# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 20:55:44 2021
#   Inital geometry file: a 136 line input string
#   Ligand name: 5'-O-[(S)-{[(2S)-2-amino-4-(methylsulfanyl)butyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N)CO[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=NC3=C(N)NC=N[C@@H]23
#
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
 MOD  MOD  5'-O-[(S)-{[(2S)-2-amino-4-(methylsulfanyl)butyl]oxy}(hydroxy)phosphoryl]adenosine  L-peptide  57  30  .  2022-07-25  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_MOD
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
 MOD  N2    N  NH2   0  -0.801   9.0497  19.5948  13.6249
 MOD  CA    C  CH1   0  -0.092  10.2485  20.4182  13.5963
 MOD  CB    C  CH2   0  -0.439  10.2240  21.3713  12.4033
 MOD  CG    C  CH2   0  -0.552  10.3049  20.6532  11.0645
 MOD  SD    S  S2    0  -0.037  10.3521  21.8788   9.7268
 MOD  CE    C  CH3   0  -0.763  10.3747  20.7729   8.2992
 MOD  C9    C  CH2   0  -0.193  10.3956  21.1740  14.9020
 MOD  O1    O  O2    0  -0.586   9.2732  22.0483  15.1069
 MOD  P1    P  P     0   1.493   9.4679  23.4977  15.7269
 MOD  O1S   O  OH1   0  -0.736   7.9913  23.6827  16.2970
 MOD  O2S   O  O     0  -0.696  10.6032  23.6852  16.6478
 MOD  O5'   O  O2    0  -0.591   9.6113  24.5092  14.4923
 MOD  C5'   C  CH2   0  -0.209   8.5589  24.7966  13.5745
 MOD  C4'   C  CH1   0  -0.018   9.0662  25.7527  12.5209
 MOD  O4'   O  O2    0  -0.495   9.4658  26.9842  13.1271
 MOD  C3'   C  CH1   0  -0.045  10.2662  25.2656  11.7086
 MOD  O3'   O  OH1   0  -0.664  10.1461  25.7770  10.4073
 MOD  C2'   C  CH1   0  -0.038  11.4370  25.9212  12.4438
 MOD  O2'   O  OH1   0  -0.656  12.5599  26.1749  11.6485
 MOD  C1'   C  CH1   0   0.221  10.8125  27.2465  12.8789
 MOD  N9    N  NR5   0  -0.523  11.4197  27.8081  14.0597
 MOD  C8    C  CR15  0   0.093  11.1783  27.4833  15.3792
 MOD  N7    N  N     0  -0.448  11.9106  28.1696  16.1979
 MOD  C5    C  CR5   0  -0.053  12.6724  28.9865  15.3968
 MOD  C6    C  C     0   0.577  13.8725  29.6902  15.7064
 MOD  N6    N  NH2   0  -0.817  14.4530  29.5681  16.8970
 MOD  N1    N  NH1   0  -0.634  14.3985  30.3802  14.7101
 MOD  C2    C  C1    0  -0.365  13.7119  30.6225  13.4162
 MOD  N3    N  N     0  -0.678  12.9856  29.4059  13.0385
 MOD  C4    C  CR15  0   0.575  12.3848  28.7667  14.0636
 MOD  HN21  H  HNH2  0   0.351   9.0275  18.9957  12.8096
 MOD  HN22  H  HNH2  0   0.349   9.0933  18.9635  14.4160
 MOD  HA    H  HCH1  0   0.222  11.1741  19.8231  13.5252
 MOD  HB1   H  HCH2  0   0.233  11.0737  22.0555  12.4908
 MOD  HB2   H  HCH2  0   0.239   9.3121  21.9733  12.4342
 MOD  HG1   H  HCH2  0   0.258   9.4376  20.0077  10.9096
 MOD  HG2   H  HCH2  0   0.261  11.2016  20.0305  11.0152
 MOD  HE1   H  HCH3  0   0.261   9.4783  20.1546   8.2686
 MOD  HE2   H  HCH3  0   0.274  10.4040  21.3881   7.4019
 MOD  HE3   H  HCH3  0   0.261  11.2561  20.1332   8.3124
 MOD  H91   H  HCH2  0   0.244  11.3363  21.7292  14.8907
 MOD  H92   H  HCH2  0   0.258  10.4347  20.4765  15.7418
 MOD  HOS1  H  HOH1  0   0.504   7.8619  24.4763  16.8339
