# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 01:12:25 2021
#   Inital geometry file: a 138 line input string
#   Ligand name: (2S)-2-amino-4-({[(2S,3S,4R,5R)-5-{6-[(3-chlorobenzyl)amino]-9H-purin-9-yl}-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(NCc4cccc(Cl)c4)ncnc23)C(O)=O
#
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
 36A  36A  '(2S)-2-amino-4-({[(2S,3S,4R,5R)-5-{6-[(3-chlorobenzyl)amino]-9H-purin-9-yl}-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name)'  ligand  59  34  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_36A
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
 36A  C     C   C     0   0.538  6.7208  -7.1529  46.6522
 36A  N     N   NH2   0  -0.802  6.8988  -7.5301  44.2251
 36A  O     O   O     0  -0.452  6.9121  -6.5410  47.6752
 36A  N1    N   N     0  -0.477  6.2301   4.2986  38.3247
 36A  C2    C   CR16  0   0.040  7.3340   3.6538  38.6810
 36A  N3    N   N     0  -0.456  7.4395   2.4478  39.2130
 36A  C4    C   CR56  0   0.489  6.2477   1.8833  39.3820
 36A  C5    C   CR56  0  -0.004  5.0068   2.4292  39.0666
 36A  C6    C   CR6   0   0.488  5.0353   3.7175  38.4981
 36A  N6    N   NH1   0  -0.645  3.9534   4.4160  38.1259
 36A  N7    N   N     0  -0.439  4.0051   1.5529  39.4018
 36A  C8    C   CR15  0   0.105  4.6202   0.5204  39.8946
 36A  N9    N   NR5   0  -0.536  5.9816   0.6562  39.9096
 36A  CA    C   CH1   0  -0.189  6.9462  -6.5414  45.2815
 36A  CB    C   CH2   0  -0.427  5.8654  -5.4699  45.0730
 36A  CD    C   CH2   0  -0.603  5.0556  -2.7577  42.0155
 36A  SD    S   S2    0  -0.020  4.8610  -3.3343  43.7236
 36A  CG    C   CH2   0  -0.575  6.0802  -4.6835  43.7878
 36A  C1'   C   CH1   0   0.169  6.9899  -0.2786  40.3894
 36A  C2'   C   CH1   0  -0.040  7.4725   0.0778  41.7958
 36A  O2'   O   OH1   0  -0.663  8.7842  -0.4014  41.9144
 36A  C27   C   CH2   0  -0.346  2.6069   3.9057  38.0930
 36A  C28   C   CR6   0   0.092  2.3463   2.8878  37.0063
 36A  C29   C   CR16  0  -0.253  3.0556   2.9165  35.8121
 36A  C3'   C   CH1   0  -0.015  6.4991  -0.7297  42.6503
 36A  O3'   O   OH1   0  -0.662  7.0146  -0.9090  43.9348
 36A  C30   C   CR6   0  -0.021  2.7609   1.9941  34.8198
 36A  C31   C   CR16  0  -0.233  1.7702   1.0405  34.9828
 36A  C32   C   CR16  0  -0.252  1.0661   1.0189  36.1795
 36A  C33   C   CR16  0  -0.275  1.3544   1.9291  37.1841
 36A  CL34  CL  CL    0  -0.135  3.6593   2.0406  33.3344
 36A  C4'   C   CH1   0   0.046  6.3575  -2.0068  41.8155
 36A  O4'   O   O2    0  -0.493  6.4315  -1.5569  40.4613
 36A  OXT   O   OH1   0  -0.576  6.2831  -8.4004  46.6217
 36A  HN    H   HNH2  0   0.360  7.0859  -7.0805  43.3382
 36A  HNA   H   HNH2  0   0.356  7.6455  -8.2034  44.3432
 36A  H2    H   HCR6  0   0.254  8.2633   4.1872  38.5117
 36A  HN6   H   HNH1  0   0.400  4.1365   5.3124  37.7037
 36A  H8    H   HCR5  0   0.297  4.1283  -0.3714  40.2494
 36A  HA    H   HCH1  0   0.256  7.9122  -6.0189  45.3535
