# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:52:03 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5'-S-(3-aminopropyl)-5'-thioadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCSC[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
 DSH  DSH  5'-S-(3-aminopropyl)-5'-thioadenosine  ligand  43  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DSH
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
 DSH  N     N  NH2   0  -0.799   6.6522  -3.2831   0.0060
 DSH  N1    N  N     0  -0.475  -4.8157  -1.7156  -0.3454
 DSH  C2    C  CR16  0   0.042  -4.7464  -0.4082  -0.5831
 DSH  N3    N  N     0  -0.454  -3.6819   0.3746  -0.5710
 DSH  C4    C  CR56  0   0.489  -2.5746  -0.3054  -0.2820
 DSH  C5    C  CR56  0  -0.011  -2.4870  -1.6634  -0.0180
 DSH  C6    C  CR6   0   0.458  -3.6942  -2.3850  -0.0567
 DSH  N6    N  NH2   0  -0.817  -3.7587  -3.6955   0.1825
 DSH  N7    N  N     0  -0.452  -1.1889  -2.0305   0.2238
 DSH  C8    C  CR15  0   0.108  -0.5127  -0.9249   0.1147
 DSH  N9    N  NR5   0  -0.541  -1.2940   0.1580  -0.1904
 DSH  CA    C  CH2   0  -0.267   6.0894  -2.0785   0.5968
 DSH  CB    C  CH2   0  -0.433   4.9615  -1.5339  -0.2697
 DSH  SD    S  S2    0  -0.013   2.9965   0.3145  -0.7245
 DSH  CG    C  CH2   0  -0.549   4.3496  -0.2781   0.3313
 DSH  C1'   C  CH1   0   0.224  -0.8728   1.5310  -0.3478
 DSH  C2'   C  CH1   0  -0.055  -0.6270   2.2572   0.9779
 DSH  O2'   O  OH1   0  -0.651  -1.8177   2.8205   1.4392
 DSH  C3'   C  CH1   0  -0.013   0.4483   3.2690   0.5688
 DSH  O3'   O  OH1   0  -0.668  -0.1174   4.3388  -0.1402
 DSH  C4'   C  CH1   0  -0.007   1.2784   2.4254  -0.3892
 DSH  O4'   O  O2    0  -0.491   0.3396   1.5651  -1.0415
 DSH  C5'   C  CH2   0  -0.580   2.3478   1.6286   0.3423
 DSH  HN    H  HNH2  0   0.348   7.4326  -3.5993   0.5673
 DSH  HNA   H  HNH2  0   0.339   5.9679  -4.0283   0.0518
 DSH  HN6   H  HNH2  0   0.403  -4.6399  -4.1768   0.1386
 DSH  HN6A  H  HNH2  0   0.411  -2.9331  -4.2268   0.3949
 DSH  H8    H  HCR5  0   0.292   0.5613  -0.8436   0.2104
 DSH  HA    H  HCH2  0   0.193   5.7127  -2.2242   1.6197
 DSH  HB    H  HCH2  0   0.232   5.3467  -1.3240  -1.2709
 DSH  HG    H  HCH2  0   0.260   3.9496  -0.4882   1.3257
 DSH  HGA   H  HCH2  0   0.260   5.1018   0.5074   0.4304
 DSH  H1'   H  HCH1  0   0.264  -1.6684   2.0321  -0.9097
 DSH  H2'   H  HCH1  0   0.252  -0.2033   1.5566   1.7075
 DSH  HO2'  H  HOH1  0   0.470  -1.7359   2.9915   2.3826
 DSH  H3'   H  HCH1  0   0.254   1.0408   3.6123   1.4272
 DSH  HO3'  H  HOH1  0   0.450  -0.9028   4.6296   0.3384
