# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 18:55:43 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 5'-O-[(S)-{[(2S)-2-amino-4-(methylsulfanyl)butanoyl]oxy}(hydroxy)phosphoryl]adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N)C(=O)O[P](O)(=O)OC[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
 ME8  ME8  5'-O-[(S)-{[(2S)-2-amino-4-(methylsulfanyl)butanoyl]oxy}(hydroxy)phosphoryl]adenosine  ligand  54  31  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ME8
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
 ME8  O     O  O     0  -0.405  30.4091  45.4637   -7.8200
 ME8  N1    N  N     0  -0.473  39.2130  46.3611   -1.1280
 ME8  O1    O  O2    0  -0.563  31.1574  43.4307   -8.3805
 ME8  P1    P  P     0   1.500  32.7063  43.6162   -7.8739
 ME8  C2    C  CR16  0   0.040  38.0861  46.0755   -0.4804
 ME8  N2    N  NH2   0  -0.799  29.0134  43.0134   -9.9364
 ME8  N3    N  N     0  -0.458  36.9350  45.6596   -0.9791
 ME8  C4    C  CR56  0   0.488  36.9914  45.5327   -2.3039
 ME8  C5    C  CR56  0  -0.000  38.0883  45.7863   -3.1120
 ME8  C6    C  CR6   0   0.455  39.2542  46.2259   -2.4578
 ME8  N6    N  NH2   0  -0.815  40.3903  46.4904   -3.1071
 ME8  N7    N  N     0  -0.449  37.7929  45.5321   -4.4244
 ME8  C8    C  CR15  0   0.107  36.5529  45.1375   -4.4073
 ME8  C9    C  C     0   0.584  30.2064  44.3844   -8.2986
 ME8  N9    N  NR5   0  -0.541  36.0044  45.1255   -3.1537
 ME8  CA    C  CH1   0  -0.190  28.8633  43.9233   -8.8215
 ME8  CB    C  CH2   0  -0.437  28.1358  43.2437   -7.6507
 ME8  SD    S  S2    0  -0.034  25.8732  42.2520   -6.5081
 ME8  CE    C  CH3   0  -0.765  24.2415  41.8856   -7.1889
 ME8  CG    C  CH2   0  -0.564  26.6980  42.8829   -7.9971
 ME8  C1'   C  CH1   0   0.178  34.6669  44.7053   -2.7410
 ME8  O1S   O  O     0  -0.665  33.4146  42.3546   -8.1282
 ME8  C2'   C  CH1   0  -0.046  33.8508  45.8849   -2.2198
 ME8  O2'   O  OH1   0  -0.662  32.8855  45.3695   -1.3468
 ME8  O2S   O  OH1   0  -0.736  33.2426  44.9269   -8.5862
 ME8  C3'   C  CH1   0  -0.041  33.2059  46.3914   -3.5150
 ME8  O3'   O  OH1   0  -0.655  32.0083  47.0850   -3.3165
 ME8  C4'   C  CH1   0   0.001  32.9414  45.0820   -4.2559
 ME8  O4'   O  O2    0  -0.494  33.9821  44.1985   -3.8460
 ME8  C5'   C  CH2   0  -0.167  32.9464  45.2626   -5.7504
 ME8  O5'   O  O2    0  -0.593  32.5701  44.0172   -6.3513
 ME8  HN2   H  HNH2  0   0.362  28.0970  42.7451  -10.2706
 ME8  HN2A  H  HNH2  0   0.360  29.4514  43.4868  -10.7171
 ME8  HN6   H  HNH2  0   0.403  41.1623  46.9062   -2.6149
 ME8  HN6A  H  HNH2  0   0.410  40.4169  46.4985   -4.1117
 ME8  HA    H  HCH1  0   0.260  28.3172  44.8447   -9.0663
 ME8  HB    H  HCH2  0   0.256  28.6839  42.3468   -7.3523
 ME8  HBA   H  HCH2  0   0.257  28.1319  43.9283   -6.7992
 ME8  HE    H  HCH3  0   0.275  23.6296  41.4920   -6.3793
 ME8  HEA   H  HCH3  0   0.262  23.7661  42.7844   -7.5789
 ME8  HEB   H  HCH3  0   0.262  24.3020  41.1361   -7.9764
 ME8  HG    H  HCH2  0   0.267  26.1602  43.7614   -8.3611
 ME8  HGA   H  HCH2  0   0.264  26.6514  42.1103   -8.7667
 ME8  H1'   H  HCH1  0   0.290  34.7879  43.9284   -1.9816
