# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 19:08:49 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: (2S)-2-amino-4-[{[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)sulfonio]butanoate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S@@+](CC[C@H](N)C([O-])=O)C[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
 SAM  SAM  "S-ADENOSYLMETHIONINE"
  ligand  49  27  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_SAM
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
 SAM  N     N  NH2    0  -0.786  -26.7981  26.7796  46.4031
 SAM  CA    C  CH1    0  -0.203  -27.9888  27.0275  45.6128
 SAM  C     C  C      0   0.425  -29.2111  26.2515  46.1464
 SAM  O     O  O      0  -0.573  -29.0034  25.2538  46.8532
 SAM  OXT   O  OC    -1  -0.603  -30.3268  26.6842  45.7661
 SAM  CB    C  CH2    0  -0.461  -27.7860  26.7024  44.1192
 SAM  CG    C  CH2    0  -0.571  -29.0298  26.7754  43.2491
 SAM  SD    S  S3     1   0.399  -29.9452  28.3173  43.5579
 SAM  CE    C  CH3    0  -0.754  -31.5960  27.8945  42.9973
 SAM  C5'   C  CH2   -1  -0.627  -29.3171  29.3250  42.1900
 SAM  C4'   C  CH1    0   0.049  -29.7831  30.7621  42.2909
 SAM  O4'   O  O2     0  -0.487  -29.5797  31.2383  43.6103
 SAM  C3'   C  CH1    0   0.017  -28.9720  31.6930  41.3870
 SAM  O3'   O  OH1    0  -0.653  -29.4996  31.6797  40.0983
 SAM  C2'   C  CH1    0  -0.066  -29.0715  33.0213  42.1435
 SAM  O2'   O  OH1    0  -0.654  -30.2906  33.6222  41.8100
 SAM  C1'   C  CH1    0   0.170  -29.0876  32.5469  43.6096
 SAM  N9    N  NR5    0  -0.537  -27.7997  32.5880  44.2793
 SAM  C8    C  CR15   0   0.114  -27.4398  33.5529  45.1828
 SAM  N7    N  N      0  -0.447  -26.2471  33.3963  45.6698
 SAM  C5    C  CR56   0  -0.006  -25.7866  32.2576  45.0640
 SAM  C6    C  CR6    0   0.459  -24.5774  31.5482  45.1860
 SAM  N6    N  NH2    0  -0.815  -23.5888  31.9458  45.9870
 SAM  N1    N  N      0  -0.469  -24.4255  30.4361  44.4594
 SAM  C2    C  CR16   0   0.049  -25.4123  30.0542  43.6552
 SAM  N3    N  N      0  -0.467  -26.5845  30.6322  43.4592
 SAM  C4    C  CR56   0   0.508  -26.7321  31.7352  44.1927
 SAM  HN1   H  HNH2   0   0.335  -25.9918  27.1857  45.9427
 SAM  HN2   H  HNH2   0   0.329  -26.6331  25.7818  46.4487
 SAM  HA    H  HCH1   0   0.224  -28.2127  28.0973  45.6909
 SAM  HB1   H  HCH2   0   0.257  -27.0143  27.3634  43.7152
 SAM  HB2   H  HCH2   0   0.261  -27.4013  25.6829  44.0217
 SAM  HG1   H  HCH2   0   0.318  -28.7901  26.7445  42.1860
 SAM  HG2   H  HCH2   0   0.320  -29.7343  25.9760  43.4646
 SAM  HE1   H  HCH3   0   0.315  -32.1895  28.8056  42.9719
 SAM  HE2   H  HCH3   0   0.304  -31.5536  27.4355  42.0125
 SAM  HE3   H  HCH3   0   0.317  -32.0092  27.2082  43.7314
 SAM  H5'1  H  HCH2   0   0.338  -28.2316  29.2761  42.2948
 SAM  H5'2  H  HCH2   0   0.325  -29.6162  28.8789  41.2406
 SAM  H4'   H  HCH1   0   0.265  -30.8471  30.8352  42.0322
 SAM  H3'   H  HCH1   0   0.248  -27.9231  31.3739  41.4026
 SAM  HO3'  H  HOH1   0   0.461  -28.8573  32.0661  39.4952
