# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 18:43:31 2021
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-[6-(4-cyclopropylphenyl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CSc1ncnc2cc(sc12)c3ccc(cc3)C4CC4
#
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
 QM2  QM2  '2-[6-(4-cyclopropylphenyl)thieno[3,2-d]pyrimidin-4-yl]sulfanylethanoic acid'  ligand  37  23  .  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_QM2
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
 QM2  N1   N  N     0  -0.432  59.9140   1.3091  -4.4452
 QM2  C2   C  CR6   0   0.110  60.9821   1.5957  -3.7261
 QM2  C4   C  CR56  0   0.356  62.2864   0.2716  -5.2319
 QM2  C5   C  CR15  0  -0.279  63.6103  -0.1866  -5.4897
 QM2  C6   C  CR5   0  -0.178  64.5121   0.2753  -4.5795
 QM2  O1   O  O     0  -0.432  57.6540   4.4018  -1.0470
 QM2  C    C  C     0   0.571  58.7277   3.8663  -1.1283
 QM2  O    O  OH1   0  -0.582  59.6735   3.9353  -0.2091
 QM2  C1   C  CH2   0  -0.677  59.1132   3.0145  -2.3117
 QM2  S    S  S2    0   0.095  60.8748   2.5965  -2.3010
 QM2  C16  C  CR16  0   0.036  60.0739   0.5229  -5.5147
 QM2  N    N  N     0  -0.437  61.1905  -0.0150  -5.9495
 QM2  S1   S  S2    0   0.246  63.7710   1.2985  -3.3723
 QM2  C3   C  CR56  0  -0.235  62.2261   1.0882  -4.0973
 QM2  C7   C  CR6   0   0.132  65.9486   0.0257  -4.5269
 QM2  C15  C  CR16  0  -0.296  66.6955   0.2823  -3.3742
 QM2  C14  C  CR16  0  -0.335  68.0560   0.0396  -3.3369
 QM2  C10  C  CR6   0   0.219  68.7278  -0.4748  -4.4472
 QM2  C9   C  CR16  0  -0.302  67.9791  -0.7312  -5.5966
 QM2  C8   C  CR16  0  -0.305  66.6186  -0.4844  -5.6409
 QM2  C11  C  CH1   0  -0.373  70.1809  -0.7477  -4.4386
 QM2  C13  C  CH2   0  -0.475  70.8773  -1.1909  -3.1785
 QM2  C12  C  CH2   0  -0.473  71.1355   0.1716  -3.7195
 QM2  H1   H  HCR5  0   0.279  63.8567  -0.8422  -6.3125
 QM2  H2   H  HOH1  0   0.494  59.3875   4.4807   0.5412
 QM2  H3   H  HCH2  0   0.330  58.8549   3.5444  -3.2275
 QM2  H4   H  HCH2  0   0.335  58.5168   2.1007  -2.2852
 QM2  H5   H  HCR6  0   0.266  59.1736   0.3121  -6.0802
 QM2  H6   H  HCR6  0   0.259  66.2186   0.6642  -2.4792
 QM2  H7   H  HCR6  0   0.258  68.5924   0.2533  -2.4202
 QM2  H8   H  HCR6  0   0.259  68.4702  -1.1262  -6.4774
 QM2  H9   H  HCR6  0   0.261  66.0805  -0.6836  -6.5587
 QM2  H10  H  HCH1  0   0.265  70.5540  -1.1810  -5.3595
 QM2  H11  H  HCH2  0   0.256  70.2762  -1.2785  -2.2814
 QM2  H12  H  HCH2  0   0.265  71.6490  -1.9428  -3.2756
 QM2  H13  H  HCH2  0   0.264  72.0873   0.3697  -4.1950
 QM2  H14  H  HCH2  0   0.255  70.7127   1.0205  -3.1959

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
 QM2  N    C16  aromatic  1.313  0.020  1.313
 QM2  N    C4   aromatic  1.341  0.020  1.341
 QM2  C16  N1   aromatic  1.337  0.020  1.337
 QM2  C8   C9   aromatic  1.383  0.020  1.383
 QM2  C8   C7   aromatic  1.396  0.020  1.396
 QM2  C9   C10  aromatic  1.396  0.020  1.396
 QM2  C5   C4   aromatic  1.424  0.020  1.424
 QM2  C5   C6   aromatic  1.362  0.020  1.362
 QM2  C4   C3   aromatic  1.399  0.020  1.399
 QM2  C6   C7   single    1.459  0.020  1.459
 QM2  C6   S1   aromatic  1.747  0.020  1.747
 QM2  C7   C15  aromatic  1.397  0.020  1.397
 QM2  N1   C2   aromatic  1.319  0.020  1.319
 QM2  C10  C11  single    1.479  0.020  1.479
 QM2  C10  C14  aromatic  1.396  0.020  1.396
 QM2  C11  C12  single    1.508  0.020  1.508