 DSH  H4'   H  HCH1  0   0.273   1.7532   3.0413  -1.1571
 DSH  H5'   H  HCH2  0   0.266   1.9690   1.1848   1.2670
 DSH  H5'A  H  HCH2  0   0.289   3.1578   2.3085   0.6141
 DSH  HAA   H  HCH2  0   0.218   6.8817  -1.3287   0.6663
 DSH  HBA   H  HCH2  0   0.229   4.1860  -2.2984  -0.3793
 DSH  H2    H  HCR6  0   0.251  -5.6904   0.0732  -0.8157

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
 DSH  N    CA    single    1.455  0.020  1.455
 DSH  N1   C2    aromatic  1.331  0.020  1.331
 DSH  N1   C6    aromatic  1.338  0.020  1.338
 DSH  C2   N3    aromatic  1.321  0.020  1.321
 DSH  N3   C4    aromatic  1.331  0.020  1.331
 DSH  C4   C5    aromatic  1.386  0.020  1.386
 DSH  C4   N9    aromatic  1.365  0.020  1.365
 DSH  C5   C6    aromatic  1.407  0.020  1.407
 DSH  C5   N7    aromatic  1.371  0.020  1.371
 DSH  C6   N6    single    1.334  0.020  1.334
 DSH  N7   C8    aromatic  1.301  0.020  1.301
 DSH  C8   N9    aromatic  1.370  0.020  1.370
 DSH  N9   C1'   single    1.445  0.020  1.445
 DSH  CA   CB    single    1.523  0.020  1.523
 DSH  CB   CG    single    1.521  0.020  1.521
 DSH  SD   CG    single    1.816  0.020  1.816
 DSH  SD   C5'   single    1.813  0.020  1.813
 DSH  C1'  C2'   single    1.531  0.020  1.531
 DSH  C1'  O4'   single    1.397  0.020  1.397
 DSH  C2'  O2'   single    1.396  0.020  1.396
 DSH  C2'  C3'   single    1.532  0.020  1.532
 DSH  C3'  O3'   single    1.403  0.020  1.403
 DSH  C3'  C4'   single    1.523  0.020  1.523
 DSH  C4'  O4'   single    1.431  0.020  1.431
 DSH  C4'  C5'   single    1.521  0.020  1.521
 DSH  N    HN    single    0.890  0.020  1.040
 DSH  N    HNA   single    0.890  0.020  1.040
 DSH  C2   H2    single    0.930  0.020  1.080
 DSH  N6   HN6   single    0.860  0.020  1.020
 DSH  N6   HN6A  single    0.860  0.020  1.020
 DSH  C8   H8    single    0.930  0.020  1.080
 DSH  CA   HA    single    0.970  0.020  1.090
 DSH  CB   HB    single    0.970  0.020  1.090
 DSH  CG   HG    single    0.970  0.020  1.090
 DSH  CG   HGA   single    0.970  0.020  1.090
 DSH  C1'  H1'   single    0.970  0.020  1.090
 DSH  C2'  H2'   single    0.970  0.020  1.090
 DSH  O2'  HO2'  single    0.850  0.020  0.980
 DSH  C3'  H3'   single    0.970  0.020  1.090
 DSH  O3'  HO3'  single    0.850  0.020  0.980
 DSH  C4'  H4'   single    0.970  0.020  1.090
 DSH  C5'  H5'   single    0.970  0.020  1.090
 DSH  C5'  H5'A  single    0.970  0.020  1.090
 DSH  CA   HAA   single    0.970  0.020  1.090
 DSH  CB   HBA   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
 DSH  HNA   N    HN   105.43  3.000
