# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:37:32 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: 7-(5-S-methyl-5-thio-beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2ccc3c(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
 MTH  MTH  7-(5-S-methyl-5-thio-beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine  ligand  36  20  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MTH
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
 MTH  CS    C  CH3   0  -0.767   4.5831  -2.5820   0.4190
 MTH  S5'   S  S2    0  -0.021   3.4418  -1.6370  -0.6136
 MTH  C5'   C  CH2   0  -0.582   3.3186  -0.1392   0.3991
 MTH  C4'   C  CH1   0  -0.001   2.6164   0.9642  -0.3763
 MTH  O4'   O  O2    0  -0.492   1.3984   0.4963  -0.9574
 MTH  C2'   C  CH1   0  -0.057   0.8340   1.6750   0.9854
 MTH  O2'   O  OH1   0  -0.651  -0.0150   2.7048   1.3950
 MTH  C3'   C  CH1   0  -0.013   2.2205   2.1291   0.5220
 MTH  O3'   O  OH1   0  -0.669   2.1326   3.2936  -0.2552
 MTH  C1'   C  CH1   0   0.215   0.2853   1.0230  -0.2869
 MTH  N9    N  NR5   0  -0.551  -0.6687  -0.0250  -0.0392
 MTH  C8    C  CR15  0  -0.008  -0.4018  -1.2468   0.5434
 MTH  C7    C  CR15  0  -0.440  -1.5541  -1.9598   0.6701
 MTH  C5    C  CR56  0  -0.089  -2.5936  -1.1390   0.1374
 MTH  C6    C  CR6   0   0.443  -3.9861  -1.2282  -0.0561
 MTH  N6    N  NH2   0  -0.823  -4.6929  -2.3089   0.2977
 MTH  N1    N  N     0  -0.479  -4.6329  -0.2078  -0.6263
 MTH  C2    C  CR16  0   0.041  -3.9325   0.8630  -0.9947
 MTH  N3    N  N     0  -0.461  -2.6387   1.0757  -0.8660
 MTH  C4    C  CR56  0   0.518  -2.0029   0.0506  -0.2949
 MTH  HCS1  H  HCH3  0   0.262   5.5235  -2.0501   0.5564
 MTH  HCS2  H  HCH3  0   0.263   4.1458  -2.7994   1.3924
 MTH  HCS3  H  HCH3  0   0.276   4.7846  -3.5232  -0.0889
 MTH  H5'1  H  HCH2  0   0.262   2.8070  -0.3762   1.3361
 MTH  H5'2  H  HCH2  0   0.287   4.3235   0.2041   0.6541
 MTH  H4'1  H  HCH1  0   0.267   3.2698   1.2970  -1.1874
 MTH  H2'1  H  HCH1  0   0.247   0.9483   0.9153   1.7687
 MTH  HO21  H  HOH1  0   0.468   0.1687   2.9098   2.3174
 MTH  H3'1  H  HCH1  0   0.249   2.9188   2.2477   1.3609
 MTH  HO31  H  HOH1  0   0.449   1.5278   3.9007   0.1879
 MTH  H1'1  H  HCH1  0   0.260  -0.2326   1.7690  -0.8982
 MTH  HC81  H  HCR5  0   0.290   0.6062  -1.5330   0.7974
 MTH  HC71  H  HCR5  0   0.256  -1.6350  -2.9530   1.0824
 MTH  HN61  H  HNH2  0   0.406  -4.2756  -3.0652   0.8095
 MTH  HN62  H  HNH2  0   0.400  -5.6942  -2.3038   0.2067
 MTH  HC21  H  HCR6  0   0.245  -4.5064   1.6592  -1.4580

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
 MTH  CS   S5'   single    1.806  0.020  1.806
 MTH  CS   HCS1  single    0.970  0.020  1.090
 MTH  CS   HCS2  single    0.970  0.020  1.090
 MTH  CS   HCS3  single    0.970  0.020  1.090
 MTH  S5'  C5'   single    1.812  0.020  1.812
 MTH  C5'  C4'   single    1.521  0.020  1.521
 MTH  C5'  H5'1  single    0.970  0.020  1.090
 MTH  C5'  H5'2  single    0.970  0.020  1.090
 MTH  C4'  O4'   single    1.428  0.020  1.428
 MTH  C4'  C3'   single    1.523  0.020  1.523