 36A  HB    H   HCH2  0   0.255  4.8803  -5.9432  45.0559
 36A  HBA   H   HCH2  0   0.256  5.8895  -4.7863  45.9235
 36A  HD    H   HCH2  0   0.299  4.9787  -3.6091  41.3367
 36A  HDA   H   HCH2  0   0.293  4.1990  -2.1050  41.8312
 36A  HG    H   HCH2  0   0.273  7.0926  -4.2767  43.7548
 36A  HGA   H   HCH2  0   0.277  5.9331  -5.3087  42.9059
 36A  H1'   H   HCH1  0   0.286  7.8143  -0.2570  39.6716
 36A  H2'   H   HCH1  0   0.265  7.4104   1.1556  41.9882
 36A  HO2'  H   HOH1  0   0.457  8.9709  -0.5514  42.8483
 36A  H27   H   HCH2  0   0.269  2.3400   3.4785  39.0596
 36A  H27A  H   HCH2  0   0.291  1.9507   4.7640  37.9434
 36A  H29   H   HCR6  0   0.268  3.8365   3.6492  35.6534
 36A  H3'   H   HCH1  0   0.229  5.5295  -0.2087  42.6729
 36A  HO3'  H   HOH1  0   0.453  6.4403  -1.5359  44.3977
 36A  H31   H   HCR6  0   0.277  1.5527   0.3275  34.1994
 36A  H32   H   HCR6  0   0.266  0.2932   0.2760  36.3260
 36A  H33   H   HCR6  0   0.252  0.8063   1.8918  38.1175
 36A  H4'   H   HCH1  0   0.250  7.2038  -2.6743  42.0171
 36A  HOXT  H   HOH1  0   0.482  6.1531  -8.7202  47.5276

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
 36A  C    O     double    1.207  0.020  1.207
 36A  C    CA    single    1.518  0.020  1.518
 36A  C    OXT   single    1.322  0.020  1.322
 36A  N    CA    single    1.448  0.020  1.448
 36A  N1   C2    aromatic  1.327  0.020  1.327
 36A  N1   C6    aromatic  1.340  0.020  1.340
 36A  C2   N3    aromatic  1.322  0.020  1.322
 36A  N3   C4    aromatic  1.330  0.020  1.330
 36A  C4   C5    aromatic  1.392  0.020  1.392
 36A  C4   N9    aromatic  1.362  0.020  1.362
 36A  C5   C6    aromatic  1.409  0.020  1.409
 36A  C5   N7    aromatic  1.372  0.020  1.372
 36A  C6   N6    single    1.341  0.020  1.341
 36A  N6   C27   single    1.440  0.020  1.440
 36A  N7   C8    aromatic  1.299  0.020  1.299
 36A  C8   N9    aromatic  1.368  0.020  1.368
 36A  N9   C1'   single    1.456  0.020  1.456
 36A  CA   CB    single    1.536  0.020  1.536
 36A  CB   CG    single    1.522  0.020  1.522
 36A  CD   SD    single    1.813  0.020  1.813
 36A  CD   C4'   single    1.516  0.020  1.516
 36A  SD   CG    single    1.820  0.020  1.820
 36A  C1'  C2'   single    1.529  0.020  1.529
 36A  C1'  O4'   single    1.397  0.020  1.397
 36A  C2'  O2'   single    1.401  0.020  1.401
 36A  C2'  C3'   single    1.526  0.020  1.526
 36A  C27  C28   single    1.512  0.020  1.512
 36A  C28  C29   aromatic  1.389  0.020  1.389
 36A  C28  C33   aromatic  1.391  0.020  1.391
 36A  C29  C30   aromatic  1.386  0.020  1.386
 36A  C3'  O3'   single    1.396  0.020  1.396
 36A  C3'  C4'   single    1.532  0.020  1.532
 36A  C30  C31   aromatic  1.385  0.020  1.385
 36A  C30  CL34  single    1.737  0.020  1.737
 36A  C31  C32   aromatic  1.389  0.020  1.389
 36A  C32  C33   aromatic  1.386  0.020  1.386
 36A  C4'  O4'   single    1.429  0.020  1.429
 36A  N    HN    single    0.890  0.020  1.040
 36A  N    HNA   single    0.890  0.020  1.040