 DSH  HNA   N    CA   109.23  3.000
 DSH  HN    N    CA   109.37  3.000
 DSH  C6    N1   C2   119.11  3.000
 DSH  H2    C2   N3   116.11  3.000
 DSH  H2    C2   N1   115.40  3.000
 DSH  N3    C2   N1   128.49  3.000
 DSH  C4    N3   C2   111.68  3.000
 DSH  N9    C4   C5   105.10  3.000
 DSH  N9    C4   N3   128.43  3.000
 DSH  C5    C4   N3   126.46  3.000
 DSH  N7    C5   C6   132.86  3.000
 DSH  N7    C5   C4   110.85  3.000
 DSH  C6    C5   C4   116.30  3.000
 DSH  N6    C6   C5   122.72  3.000
 DSH  N6    C6   N1   119.33  3.000
 DSH  C5    C6   N1   117.95  3.000
 DSH  HN6A  N6   HN6  118.46  3.000
 DSH  HN6A  N6   C6   121.19  3.000
 DSH  HN6   N6   C6   120.34  3.000
 DSH  C8    N7   C5   104.47  3.000
 DSH  H8    C8   N9   121.79  3.000
 DSH  H8    C8   N7   124.95  3.000
 DSH  N9    C8   N7   113.22  3.000
 DSH  C1'   N9   C8   127.54  3.000
 DSH  C1'   N9   C4   126.07  3.000
 DSH  C8    N9   C4   106.36  3.000
 DSH  HAA   CA   HA   106.26  3.000
 DSH  HAA   CA   CB   109.13  3.000
 DSH  HA    CA   CB   108.84  3.000
 DSH  HAA   CA   N    108.26  3.000
 DSH  HA    CA   N    113.61  3.000
 DSH  CB    CA   N    110.58  3.000
 DSH  HBA   CB   HB   106.98  3.000
 DSH  HBA   CB   CG   109.35  3.000
 DSH  HB    CB   CG   110.19  3.000
 DSH  HBA   CB   CA   109.39  3.000
 DSH  HB    CB   CA   109.20  3.000
 DSH  CG    CB   CA   111.62  3.000
 DSH  C5'   SD   CG    99.27  3.000
 DSH  HGA   CG   HG   107.94  3.000
 DSH  HGA   CG   SD   109.35  3.000
 DSH  HG    CG   SD   108.62  3.000
 DSH  HGA   CG   CB   110.65  3.000
 DSH  HG    CG   CB   110.38  3.000
 DSH  SD    CG   CB   109.86  3.000
 DSH  H1'   C1'  O4'  111.37  3.000
 DSH  H1'   C1'  C2'  110.11  3.000
 DSH  O4'   C1'  C2'  106.19  3.000
 DSH  H1'   C1'  N9   106.19  3.000
 DSH  O4'   C1'  N9   109.28  3.000
 DSH  C2'   C1'  N9   113.77  3.000
 DSH  H2'   C2'  C3'  109.17  3.000
 DSH  H2'   C2'  O2'  111.57  3.000
 DSH  C3'   C2'  O2'  114.87  3.000
 DSH  H2'   C2'  C1'  109.57  3.000
 DSH  C3'   C2'  C1'  101.22  3.000
 DSH  O2'   C2'  C1'  109.91  3.000
 DSH  HO2'  O2'  C2'  108.86  3.000
 DSH  H3'   C3'  C4'  111.77  3.000
 DSH  H3'   C3'  O3'  111.98  3.000
 DSH  C4'   C3'  O3'  108.93  3.000
 DSH  H3'   C3'  C2'  112.11  3.000
 DSH  C4'   C3'  C2'  100.64  3.000
 DSH  O3'   C3'  C2'  110.83  3.000
 DSH  HO3'  O3'  C3'  107.91  3.000
 DSH  H4'   C4'  C5'  109.13  3.000
 DSH  H4'   C4'  O4'  107.67  3.000
 DSH  C5'   C4'  O4'  111.45  3.000
 DSH  H4'   C4'  C3'  111.51  3.000
 DSH  C5'   C4'  C3'  111.77  3.000
 DSH  O4'   C4'  C3'  105.21  3.000
 DSH  C4'   O4'  C1'  110.96  3.000
