# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 01:44:56 2022
#   Inital geometry file: a 106 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}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(N)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
 SAH  SAH  '(2S)-2-amino-4-({[(2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}sulfanyl)butanoic acid (non-preferred name)'  L-peptide  45  26  .  2012-03-26  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_SAH
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
 SAH  N     N  NH2    0  -0.818  -3.5244  13.3796  24.6282
 SAH  CA    C  CH1    0  -0.216  -3.3584  12.3436  25.6373
 SAH  CB    C  CH2    0  -0.394  -2.4087  11.2563  25.1371
 SAH  CG    C  CH2    0  -0.557  -2.9267  10.5878  23.8720
 SAH  SD    S  S2     0  -0.027  -1.7980   9.2426  23.3966
 SAH  C     C  C      0   0.415  -2.8719  12.9471  26.9840
 SAH  O     O  O      0  -0.598  -2.9932  14.1805  27.1251
 SAH  OXT   O  OC    -1  -0.602  -2.4370  12.1391  27.8264
 SAH  C5'   C  CH2    0  -0.596  -2.4381   8.7821  21.7683
 SAH  C4'   C  CH1    0   0.025  -3.8091   8.1207  21.8175
 SAH  O4'   O  O2     0  -0.490  -4.2556   7.8825  20.4750
 SAH  C3'   C  CH1    0  -0.030  -3.8278   6.7634  22.5117
 SAH  O3'   O  OH1    0  -0.664  -5.1132   6.5645  23.0453
 SAH  C2'   C  CH1    0  -0.031  -3.5556   5.8267  21.3409
 SAH  O2'   O  OH1    0  -0.654  -3.9511   4.5212  21.6240
 SAH  C1'   C  CH1    0   0.196  -4.3714   6.5064  20.2359
 SAH  N9    N  NR5    0  -0.542  -3.9181   6.2109  18.9019
 SAH  C8    C  CR15   0   0.108  -2.6846   6.4734  18.3664
 SAH  N7    N  N      0  -0.446  -2.5713   6.1058  17.1257
 SAH  C5    C  CR5    0  -0.010  -3.7955   5.5698  16.8156
 SAH  C6    C  C      0   0.458  -4.3216   4.9961  15.6434
 SAH  N6    N  NH2    0  -0.816  -3.6167   4.8748  14.5176
 SAH  N1    N  N      0  -0.472  -5.5874   4.5635  15.6713
 SAH  C2    C  C1     0   0.045  -6.2917   4.6919  16.7922
 SAH  N3    N  N      0  -0.454  -5.9098   5.2055  17.9485
 SAH  C4    C  CR5    0   0.488  -4.6499   5.6306  17.9049
 SAH  HN1   H  HNH2   0   0.335  -3.7562  14.2394  25.1086
 SAH  HN2   H  HNH2   0   0.332  -4.3006  13.1614  24.0183
 SAH  HA    H  HCH1   0   0.199  -4.3168  11.8485  25.8741
 SAH  HB1   H  HCH2   0   0.214  -1.4249  11.6936  24.9412
 SAH  HB2   H  HCH2   0   0.221  -2.2802  10.5068  25.9195
 SAH  HG1   H  HCH2   0   0.254  -3.9278  10.1871  24.0459
 SAH  HG2   H  HCH2   0   0.258  -2.9839  11.3005  23.0472
 SAH  H5'1  H  HCH2   0   0.287  -2.4798   9.6710  21.1351
 SAH  H5'2  H  HCH2   0   0.286  -1.6926   8.1115  21.3337
 SAH  H4'   H  HCH1   0   0.263  -4.5217   8.7975  22.2972
 SAH  H3'   H  HCH1   0   0.252  -3.0538   6.6909  23.2841
