# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue May 26 18:53:27 2020
#   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  58  34  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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   0.388  -6.7102  -3.7931   0.7466
 36A  N     N   NH2    0  -0.787  -7.8731  -2.0159  -0.6472
 36A  O     O   O      0  -0.606  -7.8054  -3.9816   1.3117
 36A  N1    N   N      0  -0.475   3.5463   1.0835   1.5852
 36A  C2    C   CR16   0   0.041   3.1584   2.3159   1.2624
 36A  N3    N   N      0  -0.452   1.9803   2.7153   0.8191
 36A  C4    C   CR56   0   0.488   1.1223   1.7025   0.7148
 36A  C5    C   CR56   0  -0.012   1.3766   0.3744   1.0194
 36A  C6    C   CR6    0   0.514   2.6733   0.0800   1.4791
 36A  N6    N   NH1    0  -0.662   3.0489  -1.1607   1.8152
 36A  N7    N   N      0  -0.453   0.2632  -0.3958   0.8090
 36A  C8    C   CR15   0   0.110  -0.6363   0.4428   0.3842
 36A  N9    N   NR5    0  -0.540  -0.1793   1.7310   0.3051
 36A  CA    C   CH1    0  -0.212  -6.6044  -2.5885  -0.2234
 36A  CB    C   CH2    0  -0.419  -5.7340  -1.5069   0.4273
 36A  CD    C   CH2    0  -0.581  -3.8795   1.8535  -1.1254
 36A  SD    S   S2     0  -0.022  -4.4070   0.8833   0.3122
 36A  CG    C   CH2    0  -0.537  -5.3954  -0.3831  -0.5378
 36A  C1'   C   CH1    0   0.223  -0.9047   2.8945  -0.1510
 36A  C2'   C   CH1    0  -0.055  -1.0359   2.9814  -1.6741
 36A  O2'   O   OH1    0  -0.651   0.0763   3.6315  -2.2110
 36A  C27   C   CH2    0  -0.340   4.3825  -1.4906   2.2423
 36A  C28   C   CR6    0   0.097   5.4119  -1.4774   1.1358
 36A  C29   C   CR16   0  -0.248   5.0618  -1.8033  -0.1695
 36A  C3'   C   CH1    0  -0.013  -2.3597   3.7393  -1.8180
 36A  O3'   O   OH1    0  -0.668  -2.1863   5.1064  -1.5569
 36A  C30   C   CR6    0  -0.024   6.0381  -1.8278  -1.1525
 36A  C31   C   CR16   0  -0.232   7.3637  -1.5381  -0.8715
 36A  C32   C   CR16   0  -0.248   7.7051  -1.2138   0.4339
 36A  C33   C   CR16   0  -0.296   6.7386  -1.1800   1.4284
 36A  CL34  CL  CL     0  -0.134   5.5854  -2.2345  -2.7789
 36A  C4'   C   CH1    0  -0.005  -3.1634   3.1204  -0.6825
 36A  O4'   O   O2     0  -0.491  -2.2085   2.8504   0.3490
 36A  OXT   O   OC    -1  -0.622  -5.6677  -4.4623   0.9029
 36A  HN    H   HNH2   0   0.336  -8.3407  -2.6753  -1.2574
 36A  HNA   H   HNH2   0   0.324  -8.4715  -1.9600   0.1698
 36A  H2    H   HCR6   0   0.251   3.9125   3.0869   1.3782
 36A  HN6   H   HNH1   0   0.410   2.3734  -1.9002   1.7213
 36A  H8    H   HCR5   0   0.293  -1.6593   0.1881   0.1444
 36A  HA    H   HCH1   0   0.213  -6.0789  -2.9322  -1.1219
 36A  HB    H   HCH2   0   0.221  -6.2577  -1.1058   1.3028
 36A  HBA   H   HCH2   0   0.232  -4.8120  -1.9625   0.7926
 36A  HD    H   HCH2   0   0.264  -3.2457   1.2315  -1.7630
 36A  HDA   H   HCH2   0   0.288  -4.7538   2.1408  -1.7132
 36A  HG    H   HCH2   0   0.253  -4.8103  -0.7719  -1.3754
 36A  HGA   H   HCH2   0   0.261  -6.3027   0.0660  -0.9404
 36A  H1'   H   HCH1   0   0.265  -0.3594   3.7638   0.2312
 36A  H2'   H   HCH1   0   0.251  -1.1505   1.9720  -2.0892
 36A  HO2'  H   HOH1   0   0.470   0.1320   3.4270  -3.1500
 36A  H27   H   HCH2   0   0.262   4.7005  -0.8160   3.0392
 36A  H27A  H   HCH2   0   0.285   4.3382  -2.4894   2.6791
