# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:46:59 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio]-2-ammoniobutanoate 
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](C[S@+](CC[C@H]([NH3+])C([O-])=O)CC([O-])=O)[C@@H](O)[C@H]3O
#
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
 GEK  GEK  '(2S)-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(carboxylatomethyl)sulfonio]-2-ammoniobutanoate '  ligand  52  30  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GEK
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
 GEK  C     C  C      0   0.466  -6.0953  -2.5708   0.0546
 GEK  N     N  NT3    1  -0.848  -5.7254  -0.3109  -0.8469
 GEK  OXT   O  OC     0  -0.570  -5.6991  -3.7165   0.2881
 GEK  N1    N  N      0  -0.473   6.2473  -1.7099   0.9968
 GEK  C2    C  CR16   0   0.048   6.0558  -0.4106   1.2056
 GEK  N3    N  N      0  -0.457   5.0143   0.3311   0.8688
 GEK  C4    C  CR56   0   0.497   4.0826  -0.3852   0.2472
 GEK  C5    C  CR56   0  -0.011   4.1369  -1.7390  -0.0397
 GEK  C6    C  CR6    0   0.462   5.2995  -2.4171   0.3713
 GEK  N6    N  NH2    0  -0.815   5.4918  -3.7184   0.1523
 GEK  N7    N  N      0  -0.444   2.9963  -2.1477  -0.6833
 GEK  C8    C  CR15   0   0.121   2.2789  -1.0714  -0.7852
 GEK  N9    N  NR5    0  -0.542   2.8787   0.0364  -0.2450
 GEK  CA    C  CH1    0  -0.236  -5.0819  -1.6445  -0.6797
 GEK  CB    C  CH2    0  -0.479  -3.7785  -1.5182   0.0944
 GEK  SD    S  S3     1   0.406  -1.4762   0.0295   0.3378
 GEK  CE    C  CH2    0  -0.744  -2.3230   0.8933   1.6822
 GEK  CG    C  CH2    0  -0.561  -2.7418  -0.7426  -0.7119
 GEK  CZ    C  C      0   0.504  -3.5133   1.8229   1.3398
 GEK  C1'   C  CH1    0   0.211   2.3451   1.3662  -0.1553
 GEK  C2'   C  CH1    0  -0.051   2.0344   2.0151  -1.5042
 GEK  O2'   O  OH1    0  -0.649   3.1900   2.5912  -2.0264
 GEK  C3'   C  CH1    0  -0.016   0.9397   3.0128  -1.1079
 GEK  O3'   O  OH1    0  -0.661   1.4855   4.1263  -0.4587
 GEK  C4'   C  CH1    0  -0.011   0.1696   2.1917  -0.0784
 GEK  O4'   O  O2     0  -0.488   1.1206   1.3325   0.5375
 GEK  C5'   C  CH2   -1  -0.621  -0.9295   1.3740  -0.7435
 GEK  O     O  O     -1  -0.585  -7.1960  -2.0507   0.3232
 GEK  OZ1   O  O      0  -0.587  -4.0639   1.6741   0.2268
 GEK  OZ2   O  OC    -1  -0.536  -3.8068   2.6033   2.2416
 GEK  HN    H  HNT3   0   0.457  -5.8795  -0.0651  -1.8216
 GEK  HNA   H  HNT3   0   0.446  -6.6497  -0.4158  -0.3929
 GEK  HN6   H  HNH2   0   0.404   6.3007  -4.1788   0.5329
 GEK  HN6A  H  HNH2   0   0.412   4.7622  -4.2902  -0.2362
 GEK  H8    H  HCR5   0   0.282   1.3017  -1.0276  -1.2429
 GEK  HA    H  HCH1   0   0.308  -4.8913  -2.0500  -1.6748
 GEK  HB    H  HCH2   0   0.273  -3.9973  -1.0463   1.0534
 GEK  HBA   H  HCH2   0   0.302  -3.4063  -2.5161   0.3138
 GEK  HE    H  HCH2   0   0.351  -2.6424   0.1058   2.3693
 GEK  HEA   H  HCH2   0   0.343  -1.5255   1.4289   2.2008
 GEK  HG    H  HCH2   0   0.337  -2.1749  -1.4113  -1.3600
 GEK  HGA   H  HCH2   0   0.319  -3.1712   0.0459  -1.3215
