# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 16:01:25 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 6-(5-methyl-1H-pyrazol-4-yl)-2-[(pyrrolidin-1-yl)methyl]thieno[3,2-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]ncc1c2sc3C(=O)NC(=Nc3c2)CN4CCCC4
#
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
 O1S  O1S  6-(5-methyl-1H-pyrazol-4-yl)-2-[(pyrrolidin-1-yl)methyl]thieno[3,2-d]pyrimidin-4(3H)-one  ligand  39  22  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_O1S
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
 O1S  N3   N  NR15  0  -0.478   5.5431  -1.5788  -0.3664
 O1S  C6   C  CR15  0  -0.107   3.6276  -2.4244  -0.4115
 O1S  C7   C  CR5   0  -0.103   3.4437  -1.0225  -0.3911
 O1S  C8   C  CR5   0  -0.212   2.1800  -0.3255  -0.3983
 O1S  C10  C  CR56  0   0.356  -0.1048   0.0738  -0.4352
 O1S  C15  C  CH2   0  -0.277  -5.5563  -0.9411  -0.6251
 O1S  C17  C  CH2   0  -0.465  -4.8793  -2.4210   1.1735
 O1S  C21  C  CR6   0   0.539  -0.4843   2.4933  -0.3246
 O1S  C2   C  CR5   0   0.406   4.7363  -0.5092  -0.3615
 O1S  N5   N  N     0  -0.253   4.9009  -2.7440  -0.3961
 O1S  C9   C  CR15  0  -0.312   0.9334  -0.8901  -0.4596
 O1S  N11  N  N     0  -0.458  -1.4366  -0.2137  -0.4796
 O1S  C12  C  CR6   0   0.480  -2.2378   0.7961  -0.4441
 O1S  N14  N  NT    0  -0.420  -4.1651  -0.7131  -0.2680
 O1S  C16  C  CH2   0  -0.468  -5.8639  -2.3053  -0.0098
 O1S  C18  C  CH2   0  -0.282  -4.0687  -1.1242   1.1236
 O1S  N19  N  NR16  0  -0.704  -1.8113   2.0863  -0.3652
 O1S  O22  O  O     0  -0.466  -0.1697   3.6708  -0.2628
 O1S  C23  C  CR56  0  -0.406   0.3854   1.3650  -0.3605
 O1S  S24  S  S2    0   0.237   2.0989   1.4079  -0.3149
 O1S  H1   H  HNR5  0   0.423   6.5516  -1.5650  -0.3515
 O1S  H2   H  HCR5  0   0.263   2.8720  -3.1950  -0.4349
 O1S  H3   H  HCH2  0   0.231  -4.2080   1.3645   0.1402
 O1S  H4   H  HCH2  0   0.291  -4.0244   0.9088  -1.5448
 O1S  H6   H  HCH2  0   0.238  -5.6904  -0.9146  -1.7086
 O1S  H7   H  HCH2  0   0.235  -5.3875  -2.5304   2.1309
 O1S  H8   H  HCH2  0   0.236  -4.2296  -3.2880   1.0528
 O1S  H12  H  HCR5  0   0.266   0.7541  -1.9542  -0.5172
 O1S  H14  H  HCH2  0   0.235  -6.9051  -2.3742   0.3028
 O1S  H15  H  HCH2  0   0.236  -5.6922  -3.1011  -0.7347
 O1S  H16  H  HCH2  0   0.196  -4.5151  -0.3686   1.7922
 O1S  H17  H  HCH2  0   0.239  -3.0299  -1.2584   1.4252
 O1S  H18  H  HNR6  0   0.429  -2.5072   2.8217  -0.3351
 O1S  C13  C  CH2   0  -0.368  -3.7303   0.6254  -0.5277
 O1S  C1   C  CH3   0  -0.770   5.2593   0.8803  -0.3301
 O1S  H5   H  HCH2  0   0.196  -6.2173  -0.1721  -0.1917
 O1S  H9   H  HCH3  0   0.267   4.9196   1.4500  -1.1957
 O1S  H10  H  HCH3  0   0.268   4.9295   1.4080   0.5656
 O1S  H11  H  HCH3  0   0.279   6.3484   0.8885  -0.3361

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
 O1S  N5   C6   aromatic  1.313  0.020  1.313
 O1S  N5   N3   aromatic  1.331  0.020  1.331
 O1S  C6   C7   aromatic  1.414  0.020  1.414
 O1S  N3   C2   aromatic  1.340  0.020  1.340
 O1S  C9   C8   aromatic  1.370  0.020  1.370
 O1S  C9   C10  aromatic  1.417  0.020  1.417
 O1S  C7   C2   aromatic  1.391  0.020  1.391
 O1S  C7   C8   single    1.443  0.020  1.443
 O1S  N11  C10  single    1.363  0.020  1.363
 O1S  N11  C12  double    1.289  0.020  1.289
 O1S  C2   C1   single    1.485  0.020  1.485
 O1S  C8   S24  aromatic  1.737  0.020  1.737