 36A  H29   H   HCR6   0   0.269   4.0343  -2.0324  -0.4208
 36A  H3'   H   HCH1   0   0.254  -2.8290   3.5623  -2.7946
 36A  HO3'  H   HOH1   0   0.450  -1.4038   5.4059  -2.0350
 36A  H31   H   HCR6   0   0.278   8.1127  -1.5600  -1.6509
 36A  H32   H   HCR6   0   0.267   8.7341  -0.9790   0.6716
 36A  H33   H   HCR6   0   0.256   7.0186  -0.9146   2.4406
 36A  H4'   H   HCH1   0   0.272  -3.8958   3.8232  -0.2778

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     deloc     1.247  0.020  1.247
 36A  C    CA    single    1.550  0.020  1.550
 36A  C    OXT   deloc     1.249  0.020  1.249
 36A  N    CA    single    1.455  0.020  1.455
 36A  N1   C2    aromatic  1.332  0.020  1.332
 36A  N1   C6    aromatic  1.334  0.020  1.334
 36A  C2   N3    aromatic  1.321  0.020  1.321
 36A  N3   C4    aromatic  1.331  0.020  1.331
 36A  C4   C5    aromatic  1.386  0.020  1.386
 36A  C4   N9    aromatic  1.365  0.020  1.365
 36A  C5   C6    aromatic  1.407  0.020  1.407
 36A  C5   N7    aromatic  1.370  0.020  1.370
 36A  C6   N6    single    1.339  0.020  1.339
 36A  N6   C27   single    1.439  0.020  1.439
 36A  N7   C8    aromatic  1.301  0.020  1.301
 36A  C8   N9    aromatic  1.369  0.020  1.369
 36A  N9   C1'   single    1.445  0.020  1.445
 36A  CA   CB    single    1.533  0.020  1.533
 36A  CB   CG    single    1.520  0.020  1.520
 36A  CD   SD    single    1.813  0.020  1.813
 36A  CD   C4'   single    1.521  0.020  1.521
 36A  SD   CG    single    1.818  0.020  1.818
 36A  C1'  C2'   single    1.531  0.020  1.531
 36A  C1'  O4'   single    1.397  0.020  1.397
 36A  C2'  O2'   single    1.396  0.020  1.396
 36A  C2'  C3'   single    1.532  0.020  1.532
 36A  C27  C28   single    1.511  0.020  1.511
 36A  C28  C29   aromatic  1.390  0.020  1.390
 36A  C28  C33   aromatic  1.391  0.020  1.391
 36A  C29  C30   aromatic  1.386  0.020  1.386
 36A  C3'  O3'   single    1.403  0.020  1.403
 36A  C3'  C4'   single    1.523  0.020  1.523
 36A  C30  C31   aromatic  1.386  0.020  1.386
 36A  C30  CL34  single    1.736  0.020  1.736
 36A  C31  C32   aromatic  1.388  0.020  1.388
 36A  C32  C33   aromatic  1.387  0.020  1.387
 36A  C4'  O4'   single    1.431  0.020  1.431
 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

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   115.97  3.000
 36A  OXT   C    O    126.56  3.000
 36A  CA    C    O    117.45  3.000
 36A  HNA   N    HN   104.41  3.000
 36A  HNA   N    CA   107.55  3.000
 36A  HN    N    CA   108.77  3.000
 36A  C6    N1   C2   119.09  3.000
 36A  H2    C2   N3   116.18  3.000
 36A  H2    C2   N1   115.43  3.000
 36A  N3    C2   N1   128.39  3.000
 36A  C4    N3   C2   111.79  3.000
 36A  N9    C4   C5   105.12  3.000
 36A  N9    C4   N3   128.48  3.000
 36A  C5    C4   N3   126.40  3.000
 36A  N7    C5   C6   132.96  3.000
 36A  N7    C5   C4   110.84  3.000
 36A  C6    C5   C4   116.19  3.000
 36A  N6    C6   C5   122.30  3.000
 36A  N6    C6   N1   119.56  3.000
 36A  C5    C6   N1   118.14  3.000
 36A  HN6   N6   C27  118.79  3.000
 36A  HN6   N6   C6   117.98  3.000
 36A  C27   N6   C6   123.16  3.000
 36A  C8    N7   C5   104.45  3.000
 36A  H8    C8   N9   121.64  3.000
 36A  H8    C8   N7   125.08  3.000
 36A  N9    C8   N7   113.24  3.000