 MTH  C4'  H4'1  single    0.970  0.020  1.090
 MTH  O4'  C1'   single    1.402  0.020  1.402
 MTH  C2'  O2'   single    1.396  0.020  1.396
 MTH  C2'  C3'   single    1.531  0.020  1.531
 MTH  C2'  C1'   single    1.531  0.020  1.531
 MTH  C2'  H2'1  single    0.970  0.020  1.090
 MTH  O2'  HO21  single    0.850  0.020  0.980
 MTH  C3'  O3'   single    1.403  0.020  1.403
 MTH  C3'  H3'1  single    0.970  0.020  1.090
 MTH  O3'  HO31  single    0.850  0.020  0.980
 MTH  C1'  N9    single    1.439  0.020  1.439
 MTH  C1'  H1'1  single    0.970  0.020  1.090
 MTH  N9   C8    aromatic  1.380  0.020  1.380
 MTH  N9   C4    aromatic  1.361  0.020  1.361
 MTH  C8   C7    aromatic  1.361  0.020  1.361
 MTH  C8   HC81  single    0.930  0.020  1.080
 MTH  C7   C5    aromatic  1.428  0.020  1.428
 MTH  C7   HC71  single    0.930  0.020  1.080
 MTH  C5   C6    aromatic  1.409  0.020  1.409
 MTH  C5   C4    aromatic  1.397  0.020  1.397
 MTH  C6   N6    single    1.339  0.020  1.339
 MTH  C6   N1    aromatic  1.336  0.020  1.336
 MTH  N6   HN61  single    0.860  0.020  1.020
 MTH  N6   HN62  single    0.860  0.020  1.020
 MTH  N1   C2    aromatic  1.332  0.020  1.332
 MTH  C2   N3    aromatic  1.317  0.020  1.317
 MTH  C2   HC21  single    0.930  0.020  1.080
 MTH  N3   C4    aromatic  1.335  0.020  1.335

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
 MTH  HCS3  CS   HCS2  108.59  3.000
 MTH  HCS3  CS   HCS1  108.75  3.000
 MTH  HCS2  CS   HCS1  109.36  3.000
 MTH  HCS3  CS   S5'   107.62  3.000
 MTH  HCS2  CS   S5'   111.21  3.000
 MTH  HCS1  CS   S5'   111.24  3.000
 MTH  C5'   S5'  CS     98.97  3.000
 MTH  H5'2  C5'  H5'1  107.37  3.000
 MTH  H5'2  C5'  C4'   108.41  3.000
 MTH  H5'1  C5'  C4'   112.22  3.000
 MTH  H5'2  C5'  S5'   109.13  3.000
 MTH  H5'1  C5'  S5'   109.36  3.000
 MTH  C4'   C5'  S5'   110.25  3.000
 MTH  H4'1  C4'  C3'   111.10  3.000
 MTH  H4'1  C4'  O4'   107.91  3.000
 MTH  C3'   C4'  O4'   105.60  3.000
 MTH  H4'1  C4'  C5'   108.85  3.000
 MTH  C3'   C4'  C5'   111.97  3.000
 MTH  O4'   C4'  C5'   111.32  3.000
 MTH  C1'   O4'  C4'   111.06  3.000
 MTH  H2'1  C2'  C1'   109.61  3.000
 MTH  H2'1  C2'  C3'   109.10  3.000
 MTH  C1'   C2'  C3'   101.50  3.000
 MTH  H2'1  C2'  O2'   111.39  3.000
 MTH  C1'   C2'  O2'   109.87  3.000
 MTH  C3'   C2'  O2'   114.88  3.000
 MTH  HO21  O2'  C2'   108.79  3.000
 MTH  H3'1  C3'  O3'   111.93  3.000
 MTH  H3'1  C3'  C2'   112.14  3.000
 MTH  O3'   C3'  C2'   110.93  3.000
 MTH  H3'1  C3'  C4'   111.59  3.000
 MTH  O3'   C3'  C4'   108.93  3.000
 MTH  C2'   C3'  C4'   100.78  3.000
 MTH  HO31  O3'  C3'   107.89  3.000
 MTH  H1'1  C1'  N9    106.19  3.000
 MTH  H1'1  C1'  C2'   110.08  3.000
 MTH  N9    C1'  C2'   113.87  3.000
 MTH  H1'1  C1'  O4'   111.38  3.000
 MTH  N9    C1'  O4'   109.58  3.000
 MTH  C2'   C1'  O4'   105.83  3.000
 MTH  C4    N9   C8    108.56  3.000
 MTH  C4    N9   C1'   125.27  3.000
 MTH  C8    N9   C1'   126.13  3.000
 MTH  HC81  C8   C7    129.09  3.000
 MTH  HC81  C8   N9    121.03  3.000
 MTH  C7    C8   N9    109.84  3.000
 MTH  HC71  C7   C5    128.14  3.000