 36A  C2   H2    single    0.930  0.020  1.080
 36A  N6   HN6   single    0.860  0.020  1.020
 36A  C8   H8    single    0.930  0.020  1.080
 36A  CA   HA    single    0.970  0.020  1.090
 36A  CB   HB    single    0.970  0.020  1.090
 36A  CB   HBA   single    0.970  0.020  1.090
 36A  CD   HD    single    0.970  0.020  1.090
 36A  CD   HDA   single    0.970  0.020  1.090
 36A  CG   HG    single    0.970  0.020  1.090
 36A  CG   HGA   single    0.970  0.020  1.090
 36A  C1'  H1'   single    0.970  0.020  1.090
 36A  C2'  H2'   single    0.970  0.020  1.090
 36A  O2'  HO2'  single    0.850  0.020  0.980
 36A  C27  H27   single    0.970  0.020  1.090
 36A  C27  H27A  single    0.970  0.020  1.090
 36A  C29  H29   single    0.930  0.020  1.080
 36A  C3'  H3'   single    0.970  0.020  1.090
 36A  O3'  HO3'  single    0.850  0.020  0.980
 36A  C31  H31   single    0.930  0.020  1.080
 36A  C32  H32   single    0.930  0.020  1.080
 36A  C33  H33   single    0.930  0.020  1.080
 36A  C4'  H4'   single    0.970  0.020  1.090
 36A  OXT  HOXT  single    0.850  0.020  0.980

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
 36A  OXT   C    CA   114.10  3.000
 36A  OXT   C    O    123.37  3.000
 36A  CA    C    O    122.52  3.000
 36A  HNA   N    HN   105.15  3.000
 36A  HNA   N    CA   110.18  3.000
 36A  HN    N    CA   109.28  3.000
 36A  C6    N1   C2   119.75  3.000
 36A  H2    C2   N3   116.29  3.000
 36A  H2    C2   N1   115.58  3.000
 36A  N3    C2   N1   128.13  3.000
 36A  C4    N3   C2   111.52  3.000
 36A  N9    C4   C5   105.48  3.000
 36A  N9    C4   N3   127.37  3.000
 36A  C5    C4   N3   127.15  3.000
 36A  N7    C5   C6   134.21  3.000
 36A  N7    C5   C4   110.18  3.000
 36A  C6    C5   C4   115.60  3.000
 36A  N6    C6   C5   124.91  3.000
 36A  N6    C6   N1   117.24  3.000
 36A  C5    C6   N1   117.84  3.000
 36A  HN6   N6   C27  118.39  3.000
 36A  HN6   N6   C6   115.67  3.000
 36A  C27   N6   C6   125.19  3.000
 36A  C8    N7   C5   104.74  3.000
 36A  H8    C8   N9   122.15  3.000
 36A  H8    C8   N7   124.48  3.000
 36A  N9    C8   N7   113.36  3.000
 36A  C1'   N9   C8   128.97  3.000
 36A  C1'   N9   C4   124.79  3.000
 36A  C8    N9   C4   106.23  3.000
 36A  HA    CA   CB   107.17  3.000
 36A  HA    CA   N    113.62  3.000
 36A  CB    CA   N    110.75  3.000
 36A  HA    CA   C    105.21  3.000
 36A  CB    CA   C    107.40  3.000
 36A  N     CA   C    112.28  3.000
 36A  HBA   CB   HB   107.65  3.000
 36A  HBA   CB   CG   109.34  3.000
 36A  HB    CB   CG   109.74  3.000
 36A  HBA   CB   CA   108.40  3.000
 36A  HB    CB   CA   109.52  3.000
 36A  CG    CB   CA   112.07  3.000
 36A  HDA   CD   HD   107.81  3.000
 36A  HDA   CD   C4'  110.80  3.000
 36A  HD    CD   C4'  111.39  3.000
 36A  HDA   CD   SD   105.35  3.000
 36A  HD    CD   SD   109.28  3.000
 36A  C4'   CD   SD   111.95  3.000
 36A  CG    SD   CD   101.37  3.000
 36A  HGA   CG   HG   108.31  3.000
