# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 19:38:48 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: 6-(methylsulfanyl)-9-beta-D-ribofuranosyl-9H-purine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
#
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
 MTP  MTP  6-(methylsulfanyl)-9-beta-D-ribofuranosyl-9H-purine  ligand  34  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_MTP
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
 MTP  O5'   O  OH1   0  -0.668  -4.6923  -2.1544   0.8646
 MTP  C5'   C  CH2   0  -0.154  -4.0702  -1.5462  -0.2390
 MTP  C4'   C  CH1   0   0.006  -3.6518  -0.1477   0.1401
 MTP  O4'   O  O2    0  -0.494  -2.6726  -0.1759   1.1818
 MTP  C1'   C  CH1   0   0.172  -1.6434   0.7271   0.9302
 MTP  N9    N  NR5   0  -0.536  -0.4229  -0.0140   0.6112
 MTP  C8    C  CR15  0   0.113  -0.2742  -1.3469   0.3501
 MTP  N7    N  N     0  -0.445   0.9564  -1.6989   0.1073
 MTP  C5    C  CR56  0   0.115   1.6682  -0.5380   0.2180
 MTP  C6    C  CR6   0   0.043   3.0190  -0.2181   0.0777
 MTP  S6    S  S2    0   0.073   4.1606  -1.4640  -0.3379
 MTP  CS    C  CH3   0  -0.764   5.7093  -0.5431  -0.4136
 MTP  N1    N  N     0  -0.430   3.4057   1.0354   0.2596
 MTP  C2    C  CR16  0   0.042   2.4926   1.9586   0.5688
 MTP  N3    N  N     0  -0.429   1.1920   1.7853   0.7213
 MTP  C4    C  CR56  0   0.497   0.8255   0.5253   0.5366
 MTP  C2'   C  CH1   0  -0.040  -2.0887   1.5950  -0.2447
 MTP  O2'   O  OH1   0  -0.663  -2.8331   2.6602   0.2773
 MTP  C3'   C  CH1   0  -0.043  -2.9884   0.6140  -1.0043
 MTP  O3'   O  OH1   0  -0.655  -3.9604   1.2335  -1.7967
 MTP  H5'   H  HOH1  0   0.460  -5.0007  -3.0242   0.5951
 MTP  H5'1  H  HCH2  0   0.217  -4.7467  -1.4611  -1.0991
 MTP  H5'2  H  HCH2  0   0.197  -3.1923  -2.1120  -0.5814
 MTP  H4'   H  HCH1  0   0.249  -4.5286   0.4102   0.4917
 MTP  H1'   H  HCH1  0   0.290  -1.4305   1.3273   1.8188
 MTP  H8    H  HCR5  0   0.306  -1.1119  -2.0258   0.3621
 MTP  HS1   H  HCH3  0   0.280   5.9662  -0.1251   0.5560
 MTP  HS2   H  HCH3  0   0.285   6.4672  -1.2669  -0.7060
 MTP  HS3   H  HCH3  0   0.280   5.6588   0.2471  -1.1575
 MTP  H2    H  HCR6  0   0.265   2.8678   2.9657   0.7074
 MTP  H2'   H  HCH1  0   0.263  -1.2414   1.9460  -0.8454
 MTP  H1    H  HOH1  0   0.453  -3.4931   2.9076  -0.3823
 MTP  H3'   H  HCH1  0   0.247  -2.3608  -0.0670  -1.5950
 MTP  H3    H  HOH1  0   0.470  -3.5713   1.4631  -2.6469

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
 MTP  O5'  C5'   single    1.405  0.020  1.405
 MTP  O5'  H5'   single    0.850  0.020  0.980
 MTP  C5'  C4'   single    1.508  0.020  1.508
 MTP  C5'  H5'1  single    0.970  0.020  1.090
 MTP  C5'  H5'2  single    0.970  0.020  1.090
 MTP  C4'  O4'   single    1.430  0.020  1.430
 MTP  C4'  C3'   single    1.526  0.020  1.526
