# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 03:04:05 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 5'-S-methyl-5'-thioadenosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[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
 MTA  MTA  5'-S-methyl-5'-thioadenosine  ligand  35  20  .  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_MTA
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
 MTA  CS    C  CH3   0  -0.767   2.6746  -0.5416   4.4723
 MTA  S5'   S  S2    0  -0.021   1.7074   0.5426   3.3996
 MTA  C5'   C  CH2   0  -0.583   0.1810  -0.4317   3.3106
 MTA  C4'   C  CH1   0  -0.003  -0.9287   0.3888   2.6751
 MTA  O4'   O  O2    0  -0.491  -0.4914   0.9997   1.4575
 MTA  C2'   C  CH1   0  -0.054  -1.7367  -0.8986   0.8755
 MTA  O2'   O  OH1   0  -0.651  -2.8078  -1.2404   0.0481
 MTA  C3'   C  CH1   0  -0.013  -2.1289  -0.4665   2.2918
 MTA  O3'   O  OH1   0  -0.667  -3.2726   0.3448   2.2698
 MTA  C1'   C  CH1   0   0.219  -1.0584   0.3690   0.3477
 MTA  N9    N  NR5   0  -0.539  -0.0267   0.1089  -0.6293
 MTA  C8    C  CR15  0   0.110   1.2336  -0.3739  -0.3983
 MTA  N7    N  N     0  -0.451   1.9293  -0.5352  -1.4846
 MTA  C5    C  CR56  0  -0.011   1.0870  -0.1408  -2.4918
 MTA  C6    C  CR6   0   0.459   1.2337  -0.0684  -3.8893
 MTA  N6    N  NH2   0  -0.817   2.3520  -0.4338  -4.5169
 MTA  N1    N  N     0  -0.475   0.2000   0.3888  -4.6050
 MTA  C2    C  CR16  0   0.043  -0.9139   0.7530  -3.9747
 MTA  N3    N  N     0  -0.455  -1.1722   0.7247  -2.6790
 MTA  C4    C  CR56  0   0.490  -0.1350   0.2682  -1.9805
 MTA  HCS1  H  HCH3  0   0.264   2.8587  -1.5046   3.9984
 MTA  HCS2  H  HCH3  0   0.276   3.6310  -0.0551   4.6541
 MTA  HCS3  H  HCH3  0   0.263   2.1744  -0.6981   5.4269
 MTA  H5'1  H  HCH2  0   0.265   0.3756  -1.3601   2.7670
 MTA  H5'2  H  HCH2  0   0.289  -0.1293  -0.7046   4.3214
 MTA  H4'   H  HCH1  0   0.272  -1.2163   1.1884   3.3625
 MTA  H2'   H  HCH1  0   0.252  -1.0019  -1.7110   0.9350
 MTA  HO2'  H  HOH1  0   0.470  -3.0365  -2.1628   0.2009
 MTA  H3'   H  HCH1  0   0.253  -2.2458  -1.3245   2.9662
 MTA  H3T   H  HOH1  0   0.450  -3.9196  -0.0689   1.6861
 MTA  H1'   H  HCH1  0   0.265  -1.7920   1.0126  -0.1494
 MTA  H8    H  HCR5  0   0.292   1.5966  -0.5617   0.6021
 MTA  H61   H  HNH2  0   0.403   2.4196  -0.3655  -5.5176
 MTA  H62   H  HNH2  0   0.411   3.1430  -0.7865  -4.0079
 MTA  H2    H  HCR6  0   0.251  -1.7112   1.1188  -4.6131

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
 MTA  CS   S5'   single    1.806  0.020  1.806
 MTA  CS   HCS1  single    0.970  0.020  1.090
 MTA  CS   HCS2  single    0.970  0.020  1.090
 MTA  CS   HCS3  single    0.970  0.020  1.090
 MTA  S5'  C5'   single    1.813  0.020  1.813
 MTA  C5'  C4'   single    1.519  0.020  1.519
 MTA  C5'  H5'1  single    0.970  0.020  1.090
 MTA  C5'  H5'2  single    0.970  0.020  1.090
 MTA  C4'  O4'   single    1.431  0.020  1.431
 MTA  C4'  C3'   single    1.523  0.020  1.523
 MTA  C4'  H4'   single    0.970  0.020  1.090