 MOD  H5'1  H  HCH2  0   0.267   7.7140  25.2490  14.0982
 MOD  H5'2  H  HCH2  0   0.249   8.2024  23.8871  13.0831
 MOD  H4'   H  HCH1  0   0.276   8.2234  25.9416  11.8479
 MOD  H3'   H  HCH1  0   0.248  10.3390  24.1710  11.7041
 MOD  H2    H  HOH1  0   0.449  11.0222  25.7725  10.0043
 MOD  H1    H  HCH1  0   0.261  11.6954  25.3315  13.3295
 MOD  H2'   H  HOH1  0   0.472  13.1778  25.4423  11.7298
 MOD  H1'   H  HCH1  0   0.254  10.9383  27.9951  12.0850
 MOD  H8    H  HCR5  0   0.283  10.4467  26.7436  15.6603
 MOD  HN61  H  HNH2  0   0.416  14.1047  28.8996  17.5625
 MOD  HN62  H  HNH2  0   0.414  15.3144  30.0390  17.1162
 MOD  HN1   H  HNH1  0   0.387  15.3328  30.7393  14.8377
 MOD  H3    H  H     0   0.112  12.9272  31.3544  13.6582
 MOD  H4    H  HCR5  0   0.365  13.3383  28.8316  12.2860

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
 MOD  N2   CA    single  1.455  0.020  1.455
 MOD  N2   HN21  single  0.868  0.020  1.013
 MOD  N2   HN22  single  0.868  0.020  1.013
 MOD  CA   CB    single  1.521  0.033  1.521
 MOD  CA   C9    single  1.516  0.020  1.516
 MOD  CA   HA    single  0.970  0.020  0.970
 MOD  CB   CG    single  1.521  0.020  1.521
 MOD  CB   HB1   single  0.939  0.020  1.096
 MOD  CB   HB2   single  0.939  0.020  1.096
 MOD  CG   SD    single  1.815  0.020  1.815
 MOD  CG   HG1   single  0.939  0.020  1.096
 MOD  CG   HG2   single  0.939  0.020  1.096
 MOD  SD   CE    single  1.806  0.020  1.806
 MOD  CE   HE1   single  0.939  0.020  1.096
 MOD  CE   HE2   single  0.939  0.020  1.096
 MOD  CE   HE3   single  0.939  0.020  1.096
 MOD  C9   O1    single  1.437  0.020  1.437
 MOD  C9   H91   single  0.939  0.020  1.096
 MOD  C9   H92   single  0.939  0.020  1.096
 MOD  O1   P1    single  1.588  0.020  1.588
 MOD  P1   O1S   single  1.594  0.020  1.594
 MOD  P1   O2S   double  1.474  0.020  1.474
 MOD  P1   O5'   single  1.602  0.020  1.602
 MOD  O1S  HOS1  single  0.832  0.020  0.971
 MOD  O5'  C5'   single  1.426  0.020  1.426
 MOD  C5'  C4'   single  1.510  0.020  1.510
 MOD  C5'  H5'1  single  0.939  0.020  1.096
 MOD  C5'  H5'2  single  0.939  0.020  1.096
 MOD  C4'  O4'   single  1.430  0.020  1.430
 MOD  C4'  C3'   single  1.529  0.020  1.529
 MOD  C4'  H4'   single  0.939  0.020  1.096
 MOD  O4'  C1'   single  1.394  0.020  1.394
 MOD  C3'  O3'   single  1.403  0.020  1.403
 MOD  C3'  C2'   single  1.530  0.020  1.530
 MOD  C3'  H3'   single  0.939  0.020  1.096
 MOD  O3'  H2    single  0.832  0.020  0.971
 MOD  C2'  O2'   single  1.399  0.020  1.399
 MOD  C2'  C1'   single  1.528  0.020  1.528
 MOD  C2'  H1    single  0.939  0.020  1.096
 MOD  O2'  H2'   single  0.832  0.020  0.971
 MOD  C1'  N9    single  1.442  0.020  1.442
 MOD  C1'  H1'   single  0.939  0.020  1.096
 MOD  N9   C8    single  1.380  0.020  1.380
 MOD  N9   C4    single  1.360  0.020  1.360
 MOD  C8   N7    double  1.295  0.020  1.295
 MOD  C8   H8    single  0.930  0.020  1.086
 MOD  N7   C5    single  1.375  0.020  1.375
 MOD  C5   C6    double  1.425  0.020  1.425
 MOD  C5   C4    single  1.382  0.020  1.382