 SAM  H2'   H  HCH1   0   0.265  -28.2182  33.6825  41.9520
 SAM  HO2'  H  HOH1   0   0.460  -30.3398  34.4814  42.2427
 SAM  H1'   H  HCH1   0   0.281  -29.7406  33.1966  44.2007
 SAM  H8    H  HCR5   0   0.299  -28.1205  34.3523  45.4390
 SAM  HN61  H  HNH2   0   0.403  -22.7557  31.3898  46.0769
 SAM  HN62  H  HNH2   0   0.411  -23.6906  32.7532  46.5767
 SAM  H2    H  HCR6   0   0.251  -25.2292  29.1474  43.0882

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
 SAM  N    CA    single    1.451  0.020  1.451
 SAM  N    HN1   single    0.890  0.020  1.040
 SAM  N    HN2   single    0.890  0.020  1.040
 SAM  CA   C     single    1.543  0.020  1.543
 SAM  CA   CB    single    1.542  0.020  1.542
 SAM  CA   HA    single    0.970  0.020  1.090
 SAM  C    O     deloc     1.240  0.020  1.240
 SAM  C    OXT   deloc     1.256  0.020  1.256
 SAM  CB   CG    single    1.520  0.020  1.520
 SAM  CB   HB1   single    0.970  0.020  1.090
 SAM  CB   HB2   single    0.970  0.020  1.090
 SAM  CG   SD    single    1.820  0.020  1.820
 SAM  CG   HG1   single    0.970  0.020  1.090
 SAM  CG   HG2   single    0.970  0.020  1.090
 SAM  SD   CE    single    1.794  0.020  1.794
 SAM  SD   C5'   single    1.811  0.020  1.811
 SAM  CE   HE1   single    0.970  0.020  1.090
 SAM  CE   HE2   single    0.970  0.020  1.090
 SAM  CE   HE3   single    0.970  0.020  1.090
 SAM  C5'  C4'   single    1.514  0.020  1.514
 SAM  C5'  H5'1  single    0.970  0.020  1.090
 SAM  C5'  H5'2  single    0.970  0.020  1.090
 SAM  C4'  O4'   single    1.417  0.020  1.417
 SAM  C4'  C3'   single    1.530  0.020  1.530
 SAM  C4'  H4'   single    0.970  0.020  1.090
 SAM  O4'  C1'   single    1.398  0.020  1.398
 SAM  C3'  O3'   single    1.393  0.020  1.393
 SAM  C3'  C2'   single    1.532  0.020  1.532
 SAM  C3'  H3'   single    0.970  0.020  1.090
 SAM  O3'  HO3'  single    0.850  0.020  0.980
 SAM  C2'  O2'   single    1.400  0.020  1.400
 SAM  C2'  C1'   single    1.541  0.020  1.541
 SAM  C2'  H2'   single    0.970  0.020  1.090
 SAM  O2'  HO2'  single    0.850  0.020  0.980
 SAM  C1'  N9    single    1.452  0.020  1.452
 SAM  C1'  H1'   single    0.970  0.020  1.090
 SAM  N9   C8    aromatic  1.370  0.020  1.370
 SAM  N9   C4    aromatic  1.369  0.020  1.369
 SAM  C8   N7    aromatic  1.298  0.020  1.298
 SAM  C8   H8    single    0.930  0.020  1.080
 SAM  N7   C5    aromatic  1.370  0.020  1.370
 SAM  C5   C6    aromatic  1.407  0.020  1.407
 SAM  C5   C4    aromatic  1.388  0.020  1.388
 SAM  C6   N6    single    1.333  0.020  1.333
 SAM  C6   N1    aromatic  1.337  0.020  1.337
 SAM  N6   HN61  single    0.860  0.020  1.020
 SAM  N6   HN62  single    0.860  0.020  1.020
 SAM  N1   C2    aromatic  1.329  0.020  1.329
 SAM  C2   N3    aromatic  1.322  0.020  1.322
 SAM  C2   H2    single    0.930  0.020  1.080
 SAM  N3   C4    aromatic  1.333  0.020  1.333

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
 SAM  HN2   N    HN1   106.61  3.000
 SAM  HN2   N    CA    109.07  3.000
 SAM  HN1   N    CA    109.70  3.000
