# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 15:52:56 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: 2-(6-chloranyl-7-cyclopropyl-thieno[3,2-d]pyrimidin-4-yl)sulfanylethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSc1ncnc2c1sc(Cl)c2C3CC3
#
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
 M9K  M9K  '2-(6-chloranyl-7-cyclopropyl-thieno[3,2-d]pyrimidin-4-yl)sulfanylethanoic acid'  ligand  27  18  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M9K
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
 M9K  C10  C   CH2   0  -0.468  -0.5745  -7.7837  7.4579
 M9K  C02  C   C     0   0.570   7.6424  -3.3261  5.3958
 M9K  C03  C   CH2   0  -0.677   6.6592  -4.3620  5.8724
 M9K  C05  C   CR6   0   0.114   4.0549  -5.1927  5.8717
 M9K  C06  C   CR56  0  -0.219   2.6891  -5.2056  5.5842
 M9K  C07  C   CR56  0   0.241   1.9193  -6.2524  6.0994
 M9K  C08  C   CR5   0   0.392   0.5269  -6.1592  5.7378
 M9K  C09  C   CH1   0  -0.361  -0.5436  -7.0957  6.1182
 M9K  C11  C   CH2   0  -0.468  -0.3133  -8.5806  6.2255
 M9K  C12  C   CR5   0  -0.396   0.3406  -5.0515  4.9738
 M9K  C16  C   CR16  0   0.045   3.7633  -7.1102  7.0564
 M9K  N15  N   N     0  -0.430   2.4717  -7.2162  6.8462
 M9K  N17  N   N     0  -0.428   4.5788  -6.1516  6.6093
 M9K  O01  O   OH1   0  -0.580   8.8621  -3.5987  5.8207
 M9K  O18  O   O     0  -0.428   7.3473  -2.3771  4.7167
 M9K  S14  S   S2    0   0.309   1.7558  -4.0964  4.6579
 M9K  CL   CL  CL    0  -0.050  -1.1330  -4.5175  4.3053
 M9K  H1   H   HCH2  0   0.260   0.2523  -7.6191  8.1344
 M9K  H2   H   HCH2  0   0.261  -1.5421  -7.8681  7.9353
 M9K  H3   H   HCH2  0   0.334   6.9445  -5.3496  5.5081
 M9K  H4   H   HCH2  0   0.334   6.6504  -4.4005  6.9624
 M9K  H5   H   HCH1  0   0.262  -1.5158  -6.8154  5.7325
 M9K  H6   H   HCH2  0   0.261  -1.0986  -9.2197  5.8433
 M9K  H7   H   HCH2  0   0.259   0.6896  -8.9530  6.0701
 M9K  H8   H   HCR6  0   0.269   4.2283  -7.8813  7.6592
 M9K  H9   H   HOH1  0   0.491   9.4866  -2.9242  5.5121
 M9K  S04  S   S2    0   0.101   5.0327  -3.8956  5.2392

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
 M9K  CL   C12  single    1.704  0.020  1.704
 M9K  S14  C12  aromatic  1.736  0.020  1.736
 M9K  S14  C06  aromatic  1.720  0.020  1.720
 M9K  C12  C08  aromatic  1.358  0.020  1.358
 M9K  O18  C02  double    1.204  0.020  1.204
 M9K  C02  O01  single    1.320  0.020  1.320
 M9K  C02  C03  single    1.506  0.020  1.506
 M9K  S04  C03  single    1.807  0.020  1.807
 M9K  S04  C05  single    1.743  0.020  1.743
 M9K  C08  C09  single    1.472  0.020  1.472
 M9K  C08  C07  aromatic  1.442  0.020  1.442
 M9K  C06  C05  aromatic  1.396  0.020  1.396
 M9K  C06  C07  aromatic  1.398  0.020  1.398
 M9K  C09  C11  single    1.506  0.020  1.506
 M9K  C09  C10  single    1.506  0.020  1.506
 M9K  C05  N17  aromatic  1.318  0.020  1.318
 M9K  C07  N15  aromatic  1.339  0.020  1.339
 M9K  C11  C10  single    1.491  0.020  1.491
 M9K  N17  C16  aromatic  1.336  0.020  1.336
 M9K  N15  C16  aromatic  1.313  0.020  1.313
 M9K  C10  H1   single    0.970  0.020  1.090
 M9K  C10  H2   single    0.970  0.020  1.090
 M9K  C03  H3   single    0.970  0.020  1.090
 M9K  C03  H4   single    0.970  0.020  1.090
 M9K  C09  H5   single    0.970  0.020  1.090
 M9K  C11  H6   single    0.970  0.020  1.090
 M9K  C11  H7   single    0.970  0.020  1.090
 M9K  C16  H8   single    0.930  0.020  1.080
 M9K  O01  H9   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
 M9K  H2   C10  H1   114.81  3.000
 M9K  H2   C10  C11  118.67  3.000
 M9K  H1   C10  C11  117.70  3.000
 M9K  H2   C10  C09  116.50  3.000
 M9K  H1   C10  C09  118.12  3.000
 M9K  C11  C10  C09   60.35  3.000
 M9K  O18  C02  O01  124.82  3.000
 M9K  O01  C02  C03  111.06  3.000
 M9K  O18  C02  C03  124.12  3.000