 MTP  C4'  H4'   single    0.970  0.020  1.090
 MTP  O4'  C1'   single    1.392  0.020  1.392
 MTP  C1'  N9    single    1.463  0.020  1.463
 MTP  C1'  C2'   single    1.527  0.020  1.527
 MTP  C1'  H1'   single    0.970  0.020  1.090
 MTP  N9   C8    aromatic  1.366  0.020  1.366
 MTP  N9   C4    aromatic  1.362  0.020  1.362
 MTP  C8   N7    aromatic  1.303  0.020  1.303
 MTP  C8   H8    single    0.930  0.020  1.080
 MTP  N7   C5    aromatic  1.366  0.020  1.366
 MTP  C5   C6    aromatic  1.395  0.020  1.395
 MTP  C5   C4    aromatic  1.394  0.020  1.394
 MTP  C6   S6    single    1.740  0.020  1.740
 MTP  C6   N1    aromatic  1.324  0.020  1.324
 MTP  S6   CS    single    1.803  0.020  1.803
 MTP  CS   HS1   single    0.970  0.020  1.090
 MTP  CS   HS2   single    0.970  0.020  1.090
 MTP  CS   HS3   single    0.970  0.020  1.090
 MTP  N1   C2    aromatic  1.335  0.020  1.335
 MTP  C2   N3    aromatic  1.321  0.020  1.321
 MTP  C2   H2    single    0.930  0.020  1.080
 MTP  N3   C4    aromatic  1.325  0.020  1.325
 MTP  C2'  O2'   single    1.400  0.020  1.400
 MTP  C2'  C3'   single    1.533  0.020  1.533
 MTP  C2'  H2'   single    0.970  0.020  1.090
 MTP  O2'  H1    single    0.850  0.020  0.980
 MTP  C3'  O3'   single    1.399  0.020  1.399
 MTP  C3'  H3'   single    0.970  0.020  1.090
 MTP  O3'  H3    single    0.850  0.020  0.980

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
 MTP  H5'   O5'  C5'   108.26  3.000
 MTP  H5'2  C5'  H5'1  106.74  3.000
 MTP  H5'2  C5'  C4'   109.52  3.000
 MTP  H5'1  C5'  C4'   107.22  3.000
 MTP  H5'2  C5'  O5'   112.05  3.000
 MTP  H5'1  C5'  O5'   112.09  3.000
 MTP  C4'   C5'  O5'   109.07  3.000
 MTP  H4'   C4'  C3'   109.51  3.000
 MTP  H4'   C4'  O4'   108.89  3.000
 MTP  C3'   C4'  O4'   104.97  3.000
 MTP  H4'   C4'  C5'   109.29  3.000
 MTP  C3'   C4'  C5'   113.26  3.000
 MTP  O4'   C4'  C5'   110.78  3.000
 MTP  C1'   O4'  C4'   111.21  3.000
 MTP  H1'   C1'  C2'   111.73  3.000
 MTP  H1'   C1'  N9    107.03  3.000
 MTP  C2'   C1'  N9    111.31  3.000
 MTP  H1'   C1'  O4'   110.69  3.000
 MTP  C2'   C1'  O4'   106.98  3.000
 MTP  N9    C1'  O4'   109.12  3.000
 MTP  C4    N9   C8    106.03  3.000
 MTP  C4    N9   C1'   125.17  3.000
 MTP  C8    N9   C1'   128.80  3.000
 MTP  H8    C8   N7    124.46  3.000
 MTP  H8    C8   N9    121.84  3.000
 MTP  N7    C8   N9    113.70  3.000
 MTP  C5    N7   C8    104.33  3.000
 MTP  C4    C5   C6    115.69  3.000
 MTP  C4    C5   N7    110.59  3.000
 MTP  C6    C5   N7    133.72  3.000
 MTP  N1    C6   S6    121.26  3.000
 MTP  N1    C6   C5    119.07  3.000
 MTP  S6    C6   C5    119.67  3.000
 MTP  CS    S6   C6    102.00  3.000
 MTP  HS3   CS   HS2   109.41  3.000
 MTP  HS3   CS   HS1   110.01  3.000
 MTP  HS2   CS   HS1   109.33  3.000
 MTP  HS3   CS   S6    111.12  3.000