 36A  HGA   CG   SD   107.82  3.000
 36A  HG    CG   SD   110.13  3.000
 36A  HGA   CG   CB   111.56  3.000
 36A  HG    CG   CB   110.43  3.000
 36A  SD    CG   CB   108.56  3.000
 36A  H1'   C1'  O4'  110.69  3.000
 36A  H1'   C1'  C2'  111.18  3.000
 36A  O4'   C1'  C2'  106.99  3.000
 36A  H1'   C1'  N9   107.05  3.000
 36A  O4'   C1'  N9   109.12  3.000
 36A  C2'   C1'  N9   111.83  3.000
 36A  H2'   C2'  C3'  112.68  3.000
 36A  H2'   C2'  O2'  111.98  3.000
 36A  C3'   C2'  O2'  111.62  3.000
 36A  H2'   C2'  C1'  111.88  3.000
 36A  C3'   C2'  C1'  100.97  3.000
 36A  O2'   C2'  C1'  107.07  3.000
 36A  HO2'  O2'  C2'  108.45  3.000
 36A  H27A  C27  H27  106.43  3.000
 36A  H27A  C27  C28  109.12  3.000
 36A  H27   C27  C28  109.36  3.000
 36A  H27A  C27  N6   106.66  3.000
 36A  H27   C27  N6   110.33  3.000
 36A  C28   C27  N6   114.59  3.000
 36A  C33   C28  C29  119.22  3.000
 36A  C33   C28  C27  119.68  3.000
 36A  C29   C28  C27  121.07  3.000
 36A  H29   C29  C30  119.92  3.000
 36A  H29   C29  C28  120.55  3.000
 36A  C30   C29  C28  119.54  3.000
 36A  H3'   C3'  C4'  108.92  3.000
 36A  H3'   C3'  O3'  111.54  3.000
 36A  C4'   C3'  O3'  115.37  3.000
 36A  H3'   C3'  C2'  108.83  3.000
 36A  C4'   C3'  C2'  101.24  3.000
 36A  O3'   C3'  C2'  110.34  3.000
 36A  HO3'  O3'  C3'  107.71  3.000
 36A  CL34  C30  C31  119.29  3.000
 36A  CL34  C30  C29  118.97  3.000
 36A  C31   C30  C29  121.73  3.000
 36A  H31   C31  C32  120.80  3.000
 36A  H31   C31  C30  120.84  3.000
 36A  C32   C31  C30  118.36  3.000
 36A  H32   C32  C33  120.09  3.000
 36A  H32   C32  C31  119.31  3.000
 36A  C33   C32  C31  120.60  3.000
 36A  H33   C33  C32  119.79  3.000
 36A  H33   C33  C28  119.66  3.000
 36A  C32   C33  C28  120.55  3.000
 36A  H4'   C4'  O4'  109.02  3.000
 36A  H4'   C4'  C3'  109.63  3.000
 36A  O4'   C4'  C3'  104.42  3.000
 36A  H4'   C4'  CD   109.69  3.000
 36A  O4'   C4'  CD   108.99  3.000
 36A  C3'   C4'  CD   114.86  3.000
 36A  C4'   O4'  C1'  110.95  3.000
 36A  HOXT  OXT  C    109.51  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
 36A  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 36A  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 36A  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 36A  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 36A  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 36A  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 36A  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 36A  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 36A  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 36A  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 36A  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 36A  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 36A  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 36A  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 36A  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 36A  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 36A  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 36A  CONST_18  C31   C30  C29  C28     0.00   0.0  0