 M9K  H4   C03  H3   107.69  3.000
 M9K  H4   C03  S04  110.61  3.000
 M9K  H3   C03  S04  110.62  3.000
 M9K  H4   C03  C02  110.24  3.000
 M9K  H3   C03  C02  110.28  3.000
 M9K  S04  C03  C02  107.42  3.000
 M9K  S04  C05  N17  121.42  3.000
 M9K  N17  C05  C06  119.83  3.000
 M9K  S04  C05  C06  118.75  3.000
 M9K  S14  C06  C07  112.50  3.000
 M9K  C07  C06  C05  118.03  3.000
 M9K  S14  C06  C05  129.48  3.000
 M9K  N15  C07  C08  125.81  3.000
 M9K  N15  C07  C06  121.17  3.000
 M9K  C08  C07  C06  113.02  3.000
 M9K  C12  C08  C09  124.35  3.000
 M9K  C09  C08  C07  126.61  3.000
 M9K  C12  C08  C07  109.04  3.000
 M9K  H5   C09  C11  114.70  3.000
 M9K  H5   C09  C08  113.34  3.000
 M9K  C11  C09  C08  122.29  3.000
 M9K  H5   C09  C10  114.62  3.000
 M9K  C11  C09  C10   59.31  3.000
 M9K  C08  C09  C10  122.36  3.000
 M9K  H7   C11  H6   114.77  3.000
 M9K  H7   C11  C09  118.12  3.000
 M9K  H6   C11  C09  116.48  3.000
 M9K  H7   C11  C10  117.75  3.000
 M9K  H6   C11  C10  118.72  3.000
 M9K  C09  C11  C10   60.34  3.000
 M9K  CL   C12  S14  117.46  3.000
 M9K  S14  C12  C08  116.05  3.000
 M9K  CL   C12  C08  126.49  3.000
 M9K  H8   C16  N17  115.79  3.000
 M9K  H8   C16  N15  116.98  3.000
 M9K  N17  C16  N15  127.23  3.000
 M9K  C16  N15  C07  115.93  3.000
 M9K  C16  N17  C05  117.82  3.000
 M9K  H9   O01  C02  110.42  3.000
 M9K  C12  S14  C06   89.40  3.000
 M9K  C05  S04  C03  100.70  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
 M9K  CONST_01  C12  S14  C06  C05   180.00   0.0  0
 M9K  CONST_02  C08  C07  C06  C05   180.00   0.0  0
 M9K  CONST_03  N15  C07  C06  C05     0.00   0.0  0
 M9K  CONST_04  N15  C16  N17  C05     0.00   0.0  0
 M9K  CONST_05  C08  C12  S14  C06     0.00   0.0  0
 M9K  CONST_06  C16  N17  C05  C06     0.00   0.0  0
 M9K  CONST_07  C12  C08  C07  C06     0.00   0.0  0
 M9K  CONST_08  C16  N15  C07  C06     0.00   0.0  0
 M9K  CONST_09  S14  C12  C08  C07     0.00   0.0  0
 M9K  CONST_10  C12  S14  C06  C07     0.00   0.0  0
 M9K  CONST_11  N17  C05  C06  C07     0.00   0.0  0
 M9K  CONST_12  N17  C16  N15  C07     0.00   0.0  0
 M9K  CONST_13  S14  C06  C07  C08     0.00   0.0  0
 M9K  CONST_14  C16  N15  C07  C08   180.00   0.0  0
 M9K  CONST_15  N15  C07  C08  C12   180.00   0.0  0
 M9K  CONST_16  S14  C06  C07  N15   180.00   0.0  0
 M9K  CONST_17  S14  C06  C05  N17   180.00   0.0  0
 M9K  CONST_18  C09  C08  C07  C06   180.00   0.0  0
 M9K  CONST_19  S14  C12  C08  C09   180.00   0.0  0
 M9K  CONST_20  N15  C07  C08  C09     0.00   0.0  0
 M9K  CONST_21  CL   C12  S14  C06   180.00   0.0  0
 M9K  CONST_22  CL   C12  C08  C07   180.00   0.0  0
 M9K  CONST_23  S04  C05  C06  C07   180.00   0.0  0
 M9K  CONST_24  CL   C12  C08  C09     0.00   0.0  0
 M9K  CONST_25  S04  C05  N17  C16   180.00   0.0  0
 M9K  CONST_26  S14  C06  C05  S04     0.00   0.0  0
 M9K  CONST_27  H8   C16  N17  C05   180.00   0.0  0
 M9K  CONST_28  H9   O01  C02  C03   180.00   0.0  0
 M9K  Var_01    C12  C08  C09  C10  -144.51  30.0  2
 M9K  Var_02    C08  C09  C11  C10   111.17  30.0  1
 M9K  Var_03    C06  C05  S04  C03  -179.39  30.0  2
 M9K  Var_04    H3   C03  S04  C05    59.17  30.0  3
 M9K  Var_05    S04  C03  C02  O01   179.99  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
 M9K  chir_01  C09  C08  C11  C10  both

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
 M9K  plan-1  C05  0.020
 M9K  plan-1  C06  0.020
 M9K  plan-1  C07  0.020
 M9K  plan-1  C08  0.020
 M9K  plan-1  C09  0.020
 M9K  plan-1  C12  0.020
 M9K  plan-1  C16  0.020
 M9K  plan-1  N15  0.020
 M9K  plan-1  N17  0.020
 M9K  plan-1  S14  0.020
 M9K  plan-1  CL   0.020
 M9K  plan-1  H8   0.020
 M9K  plan-1  S04  0.020
 M9K  plan-2  C02  0.020
 M9K  plan-2  C03  0.020
 M9K  plan-2  O01  0.020
 M9K  plan-2  O18  0.020
 M9K  plan-2  H9   0.020

