# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:13:30 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 5'-deoxy-5'-(dimethyl-lambda~4~-sulfanyl)adenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[SH](C)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
 M2T  M2T  5'-deoxy-5'-(dimethyl-lambda~4~-sulfanyl)adenosine  ligand  40  21  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M2T
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
 M2T  CG    C  CH3   0  -0.885   5.2857  -1.9162  -1.8047
 M2T  SD    S  SH1   0   0.179   3.9962  -1.1456  -0.4929
 M2T  CE    C  CH3   0  -0.729   5.0475  -1.7032   0.8691
 M2T  C5'   C  CH2   0  -0.699   2.9349   0.0158   0.8651
 M2T  C4'   C  CR15  0   0.060   2.0785   0.9524   0.0692
 M2T  O4'   O  O     0  -0.498   1.2157   0.2102  -0.8127
 M2T  C1'   C  CR15  0   0.175  -0.0547   0.7698  -0.8756
 M2T  N9    N  NR5   0  -0.535  -0.9998  -0.1248  -0.2081
 M2T  C4    C  CR56  0   0.484  -2.3578  -0.0287  -0.2718
 M2T  N3    N  N     0  -0.459  -3.0890   0.8775  -0.9196
 M2T  C2    C  CR16  0   0.038  -4.3831   0.6608  -0.7631
 M2T  N1    N  N     0  -0.474  -4.9827  -0.3045  -0.0703
 M2T  C6    C  CR6   0   0.455  -4.2345  -1.2060   0.5753
 M2T  N6    N  NH2   0  -0.817  -4.8339  -2.1668   1.2810
 M2T  C5    C  CR56  0  -0.003  -2.8351  -1.0865   0.4868
 M2T  N7    N  N     0  -0.453  -1.7996  -1.8203   1.0014
 M2T  C8    C  CR15  0   0.100  -0.7296  -1.2197   0.5645
 M2T  C2'   C  CR15  0  -0.040   0.0163   2.1247  -0.1731
 M2T  O2'   O  OH1   0  -0.667   0.4278   3.0760  -1.1175
 M2T  C3'   C  CR15  0  -0.026   1.1204   1.8542   0.8534
 M2T  O3'   O  OH1   0  -0.660   1.7873   3.0089   1.2826
 M2T  HG    H  HCH3  0   0.225   5.2436  -3.0066  -1.7795
 M2T  HGA   H  HCH3  0   0.223   4.9555  -1.5719  -2.7867
 M2T  HGB   H  HCH3  0   0.221   6.3150  -1.5895  -1.6388
 M2T  HE    H  HCH3  0   0.281   4.4453  -1.7749   1.7703
 M2T  HEA   H  HCH3  0   0.279   5.4661  -2.6706   0.6035
 M2T  HEB   H  HCH3  0   0.289   5.8514  -0.9878   1.0205
 M2T  H5'   H  HCH2  0   0.210   2.3366  -0.6362   1.5111
 M2T  H5'A  H  HCH2  0   0.222   3.6173   0.5976   1.4926
 M2T  H4'   H  HCR5  0   0.217   2.7277   1.5948  -0.5486
 M2T  H1'   H  HCR5  0   0.278  -0.3861   0.8710  -1.9134
 M2T  H2    H  HCR6  0   0.251  -5.0481   1.3575  -1.2623
 M2T  HN6   H  HNH2  0   0.403  -5.8348  -2.2590   1.2594
 M2T  HN6A  H  HNH2  0   0.410  -4.3008  -2.9002   1.7140
 M2T  H8    H  HCR5  0   0.297   0.2805  -1.5382   0.7676
 M2T  H2'   H  HCR5  0   0.253  -0.9396   2.4015   0.2879
 M2T  HO2'  H  HOH1  0   0.450   0.9575   3.7358  -0.6523
 M2T  H3'   H  HCR5  0   0.234   0.7023   1.2960   1.7008
 M2T  HO3'  H  HOH1  0   0.466   1.2653   3.4303   1.9730
 M2T  HSD   H  HSH1  0   0.244   4.3722   0.0467  -0.9880

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
 M2T  SD   CG    single    1.994  0.020  1.994
 M2T  CG   HG    single    0.970  0.020  1.090
 M2T  CG   HGA   single    0.970  0.020  1.090
 M2T  CG   HGB   single    0.970  0.020  1.090
 M2T  CE   SD    single    1.809  0.020  1.809
 M2T  SD   C5'   single    2.078  0.020  2.078
 M2T  CE   HE    single    0.970  0.020  1.090
 M2T  CE   HEA   single    0.970  0.020  1.090
 M2T  CE   HEB   single    0.970  0.020  1.090
 M2T  C4'  C5'   single    1.498  0.020  1.498