 SAM  HA    CA   CB    107.56  3.000
 SAM  HA    CA   C     107.73  3.000
 SAM  CB    CA   C     109.46  3.000
 SAM  HA    CA   N     107.21  3.000
 SAM  CB    CA   N     112.57  3.000
 SAM  C     CA   N     112.08  3.000
 SAM  OXT   C    O     126.77  3.000
 SAM  OXT   C    CA    115.20  3.000
 SAM  O     C    CA    117.97  3.000
 SAM  HB2   CB   HB1   106.39  3.000
 SAM  HB2   CB   CG    106.35  3.000
 SAM  HB1   CB   CG    109.70  3.000
 SAM  HB2   CB   CA    109.21  3.000
 SAM  HB1   CB   CA    108.86  3.000
 SAM  CG    CB   CA    115.90  3.000
 SAM  HG2   CG   HG1   108.35  3.000
 SAM  HG2   CG   SD    105.28  3.000
 SAM  HG1   CG   SD    107.46  3.000
 SAM  HG2   CG   CB    112.43  3.000
 SAM  HG1   CG   CB    112.15  3.000
 SAM  SD    CG   CB    110.81  3.000
 SAM  C5'   SD   CE    102.37  3.000
 SAM  C5'   SD   CG     99.72  3.000
 SAM  CE    SD   CG    102.13  3.000
 SAM  HE3   CE   HE2   111.11  3.000
 SAM  HE3   CE   HE1   109.71  3.000
 SAM  HE2   CE   HE1   110.71  3.000
 SAM  HE3   CE   SD    106.72  3.000
 SAM  HE2   CE   SD    110.28  3.000
 SAM  HE1   CE   SD    108.18  3.000
 SAM  H5'2  C5'  H5'1  109.75  3.000
 SAM  H5'2  C5'  C4'   111.21  3.000
 SAM  H5'1  C5'  C4'   110.01  3.000
 SAM  H5'2  C5'  SD    109.55  3.000
 SAM  H5'1  C5'  SD    104.32  3.000
 SAM  C4'   C5'  SD    111.77  3.000
 SAM  H4'   C4'  C3'   109.52  3.000
 SAM  H4'   C4'  O4'   109.65  3.000
 SAM  C3'   C4'  O4'   105.63  3.000
 SAM  H4'   C4'  C5'   110.24  3.000
 SAM  C3'   C4'  C5'   112.02  3.000
 SAM  O4'   C4'  C5'   109.68  3.000
 SAM  C1'   O4'  C4'   111.38  3.000
 SAM  H3'   C3'  C2'   107.90  3.000
 SAM  H3'   C3'  O3'   111.89  3.000
 SAM  C2'   C3'  O3'   116.14  3.000
 SAM  H3'   C3'  C4'   108.76  3.000
 SAM  C2'   C3'  C4'   101.62  3.000
 SAM  O3'   C3'  C4'   109.88  3.000
 SAM  HO3'  O3'  C3'   108.86  3.000
 SAM  H2'   C2'  C1'   111.10  3.000
 SAM  H2'   C2'  O2'   112.18  3.000
 SAM  C1'   C2'  O2'   110.47  3.000
 SAM  H2'   C2'  C3'   112.72  3.000
 SAM  C1'   C2'  C3'   101.74  3.000
 SAM  O2'   C2'  C3'   108.13  3.000
 SAM  HO2'  O2'  C2'   108.69  3.000
 SAM  H1'   C1'  N9    105.26  3.000
 SAM  H1'   C1'  C2'   109.71  3.000
 SAM  N9    C1'  C2'   114.88  3.000
 SAM  H1'   C1'  O4'   110.21  3.000
 SAM  N9    C1'  O4'   109.78  3.000
 SAM  C2'   C1'  O4'   107.00  3.000
 SAM  C4    N9   C8    106.00  3.000
 SAM  C4    N9   C1'   130.15  3.000
 SAM  C8    N9   C1'   123.85  3.000
 SAM  H8    C8   N7    125.39  3.000
 SAM  H8    C8   N9    120.78  3.000
 SAM  N7    C8   N9    113.82  3.000
 SAM  C5    N7   C8    104.09  3.000
 SAM  C4    C5   C6    116.75  3.000
 SAM  C4    C5   N7    111.19  3.000
 SAM  C6    C5   N7    132.05  3.000
 SAM  N1    C6   N6    119.36  3.000
 SAM  N1    C6   C5    118.02  3.000
 SAM  N6    C6   C5    122.61  3.000
 SAM  HN62  N6   HN61  118.41  3.000
 SAM  HN62  N6   C6    121.13  3.000
 SAM  HN61  N6   C6    120.21  3.000
 SAM  C2    N1   C6    118.91  3.000
 SAM  H2    C2   N3    115.96  3.000
 SAM  H2    C2   N1    115.53  3.000