 O1S  C13  C12  single    1.505  0.020  1.505
 O1S  C13  N14  single    1.431  0.020  1.431
 O1S  C10  C23  aromatic  1.383  0.020  1.383
 O1S  C12  N19  single    1.361  0.020  1.361
 O1S  C18  N14  single    1.454  0.020  1.454
 O1S  C18  C17  single    1.530  0.020  1.530
 O1S  C15  N14  single    1.454  0.020  1.454
 O1S  C15  C16  single    1.528  0.020  1.528
 O1S  C17  C16  single    1.544  0.020  1.544
 O1S  C23  S24  aromatic  1.715  0.020  1.715
 O1S  C23  C21  single    1.425  0.020  1.425
 O1S  N19  C21  single    1.389  0.020  1.389
 O1S  C21  O22  double    1.220  0.020  1.220
 O1S  N3   H1   single    0.860  0.020  1.020
 O1S  C6   H2   single    0.930  0.020  1.080
 O1S  C13  H3   single    0.970  0.020  1.090
 O1S  C13  H4   single    0.970  0.020  1.090
 O1S  C15  H5   single    0.970  0.020  1.090
 O1S  C15  H6   single    0.970  0.020  1.090
 O1S  C17  H7   single    0.970  0.020  1.090
 O1S  C17  H8   single    0.970  0.020  1.090
 O1S  C1   H9   single    0.970  0.020  1.090
 O1S  C1   H10  single    0.970  0.020  1.090
 O1S  C1   H11  single    0.970  0.020  1.090
 O1S  C9   H12  single    0.930  0.020  1.080
 O1S  C16  H14  single    0.970  0.020  1.090
 O1S  C16  H15  single    0.970  0.020  1.090
 O1S  C18  H16  single    0.970  0.020  1.090
 O1S  C18  H17  single    0.970  0.020  1.090
 O1S  N19  H18  single    0.860  0.020  1.020

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
 O1S  H1   N3   N5   119.65  3.000
 O1S  H1   N3   C2   126.24  3.000
 O1S  N5   N3   C2   114.11  3.000
 O1S  H2   C6   N5   120.35  3.000
 O1S  H2   C6   C7   128.09  3.000
 O1S  N5   C6   C7   111.55  3.000
 O1S  C2   C7   C8   129.46  3.000
 O1S  C8   C7   C6   126.34  3.000
 O1S  C2   C7   C6   104.19  3.000
 O1S  S24  C8   C9   111.78  3.000
 O1S  S24  C8   C7   121.50  3.000
 O1S  C9   C8   C7   126.72  3.000
 O1S  C23  C10  N11  123.02  3.000
 O1S  C23  C10  C9   112.10  3.000
 O1S  N11  C10  C9   124.88  3.000
 O1S  H6   C15  H5   107.43  3.000
 O1S  H6   C15  C16  113.36  3.000
 O1S  H5   C15  C16  110.10  3.000
 O1S  H6   C15  N14  110.93  3.000
 O1S  H5   C15  N14  111.57  3.000
 O1S  C16  C15  N14  103.51  3.000
 O1S  H8   C17  H7   107.18  3.000
 O1S  H8   C17  C18  110.78  3.000
 O1S  H7   C17  C18  111.16  3.000
 O1S  H8   C17  C16  110.79  3.000
 O1S  H7   C17  C16  112.56  3.000
 O1S  C18  C17  C16  104.44  3.000
 O1S  C23  C21  O22  127.44  3.000
 O1S  O22  C21  N19  122.05  3.000
 O1S  C23  C21  N19  110.51  3.000
 O1S  C1   C2   C7   132.29  3.000
 O1S  C1   C2   N3   122.34  3.000
 O1S  C7   C2   N3   105.36  3.000
 O1S  C6   N5   N3   104.78  3.000
 O1S  H12  C9   C10  123.32  3.000
 O1S  H12  C9   C8   124.00  3.000
 O1S  C10  C9   C8   112.68  3.000
 O1S  C12  N11  C10  116.16  3.000
 O1S  N19  C12  N11  123.31  3.000
 O1S  N19  C12  C13  114.93  3.000
 O1S  N11  C12  C13  121.73  3.000
 O1S  C18  N14  C15  104.72  3.000
 O1S  C15  N14  C13  113.12  3.000
 O1S  C18  N14  C13  114.70  3.000
 O1S  H15  C16  H14  107.17  3.000
 O1S  H15  C16  C17  110.77  3.000
 O1S  H14  C16  C17  112.64  3.000
 O1S  H15  C16  C15  110.63  3.000
 O1S  H14  C16  C15  111.37  3.000
 O1S  C17  C16  C15  104.31  3.000
 O1S  H17  C18  H16  107.59  3.000
 O1S  H17  C18  N14  111.27  3.000
 O1S  H16  C18  N14  111.07  3.000
 O1S  H17  C18  C17  113.05  3.000
 O1S  H16  C18  C17  110.27  3.000
 O1S  N14  C18  C17  103.63  3.000