 QM2  C11  C13  single    1.506  0.020  1.506
 QM2  C3   C2   aromatic  1.394  0.020  1.394
 QM2  C3   S1   aromatic  1.719  0.020  1.719
 QM2  C12  C13  single    1.489  0.020  1.489
 QM2  C2   S    single    1.745  0.020  1.745
 QM2  C15  C14  aromatic  1.382  0.020  1.382
 QM2  C1   S    single    1.810  0.020  1.810
 QM2  C1   C    single    1.508  0.020  1.508
 QM2  C    O1   double    1.203  0.020  1.203
 QM2  C    O    single    1.321  0.020  1.321
 QM2  C5   H1   single    0.930  0.020  1.080
 QM2  O    H2   single    0.850  0.020  0.980
 QM2  C1   H3   single    0.970  0.020  1.090
 QM2  C1   H4   single    0.970  0.020  1.090
 QM2  C16  H5   single    0.930  0.020  1.080
 QM2  C15  H6   single    0.930  0.020  1.080
 QM2  C14  H7   single    0.930  0.020  1.080
 QM2  C9   H8   single    0.930  0.020  1.080
 QM2  C8   H9   single    0.930  0.020  1.080
 QM2  C11  H10  single    0.970  0.020  1.090
 QM2  C13  H11  single    0.970  0.020  1.090
 QM2  C13  H12  single    0.970  0.020  1.090
 QM2  C12  H13  single    0.970  0.020  1.090
 QM2  C12  H14  single    0.970  0.020  1.090

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
 QM2  C16  N1   C2   117.84  3.000
 QM2  C3   C2   S    118.76  3.000
 QM2  S    C2   N1   121.34  3.000
 QM2  C3   C2   N1   119.90  3.000
 QM2  C3   C4   N    121.57  3.000
 QM2  C3   C4   C5   111.99  3.000
 QM2  N    C4   C5   126.44  3.000
 QM2  H1   C5   C6   124.31  3.000
 QM2  H1   C5   C4   123.02  3.000
 QM2  C6   C5   C4   112.67  3.000
 QM2  C7   C6   S1   119.53  3.000
 QM2  S1   C6   C5   112.30  3.000
 QM2  C7   C6   C5   128.17  3.000
 QM2  C1   C    O    113.11  3.000
 QM2  O    C    O1   124.68  3.000
 QM2  C1   C    O1   122.20  3.000
 QM2  H2   O    C    110.88  3.000
 QM2  H4   C1   H3   107.34  3.000
 QM2  H4   C1   S    109.77  3.000
 QM2  H3   C1   S    110.37  3.000
 QM2  H4   C1   C    108.30  3.000
 QM2  H3   C1   C    108.93  3.000
 QM2  S    C1   C    111.99  3.000
 QM2  C1   S    C2   100.80  3.000
 QM2  H5   C16  N    116.99  3.000
 QM2  H5   C16  N1   115.61  3.000
 QM2  N    C16  N1   127.40  3.000
 QM2  C16  N    C4   115.47  3.000
 QM2  C3   S1   C6    91.04  3.000
 QM2  S1   C3   C4   112.00  3.000
 QM2  S1   C3   C2   130.17  3.000
 QM2  C4   C3   C2   117.83  3.000
 QM2  C8   C7   C15  117.95  3.000
 QM2  C15  C7   C6   121.64  3.000
 QM2  C8   C7   C6   120.40  3.000
 QM2  H6   C15  C14  118.22  3.000
 QM2  H6   C15  C7   120.71  3.000
 QM2  C14  C15  C7   121.06  3.000
 QM2  H7   C14  C10  120.50  3.000
 QM2  H7   C14  C15  118.38  3.000
 QM2  C10  C14  C15  121.12  3.000
 QM2  C11  C10  C9   119.88  3.000
 QM2  C11  C10  C14  122.44  3.000
 QM2  C9   C10  C14  117.68  3.000
 QM2  H8   C9   C8   119.01  3.000
 QM2  H8   C9   C10  119.57  3.000
 QM2  C8   C9   C10  121.41  3.000
 QM2  H9   C8   C9   118.90  3.000
 QM2  H9   C8   C7   120.34  3.000
 QM2  C9   C8   C7   120.76  3.000
 QM2  H10  C11  C12  115.53  3.000
 QM2  H10  C11  C13  115.72  3.000
 QM2  C12  C11  C13   59.19  3.000
 QM2  H10  C11  C10  114.03  3.000
 QM2  C13  C11  C10  120.89  3.000
 QM2  C12  C11  C10  120.82  3.000
 QM2  H12  C13  H11  114.44  3.000
 QM2  H12  C13  C12  118.67  3.000
 QM2  H11  C13  C12  118.11  3.000
 QM2  H12  C13  C11  117.34  3.000
 QM2  H11  C13  C11  117.39  3.000
 QM2  C12  C13  C11   60.46  3.000
 QM2  H14  C12  H13  114.35  3.000