 ME8  H2'   H  HCH1  0   0.266  34.4775  46.6426   -1.7367
 ME8  HO2'  H  HOH1  0   0.454  32.1395  45.9814   -1.3339
 ME8  HO2S  H  HOH1  0   0.511  33.8032  44.7654   -9.3583
 ME8  H3'   H  HCH1  0   0.254  33.9352  46.9981   -4.0680
 ME8  HO3'  H  HOH1  0   0.471  32.2020  48.0225   -3.2189
 ME8  H4'   H  HCH1  0   0.263  31.9745  44.6703   -3.9431
 ME8  H5'   H  HCH2  0   0.264  32.2262  46.0368   -6.0167
 ME8  H5'A  H  HCH2  0   0.243  33.9323  45.5755   -6.0985
 ME8  H8    H  HCR5  0   0.290  36.0005  44.8308   -5.2802
 ME8  H2    H  HCR6  0   0.253  38.1225  46.2026    0.5963

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
 ME8  N1   C2    aromatic  1.331  0.020  1.331
 ME8  O1   P1    single    1.640  0.020  1.640
 ME8  O1   C9    single    1.349  0.020  1.349
 ME8  P1   O5'   single    1.580  0.020  1.580
 ME8  C2   H2    single    0.930  0.020  1.080
 ME8  N2   CA    single    1.447  0.020  1.447
 ME8  N2   HN2   single    0.890  0.020  1.040
 ME8  N2   HN2A  single    0.890  0.020  1.040
 ME8  N3   C2    aromatic  1.322  0.020  1.322
 ME8  C4   N3    aromatic  1.332  0.020  1.332
 ME8  C5   C4    aromatic  1.386  0.020  1.386
 ME8  C5   C6    aromatic  1.407  0.020  1.407
 ME8  C6   N1    aromatic  1.337  0.020  1.337
 ME8  N6   C6    single    1.335  0.020  1.335
 ME8  N6   HN6   single    0.860  0.020  1.020
 ME8  N6   HN6A  single    0.860  0.020  1.020
 ME8  N7   C5    aromatic  1.369  0.020  1.369
 ME8  C8   N7    aromatic  1.301  0.020  1.301
 ME8  C8   N9    aromatic  1.368  0.020  1.368
 ME8  C9   O     double    1.198  0.020  1.198
 ME8  N9   C4    aromatic  1.365  0.020  1.365
 ME8  N9   C1'   single    1.461  0.020  1.461
 ME8  CA   C9    single    1.513  0.020  1.513
 ME8  CA   CB    single    1.537  0.020  1.537
 ME8  CA   HA    single    0.970  0.020  1.090
 ME8  CB   HB    single    0.970  0.020  1.090
 ME8  CB   HBA   single    0.970  0.020  1.090
 ME8  CE   SD    single    1.806  0.020  1.806
 ME8  CE   HE    single    0.970  0.020  1.090
 ME8  CE   HEA   single    0.970  0.020  1.090
 ME8  CE   HEB   single    0.970  0.020  1.090
 ME8  CG   CB    single    1.522  0.020  1.522
 ME8  CG   SD    single    1.815  0.020  1.815
 ME8  CG   HG    single    0.970  0.020  1.090
 ME8  CG   HGA   single    0.970  0.020  1.090
 ME8  C1'  C2'   single    1.526  0.020  1.526
 ME8  C1'  H1'   single    0.970  0.020  1.090
 ME8  O1S  P1    double    1.469  0.020  1.469
 ME8  C2'  O2'   single    1.400  0.020  1.400
 ME8  C2'  H2'   single    0.970  0.020  1.090
 ME8  O2'  HO2'  single    0.850  0.020  0.980
 ME8  O2S  P1    single    1.585  0.020  1.585
 ME8  O2S  HO2S  single    0.850  0.020  0.980
 ME8  C3'  C2'   single    1.533  0.020  1.533
 ME8  C3'  O3'   single    1.398  0.020  1.398
 ME8  C3'  H3'   single    0.970  0.020  1.090
 ME8  O3'  HO3'  single    0.850  0.020  0.980
 ME8  C4'  C3'   single    1.528  0.020  1.528
 ME8  C4'  O4'   single    1.425  0.020  1.425
 ME8  C4'  H4'   single    0.970  0.020  1.090
 ME8  O4'  C1'   single    1.395  0.020  1.395
 ME8  C5'  C4'   single    1.505  0.020  1.505
 ME8  C5'  H5'   single    0.970  0.020  1.090
 ME8  C5'  H5'A  single    0.970  0.020  1.090