 O1S  H18  N19  C12  118.34  3.000
 O1S  H18  N19  C21  116.29  3.000
 O1S  C12  N19  C21  125.37  3.000
 O1S  S24  C23  C21  126.11  3.000
 O1S  C21  C23  C10  121.61  3.000
 O1S  S24  C23  C10  112.27  3.000
 O1S  C23  S24  C8    91.17  3.000
 O1S  H4   C13  H3   105.78  3.000
 O1S  H4   C13  N14  109.19  3.000
 O1S  H3   C13  N14  112.62  3.000
 O1S  H4   C13  C12  106.77  3.000
 O1S  H3   C13  C12  108.63  3.000
 O1S  N14  C13  C12  113.42  3.000
 O1S  H11  C1   H10  107.66  3.000
 O1S  H11  C1   H9   107.65  3.000
 O1S  H10  C1   H9   107.75  3.000
 O1S  H11  C1   C2   111.05  3.000
 O1S  H10  C1   C2   111.32  3.000
 O1S  H9   C1   C2   111.24  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
 O1S  CONST_01  C7   C6   N5   N3      0.00   0.0  0
 O1S  CONST_02  C6   C7   C2   N3      0.00   0.0  0
 O1S  CONST_03  C8   C7   C2   N3    180.00   0.0  0
 O1S  CONST_04  C2   N3   N5   C6      0.00   0.0  0
 O1S  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 O1S  CONST_06  S24  C8   C7   C6    180.00   0.0  0
 O1S  CONST_07  N5   N3   C2   C7      0.00   0.0  0
 O1S  CONST_08  C10  C9   C8   C7    180.00   0.0  0
 O1S  CONST_09  C23  S24  C8   C7    180.00   0.0  0
 O1S  CONST_10  C23  C10  C9   C8      0.00   0.0  0
 O1S  CONST_11  N5   C6   C7   C8    180.00   0.0  0
 O1S  CONST_12  C10  C23  S24  C8      0.00   0.0  0
 O1S  CONST_13  S24  C8   C9   C10     0.00   0.0  0
 O1S  CONST_14  N5   C6   C7   C2      0.00   0.0  0
 O1S  CONST_15  C9   C8   C7   C2    180.00   0.0  0
 O1S  CONST_16  S24  C8   C7   C2      0.00   0.0  0
 O1S  CONST_17  C23  S24  C8   C9      0.00   0.0  0
 O1S  CONST_18  S24  C23  C10  C9      0.00   0.0  0
 O1S  CONST_19  N19  C12  N11  C10     0.00   0.0  0
 O1S  CONST_20  N11  C12  N19  C21     0.00   0.0  0
 O1S  CONST_21  C23  C21  N19  C12     0.00   0.0  0
 O1S  CONST_22  C1   C2   C7   C6    180.00   0.0  0
 O1S  CONST_23  C1   C2   C7   C8      0.00   0.0  0
 O1S  CONST_24  N5   N3   C2   C1    180.00   0.0  0
 O1S  CONST_25  C13  C12  N11  C10   180.00   0.0  0
 O1S  CONST_26  C21  N19  C12  C13   180.00   0.0  0
 O1S  CONST_27  O22  C21  N19  C12   180.00   0.0  0
 O1S  CONST_28  H2   C6   N5   N3    180.00   0.0  0
 O1S  CONST_29  H1   N3   N5   C6    180.00   0.0  0
 O1S  CONST_30  H12  C9   C8   C7      0.00   0.0  0
 O1S  CONST_31  H18  N19  C12  N11   180.00   0.0  0
 O1S  Var_01    C17  C18  N14  C15    42.63  30.0  1
 O1S  Var_02    C18  C17  C16  C15    -1.05  30.0  1
 O1S  Var_03    N14  C15  C16  C17    26.33  30.0  1
 O1S  Var_04    C16  C17  C18  N14   -24.60  30.0  1
 O1S  Var_05    C18  N14  C15  C16   -43.35  30.0  1
 O1S  Var_06    C12  C13  N14  C15  -167.63  30.0  1
 O1S  Var_07    N14  C13  C12  N11    16.67  30.0  2
 O1S  Var_08    H9   C1   C2   N3    121.20  30.0  2

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
 O1S  plan-1  N3   0.020
 O1S  plan-1  C6   0.020
 O1S  plan-1  C7   0.020
 O1S  plan-1  C8   0.020
 O1S  plan-1  C2   0.020
 O1S  plan-1  N5   0.020
 O1S  plan-1  H1   0.020
 O1S  plan-1  H2   0.020
 O1S  plan-1  C1   0.020
 O1S  plan-2  C7   0.020
 O1S  plan-2  C8   0.020
 O1S  plan-2  C10  0.020
 O1S  plan-2  C21  0.020
 O1S  plan-2  C9   0.020
 O1S  plan-2  N11  0.020
 O1S  plan-2  C12  0.020
 O1S  plan-2  N19  0.020
 O1S  plan-2  O22  0.020
 O1S  plan-2  C23  0.020
 O1S  plan-2  S24  0.020
 O1S  plan-2  H12  0.020
 O1S  plan-2  H18  0.020
 O1S  plan-2  C13  0.020