 MTP  HS2   CS   S6    105.65  3.000
 MTP  HS1   CS   S6    111.22  3.000
 MTP  C2    N1   C6    119.13  3.000
 MTP  H2    C2   N3    116.62  3.000
 MTP  H2    C2   N1    115.82  3.000
 MTP  N3    C2   N1    127.55  3.000
 MTP  C4    N3   C2    112.39  3.000
 MTP  N3    C4   C5    126.16  3.000
 MTP  N3    C4   N9    128.49  3.000
 MTP  C5    C4   N9    105.35  3.000
 MTP  H2'   C2'  C3'   112.77  3.000
 MTP  H2'   C2'  O2'   111.80  3.000
 MTP  C3'   C2'  O2'   111.07  3.000
 MTP  H2'   C2'  C1'   112.22  3.000
 MTP  C3'   C2'  C1'   100.88  3.000
 MTP  O2'   C2'  C1'   107.49  3.000
 MTP  H1    O2'  C2'   107.68  3.000
 MTP  H3'   C3'  O3'   111.53  3.000
 MTP  H3'   C3'  C2'   109.14  3.000
 MTP  O3'   C3'  C2'   113.90  3.000
 MTP  H3'   C3'  C4'   110.01  3.000
 MTP  O3'   C3'  C4'   110.11  3.000
 MTP  C2'   C3'  C4'   101.71  3.000
 MTP  H3    O3'  C3'   108.97  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
 MTP  CONST_01  C5   N7  C8  N9     0.00   0.0  0
 MTP  CONST_02  N7   C5  C4  N9     0.00   0.0  0
 MTP  CONST_03  C6   C5  C4  N9   180.00   0.0  0
 MTP  CONST_04  C2   N3  C4  N9   180.00   0.0  0
 MTP  CONST_05  C5   C4  N9  C8     0.00   0.0  0
 MTP  CONST_06  N3   C4  N9  C8   180.00   0.0  0
 MTP  CONST_07  C6   C5  N7  C8   180.00   0.0  0
 MTP  CONST_08  C4   C5  N7  C8     0.00   0.0  0
 MTP  CONST_09  C4   N9  C8  N7     0.00   0.0  0
 MTP  CONST_10  N1   C6  C5  N7   180.00   0.0  0
 MTP  CONST_11  N3   C4  C5  N7   180.00   0.0  0
 MTP  CONST_12  C2   N1  C6  C5     0.00   0.0  0
 MTP  CONST_13  C2   N3  C4  C5     0.00   0.0  0
 MTP  CONST_14  N3   C4  C5  C6     0.00   0.0  0
 MTP  CONST_15  N3   C2  N1  C6     0.00   0.0  0
 MTP  CONST_16  C4   C5  C6  N1     0.00   0.0  0
 MTP  CONST_17  C4   N3  C2  N1     0.00   0.0  0
 MTP  CONST_18  N7   C8  N9  C1'  180.00   0.0  0
 MTP  CONST_19  C5   C4  N9  C1'  180.00   0.0  0
 MTP  CONST_20  N3   C4  N9  C1'    0.00   0.0  0
 MTP  CONST_21  S6   C6  C5  N7     0.00   0.0  0
 MTP  CONST_22  C4   C5  C6  S6   180.00   0.0  0
 MTP  CONST_23  C2   N1  C6  S6   180.00   0.0  0
 MTP  CONST_24  H8   C8  N9  C1'    0.00   0.0  0
 MTP  CONST_25  H2   C2  N1  C6   180.00   0.0  0
 MTP  Var_01    N1   C6  S6  CS    -0.47  30.0  1
 MTP  Var_02    HS1  CS  S6  C6    63.38  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
 MTP  chir_01  C4'  C5'  O4'  C3'  negativ
 MTP  chir_02  C1'  O4'  N9   C2'  negativ
 MTP  chir_03  C2'  O2'  C1'  C3'  negativ
 MTP  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
 MTP  plan-1  C1'  0.020
 MTP  plan-1  N9   0.020
 MTP  plan-1  C8   0.020
 MTP  plan-1  N7   0.020
 MTP  plan-1  C5   0.020
 MTP  plan-1  C6   0.020
 MTP  plan-1  S6   0.020
 MTP  plan-1  N1   0.020
 MTP  plan-1  C2   0.020
 MTP  plan-1  N3   0.020
 MTP  plan-1  C4   0.020
 MTP  plan-1  H8   0.020
 MTP  plan-1  H2   0.020