 MOD  C6   N6    single  1.330  0.020  1.330
 MOD  C6   N1    single  1.321  0.020  1.321
 MOD  N6   HN61  single  0.868  0.020  1.013
 MOD  N6   HN62  single  0.868  0.020  1.013
 MOD  N1   C2    single  1.485  0.020  1.485
 MOD  N1   HN1   single  0.868  0.020  1.013
 MOD  C2   N3    double  1.466  0.020  1.466
 MOD  C2   H3    single  0.930  0.020  1.086
 MOD  N3   C4    single  1.349  0.020  1.349
 MOD  C4   H4    single  0.939  0.020  1.096

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
 MOD  HN22  N2   HN21  105.14  3.000
 MOD  HN22  N2   CA    109.43  3.000
 MOD  HN21  N2   CA    109.72  3.000
 MOD  HA    CA   C9    104.07  3.000
 MOD  HA    CA   CB    109.00  3.000
 MOD  C9    CA   CB    111.30  3.000
 MOD  HA    CA   N2    112.81  3.000
 MOD  C9    CA   N2    110.20  3.000
 MOD  CB    CA   N2    110.82  3.000
 MOD  HB2   CB   HB1   107.53  3.000
 MOD  HB2   CB   CG    109.22  3.000
 MOD  HB1   CB   CG    108.92  3.000
 MOD  HB2   CB   CA    109.57  3.000
 MOD  HB1   CB   CA    108.38  3.000
 MOD  CG    CB   CA    113.08  3.000
 MOD  HG2   CG   HG1   107.97  3.000
 MOD  HG2   CG   SD    109.28  3.000
 MOD  HG1   CG   SD    108.38  3.000
 MOD  HG2   CG   CB    110.63  3.000
 MOD  HG1   CG   CB    111.20  3.000
 MOD  SD    CG   CB    109.34  3.000
 MOD  CE    SD   CG     99.75  3.000
 MOD  HE3   CE   HE2   108.67  3.000
 MOD  HE3   CE   HE1   109.44  3.000
 MOD  HE2   CE   HE1   108.65  3.000
 MOD  HE3   CE   SD    111.11  3.000
 MOD  HE2   CE   SD    107.81  3.000
 MOD  HE1   CE   SD    111.07  3.000
 MOD  H92   C9   H91   107.55  3.000
 MOD  H92   C9   O1    107.86  3.000
 MOD  H91   C9   O1    111.39  3.000
 MOD  H92   C9   CA    110.32  3.000
 MOD  H91   C9   CA    109.15  3.000
 MOD  O1    C9   CA    110.51  3.000
 MOD  P1    O1   C9    121.00  3.000
 MOD  O5'   P1   O2S   109.40  3.000
 MOD  O5'   P1   O1S   106.58  3.000
 MOD  O2S   P1   O1S   118.39  3.000
 MOD  O5'   P1   O1    106.63  3.000
 MOD  O2S   P1   O1    117.02  3.000
 MOD  O1S   P1   O1     97.59  3.000
 MOD  HOS1  O1S  P1    114.70  3.000
 MOD  C5'   O5'  P1    123.86  3.000
 MOD  H5'2  C5'  H5'1  107.93  3.000
 MOD  H5'2  C5'  C4'   108.82  3.000
 MOD  H5'1  C5'  C4'   109.40  3.000
 MOD  H5'2  C5'  O5'   111.24  3.000
 MOD  H5'1  C5'  O5'   110.23  3.000
 MOD  C4'   C5'  O5'   109.19  3.000
 MOD  H4'   C4'  C3'   109.42  3.000
 MOD  H4'   C4'  O4'   109.09  3.000
 MOD  C3'   C4'  O4'   106.28  3.000
 MOD  H4'   C4'  C5'   106.22  3.000
 MOD  C3'   C4'  C5'   115.64  3.000
 MOD  O4'   C4'  C5'   110.08  3.000
 MOD  C1'   O4'  C4'   110.88  3.000
 MOD  H3'   C3'  C2'   112.25  3.000
 MOD  H3'   C3'  O3'   111.44  3.000
 MOD  C2'   C3'  O3'   110.79  3.000
 MOD  H3'   C3'  C4'   111.85  3.000
 MOD  C2'   C3'  C4'   102.05  3.000
 MOD  O3'   C3'  C4'   108.03  3.000
 MOD  H2    O3'  C3'   107.94  3.000
 MOD  H1    C2'  C1'   109.46  3.000
 MOD  H1    C2'  O2'   111.59  3.000
 MOD  C1'   C2'  O2'   109.43  3.000
 MOD  H1    C2'  C3'   109.78  3.000
 MOD  C1'   C2'  C3'   101.28  3.000
 MOD  O2'   C2'  C3'   114.75  3.000
 MOD  H2'   O2'  C2'   109.23  3.000
