# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 05:40:02 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (2R,3R,4S)-2-(hydroxymethyl)-1-[(4-hydroxythieno[3,2-d]pyrimidin-7-yl)methyl]pyrrolidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@@H](O)CN1Cc2csc3c(O)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
 MBY  MBY  (2R,3R,4S)-2-(hydroxymethyl)-1-[(4-hydroxythieno[3,2-d]pyrimidin-7-yl)methyl]pyrrolidine-3,4-diol  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_MBY
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
 MBY  O6   O  OH1   0  -0.594  -4.2588   1.5087   0.6635
 MBY  C6   C  CR6   0   0.506  -3.1999   1.2160  -0.0683
 MBY  N1   N  N     0  -0.463  -2.9073   1.9236  -1.1359
 MBY  C2   C  CR16  0   0.038  -1.8254   1.5692  -1.8401
 MBY  N3   N  N     0  -0.433  -1.0007   0.5821  -1.5858
 MBY  C4   C  CR56  0   0.287  -1.2860  -0.1443  -0.4920
 MBY  C5   C  CR56  0  -0.328  -2.3952   0.1395   0.3056
 MBY  C9   C  CR5   0   0.196  -0.5498  -1.2802  -0.0124
 MBY  C8   C  CR15  0  -0.531  -1.1396  -1.7945   1.0968
 MBY  S7   S  S2    0   0.248  -2.5555  -0.9555   1.6204
 MBY  C7   C  CH2   0  -0.395   0.7171  -1.8064  -0.6349
 MBY  N4'  N  NR5   0  -0.439   1.9326  -1.1895  -0.1654
 MBY  C4'  C  CR15  0  -0.087   2.2107   0.1843  -0.5398
 MBY  C5'  C  CH2   0  -0.180   2.5429   0.3540  -2.0078
 MBY  O5'  O  OH1   0  -0.670   3.6503  -0.4436  -2.3562
 MBY  C3'  C  CR15  0   0.039   3.3523   0.5352   0.4203
 MBY  O3'  O  OH1   0  -0.671   3.6157   1.9057   0.5469
 MBY  C2'  C  CR15  0  -0.029   2.8627  -0.0777   1.7240
 MBY  O2'  O  OH1   0  -0.669   1.8761   0.7777   2.2557
 MBY  C1'  C  CH2   0  -0.282   2.2915  -1.4055   1.2314
 MBY  H2   H  HCR6  0   0.262  -1.6177   2.1715  -2.7173
 MBY  H3   H  HCR5  0   0.308  -0.8181  -2.6643   1.6516
 MBY  H4   H  HCH2  0   0.257   0.7819  -2.8813  -0.4477
 MBY  H5   H  HCH2  0   0.256   0.6578  -1.6892  -1.7190
 MBY  H7   H  HCR5  0   0.220   1.3737   0.8702  -0.3364
 MBY  H8   H  HCH2  0   0.212   1.6572   0.1036  -2.6055
 MBY  H9   H  HCH2  0   0.194   2.7358   1.4218  -2.1832
 MBY  H10  H  HOH1  0   0.453   3.8745  -0.2557  -3.2715
 MBY  H11  H  HCR5  0   0.223   4.2507  -0.0172   0.1159
 MBY  H12  H  HOH1  0   0.452   4.1893   2.1722  -0.1767
 MBY  H13  H  HCR5  0   0.226   3.6773  -0.2339   2.4427
 MBY  H14  H  HOH1  0   0.447   1.4155   0.3083   2.9571
 MBY  H15  H  HCH2  0   0.224   1.4388  -1.7032   1.8534
 MBY  H16  H  HCH2  0   0.225   3.0366  -2.2040   1.3235
 MBY  H17  H  HOH1  0   0.499  -4.7253   2.2649   0.2784

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
 MBY  O2'  C2'  single    1.410  0.020  1.410
 MBY  O3'  C3'  single    1.401  0.020  1.401
 MBY  C2'  C3'  single    1.522  0.020  1.522
 MBY  C2'  C1'  single    1.527  0.020  1.527
 MBY  C3'  C4'  single    1.532  0.020  1.532
 MBY  C1'  N4'  single    1.458  0.020  1.458