 ME8  O5'  C5'   single    1.433  0.020  1.433
 ME8  C8   H8    single    0.930  0.020  1.080

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
 ME8  C6    N1   C2   119.23  3.000
 ME8  C9    O1   P1   124.53  3.000
 ME8  O5'   P1   O2S  104.61  3.000
 ME8  O2S   P1   O1S  117.98  3.000
 ME8  O5'   P1   O1S  115.23  3.000
 ME8  O2S   P1   O1   105.91  3.000
 ME8  O1S   P1   O1   107.74  3.000
 ME8  O5'   P1   O1   104.18  3.000
 ME8  H2    C2   N3   116.15  3.000
 ME8  N3    C2   N1   128.42  3.000
 ME8  H2    C2   N1   115.43  3.000
 ME8  HN2A  N2   HN2  105.13  3.000
 ME8  HN2A  N2   CA   110.18  3.000
 ME8  HN2   N2   CA   109.11  3.000
 ME8  C4    N3   C2   111.62  3.000
 ME8  N9    C4   C5   105.31  3.000
 ME8  N9    C4   N3   128.11  3.000
 ME8  C5    C4   N3   126.58  3.000
 ME8  N7    C5   C6   133.03  3.000
 ME8  N7    C5   C4   110.74  3.000
 ME8  C6    C5   C4   116.22  3.000
 ME8  N6    C6   C5   122.74  3.000
 ME8  N6    C6   N1   119.33  3.000
 ME8  C5    C6   N1   117.92  3.000
 ME8  HN6A  N6   HN6  117.75  3.000
 ME8  HN6A  N6   C6   120.69  3.000
 ME8  HN6   N6   C6   119.82  3.000
 ME8  C8    N7   C5   104.43  3.000
 ME8  H8    C8   N9   122.28  3.000
 ME8  H8    C8   N7   124.34  3.000
 ME8  N9    C8   N7   113.37  3.000
 ME8  CA    C9   O1   112.90  3.000
 ME8  CA    C9   O    124.25  3.000
 ME8  O1    C9   O    122.81  3.000
 ME8  C1'   N9   C8   128.91  3.000
 ME8  C1'   N9   C4   124.88  3.000
 ME8  C8    N9   C4   106.14  3.000
 ME8  HA    CA   CB   107.78  3.000
 ME8  HA    CA   C9   105.23  3.000
 ME8  CB    CA   C9   106.96  3.000
 ME8  HA    CA   N2   114.03  3.000
 ME8  CB    CA   N2   110.98  3.000
 ME8  C9    CA   N2   111.46  3.000
 ME8  HBA   CB   HB   107.66  3.000
 ME8  HBA   CB   CG   108.81  3.000
 ME8  HB    CB   CG   109.96  3.000
 ME8  CG    CB   CA   112.24  3.000
 ME8  HBA   CB   CA   108.56  3.000
 ME8  HB    CB   CA   109.49  3.000
 ME8  CG    SD   CE    99.89  3.000
 ME8  HEB   CE   HEA  109.48  3.000
 ME8  HEB   CE   HE   108.68  3.000
 ME8  HEA   CE   HE   108.63  3.000
 ME8  HEB   CE   SD   111.23  3.000
 ME8  HEA   CE   SD   111.22  3.000
 ME8  HE    CE   SD   107.51  3.000
 ME8  HGA   CG   HG   108.26  3.000
 ME8  HGA   CG   SD   108.24  3.000
 ME8  HG    CG   SD   109.21  3.000
 ME8  HGA   CG   CB   111.62  3.000
 ME8  HG    CG   CB   110.50  3.000
 ME8  SD    CG   CB   108.95  3.000
 ME8  H1'   C1'  O4'  110.27  3.000
 ME8  O4'   C1'  C2'  106.78  3.000
 ME8  H1'   C1'  C2'  111.80  3.000
 ME8  O4'   C1'  N9   109.26  3.000
 ME8  H1'   C1'  N9   107.41  3.000
 ME8  C2'   C1'  N9   111.32  3.000
 ME8  H2'   C2'  C3'  112.63  3.000
 ME8  C3'   C2'  O2'  111.01  3.000
 ME8  H2'   C2'  O2'  111.97  3.000
 ME8  C3'   C2'  C1'  101.06  3.000
 ME8  H2'   C2'  C1'  112.29  3.000
 ME8  O2'   C2'  C1'  107.29  3.000
 ME8  HO2'  O2'  C2'  107.93  3.000
 ME8  HO2S  O2S  P1   114.61  3.000
 ME8  H3'   C3'  C4'  110.14  3.000
 ME8  C4'   C3'  O3'  110.23  3.000
 ME8  H3'   C3'  O3'  111.48  3.000
 ME8  C4'   C3'  C2'  101.50  3.000
 ME8  H3'   C3'  C2'  109.19  3.000
 ME8  O3'   C3'  C2'  113.85  3.000
 ME8  HO3'  O3'  C3'  108.99  3.000