 GEK  H1'   H  HCH1   0   0.276   3.0884   1.9586   0.3870
 GEK  H2'   H  HCH1   0   0.255   1.6090   1.2700  -2.1888
 GEK  HO2'  H  HOH1   0   0.473   3.0813   2.7087  -2.9756
 GEK  H3'   H  HCH1   0   0.269   0.3110   3.2993  -1.9612
 GEK  HO3'  H  HOH1   0   0.455   2.2253   4.4493  -0.9872
 GEK  H4'   H  HCH1   0   0.296  -0.2690   2.8405   0.6844
 GEK  H5'   H  HCH2   0   0.333  -0.5908   0.8801  -1.6572
 GEK  H5'A  H  HCH2   0   0.349  -1.7942   1.9915  -0.9863
 GEK  H22   H  HNT3   0   0.474  -5.2013   0.4691  -0.4007
 GEK  H2    H  HCR6   0   0.254   6.8612   0.1028   1.7196

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
 GEK  C    OXT   deloc     1.235  0.020  1.235
 GEK  C    CA    single    1.557  0.020  1.557
 GEK  C    O     deloc     1.247  0.020  1.247
 GEK  N    CA    single    1.490  0.020  1.490
 GEK  N    HN    single    0.890  0.020  1.040
 GEK  N    HNA   single    0.890  0.020  1.040
 GEK  N1   C2    aromatic  1.330  0.020  1.330
 GEK  N1   C6    aromatic  1.338  0.020  1.338
 GEK  C2   N3    aromatic  1.322  0.020  1.322
 GEK  C2   H2    single    0.930  0.020  1.080
 GEK  N3   C4    aromatic  1.330  0.020  1.330
 GEK  C4   C5    aromatic  1.385  0.020  1.385
 GEK  C4   N9    aromatic  1.367  0.020  1.367
 GEK  C5   C6    aromatic  1.407  0.020  1.407
 GEK  C5   N7    aromatic  1.372  0.020  1.372
 GEK  C6   N6    single    1.333  0.020  1.333
 GEK  N6   HN6   single    0.860  0.020  1.020
 GEK  N6   HN6A  single    0.860  0.020  1.020
 GEK  N7   C8    aromatic  1.297  0.020  1.297
 GEK  C8   N9    aromatic  1.371  0.020  1.371
 GEK  C8   H8    single    0.930  0.020  1.080
 GEK  N9   C1'   single    1.436  0.020  1.436
 GEK  CA   CB    single    1.521  0.020  1.521
 GEK  CA   HA    single    0.970  0.020  1.090
 GEK  CB   CG    single    1.525  0.020  1.525
 GEK  CB   HB    single    0.970  0.020  1.090
 GEK  CB   HBA   single    0.970  0.020  1.090
 GEK  SD   CE    single    1.808  0.020  1.808
 GEK  SD   CG    single    1.817  0.020  1.817
 GEK  SD   C5'   single    1.810  0.020  1.810
 GEK  CE   CZ    single    1.549  0.020  1.549
 GEK  CE   HE    single    0.970  0.020  1.090
 GEK  CE   HEA   single    0.970  0.020  1.090
 GEK  CG   HG    single    0.970  0.020  1.090
 GEK  CG   HGA   single    0.970  0.020  1.090
 GEK  CZ   OZ1   deloc     1.251  0.020  1.251
 GEK  CZ   OZ2   deloc     1.228  0.020  1.228
 GEK  C1'  C2'   single    1.529  0.020  1.529
 GEK  C1'  O4'   single    1.407  0.020  1.407
 GEK  C1'  H1'   single    0.970  0.020  1.090
 GEK  C2'  O2'   single    1.393  0.020  1.393
 GEK  C2'  C3'   single    1.533  0.020  1.533
 GEK  C2'  H2'   single    0.970  0.020  1.090
 GEK  O2'  HO2'  single    0.850  0.020  0.980
 GEK  C3'  O3'   single    1.400  0.020  1.400
 GEK  C3'  C4'   single    1.526  0.020  1.526
 GEK  C3'  H3'   single    0.970  0.020  1.090
 GEK  O3'  HO3'  single    0.850  0.020  0.980
 GEK  C4'  O4'   single    1.422  0.020  1.422
 GEK  C4'  C5'   single    1.523  0.020  1.523
 GEK  C4'  H4'   single    0.970  0.020  1.090
 GEK  C5'  H5'   single    0.970  0.020  1.090