 M2T  C5'  H5'   single    0.970  0.020  1.090
 M2T  C5'  H5'A  single    0.970  0.020  1.090
 M2T  O4'  C4'   single    1.440  0.020  1.440
 M2T  C4'  C3'   single    1.532  0.020  1.532
 M2T  C4'  H4'   single    0.970  0.020  1.090
 M2T  C1'  O4'   single    1.390  0.020  1.390
 M2T  N9   C1'   single    1.463  0.020  1.463
 M2T  C1'  C2'   single    1.528  0.020  1.528
 M2T  C1'  H1'   single    0.970  0.020  1.090
 M2T  C8   N9    aromatic  1.367  0.020  1.367
 M2T  N9   C4    aromatic  1.363  0.020  1.363
 M2T  C5   C4    aromatic  1.386  0.020  1.386
 M2T  C4   N3    aromatic  1.332  0.020  1.332
 M2T  N3   C2    aromatic  1.321  0.020  1.321
 M2T  N1   C2    aromatic  1.331  0.020  1.331
 M2T  C2   H2    single    0.930  0.020  1.080
 M2T  C6   N1    aromatic  1.338  0.020  1.338
 M2T  C5   C6    aromatic  1.407  0.020  1.407
 M2T  N6   C6    single    1.334  0.020  1.334
 M2T  N6   HN6   single    0.860  0.020  1.020
 M2T  N6   HN6A  single    0.860  0.020  1.020
 M2T  N7   C5    aromatic  1.369  0.020  1.369
 M2T  N7   C8    aromatic  1.302  0.020  1.302
 M2T  C8   H8    single    0.930  0.020  1.080
 M2T  O2'  C2'   single    1.402  0.020  1.402
 M2T  C2'  C3'   single    1.532  0.020  1.532
 M2T  C2'  H2'   single    0.970  0.020  1.090
 M2T  O2'  HO2'  single    0.850  0.020  0.980
 M2T  O3'  C3'   single    1.401  0.020  1.401
 M2T  C3'  H3'   single    0.970  0.020  1.090
 M2T  O3'  HO3'  single    0.850  0.020  0.980
 M2T  SD   HSD   single    1.200  0.020  1.300

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
 M2T  HGB   CG   HGA  109.10  3.000
 M2T  HGB   CG   HG   109.36  3.000
 M2T  HGA   CG   HG   108.91  3.000
 M2T  HGB   CG   SD   113.18  3.000
 M2T  HGA   CG   SD   105.92  3.000
 M2T  HG    CG   SD   110.24  3.000
 M2T  HSD   SD   C5'   83.56  3.000
 M2T  HSD   SD   CE   112.84  3.000
 M2T  C5'   SD   CE    88.69  3.000
 M2T  HSD   SD   CG    85.39  3.000
 M2T  C5'   SD   CG   167.39  3.000
 M2T  CE    SD   CG    90.02  3.000
 M2T  HEB   CE   HEA  109.57  3.000
 M2T  HEB   CE   HE   109.76  3.000
 M2T  HEA   CE   HE   110.95  3.000
 M2T  HEB   CE   SD   109.39  3.000
 M2T  HEA   CE   SD   108.31  3.000
 M2T  HE    CE   SD   108.84  3.000
 M2T  H5'A  C5'  H5'  108.59  3.000
 M2T  H5'A  C5'  C4'  109.19  3.000
 M2T  H5'   C5'  C4'  111.91  3.000
 M2T  H5'A  C5'  SD   110.69  3.000
 M2T  H5'   C5'  SD   109.36  3.000
 M2T  C4'   C5'  SD   107.11  3.000
 M2T  H4'   C4'  C3'  108.19  3.000
 M2T  H4'   C4'  O4'  108.06  3.000
 M2T  C3'   C4'  O4'  104.02  3.000
 M2T  H4'   C4'  C5'  108.98  3.000
 M2T  C3'   C4'  C5'  116.98  3.000
 M2T  O4'   C4'  C5'  110.22  3.000
 M2T  C1'   O4'  C4'  111.60  3.000
 M2T  H1'   C1'  C2'  111.61  3.000
 M2T  H1'   C1'  N9   107.09  3.000
 M2T  C2'   C1'  N9   111.26  3.000
 M2T  H1'   C1'  O4'  110.92  3.000
 M2T  C2'   C1'  O4'  107.08  3.000
 M2T  N9    C1'  O4'  108.89  3.000
 M2T  C8    N9   C4   106.25  3.000
 M2T  C4    N9   C1'  125.41  3.000
 M2T  C8    N9   C1'  128.33  3.000
 M2T  C5    C4   N3   126.59  3.000
 M2T  N3    C4   N9   128.13  3.000
 M2T  C5    C4   N9   105.29  3.000
 M2T  C2    N3   C4   111.61  3.000
 M2T  H2    C2   N1   115.41  3.000
 M2T  H2    C2   N3   116.14  3.000
 M2T  N1    C2   N3   128.45  3.000
 M2T  C6    N1   C2   119.21  3.000
 M2T  C5    C6   N6   122.76  3.000