 36A  CONST_19  C31   C32  C33  C28     0.00   0.0  0
 36A  CONST_20  C32   C33  C28  C29     0.00   0.0  0
 36A  CONST_21  C32   C31  C30  C29     0.00   0.0  0
 36A  CONST_22  C33   C28  C29  C30     0.00   0.0  0
 36A  CONST_23  C33   C32  C31  C30     0.00   0.0  0
 36A  CONST_24  C1'   N9   C4   N3      0.00   0.0  0
 36A  CONST_25  C1'   N9   C4   C5    180.00   0.0  0
 36A  CONST_26  C1'   N9   C8   N7    180.00   0.0  0
 36A  CONST_27  N6    C6   N1   C2    180.00   0.0  0
 36A  CONST_28  N6    C6   C5   C4    180.00   0.0  0
 36A  CONST_29  N7    C5   C6   N6      0.00   0.0  0
 36A  CONST_30  C30   C29  C28  C27   180.00   0.0  0
 36A  CONST_31  C32   C33  C28  C27   180.00   0.0  0
 36A  CONST_32  CL34  C30  C29  C28   180.00   0.0  0
 36A  CONST_33  CL34  C30  C31  C32   180.00   0.0  0
 36A  CONST_34  H2    C2   N3   C4    180.00   0.0  0
 36A  CONST_35  H8    C8   N9   C4    180.00   0.0  0
 36A  CONST_36  H32   C32  C33  C28   180.00   0.0  0
 36A  CONST_37  H33   C33  C28  C29   180.00   0.0  0
 36A  CONST_38  H31   C31  C30  C29   180.00   0.0  0
 36A  CONST_39  H29   C29  C30  C31   180.00   0.0  0
 36A  CONST_40  C27   N6   C6   N1    180.00   0.0  0
 36A  CONST_41  C27   N6   C6   C5      0.00   0.0  0
 36A  CONST_42  HN6   N6   C6   N1      0.00   0.0  0
 36A  CONST_43  HOXT  OXT  C    O       0.00   0.0  0
 36A  Var_01    C28   C27  N6   C6    -70.18  30.0  3
 36A  Var_02    C29   C28  C27  N6    -29.22  30.0  2
 36A  Var_03    C4'   CD   SD   CG    -72.25  30.0  2
 36A  Var_04    SD    CG   CB   CA   -174.07  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
 36A  chir_01  CA   C    N    CB   negativ
 36A  chir_02  C1'  N9   C2'  O4'  negativ
 36A  chir_03  C2'  O2'  C1'  C3'  negativ
 36A  chir_04  C3'  O3'  C2'  C4'  negativ
 36A  chir_05  C4'  O4'  C3'  CD   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
 36A  plan-1  C27   0.020
 36A  plan-1  C28   0.020
 36A  plan-1  C29   0.020
 36A  plan-1  C30   0.020
 36A  plan-1  C31   0.020
 36A  plan-1  C32   0.020
 36A  plan-1  C33   0.020
 36A  plan-1  CL34  0.020
 36A  plan-1  H29   0.020
 36A  plan-1  H31   0.020
 36A  plan-1  H32   0.020
 36A  plan-1  H33   0.020
 36A  plan-2  N1    0.020
 36A  plan-2  C2    0.020
 36A  plan-2  N3    0.020
 36A  plan-2  C4    0.020
 36A  plan-2  C5    0.020
 36A  plan-2  C6    0.020
 36A  plan-2  N6    0.020
 36A  plan-2  N7    0.020
 36A  plan-2  C8    0.020
 36A  plan-2  N9    0.020
 36A  plan-2  C1'   0.020
 36A  plan-2  H2    0.020
 36A  plan-2  H8    0.020
 36A  plan-3  C6    0.020
 36A  plan-3  N6    0.020
 36A  plan-3  C27   0.020
 36A  plan-3  HN6   0.020
 36A  plan-4  C     0.020
 36A  plan-4  O     0.020
 36A  plan-4  CA    0.020
 36A  plan-4  OXT   0.020
 36A  plan-4  HOXT  0.020

