir_07  C11  O13  C10  C12  positiv
 48N  chir_08  C12  O14  N2   C11  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
 48N  plan-1  C12  0.020
 48N  plan-1  N2   0.020
 48N  plan-1  C13  0.020
 48N  plan-1  N3   0.020
 48N  plan-1  C14  0.020
 48N  plan-1  N4   0.020
 48N  plan-1  C15  0.020
 48N  plan-1  N5   0.020
 48N  plan-1  C16  0.020
 48N  plan-1  N6   0.020
 48N  plan-1  C17  0.020
 48N  plan-1  H21  0.020
 48N  plan-1  H24  0.020
 48N  plan-2  C15  0.020
 48N  plan-2  N5   0.020
 48N  plan-2  H22  0.020
 48N  plan-2  H23  0.020
 48N  plan-3  C2   0.020
 48N  plan-3  C3   0.020
 48N  plan-3  O8   0.020
 48N  plan-3  C4   0.020
 48N  plan-4  C6   0.020
 48N  plan-4  C7   0.020
 48N  plan-4  O9   0.020
 48N  plan-4  O10  0.020
 48N  plan-5  C4   0.020
 48N  plan-5  N1   0.020
 48N  plan-5  C6   0.020
 48N  plan-5  C7   0.020
 48N  plan-5  H11  0.020