 QM2  H14  C12  C13  118.29  3.000
 QM2  H13  C12  C13  118.67  3.000
 QM2  H14  C12  C11  117.46  3.000
 QM2  H13  C12  C11  117.31  3.000
 QM2  C13  C12  C11   60.36  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
 QM2  CONST_01  C4   N    C16  N1     0.00   0.0  0
 QM2  CONST_02  C4   C3   C2   N1     0.00   0.0  0
 QM2  CONST_03  S1   C3   C2   N1   180.00   0.0  0
 QM2  CONST_04  N    C16  N1   C2     0.00   0.0  0
 QM2  CONST_05  N    C4   C3   C2     0.00   0.0  0
 QM2  CONST_06  C5   C4   C3   C2   180.00   0.0  0
 QM2  CONST_07  C6   S1   C3   C2   180.00   0.0  0
 QM2  CONST_08  C7   C6   C5   C4   180.00   0.0  0
 QM2  CONST_09  S1   C6   C5   C4     0.00   0.0  0
 QM2  CONST_10  C6   S1   C3   C4     0.00   0.0  0
 QM2  CONST_11  C16  N    C4   C5   180.00   0.0  0
 QM2  CONST_12  S1   C3   C4   C5     0.00   0.0  0
 QM2  CONST_15  C3   S1   C6   C5     0.00   0.0  0
 QM2  CONST_16  N    C4   C5   C6   180.00   0.0  0
 QM2  CONST_17  C3   C4   C5   C6     0.00   0.0  0
 QM2  CONST_18  C9   C8   C7   C6   180.00   0.0  0
 QM2  CONST_19  C14  C15  C7   C6   180.00   0.0  0
 QM2  CONST_20  C3   C4   N    C16    0.00   0.0  0
 QM2  CONST_21  C3   C2   N1   C16    0.00   0.0  0
 QM2  CONST_22  S1   C3   C4   N    180.00   0.0  0
 QM2  CONST_25  C7   C6   S1   C3   180.00   0.0  0
 QM2  CONST_26  C10  C9   C8   C7     0.00   0.0  0
 QM2  CONST_27  C10  C14  C15  C7     0.00   0.0  0
 QM2  CONST_28  C9   C8   C7   C15    0.00   0.0  0
 QM2  CONST_29  C9   C10  C14  C15    0.00   0.0  0
 QM2  CONST_30  C8   C9   C10  C14    0.00   0.0  0
 QM2  CONST_31  C8   C7   C15  C14    0.00   0.0  0
 QM2  CONST_32  C11  C10  C14  C15  180.00   0.0  0
 QM2  CONST_33  C11  C10  C9   C8   180.00   0.0  0
 QM2  CONST_34  S    C2   C3   C4   180.00   0.0  0
 QM2  CONST_35  C16  N1   C2   S    180.00   0.0  0
 QM2  CONST_36  S1   C3   C2   S      0.00   0.0  0
 QM2  CONST_37  H5   C16  N1   C2   180.00   0.0  0
 QM2  CONST_38  H9   C8   C7   C6     0.00   0.0  0
 QM2  CONST_39  H6   C15  C7   C6     0.00   0.0  0
 QM2  CONST_40  H1   C5   C4   N      0.00   0.0  0
 QM2  CONST_41  H8   C9   C8   C7   180.00   0.0  0
 QM2  CONST_42  H7   C14  C15  C7   180.00   0.0  0
 QM2  CONST_43  H2   O    C    O1     0.00   0.0  0
 QM2  Var_01    C12  C11  C10  C14  -37.61  30.0  2
 QM2  Var_02    C13  C12  C11  C10  109.90  30.0  1
 QM2  Var_03    C3   C2   S    C1   178.22  30.0  1
 QM2  Var_04    C    C1   S    C2   178.31  30.0  1
 QM2  Var_05    S    C1   C    O1   169.52  30.0  2

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
 QM2  chir_01  C11  C10  C12  C13  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
 QM2  plan-1  C6   0.020
 QM2  plan-1  C7   0.020
 QM2  plan-1  C15  0.020
 QM2  plan-1  C14  0.020
 QM2  plan-1  C10  0.020
 QM2  plan-1  C9   0.020
 QM2  plan-1  C8   0.020
 QM2  plan-1  C11  0.020
 QM2  plan-1  H6   0.020
 QM2  plan-1  H7   0.020
 QM2  plan-1  H8   0.020
 QM2  plan-1  H9   0.020
 QM2  plan-2  N1   0.020
 QM2  plan-2  C2   0.020
 QM2  plan-2  C4   0.020
 QM2  plan-2  C5   0.020
 QM2  plan-2  C6   0.020
 QM2  plan-2  S    0.020
 QM2  plan-2  C16  0.020
 QM2  plan-2  N    0.020
 QM2  plan-2  S1   0.020
 QM2  plan-2  C3   0.020
 QM2  plan-2  C7   0.020
 QM2  plan-2  H1   0.020
 QM2  plan-2  H5   0.020
 QM2  plan-3  O1   0.020
 QM2  plan-3  C    0.020
 QM2  plan-3  O    0.020
 QM2  plan-3  C1   0.020
 QM2  plan-3  H2   0.020