 ME8  H4'   C4'  C5'  109.34  3.000
 ME8  C5'   C4'  O4'  110.94  3.000
 ME8  H4'   C4'  O4'  109.22  3.000
 ME8  C5'   C4'  C3'  112.22  3.000
 ME8  H4'   C4'  C3'  109.64  3.000
 ME8  O4'   C4'  C3'  105.39  3.000
 ME8  C4'   O4'  C1'  111.16  3.000
 ME8  H5'A  C5'  H5'  108.37  3.000
 ME8  H5'A  C5'  O5'  110.65  3.000
 ME8  H5'   C5'  O5'  109.95  3.000
 ME8  O5'   C5'  C4'  108.13  3.000
 ME8  H5'A  C5'  C4'  110.73  3.000
 ME8  H5'   C5'  C4'  108.99  3.000
 ME8  C5'   O5'  P1   127.00  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
 ME8  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 ME8  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 ME8  CONST_03  N7    C5   C6   N1   180.00   0.0  0
 ME8  CONST_04  C5    C6   N1   C2     0.00   0.0  0
 ME8  CONST_05  C5    C4   N3   C2     0.00   0.0  0
 ME8  CONST_06  N9    C4   N3   C2   180.00   0.0  0
 ME8  CONST_07  C6    N1   C2   N3     0.00   0.0  0
 ME8  CONST_08  C6    C5   C4   N3     0.00   0.0  0
 ME8  CONST_09  N7    C5   C4   N3   180.00   0.0  0
 ME8  CONST_10  C8    N9   C4   N3   180.00   0.0  0
 ME8  CONST_11  C8    N7   C5   C4     0.00   0.0  0
 ME8  CONST_12  N7    C8   N9   C4     0.00   0.0  0
 ME8  CONST_13  C8    N9   C4   C5     0.00   0.0  0
 ME8  CONST_14  N9    C8   N7   C5     0.00   0.0  0
 ME8  CONST_15  N9    C4   C5   C6   180.00   0.0  0
 ME8  CONST_16  C8    N7   C5   C6   180.00   0.0  0
 ME8  CONST_17  N9    C4   C5   N7     0.00   0.0  0
 ME8  CONST_18  C1'   N9   C4   N3     0.00   0.0  0
 ME8  CONST_19  C1'   N9   C4   C5   180.00   0.0  0
 ME8  CONST_20  C1'   N9   C8   N7   180.00   0.0  0
 ME8  CONST_21  N6    C6   N1   C2   180.00   0.0  0
 ME8  CONST_22  N6    C6   C5   C4   180.00   0.0  0
 ME8  CONST_23  N7    C5   C6   N6     0.00   0.0  0
 ME8  CONST_24  H2    C2   N3   C4   180.00   0.0  0
 ME8  CONST_25  H8    C8   N9   C4   180.00   0.0  0
 ME8  CONST_26  HN6   N6   C6   N1     0.00   0.0  0
 ME8  CONST_27  HN6A  N6   C6   N1   180.00   0.0  0
 ME8  Var_01    C4'   C5'  O5'  P1  -166.84  30.0  3
 ME8  Var_02    CA    C9   O1   P1  -178.99  30.0  3
 ME8  Var_03    O5'   P1   O1   C9    56.80  30.0  3
 ME8  Var_04    SD    CG   CB   CA  -174.04  30.0  1
 ME8  Var_05    HE    CE   SD   CG  -179.86  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
 ME8  chir_02  CA   N2   C9   CB   positiv
 ME8  chir_03  C1'  N9   C2'  O4'  negativ
 ME8  chir_04  C2'  O2'  C3'  C1'  positiv
 ME8  chir_05  C3'  O3'  C4'  C2'  positiv
 ME8  chir_06  C4'  O4'  C3'  C5'  negativ
 ME8  chir_07  P1   O5'  O1S  O2S  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
 ME8  plan-1  N1    0.020
 ME8  plan-1  C2    0.020
 ME8  plan-1  N3    0.020
 ME8  plan-1  C4    0.020
 ME8  plan-1  C5    0.020
 ME8  plan-1  C6    0.020
 ME8  plan-1  N6    0.020
 ME8  plan-1  N7    0.020
 ME8  plan-1  C8    0.020
 ME8  plan-1  N9    0.020
 ME8  plan-1  C1'   0.020
 ME8  plan-1  H8    0.020
 ME8  plan-1  H2    0.020
 ME8  plan-2  C6    0.020
 ME8  plan-2  N6    0.020
 ME8  plan-2  HN6   0.020
 ME8  plan-2  HN6A  0.020
 ME8  plan-3  O     0.020
 ME8  plan-3  O1    0.020
 ME8  plan-3  C9    0.020
 ME8  plan-3  CA    0.020