 36A  C1'   N9   C8   127.46  3.000
 36A  C1'   N9   C4   126.18  3.000
 36A  C8    N9   C4   106.34  3.000
 36A  HA    CA   CB   107.27  3.000
 36A  HA    CA   N    107.62  3.000
 36A  CB    CA   N    109.94  3.000
 36A  HA    CA   C    107.58  3.000
 36A  CB    CA   C    108.74  3.000
 36A  N     CA   C    115.37  3.000
 36A  HBA   CB   HB   106.80  3.000
 36A  HBA   CB   CG   109.45  3.000
 36A  HB    CB   CG   110.07  3.000
 36A  HBA   CB   CA   109.10  3.000
 36A  HB    CB   CA   109.02  3.000
 36A  CG    CB   CA   112.25  3.000
 36A  HDA   CD   HD   107.45  3.000
 36A  HDA   CD   C4'  108.33  3.000
 36A  HD    CD   C4'  111.76  3.000
 36A  HDA   CD   SD   109.56  3.000
 36A  HD    CD   SD   109.07  3.000
 36A  C4'   CD   SD   110.60  3.000
 36A  CG    SD   CD    99.22  3.000
 36A  HGA   CG   HG   108.02  3.000
 36A  HGA   CG   SD   109.78  3.000
 36A  HG    CG   SD   108.37  3.000
 36A  HGA   CG   CB   110.73  3.000
 36A  HG    CG   CB   110.05  3.000
 36A  SD    CG   CB   109.84  3.000
 36A  H1'   C1'  O4'  111.40  3.000
 36A  H1'   C1'  C2'  110.17  3.000
 36A  O4'   C1'  C2'  106.13  3.000
 36A  H1'   C1'  N9   106.20  3.000
 36A  O4'   C1'  N9   109.27  3.000
 36A  C2'   C1'  N9   113.74  3.000
 36A  H2'   C2'  C3'  109.23  3.000
 36A  H2'   C2'  O2'  111.47  3.000
 36A  C3'   C2'  O2'  114.96  3.000
 36A  H2'   C2'  C1'  109.45  3.000
 36A  C3'   C2'  C1'  101.28  3.000
 36A  O2'   C2'  C1'  109.93  3.000
 36A  HO2'  O2'  C2'  108.81  3.000
 36A  H27A  C27  H27  106.57  3.000
 36A  H27A  C27  C28  109.19  3.000
 36A  H27   C27  C28  109.31  3.000
 36A  H27A  C27  N6   106.92  3.000
 36A  H27   C27  N6   110.19  3.000
 36A  C28   C27  N6   114.34  3.000
 36A  C33   C28  C29  119.20  3.000
 36A  C33   C28  C27  119.84  3.000
 36A  C29   C28  C27  120.92  3.000
 36A  H29   C29  C30  120.02  3.000
 36A  H29   C29  C28  120.45  3.000
 36A  C30   C29  C28  119.53  3.000
 36A  H3'   C3'  C4'  111.85  3.000
 36A  H3'   C3'  O3'  112.06  3.000
 36A  C4'   C3'  O3'  108.82  3.000
 36A  H3'   C3'  C2'  111.91  3.000
 36A  C4'   C3'  C2'  100.65  3.000
 36A  O3'   C3'  C2'  110.97  3.000
 36A  HO3'  O3'  C3'  108.09  3.000
 36A  CL34  C30  C31  119.23  3.000
 36A  CL34  C30  C29  119.01  3.000
 36A  C31   C30  C29  121.76  3.000
 36A  H31   C31  C32  120.83  3.000
 36A  H31   C31  C30  120.81  3.000
 36A  C32   C31  C30  118.36  3.000
 36A  H32   C32  C33  120.00  3.000
 36A  H32   C32  C31  119.42  3.000
 36A  C33   C32  C31  120.58  3.000
 36A  H33   C33  C32  119.72  3.000
 36A  H33   C33  C28  119.71  3.000
 36A  C32   C33  C28  120.57  3.000
 36A  H4'   C4'  O4'  107.55  3.000
 36A  H4'   C4'  C3'  111.63  3.000
 36A  O4'   C4'  C3'  105.19  3.000
 36A  H4'   C4'  CD   109.14  3.000
 36A  O4'   C4'  CD   111.51  3.000
 36A  C3'   C4'  CD   111.71  3.000
 36A  C4'   O4'  C1'  111.02  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     0.00   0.0  0
 36A  CONST_41  C27   N6   C6   C5   180.00   0.0  0
 36A  CONST_42  HN6   N6   C6   N1   180.00   0.0  0
 36A  Var_01    C28   C27  N6   C6   -72.75  30.0  3
 36A  Var_02    C29   C28  C27  N6   -30.98  30.0  2
 36A  Var_03    C4'   CD   SD   CG   172.52  30.0  2
 36A  Var_04    SD    CG   CB   CA   178.31  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