 MOD  H1'   C1'  N9    106.16  3.000
 MOD  H1'   C1'  C2'   109.78  3.000
 MOD  N9    C1'  C2'   113.50  3.000
 MOD  H1'   C1'  O4'   111.56  3.000
 MOD  N9    C1'  O4'   109.53  3.000
 MOD  C2'   C1'  O4'   106.40  3.000
 MOD  C4    N9   C8    106.69  3.000
 MOD  C4    N9   C1'   125.14  3.000
 MOD  C8    N9   C1'   128.15  3.000
 MOD  H8    C8   N7    125.64  3.000
 MOD  H8    C8   N9    121.98  3.000
 MOD  N7    C8   N9    112.38  3.000
 MOD  C5    N7   C8    105.06  3.000
 MOD  C4    C5   C6    117.61  3.000
 MOD  C4    C5   N7    110.64  3.000
 MOD  C6    C5   N7    129.31  3.000
 MOD  N1    C6   N6    123.31  3.000
 MOD  N1    C6   C5    115.42  3.000
 MOD  N6    C6   C5    121.10  3.000
 MOD  HN62  N6   HN61  117.62  3.000
 MOD  HN62  N6   C6    121.72  3.000
 MOD  HN61  N6   C6    120.15  3.000
 MOD  HN1   N1   C2    118.70  3.000
 MOD  HN1   N1   C6    117.33  3.000
 MOD  C2    N1   C6    123.95  3.000
 MOD  H3    C2   N3    104.79  3.000
 MOD  H3    C2   N1    104.28  3.000
 MOD  N3    C2   N1    108.54  3.000
 MOD  C4    N3   C2    114.71  3.000
 MOD  H4    C4   N3     26.52  3.000
 MOD  H4    C4   C5    138.29  3.000
 MOD  N3    C4   C5    124.41  3.000
 MOD  H4    C4   N9    110.82  3.000
 MOD  N3    C4   N9    130.36  3.000
 MOD  C5    C4   N9    105.22  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
 MOD  CONST_01  N7    C8   N9   C1'   180.00   0.0  0
 MOD  CONST_02  C5    N7   C8   N9      0.00   0.0  0
 MOD  CONST_03  C4    C5   N7   C8      0.00   0.0  0
 MOD  CONST_04  C4    N9   C8   N7      0.00   0.0  0
 MOD  CONST_05  C2    N1   C6   C5      0.00   0.0  0
 MOD  CONST_08  C2    N1   C6   N6    180.00   0.0  0
 MOD  CONST_09  H8    C8   N9   C1'     0.00   0.0  0
 MOD  CONST_10  HN1   N1   C6   C5    180.00   0.0  0
 MOD  CONST_12  HN61  N6   C6   C5      0.00   0.0  0
 MOD  CONST_13  HN62  N6   C6   C5    180.00   0.0  0
 MOD  Var_01    N1    C6   C5   N7    178.54   0.0  0
 MOD  Var_02    C4    C5   C6   N1     18.08   0.0  0
 MOD  Var_03    C4'   C5'  O5'  P1   -178.14  30.0  3
 MOD  Var_04    SD    CG   CB   CA   -177.19  30.0  3
 MOD  Var_05    O1S   P1   O1   C9   -156.15  30.0  3
 MOD  Var_06    HE1   CE   SD   CG     61.07  30.0  3
 MOD  Var_07    H91   C9   O1   P1    -19.34  30.0  1

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
 MOD  chir_01  CA   N2   CB   C9   negativ
 MOD  chir_03  C4'  O4'  C5'  C3'  positiv
 MOD  chir_04  C3'  O3'  C4'  C2'  positiv
 MOD  chir_05  C2'  O2'  C3'  C1'  positiv
 MOD  chir_06  C1'  O4'  N9   C2'  negativ
 MOD  chir_07  C4   N9   N3   C5   positiv
 MOD  chir_08  P1   O1S  O2S  O5'  both

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
 MOD  plan-1  C1'   0.020
 MOD  plan-1  N9    0.020
 MOD  plan-1  C8    0.020
 MOD  plan-1  N7    0.020
 MOD  plan-1  C5    0.020
 MOD  plan-1  C6    0.020
 MOD  plan-1  N6    0.020
 MOD  plan-1  N1    0.020
 MOD  plan-1  C2    0.020
 MOD  plan-1  N3    0.020
 MOD  plan-1  C4    0.020
 MOD  plan-1  H8    0.020
 MOD  plan-1  HN61  0.020
 MOD  plan-1  HN62  0.020
 MOD  plan-1  HN1   0.020
 MOD  plan-1  H3    0.020