 GEK  C5'  H5'A  single    0.970  0.020  1.090
 GEK  N    H22   single    0.890  0.020  1.040

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
 GEK  O     C    CA   115.35  3.000
 GEK  O     C    OXT  129.03  3.000
 GEK  CA    C    OXT  115.62  3.000
 GEK  H22   N    HNA  109.74  3.000
 GEK  H22   N    HN   107.83  3.000
 GEK  HNA   N    HN   108.04  3.000
 GEK  H22   N    CA   113.91  3.000
 GEK  HNA   N    CA   104.22  3.000
 GEK  HN    N    CA   112.91  3.000
 GEK  C6    N1   C2   119.20  3.000
 GEK  H2    C2   N3   116.11  3.000
 GEK  H2    C2   N1   115.46  3.000
 GEK  N3    C2   N1   128.43  3.000
 GEK  C4    N3   C2   111.65  3.000
 GEK  N9    C4   C5   105.15  3.000
 GEK  N9    C4   N3   128.26  3.000
 GEK  C5    C4   N3   126.59  3.000
 GEK  N7    C5   C6   132.86  3.000
 GEK  N7    C5   C4   110.84  3.000
 GEK  C6    C5   C4   116.29  3.000
 GEK  N6    C6   C5   122.78  3.000
 GEK  N6    C6   N1   119.37  3.000
 GEK  C5    C6   N1   117.85  3.000
 GEK  HN6A  N6   HN6  118.02  3.000
 GEK  HN6A  N6   C6   120.93  3.000
 GEK  HN6   N6   C6   120.04  3.000
 GEK  C8    N7   C5   104.45  3.000
 GEK  H8    C8   N9   122.02  3.000
 GEK  H8    C8   N7   124.56  3.000
 GEK  N9    C8   N7   113.42  3.000
 GEK  C1'   N9   C8   127.63  3.000
 GEK  C1'   N9   C4   126.18  3.000
 GEK  C8    N9   C4   106.14  3.000
 GEK  HA    CA   CB   110.20  3.000
 GEK  HA    CA   N    107.80  3.000
 GEK  CB    CA   N    110.66  3.000
 GEK  HA    CA   C    108.83  3.000
 GEK  CB    CA   C    111.53  3.000
 GEK  N     CA   C    107.71  3.000
 GEK  HBA   CB   HB   106.75  3.000
 GEK  HBA   CB   CG   109.91  3.000
 GEK  HB    CB   CG   112.40  3.000
 GEK  HBA   CB   CA   108.65  3.000
 GEK  HB    CB   CA   108.15  3.000
 GEK  CG    CB   CA   110.83  3.000
 GEK  C5'   SD   CG   100.43  3.000
 GEK  C5'   SD   CE   103.34  3.000
 GEK  CG    SD   CE   107.84  3.000
 GEK  HEA   CE   HE   105.57  3.000
 GEK  HEA   CE   CZ   111.84  3.000
 GEK  HE    CE   CZ   110.30  3.000
 GEK  HEA   CE   SD   104.21  3.000
 GEK  HE    CE   SD   105.08  3.000
 GEK  CZ    CE   SD   118.83  3.000
 GEK  HGA   CG   HG   108.51  3.000
 GEK  HGA   CG   SD   106.94  3.000
 GEK  HG    CG   SD   104.00  3.000
 GEK  HGA   CG   CB   113.42  3.000
 GEK  HG    CG   CB   110.84  3.000
 GEK  SD    CG   CB   112.59  3.000
 GEK  OZ2   CZ   OZ1  128.60  3.000
 GEK  OZ2   CZ   CE   113.75  3.000
 GEK  OZ1   CZ   CE   117.63  3.000
 GEK  H1'   C1'  O4'  111.10  3.000
 GEK  H1'   C1'  C2'  110.21  3.000
 GEK  O4'   C1'  C2'  105.53  3.000
 GEK  H1'   C1'  N9   106.26  3.000
 GEK  O4'   C1'  N9   109.39  3.000
 GEK  C2'   C1'  N9   114.43  3.000
 GEK  H2'   C2'  C3'  109.04  3.000
 GEK  H2'   C2'  O2'  111.63  3.000
 GEK  C3'   C2'  O2'  114.84  3.000
 GEK  H2'   C2'  C1'  109.93  3.000
 GEK  C3'   C2'  C1'  101.14  3.000
 GEK  O2'   C2'  C1'  109.74  3.000
 GEK  HO2'  O2'  C2'  109.05  3.000
 GEK  H3'   C3'  C4'  112.08  3.000
 GEK  H3'   C3'  O3'  112.10  3.000
 GEK  C4'   C3'  O3'  108.18  3.000
 GEK  H3'   C3'  C2'  112.19  3.000