 SAH  HO3'  H  HOH1   0   0.452  -5.1756   5.6567  23.3609
 SAH  H2'   H  HCH1   0   0.246  -2.4867   5.8827  21.0918
 SAH  HO2'  H  HOH1   0   0.465  -3.5869   3.9275  20.9600
 SAH  H1'   H  HCH1   0   0.256  -5.4139   6.1735  20.2849
 SAH  H8    H  HCR5   0   0.301  -1.9061   6.9497  18.9446
 SAH  HN61  H  HNH2   0   0.402  -4.0203   4.4249  13.7141
 SAH  HN62  H  HNH2   0   0.410  -2.6514   5.1508  14.4759
 SAH  H2    H  H      0   0.250  -7.3114   4.3241  16.7463

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
 SAH  N    CA    single    1.458  0.019  1.458
 SAH  N    HN1   single    0.890  0.020  1.040
 SAH  N    HN2   single    0.890  0.020  1.040
 SAH  CA   CB    single    1.530  0.020  1.530
 SAH  CA   C     single    1.525  0.021  1.525
 SAH  CA   HA    single    0.970  0.020  0.970
 SAH  CB   CG    single    1.522  0.020  1.522
 SAH  CB   HB1   single    0.970  0.020  1.090
 SAH  CB   HB2   single    0.970  0.020  1.090
 SAH  CG   SD    single    1.819  0.020  1.819
 SAH  CG   HG1   single    0.970  0.020  1.090
 SAH  CG   HG2   single    0.970  0.020  1.090
 SAH  SD   C5'   single    1.809  0.020  1.809
 SAH  C    O     deloc     1.231  0.020  1.231
 SAH  C    OXT   deloc     1.246  0.020  1.246
 SAH  C5'  C4'   single    1.523  0.020  1.523
 SAH  C5'  H5'1  single    0.970  0.020  1.090
 SAH  C5'  H5'2  single    0.970  0.020  1.090
 SAH  C4'  O4'   single    1.435  0.020  1.435
 SAH  C4'  C3'   single    1.525  0.020  1.525
 SAH  C4'  H4'   single    0.970  0.020  1.090
 SAH  O4'  C1'   single    1.402  0.020  1.402
 SAH  C3'  O3'   single    1.406  0.020  1.406
 SAH  C3'  C2'   single    1.524  0.020  1.524
 SAH  C3'  H3'   single    0.970  0.020  1.090
 SAH  O3'  HO3'  single    0.850  0.020  0.980
 SAH  C2'  O2'   single    1.393  0.020  1.393
 SAH  C2'  C1'   single    1.532  0.020  1.532
 SAH  C2'  H2'   single    0.970  0.020  1.090
 SAH  O2'  HO2'  single    0.850  0.020  0.980
 SAH  C1'  N9    single    1.440  0.020  1.440
 SAH  C1'  H1'   single    0.970  0.020  1.090
 SAH  N9   C8    aromatic  1.370  0.020  1.370
 SAH  N9   C4    aromatic  1.366  0.020  1.366
 SAH  C8   N7    aromatic  1.299  0.020  1.299
 SAH  C8   H8    single    0.930  0.020  1.080
 SAH  N7   C5    aromatic  1.372  0.020  1.372
 SAH  C5   C6    aromatic  1.407  0.020  1.407
 SAH  C5   C4    aromatic  1.386  0.020  1.386
 SAH  C6   N6    single    1.334  0.020  1.334
 SAH  C6   N1    aromatic  1.338  0.020  1.338
 SAH  N6   HN61  single    0.860  0.020  1.020
 SAH  N6   HN62  single    0.860  0.020  1.020
 SAH  N1   C2    aromatic  1.330  0.020  1.330
 SAH  C2   N3    aromatic  1.322  0.020  1.322
 SAH  C2   H2    single    0.930  0.020  1.080
 SAH  N3   C4    aromatic  1.330  0.020  1.330