 MTA  O4'  C1'   single    1.397  0.020  1.397
 MTA  C2'  O2'   single    1.396  0.020  1.396
 MTA  C2'  C3'   single    1.532  0.020  1.532
 MTA  C2'  C1'   single    1.532  0.020  1.532
 MTA  C2'  H2'   single    0.970  0.020  1.090
 MTA  O2'  HO2'  single    0.850  0.020  0.980
 MTA  C3'  O3'   single    1.402  0.020  1.402
 MTA  C3'  H3'   single    0.970  0.020  1.090
 MTA  O3'  H3T   single    0.850  0.020  0.980
 MTA  C1'  N9    single    1.445  0.020  1.445
 MTA  C1'  H1'   single    0.970  0.020  1.090
 MTA  N9   C8    aromatic  1.369  0.020  1.369
 MTA  N9   C4    aromatic  1.365  0.020  1.365
 MTA  C8   N7    aromatic  1.300  0.020  1.300
 MTA  C8   H8    single    0.930  0.020  1.080
 MTA  N7   C5    aromatic  1.371  0.020  1.371
 MTA  C5   C6    aromatic  1.407  0.020  1.407
 MTA  C5   C4    aromatic  1.386  0.020  1.386
 MTA  C6   N6    single    1.333  0.020  1.333
 MTA  C6   N1    aromatic  1.338  0.020  1.338
 MTA  N6   H61   single    0.860  0.020  1.020
 MTA  N6   H62   single    0.860  0.020  1.020
 MTA  N1   C2    aromatic  1.331  0.020  1.331
 MTA  C2   N3    aromatic  1.321  0.020  1.321
 MTA  C2   H2    single    0.930  0.020  1.080
 MTA  N3   C4    aromatic  1.331  0.020  1.331

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
 MTA  HCS3  CS   HCS2  108.75  3.000
 MTA  HCS3  CS   HCS1  109.40  3.000
 MTA  HCS2  CS   HCS1  108.63  3.000
 MTA  HCS3  CS   S5'   111.16  3.000
 MTA  HCS2  CS   S5'   107.54  3.000
 MTA  HCS1  CS   S5'   111.28  3.000
 MTA  C5'   S5'  CS     99.06  3.000
 MTA  H5'2  C5'  H5'1  107.37  3.000
 MTA  H5'2  C5'  C4'   108.34  3.000
 MTA  H5'1  C5'  C4'   112.37  3.000
 MTA  H5'2  C5'  S5'   109.15  3.000
 MTA  H5'1  C5'  S5'   109.33  3.000
 MTA  C4'   C5'  S5'   110.20  3.000
 MTA  H4'   C4'  C3'   111.21  3.000
 MTA  H4'   C4'  O4'   107.66  3.000
 MTA  C3'   C4'  O4'   105.46  3.000
 MTA  H4'   C4'  C5'   108.91  3.000
 MTA  C3'   C4'  C5'   112.18  3.000
 MTA  O4'   C4'  C5'   111.30  3.000
 MTA  C1'   O4'  C4'   111.06  3.000
 MTA  H2'   C2'  C1'   109.57  3.000
 MTA  H2'   C2'  C3'   109.28  3.000
 MTA  C1'   C2'  C3'   101.45  3.000
 MTA  H2'   C2'  O2'   111.40  3.000
 MTA  C1'   C2'  O2'   109.77  3.000
 MTA  C3'   C2'  O2'   114.87  3.000
 MTA  HO2'  O2'  C2'   108.83  3.000
 MTA  H3'   C3'  O3'   112.03  3.000
 MTA  H3'   C3'  C2'   112.02  3.000
 MTA  O3'   C3'  C2'   110.94  3.000
 MTA  H3'   C3'  C4'   111.62  3.000
 MTA  O3'   C3'  C4'   108.77  3.000
 MTA  C2'   C3'  C4'   100.91  3.000
 MTA  H3T   O3'  C3'   107.97  3.000
 MTA  H1'   C1'  N9    106.09  3.000
 MTA  H1'   C1'  C2'   110.25  3.000
 MTA  N9    C1'  C2'   113.60  3.000
 MTA  H1'   C1'  O4'   111.55  3.000
 MTA  N9    C1'  O4'   109.19  3.000
 MTA  C2'   C1'  O4'   106.25  3.000
 MTA  C4    N9   C8    106.33  3.000
 MTA  C4    N9   C1'   126.29  3.000
 MTA  C8    N9   C1'   127.36  3.000
 MTA  H8    C8   N7    124.90  3.000
 MTA  H8    C8   N9    121.78  3.000
 MTA  N7    C8   N9    113.29  3.000
 MTA  C5    N7   C8    104.44  3.000