 GEK  C4'   C3'  C2'  100.64  3.000
 GEK  O3'   C3'  C2'  111.05  3.000
 GEK  HO3'  O3'  C3'  108.14  3.000
 GEK  H4'   C4'  C5'  109.50  3.000
 GEK  H4'   C4'  O4'  108.95  3.000
 GEK  C5'   C4'  O4'  110.33  3.000
 GEK  H4'   C4'  C3'  110.73  3.000
 GEK  C5'   C4'  C3'  111.02  3.000
 GEK  O4'   C4'  C3'  106.26  3.000
 GEK  C4'   O4'  C1'  110.74  3.000
 GEK  H5'A  C5'  H5'  108.41  3.000
 GEK  H5'A  C5'  C4'  111.45  3.000
 GEK  H5'   C5'  C4'  112.60  3.000
 GEK  H5'A  C5'  SD   108.32  3.000
 GEK  H5'   C5'  SD   104.92  3.000
 GEK  C4'   C5'  SD   110.85  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
 GEK  CONST_01  C4    N3  C2  N1    0.00   0.0  0
 GEK  CONST_02  C4    C5  C6  N1    0.00   0.0  0
 GEK  CONST_03  N7    C5  C6  N1  180.00   0.0  0
 GEK  CONST_04  C5    C6  N1  C2    0.00   0.0  0
 GEK  CONST_05  C5    C4  N3  C2    0.00   0.0  0
 GEK  CONST_06  N9    C4  N3  C2  180.00   0.0  0
 GEK  CONST_07  C6    N1  C2  N3    0.00   0.0  0
 GEK  CONST_08  C6    C5  C4  N3    0.00   0.0  0
 GEK  CONST_09  N7    C5  C4  N3  180.00   0.0  0
 GEK  CONST_10  C8    N9  C4  N3  180.00   0.0  0
 GEK  CONST_11  C8    N7  C5  C4    0.00   0.0  0
 GEK  CONST_12  N7    C8  N9  C4    0.00   0.0  0
 GEK  CONST_13  C8    N9  C4  C5    0.00   0.0  0
 GEK  CONST_14  N9    C8  N7  C5    0.00   0.0  0
 GEK  CONST_15  N9    C4  C5  C6  180.00   0.0  0
 GEK  CONST_16  C8    N7  C5  C6  180.00   0.0  0
 GEK  CONST_17  N9    C4  C5  N7    0.00   0.0  0
 GEK  CONST_18  C1'   N9  C4  N3    0.00   0.0  0
 GEK  CONST_19  C1'   N9  C4  C5  180.00   0.0  0
 GEK  CONST_20  C1'   N9  C8  N7  180.00   0.0  0
 GEK  CONST_21  N6    C6  N1  C2  180.00   0.0  0
 GEK  CONST_22  N6    C6  C5  C4  180.00   0.0  0
 GEK  CONST_23  N7    C5  C6  N6    0.00   0.0  0
 GEK  CONST_24  H2    C2  N3  C4  180.00   0.0  0
 GEK  CONST_25  H8    C8  N9  C4  180.00   0.0  0
 GEK  CONST_26  HN6   N6  C6  N1    0.00   0.0  0
 GEK  CONST_27  HN6A  N6  C6  N1  180.00   0.0  0
 GEK  Var_01    SD    CG  CB  CA  156.23  30.0  3
 GEK  Var_02    OZ1   CZ  CE  SD   18.54  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
 GEK  chir_01  CA   C    N    CB   negativ
 GEK  chir_02  SD   C5'  CG   CE   positiv
 GEK  chir_03  C1'  O4'  N9   C2'  negativ
 GEK  chir_04  C2'  O2'  C1'  C3'  negativ
 GEK  chir_05  C3'  O3'  C2'  C4'  negativ
 GEK  chir_06  C4'  O4'  C3'  C5'  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
 GEK  plan-1  N1    0.020
 GEK  plan-1  C2    0.020
 GEK  plan-1  N3    0.020
 GEK  plan-1  C4    0.020
 GEK  plan-1  C5    0.020
 GEK  plan-1  C6    0.020
 GEK  plan-1  N6    0.020
 GEK  plan-1  N7    0.020
 GEK  plan-1  C8    0.020
 GEK  plan-1  N9    0.020
 GEK  plan-1  C1'   0.020
 GEK  plan-1  H8    0.020
 GEK  plan-1  H2    0.020
 GEK  plan-2  C6    0.020
 GEK  plan-2  N6    0.020
 GEK  plan-2  HN6   0.020
 GEK  plan-2  HN6A  0.020
 GEK  plan-3  C     0.020
 GEK  plan-3  OXT   0.020
 GEK  plan-3  CA    0.020
 GEK  plan-3  O     0.020
 GEK  plan-4  CE    0.020
 GEK  plan-4  CZ    0.020
 GEK  plan-4  OZ1   0.020
 GEK  plan-4  OZ2   0.020