 MTH  HC71  C7   C8    125.56  3.000
 MTH  C5    C7   C8    106.29  3.000
 MTH  C4    C5   C6    115.43  3.000
 MTH  C4    C5   C7    107.29  3.000
 MTH  C6    C5   C7    137.27  3.000
 MTH  N1    C6   N6    118.27  3.000
 MTH  N1    C6   C5    119.27  3.000
 MTH  N6    C6   C5    122.46  3.000
 MTH  HN62  N6   HN61  117.63  3.000
 MTH  HN62  N6   C6    119.85  3.000
 MTH  HN61  N6   C6    121.55  3.000
 MTH  C2    N1   C6    118.53  3.000
 MTH  HC21  C2   N3    116.26  3.000
 MTH  HC21  C2   N1    115.47  3.000
 MTH  N3    C2   N1    128.27  3.000
 MTH  C4    N3   C2    112.68  3.000
 MTH  N3    C4   C5    125.81  3.000
 MTH  N3    C4   N9    126.18  3.000
 MTH  C5    C4   N9    108.01  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
 MTH  CONST_01  C5    C7   C8   N9     0.00   0.0  0
 MTH  CONST_02  C7    C5   C4   N9     0.00   0.0  0
 MTH  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 MTH  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 MTH  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 MTH  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 MTH  CONST_07  C6    C5   C7   C8   180.00   0.0  0
 MTH  CONST_08  C4    C5   C7   C8     0.00   0.0  0
 MTH  CONST_09  C4    N9   C8   C7     0.00   0.0  0
 MTH  CONST_10  N1    C6   C5   C7   180.00   0.0  0
 MTH  CONST_11  N3    C4   C5   C7   180.00   0.0  0
 MTH  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 MTH  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 MTH  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 MTH  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 MTH  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 MTH  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 MTH  CONST_18  C7    C8   N9   C1'  180.00   0.0  0
 MTH  CONST_19  C5    C4   N9   C1'  180.00   0.0  0
 MTH  CONST_20  N3    C4   N9   C1'    0.00   0.0  0
 MTH  CONST_21  N6    C6   C5   C7     0.00   0.0  0
 MTH  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 MTH  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 MTH  CONST_24  HC81  C8   N9   C1'    0.00   0.0  0
 MTH  CONST_25  HC71  C7   C8   N9   180.00   0.0  0
 MTH  CONST_26  HC21  C2   N1   C6   180.00   0.0  0
 MTH  CONST_27  HN61  N6   C6   C5     0.00   0.0  0
 MTH  CONST_28  HN62  N6   C6   C5   180.00   0.0  0
 MTH  Var_01    C4'   C5'  S5'  CS   168.84  30.0  3
 MTH  Var_02    HCS1  CS   S5'  C5'  -59.16  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
 MTH  chir_01  C4'  C5'  O4'  C3'  negativ
 MTH  chir_02  C2'  O2'  C3'  C1'  positiv
 MTH  chir_03  C3'  O3'  C4'  C2'  positiv
 MTH  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
 MTH  plan-1  C1'   0.020
 MTH  plan-1  N9    0.020
 MTH  plan-1  C8    0.020
 MTH  plan-1  C7    0.020
 MTH  plan-1  C5    0.020
 MTH  plan-1  C6    0.020
 MTH  plan-1  N6    0.020
 MTH  plan-1  N1    0.020
 MTH  plan-1  C2    0.020
 MTH  plan-1  N3    0.020
 MTH  plan-1  C4    0.020
 MTH  plan-1  HC81  0.020
 MTH  plan-1  HC71  0.020
 MTH  plan-1  HC21  0.020
 MTH  plan-2  C6    0.020
 MTH  plan-2  N6    0.020
 MTH  plan-2  HN61  0.020
 MTH  plan-2  HN62  0.020