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
 SAH  HN2   N    HN1   107.09  3.000
 SAH  HN2   N    CA    110.62  3.000
 SAH  HN1   N    CA    107.56  3.000
 SAH  HA    CA   C     109.00  3.000
 SAH  HA    CA   CB    109.00  3.000
 SAH  C     CA   CB    110.10  1.900
 SAH  HA    CA   N     110.00  3.000
 SAH  C     CA   N     111.00  2.800
 SAH  CB    CA   N     110.50  1.700
 SAH  HB2   CB   HB1   107.28  3.000
 SAH  HB2   CB   CG    109.54  3.000
 SAH  HB1   CB   CG    109.43  3.000
 SAH  HB2   CB   CA    109.11  3.000
 SAH  HB1   CB   CA    109.46  3.000
 SAH  CG    CB   CA    111.91  3.000
 SAH  HG2   CG   HG1   108.17  3.000
 SAH  HG2   CG   SD    108.53  3.000
 SAH  HG1   CG   SD    109.82  3.000
 SAH  HG2   CG   CB    111.05  3.000
 SAH  HG1   CG   CB    109.93  3.000
 SAH  SD    CG   CB    109.32  3.000
 SAH  C5'   SD   CG    101.77  3.000
 SAH  OXT   C    O     126.79  3.000
 SAH  OXT   C    CA    116.32  3.000
 SAH  O     C    CA    120.80  1.700
 SAH  H5'2  C5'  H5'1  107.15  3.000
 SAH  H5'2  C5'  C4'   111.13  3.000
 SAH  H5'1  C5'  C4'   109.74  3.000
 SAH  H5'2  C5'  SD    105.83  3.000
 SAH  H5'1  C5'  SD    109.15  3.000
 SAH  C4'   C5'  SD    113.58  3.000
 SAH  H4'   C4'  C3'   110.07  3.000
 SAH  H4'   C4'  O4'   108.09  3.000
 SAH  C3'   C4'  O4'   105.93  3.000
 SAH  H4'   C4'  C5'   109.39  3.000
 SAH  C3'   C4'  C5'   114.35  3.000
 SAH  O4'   C4'  C5'   108.78  3.000
 SAH  C1'   O4'  C4'   110.39  3.000
 SAH  H3'   C3'  C2'   112.00  3.000
 SAH  H3'   C3'  O3'   111.65  3.000
 SAH  C2'   C3'  O3'   111.59  3.000
 SAH  H3'   C3'  C4'   111.79  3.000
 SAH  C2'   C3'  C4'   101.25  3.000
 SAH  O3'   C3'  C4'   108.06  3.000
 SAH  HO3'  O3'  C3'   108.48  3.000
 SAH  H2'   C2'  C1'   109.38  3.000
 SAH  H2'   C2'  O2'   111.71  3.000
 SAH  C1'   C2'  O2'   114.27  3.000
 SAH  H2'   C2'  C3'   108.46  3.000
 SAH  C1'   C2'  C3'   100.73  3.000
 SAH  O2'   C2'  C3'   111.66  3.000
 SAH  HO2'  O2'  C2'   109.30  3.000
 SAH  H1'   C1'  N9    106.18  3.000
 SAH  H1'   C1'  C2'   109.86  3.000
 SAH  N9    C1'  C2'   114.17  3.000
 SAH  H1'   C1'  O4'   111.68  3.000
 SAH  N9    C1'  O4'   109.49  3.000
 SAH  C2'   C1'  O4'   105.57  3.000
 SAH  C4    N9   C8    106.17  3.000
 SAH  C4    N9   C1'   126.49  3.000
 SAH  C8    N9   C1'   127.33  3.000
 SAH  H8    C8   N7    124.97  3.000
 SAH  H8    C8   N9    121.61  3.000
 SAH  N7    C8   N9    113.43  3.000
 SAH  C5    N7   C8    104.40  3.000
 SAH  C4    C5   C6    116.24  3.000
 SAH  C4    C5   N7    110.81  3.000
 SAH  C6    C5   N7    132.94  3.000
 SAH  N1    C6   N6    119.23  3.000
 SAH  N1    C6   C5    117.92  3.000
 SAH  N6    C6   C5    122.86  3.000
 SAH  HN62  N6   HN61  118.38  3.000
 SAH  HN62  N6   C6    121.19  3.000