 M2T  N6    C6   N1   119.29  3.000
 M2T  C5    C6   N1   117.94  3.000
 M2T  HN6A  N6   HN6  118.06  3.000
 M2T  HN6A  N6   C6   121.01  3.000
 M2T  HN6   N6   C6   120.13  3.000
 M2T  N7    C5   C6   133.06  3.000
 M2T  N7    C5   C4   110.74  3.000
 M2T  C6    C5   C4   116.20  3.000
 M2T  C8    N7   C5   104.36  3.000
 M2T  H8    C8   N7   124.76  3.000
 M2T  H8    C8   N9   121.88  3.000
 M2T  N7    C8   N9   113.36  3.000
 M2T  H2'   C2'  C3'  113.03  3.000
 M2T  H2'   C2'  O2'  111.57  3.000
 M2T  C3'   C2'  O2'  111.08  3.000
 M2T  H2'   C2'  C1'  112.12  3.000
 M2T  C3'   C2'  C1'  100.67  3.000
 M2T  O2'   C2'  C1'  107.79  3.000
 M2T  HO2'  O2'  C2'  107.46  3.000
 M2T  H3'   C3'  O3'  111.35  3.000
 M2T  H3'   C3'  C2'  109.43  3.000
 M2T  O3'   C3'  C2'  113.76  3.000
 M2T  H3'   C3'  C4'  109.52  3.000
 M2T  O3'   C3'  C4'  110.14  3.000
 M2T  C2'   C3'  C4'  102.23  3.000
 M2T  HO3'  O3'  C3'  108.81  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
 M2T  CONST_01  C5    N7   C8  N9      0.00   0.0  0
 M2T  CONST_02  C6    C5   C4  N9    180.00   0.0  0
 M2T  CONST_03  N7    C5   C4  N9      0.00   0.0  0
 M2T  CONST_04  C2    N3   C4  N9    180.00   0.0  0
 M2T  CONST_05  N7    C8   N9  C4      0.00   0.0  0
 M2T  CONST_06  N1    C6   C5  C4      0.00   0.0  0
 M2T  CONST_07  C8    N7   C5  C4      0.00   0.0  0
 M2T  CONST_08  N1    C2   N3  C4      0.00   0.0  0
 M2T  CONST_09  C8    N9   C4  N3    180.00   0.0  0
 M2T  CONST_10  C6    C5   C4  N3      0.00   0.0  0
 M2T  CONST_11  N7    C5   C4  N3    180.00   0.0  0
 M2T  CONST_12  C6    N1   C2  N3      0.00   0.0  0
 M2T  CONST_13  C5    C4   N3  C2      0.00   0.0  0
 M2T  CONST_14  C5    C6   N1  C2      0.00   0.0  0
 M2T  CONST_15  N7    C5   C6  N1    180.00   0.0  0
 M2T  CONST_16  C8    N7   C5  C6    180.00   0.0  0
 M2T  CONST_17  C8    N9   C4  C5      0.00   0.0  0
 M2T  CONST_18  N7    C8   N9  C1'   180.00   0.0  0
 M2T  CONST_19  C5    C4   N9  C1'   180.00   0.0  0
 M2T  CONST_20  N3    C4   N9  C1'     0.00   0.0  0
 M2T  CONST_21  N6    C6   C5  C4    180.00   0.0  0
 M2T  CONST_22  N6    C6   N1  C2    180.00   0.0  0
 M2T  CONST_23  N7    C5   C6  N6      0.00   0.0  0
 M2T  CONST_24  H8    C8   N9  C1'     0.00   0.0  0
 M2T  CONST_25  H2    C2   N3  C4    180.00   0.0  0
 M2T  CONST_26  HN6   N6   C6  N1      0.00   0.0  0
 M2T  CONST_27  HN6A  N6   C6  N1    180.00   0.0  0
 M2T  Var_01    C4'   C5'  SD  CG     83.02  30.0  3
 M2T  Var_02    HE    CE   SD  CG   -158.16  30.0  3
 M2T  Var_03    HG    CG   SD  CE     71.16  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
 M2T  chir_01  C4'  C5'  O4'  C3'  negativ
 M2T  chir_02  C1'  O4'  N9   C2'  negativ
 M2T  chir_03  C2'  O2'  C1'  C3'  negativ
 M2T  chir_04  C3'  O3'  C4'  C2'  positiv

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
 M2T  plan-1  C1'   0.020
 M2T  plan-1  N9    0.020
 M2T  plan-1  C4    0.020
 M2T  plan-1  N3    0.020
 M2T  plan-1  C2    0.020
 M2T  plan-1  N1    0.020
 M2T  plan-1  C6    0.020
 M2T  plan-1  N6    0.020
 M2T  plan-1  C5    0.020
 M2T  plan-1  N7    0.020
 M2T  plan-1  C8    0.020
 M2T  plan-1  H2    0.020
 M2T  plan-1  H8    0.020
 M2T  plan-2  C6    0.020
 M2T  plan-2  N6    0.020
 M2T  plan-2  HN6   0.020
 M2T  plan-2  HN6A  0.020