 MTA  C4    C5   C6    116.30  3.000
 MTA  C4    C5   N7    110.83  3.000
 MTA  C6    C5   N7    132.87  3.000
 MTA  N1    C6   N6    119.33  3.000
 MTA  N1    C6   C5    117.93  3.000
 MTA  N6    C6   C5    122.74  3.000
 MTA  H62   N6   H61   118.38  3.000
 MTA  H62   N6   C6    121.21  3.000
 MTA  H61   N6   C6    120.41  3.000
 MTA  C2    N1   C6    119.14  3.000
 MTA  H2    C2   N3    116.13  3.000
 MTA  H2    C2   N1    115.39  3.000
 MTA  N3    C2   N1    128.48  3.000
 MTA  C4    N3   C2    111.68  3.000
 MTA  N3    C4   C5    126.48  3.000
 MTA  N3    C4   N9    128.41  3.000
 MTA  C5    C4   N9    105.11  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
 MTA  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 MTA  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 MTA  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 MTA  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 MTA  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 MTA  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 MTA  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 MTA  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 MTA  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 MTA  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 MTA  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 MTA  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 MTA  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 MTA  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 MTA  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 MTA  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 MTA  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 MTA  CONST_18  N7    C8   N9   C1'  180.00   0.0  0
 MTA  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 MTA  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 MTA  CONST_21  N6    C6   C5   N7     0.00   0.0  0
 MTA  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 MTA  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 MTA  CONST_24  H8    C8   N9   C1'    0.00   0.0  0
 MTA  CONST_25  H2    C2   N1   C6   180.00   0.0  0
 MTA  CONST_26  H61   N6   C6   C5   180.00   0.0  0
 MTA  CONST_27  H62   N6   C6   C5     0.00   0.0  0
 MTA  Var_01    C4'   C5'  S5'  CS   168.88  30.0  3
 MTA  Var_02    HCS1  CS   S5'  C5'   63.44  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
 MTA  chir_01  C4'  C5'  O4'  C3'  negativ
 MTA  chir_02  C2'  O2'  C3'  C1'  positiv
 MTA  chir_03  C3'  O3'  C2'  C4'  negativ
 MTA  chir_04  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
 MTA  plan-1  C1'  0.020
 MTA  plan-1  N9   0.020
 MTA  plan-1  C8   0.020
 MTA  plan-1  N7   0.020
 MTA  plan-1  C5   0.020
 MTA  plan-1  C6   0.020
 MTA  plan-1  N6   0.020
 MTA  plan-1  N1   0.020
 MTA  plan-1  C2   0.020
 MTA  plan-1  N3   0.020
 MTA  plan-1  C4   0.020
 MTA  plan-1  H8   0.020
 MTA  plan-1  H2   0.020
 MTA  plan-2  C6   0.020
 MTA  plan-2  N6   0.020
 MTA  plan-2  H61  0.020
 MTA  plan-2  H62  0.020