 SAH  HN61  N6   C6    120.20  3.000
 SAH  C2    N1   C6    119.17  3.000
 SAH  H2    C2   N3    116.12  3.000
 SAH  H2    C2   N1    115.42  3.000
 SAH  N3    C2   N1    128.45  3.000
 SAH  C4    N3   C2    111.67  3.000
 SAH  N3    C4   C5    126.55  3.000
 SAH  N3    C4   N9    128.26  3.000
 SAH  C5    C4   N9    105.19  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
 SAH  CONST_01  C5    N7   C8  N9      0.00   0.0  0
 SAH  CONST_02  N7    C5   C4  N9      0.00   0.0  0
 SAH  CONST_03  C6    C5   C4  N9    180.00   0.0  0
 SAH  CONST_04  C2    N3   C4  N9    180.00   0.0  0
 SAH  CONST_05  C5    C4   N9  C8      0.00   0.0  0
 SAH  CONST_06  N3    C4   N9  C8    180.00   0.0  0
 SAH  CONST_07  C6    C5   N7  C8    180.00   0.0  0
 SAH  CONST_08  C4    C5   N7  C8      0.00   0.0  0
 SAH  CONST_09  C4    N9   C8  N7      0.00   0.0  0
 SAH  CONST_10  N1    C6   C5  N7    180.00   0.0  0
 SAH  CONST_11  N3    C4   C5  N7    180.00   0.0  0
 SAH  CONST_12  C2    N1   C6  C5      0.00   0.0  0
 SAH  CONST_13  C2    N3   C4  C5      0.00   0.0  0
 SAH  CONST_14  N3    C4   C5  C6      0.00   0.0  0
 SAH  CONST_15  N3    C2   N1  C6      0.00   0.0  0
 SAH  CONST_16  C4    C5   C6  N1      0.00   0.0  0
 SAH  CONST_17  C4    N3   C2  N1      0.00   0.0  0
 SAH  CONST_18  N7    C8   N9  C1'   180.00   0.0  0
 SAH  CONST_19  C5    C4   N9  C1'   180.00   0.0  0
 SAH  CONST_20  N3    C4   N9  C1'     0.00   0.0  0
 SAH  CONST_21  N6    C6   C5  N7      0.00   0.0  0
 SAH  CONST_22  C4    C5   C6  N6    180.00   0.0  0
 SAH  CONST_23  C2    N1   C6  N6    180.00   0.0  0
 SAH  CONST_24  H8    C8   N9  C1'     0.00   0.0  0
 SAH  CONST_25  H2    C2   N1  C6    180.00   0.0  0
 SAH  CONST_26  HN61  N6   C6  C5    180.00   0.0  0
 SAH  CONST_27  HN62  N6   C6  C5      0.00   0.0  0
 SAH  Var_01    C4'   C5'  SD  CG    -68.60  30.0  3
 SAH  Var_02    SD    CG   CB  CA   -176.59  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
 SAH  chir_01  CA   N    CB   C    negativ
 SAH  chir_02  C4'  O4'  C5'  C3'  positiv
 SAH  chir_03  C3'  O3'  C4'  C2'  positiv
 SAH  chir_04  C2'  O2'  C3'  C1'  positiv
 SAH  chir_05  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
 SAH  plan-1  C1'   0.020
 SAH  plan-1  N9    0.020
 SAH  plan-1  C8    0.020
 SAH  plan-1  N7    0.020
 SAH  plan-1  C5    0.020
 SAH  plan-1  C6    0.020
 SAH  plan-1  N6    0.020
 SAH  plan-1  N1    0.020
 SAH  plan-1  C2    0.020
 SAH  plan-1  N3    0.020
 SAH  plan-1  C4    0.020
 SAH  plan-1  H8    0.020
 SAH  plan-1  H2    0.020
 SAH  plan-2  C6    0.020
 SAH  plan-2  N6    0.020
 SAH  plan-2  HN61  0.020
 SAH  plan-2  HN62  0.020
 SAH  plan-3  CA    0.020
 SAH  plan-3  C     0.020
 SAH  plan-3  O     0.020
 SAH  plan-3  OXT   0.020