 MBY  C4'  N4'  single    1.451  0.020  1.451
 MBY  C4'  C5'  single    1.515  0.020  1.515
 MBY  N4'  C7   single    1.442  0.020  1.442
 MBY  C5'  O5'  single    1.408  0.020  1.408
 MBY  C2   N3   aromatic  1.311  0.020  1.311
 MBY  C2   N1   aromatic  1.339  0.020  1.339
 MBY  N3   C4   aromatic  1.344  0.020  1.344
 MBY  N1   C6   aromatic  1.314  0.020  1.314
 MBY  C4   C9   aromatic  1.436  0.020  1.436
 MBY  C4   C5   aromatic  1.395  0.020  1.395
 MBY  C7   C9   single    1.506  0.020  1.506
 MBY  C6   C5   aromatic  1.395  0.020  1.395
 MBY  C6   O6   single    1.320  0.020  1.320
 MBY  C9   C8   aromatic  1.357  0.020  1.357
 MBY  C5   S7   aromatic  1.719  0.020  1.719
 MBY  C8   S7   aromatic  1.727  0.020  1.727
 MBY  C2   H2   single    0.930  0.020  1.080
 MBY  C8   H3   single    0.930  0.020  1.080
 MBY  C7   H4   single    0.970  0.020  1.090
 MBY  C7   H5   single    0.970  0.020  1.090
 MBY  C4'  H7   single    0.970  0.020  1.090
 MBY  C5'  H8   single    0.970  0.020  1.090
 MBY  C5'  H9   single    0.970  0.020  1.090
 MBY  O5'  H10  single    0.850  0.020  0.980
 MBY  C3'  H11  single    0.970  0.020  1.090
 MBY  O3'  H12  single    0.850  0.020  0.980
 MBY  C2'  H13  single    0.970  0.020  1.090
 MBY  O2'  H14  single    0.850  0.020  0.980
 MBY  C1'  H15  single    0.970  0.020  1.090
 MBY  C1'  H16  single    0.970  0.020  1.090
 MBY  O6   H17  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
 MBY  H17  O6   C6   109.83  3.000
 MBY  C5   C6   N1   120.33  3.000
 MBY  C5   C6   O6   119.03  3.000
 MBY  N1   C6   O6   120.64  3.000
 MBY  C2   N1   C6   117.70  3.000
 MBY  H2   C2   N3   117.05  3.000
 MBY  H2   C2   N1   115.68  3.000
 MBY  N3   C2   N1   127.27  3.000
 MBY  C4   N3   C2   115.55  3.000
 MBY  C9   C4   C5   112.18  3.000
 MBY  C5   C4   N3   121.61  3.000
 MBY  C9   C4   N3   126.20  3.000
 MBY  S7   C5   C4   112.45  3.000
 MBY  S7   C5   C6   130.01  3.000
 MBY  C4   C5   C6   117.53  3.000
 MBY  C7   C9   C8   124.80  3.000
 MBY  C8   C9   C4   110.47  3.000
 MBY  C7   C9   C4   124.71  3.000
 MBY  H3   C8   S7   118.64  3.000
 MBY  H3   C8   C9   126.52  3.000
 MBY  S7   C8   C9   114.83  3.000
 MBY  C8   S7   C5    90.07  3.000
 MBY  H5   C7   H4   106.19  3.000
 MBY  H5   C7   N4'  108.85  3.000
 MBY  H4   C7   N4'  108.37  3.000
 MBY  H5   C7   C9   109.09  3.000
 MBY  H4   C7   C9   108.82  3.000
 MBY  N4'  C7   C9   115.15  3.000
 MBY  C1'  N4'  C4'  109.89  3.000
 MBY  C4'  N4'  C7   118.87  3.000
 MBY  C1'  N4'  C7   117.13  3.000
 MBY  H7   C4'  C3'  107.94  3.000
 MBY  H7   C4'  C5'  106.02  3.000
 MBY  C3'  C4'  C5'  114.72  3.000
 MBY  H7   C4'  N4'  113.36  3.000
 MBY  C5'  C4'  N4'  113.47  3.000
 MBY  C3'  C4'  N4'  101.42  3.000
 MBY  H9   C5'  H8   106.04  3.000
 MBY  H9   C5'  O5'  111.88  3.000
 MBY  H8   C5'  O5'  111.76  3.000