 SAM  N3    C2   N1    128.51  3.000
 SAM  C4    N3   C2    112.25  3.000
 SAM  N3    C4   C5    125.56  3.000
 SAM  N3    C4   N9    129.55  3.000
 SAM  C5    C4   N9    104.90  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
 SAM  CONST_01  C5    N7  C8  N9     0.00   0.0  0
 SAM  CONST_02  N7    C5  C4  N9     0.00   0.0  0
 SAM  CONST_03  C6    C5  C4  N9   180.00   0.0  0
 SAM  CONST_04  C2    N3  C4  N9   180.00   0.0  0
 SAM  CONST_05  C5    C4  N9  C8     0.00   0.0  0
 SAM  CONST_06  N3    C4  N9  C8   180.00   0.0  0
 SAM  CONST_07  C6    C5  N7  C8   180.00   0.0  0
 SAM  CONST_08  C4    C5  N7  C8     0.00   0.0  0
 SAM  CONST_09  C4    N9  C8  N7     0.00   0.0  0
 SAM  CONST_10  N1    C6  C5  N7   180.00   0.0  0
 SAM  CONST_11  N3    C4  C5  N7   180.00   0.0  0
 SAM  CONST_12  C2    N1  C6  C5     0.00   0.0  0
 SAM  CONST_13  C2    N3  C4  C5     0.00   0.0  0
 SAM  CONST_14  N3    C4  C5  C6     0.00   0.0  0
 SAM  CONST_15  N3    C2  N1  C6     0.00   0.0  0
 SAM  CONST_16  C4    C5  C6  N1     0.00   0.0  0
 SAM  CONST_17  C4    N3  C2  N1     0.00   0.0  0
 SAM  CONST_18  N7    C8  N9  C1'  180.00   0.0  0
 SAM  CONST_19  C5    C4  N9  C1'  180.00   0.0  0
 SAM  CONST_20  N3    C4  N9  C1'    0.00   0.0  0
 SAM  CONST_21  N6    C6  C5  N7     0.00   0.0  0
 SAM  CONST_22  C4    C5  C6  N6   180.00   0.0  0
 SAM  CONST_23  C2    N1  C6  N6   180.00   0.0  0
 SAM  CONST_24  H8    C8  N9  C1'    0.00   0.0  0
 SAM  CONST_25  H8    C8  N7  C5   180.00   0.0  0
 SAM  CONST_26  H2    C2  N1  C6   180.00   0.0  0
 SAM  CONST_27  H8    C8  N9  C4   180.00   0.0  0
 SAM  CONST_28  H2    C2  N3  C4   180.00   0.0  0
 SAM  CONST_29  HN61  N6  C6  C5   180.00   0.0  0
 SAM  CONST_30  HN62  N6  C6  C5     0.00   0.0  0
 SAM  CONST_31  HN61  N6  C6  N1     0.00   0.0  0
 SAM  CONST_32  HN62  N6  C6  N1   180.00   0.0  0
 SAM  Var_01    SD    CG  CB  CA    47.84  30.0  3
 SAM  Var_02    HG1   CG  CB  CA   167.93  30.0  3
 SAM  Var_03    HG2   CG  CB  CA   -69.67  30.0  3
 SAM  Var_04    HB1   CB  CG  SD   -75.91  30.0  2
 SAM  Var_05    HB2   CB  CG  SD   169.42  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
 SAM  chir_01  CA   N    C    CB   positiv
 SAM  chir_02  SD   C5'  CE   CG   negativ
 SAM  chir_03  C4'  O4'  C3'  C5'  negativ
 SAM  chir_04  C3'  O3'  C4'  C2'  positiv
 SAM  chir_05  C2'  O2'  C3'  C1'  positiv
 SAM  chir_06  C1'  O4'  N9   C2'  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
 SAM  plan-1  C1'   0.020
 SAM  plan-1  N9    0.020
 SAM  plan-1  C8    0.020
 SAM  plan-1  N7    0.020
 SAM  plan-1  C5    0.020
 SAM  plan-1  C6    0.020
 SAM  plan-1  N6    0.020
 SAM  plan-1  N1    0.020
 SAM  plan-1  C2    0.020
 SAM  plan-1  N3    0.020
 SAM  plan-1  C4    0.020
 SAM  plan-1  H8    0.020
 SAM  plan-1  H2    0.020
 SAM  plan-2  C6    0.020
 SAM  plan-2  N6    0.020
 SAM  plan-2  HN61  0.020
 SAM  plan-2  HN62  0.020
 SAM  plan-3  CA    0.020
 SAM  plan-3  C     0.020
 SAM  plan-3  O     0.020
 SAM  plan-3  OXT   0.020