 DSH  H5'A  C5'  H5'  107.41  3.000
 DSH  H5'A  C5'  C4'  108.37  3.000
 DSH  H5'   C5'  C4'  112.07  3.000
 DSH  H5'A  C5'  SD   109.41  3.000
 DSH  H5'   C5'  SD   109.12  3.000
 DSH  C4'   C5'  SD   110.39  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
 DSH  CONST_01  C4    N3   C2  N1     0.00   0.0  0
 DSH  CONST_02  C4    C5   C6  N1     0.00   0.0  0
 DSH  CONST_03  N7    C5   C6  N1   180.00   0.0  0
 DSH  CONST_04  C5    C6   N1  C2     0.00   0.0  0
 DSH  CONST_05  C5    C4   N3  C2     0.00   0.0  0
 DSH  CONST_06  N9    C4   N3  C2   180.00   0.0  0
 DSH  CONST_07  C6    N1   C2  N3     0.00   0.0  0
 DSH  CONST_08  C6    C5   C4  N3     0.00   0.0  0
 DSH  CONST_09  N7    C5   C4  N3   180.00   0.0  0
 DSH  CONST_10  C8    N9   C4  N3   180.00   0.0  0
 DSH  CONST_11  C8    N7   C5  C4     0.00   0.0  0
 DSH  CONST_12  N7    C8   N9  C4     0.00   0.0  0
 DSH  CONST_13  C8    N9   C4  C5     0.00   0.0  0
 DSH  CONST_14  N9    C8   N7  C5     0.00   0.0  0
 DSH  CONST_15  N9    C4   C5  C6   180.00   0.0  0
 DSH  CONST_16  C8    N7   C5  C6   180.00   0.0  0
 DSH  CONST_17  N9    C4   C5  N7     0.00   0.0  0
 DSH  CONST_18  C1'   N9   C4  N3     0.00   0.0  0
 DSH  CONST_19  C1'   N9   C4  C5   180.00   0.0  0
 DSH  CONST_20  C1'   N9   C8  N7   180.00   0.0  0
 DSH  CONST_21  N6    C6   N1  C2   180.00   0.0  0
 DSH  CONST_22  N6    C6   C5  C4   180.00   0.0  0
 DSH  CONST_23  N7    C5   C6  N6     0.00   0.0  0
 DSH  CONST_24  H2    C2   N3  C4   180.00   0.0  0
 DSH  CONST_25  H8    C8   N9  C4   180.00   0.0  0
 DSH  CONST_26  HN6   N6   C6  N1     0.00   0.0  0
 DSH  CONST_27  HN6A  N6   C6  N1   180.00   0.0  0
 DSH  Var_01    C4'   C5'  SD  CG   173.11  30.0  3
 DSH  Var_02    CG    CB   CA  N    179.64  30.0  3
 DSH  Var_03    SD    CG   CB  CA  -179.13  30.0  3
 DSH  Var_04    HN    N    CA  CB   176.81  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
 DSH  chir_01  C1'  N9   C2'  O4'  negativ
 DSH  chir_02  C2'  O2'  C3'  C1'  positiv
 DSH  chir_03  C3'  O3'  C4'  C2'  positiv
 DSH  chir_04  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
 DSH  plan-1  N1    0.020
 DSH  plan-1  C2    0.020
 DSH  plan-1  N3    0.020
 DSH  plan-1  C4    0.020
 DSH  plan-1  C5    0.020
 DSH  plan-1  C6    0.020
 DSH  plan-1  N6    0.020
 DSH  plan-1  N7    0.020
 DSH  plan-1  C8    0.020
 DSH  plan-1  N9    0.020
 DSH  plan-1  C1'   0.020
 DSH  plan-1  H8    0.020
 DSH  plan-1  H2    0.020
 DSH  plan-2  C6    0.020
 DSH  plan-2  N6    0.020
 DSH  plan-2  HN6   0.020
 DSH  plan-2  HN6A  0.020