 MBY  H9   C5'  C4'  107.58  3.000
 MBY  H8   C5'  C4'  108.98  3.000
 MBY  O5'  C5'  C4'  110.41  3.000
 MBY  H10  O5'  C5'  107.96  3.000
 MBY  H11  C3'  C2'  107.35  3.000
 MBY  H11  C3'  O3'  111.31  3.000
 MBY  C2'  C3'  O3'  112.15  3.000
 MBY  H11  C3'  C4'  108.71  3.000
 MBY  C2'  C3'  C4'  101.82  3.000
 MBY  O3'  C3'  C4'  114.87  3.000
 MBY  H12  O3'  C3'  108.38  3.000
 MBY  H13  C2'  C1'  111.41  3.000
 MBY  H13  C2'  O2'  111.03  3.000
 MBY  C1'  C2'  O2'  112.80  3.000
 MBY  H13  C2'  C3'  112.31  3.000
 MBY  C1'  C2'  C3'  101.20  3.000
 MBY  O2'  C2'  C3'  107.69  3.000
 MBY  H14  O2'  C2'  108.30  3.000
 MBY  H16  C1'  H15  106.45  3.000
 MBY  H16  C1'  C2'  110.61  3.000
 MBY  H15  C1'  C2'  110.11  3.000
 MBY  H16  C1'  N4'  110.84  3.000
 MBY  H15  C1'  N4'  113.09  3.000
 MBY  C2'  C1'  N4'  105.80  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
 MBY  CONST_01  N3   C2   N1   C6     0.00   0.0  0
 MBY  CONST_02  N3   C4   C5   C6     0.00   0.0  0
 MBY  CONST_03  C9   C4   C5   C6   180.00   0.0  0
 MBY  CONST_04  C8   S7   C5   C6   180.00   0.0  0
 MBY  CONST_05  C4   N3   C2   N1     0.00   0.0  0
 MBY  CONST_06  C4   C5   C6   N1     0.00   0.0  0
 MBY  CONST_07  S7   C5   C6   N1   180.00   0.0  0
 MBY  CONST_08  C9   C4   N3   C2   180.00   0.0  0
 MBY  CONST_09  C5   C4   N3   C2     0.00   0.0  0
 MBY  CONST_10  C5   C6   N1   C2     0.00   0.0  0
 MBY  CONST_11  C8   C9   C4   N3   180.00   0.0  0
 MBY  CONST_12  S7   C5   C4   N3   180.00   0.0  0
 MBY  CONST_13  S7   C8   C9   C4     0.00   0.0  0
 MBY  CONST_14  C8   S7   C5   C4     0.00   0.0  0
 MBY  CONST_15  C8   C9   C4   C5     0.00   0.0  0
 MBY  CONST_16  C9   C8   S7   C5     0.00   0.0  0
 MBY  CONST_17  S7   C5   C4   C9     0.00   0.0  0
 MBY  CONST_18  C2   N1   C6   O6   180.00   0.0  0
 MBY  CONST_19  C4   C5   C6   O6   180.00   0.0  0
 MBY  CONST_20  S7   C5   C6   O6     0.00   0.0  0
 MBY  CONST_21  C7   C9   C4   N3     0.00   0.0  0
 MBY  CONST_22  C7   C9   C4   C5   180.00   0.0  0
 MBY  CONST_23  C7   C9   C8   S7   180.00   0.0  0
 MBY  CONST_24  H2   C2   N1   C6   180.00   0.0  0
 MBY  CONST_25  H3   C8   C9   C4   180.00   0.0  0
 MBY  Var_01    C2'  C1'  N4'  C4'   -1.63  30.0  1
 MBY  Var_02    N4'  C7   C9   C4    86.96  30.0  2
 MBY  Var_03    C1'  N4'  C7   C9    65.75  30.0  1

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
 MBY  chir_01  C4'  C3'  N4'  C5'  positiv
 MBY  chir_02  C3'  O3'  C4'  C2'  positiv
 MBY  chir_03  C2'  O2'  C3'  C1'  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
 MBY  plan-1  O6  0.020
 MBY  plan-1  C6  0.020
 MBY  plan-1  N1  0.020
 MBY  plan-1  C2  0.020
 MBY  plan-1  N3  0.020
 MBY  plan-1  C4  0.020
 MBY  plan-1  C5  0.020
 MBY  plan-1  C9  0.020
 MBY  plan-1  C8  0.020
 MBY  plan-1  S7  0.020
 MBY  plan-1  C7  0.020
 MBY  plan-1  H2  0.020
 MBY  plan-1  H3  0.020

