# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 18:24:49 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 3-[5-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]sulfanylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cc1)c2csc3ncnc(SCCC(O)=O)c23
#
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
 7EY  7EY  '3-[5-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]sulfanylpropanoic acid'  ligand  35  22  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7EY
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
 7EY  C4   C  CR56   0   0.012  -2.3885   2.1241  -0.0612
 7EY  C5   C  CR56   0   0.097  -1.5063   1.0364  -0.0583
 7EY  C6   C  CR6    0   0.045  -0.1412   1.3937  -0.0143
 7EY  N1   N  N      0  -0.419   0.2151   2.6668  -0.0273
 7EY  N3   N  N      0  -0.412  -2.0341   3.4034  -0.0691
 7EY  OAB  O  O      0  -0.602   5.1770   2.1492   0.3211
 7EY  CAP  C  C      0   0.428   5.1658   0.9045   0.3414
 7EY  OAC  O  OC    -1  -0.621   6.1521   0.1471   0.4215
 7EY  CAK  C  CH2    0  -0.599   3.7934   0.2032   0.2524
 7EY  CAJ  C  CH2    0  -0.531   2.6217   1.1681   0.2000
 7EY  SAN  S  S2     0   0.065   1.1008   0.1748   0.0874
 7EY  C2   C  CR16   0   0.044  -0.7331   3.6004  -0.0635
 7EY  SAO  S  S2     0   0.241  -4.0365   1.6094  -0.0254
 7EY  CAI  C  CR15   0  -0.537  -3.5418  -0.0452  -0.0178
 7EY  CAS  C  CR5    0   0.198  -2.1981  -0.2254  -0.0461
 7EY  CAR  C  CR6    0  -0.006  -1.5799  -1.5646  -0.0807
 7EY  CAG  C  CR16   0  -0.269  -1.7013  -2.4293   1.0034
 7EY  CAE  C  CR16   0  -0.288  -1.1434  -3.6982   0.9585
 7EY  CAQ  C  CR6    0   0.092  -0.4550  -4.1416  -0.1686
 7EY  CAA  C  CH3    0  -0.722   0.1187  -5.5271  -0.2240
 7EY  CAF  C  CR16   0  -0.287  -0.3412  -3.2718  -1.2514
 7EY  CAH  C  CR16   0  -0.259  -0.8951  -2.0025  -1.2117
 7EY  H2   H  HCH2   0   0.242   3.7932  -0.4390  -0.6345
 7EY  H3   H  HCH2   0   0.241   3.6937  -0.4733   1.1072
 7EY  H4   H  HCH2   0   0.269   2.5752   1.7903   1.0920
 7EY  H5   H  HCH2   0   0.270   2.6830   1.8215  -0.6674
 7EY  H6   H  HCR6   0   0.267  -0.3916   4.6288  -0.0815
 7EY  H7   H  HCR5   0   0.306  -4.2915  -0.8220  -0.0151
 7EY  H9   H  HCR6   0   0.249  -2.2253  -2.1029   1.8933
 7EY  H10  H  HCR6   0   0.249  -1.2435  -4.3536   1.8160
 7EY  H11  H  HCH3   0   0.249  -0.6347  -6.2458  -0.5534
 7EY  H12  H  HCH3   0   0.244   0.9539  -5.5895  -0.9208
 7EY  H13  H  HCH3   0   0.244   0.4689  -5.8543   0.7546
 7EY  H14  H  HCR6   0   0.248   0.1870  -3.5921  -2.1415
 7EY  H15  H  HCR6   0   0.253  -0.7961  -1.3469  -2.0681

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
 7EY  C4   C5   aromatic  1.400  0.020  1.400
 7EY  C4   N3   aromatic  1.327  0.020  1.327
 7EY  C4   SAO  aromatic  1.727  0.020  1.727
 7EY  C5   C6   aromatic  1.412  0.020  1.412
 7EY  C5   CAS  aromatic  1.439  0.020  1.439
 7EY  C6   N1   aromatic  1.322  0.020  1.322
 7EY  C6   SAN  single    1.743  0.020  1.743
 7EY  N1   C2   aromatic  1.331  0.020  1.331
 7EY  N3   C2   aromatic  1.316  0.020  1.316
 7EY  OAB  CAP  deloc     1.245  0.020  1.245
 7EY  CAP  OAC  deloc     1.246  0.020  1.246
 7EY  CAP  CAK  single    1.544  0.020  1.544
 7EY  CAK  CAJ  single    1.519  0.020  1.519
 7EY  CAJ  SAN  single    1.820  0.020  1.820
 7EY  SAO  CAI  aromatic  1.727  0.020  1.727
 7EY  CAI  CAS  aromatic  1.356  0.020  1.356
 7EY  CAS  CAR  single    1.475  0.020  1.475
 7EY  CAR  CAG  aromatic  1.392  0.020  1.392
 7EY  CAR  CAH  aromatic  1.393  0.020  1.393
 7EY  CAG  CAE  aromatic  1.387  0.020  1.387
 7EY  CAE  CAQ  aromatic  1.393  0.020  1.393
 7EY  CAQ  CAA  single    1.501  0.020  1.501
 7EY  CAQ  CAF  aromatic  1.393  0.020  1.393
 7EY  CAF  CAH  aromatic  1.385  0.020  1.385
 7EY  CAK  H2   single    0.970  0.020  1.090
 7EY  CAK  H3   single    0.970  0.020  1.090
 7EY  CAJ  H4   single    0.970  0.020  1.090
 7EY  CAJ  H5   single    0.970  0.020  1.090
 7EY  C2   H6   single    0.930  0.020  1.080
 7EY  CAI  H7   single    0.930  0.020  1.080
 7EY  CAG  H9   single    0.930  0.020  1.080
 7EY  CAE  H10  single    0.930  0.020  1.080
 7EY  CAA  H11  single    0.970  0.020  1.090
 7EY  CAA  H12  single    0.970  0.020  1.090
 7EY  CAA  H13  single    0.970  0.020  1.090
 7EY  CAF  H14  single    0.930  0.020  1.080
 7EY  CAH  H15  single    0.930  0.020  1.080

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
 7EY  SAO  C4   N3   122.83  3.000
 7EY  SAO  C4   C5   111.69  3.000
 7EY  N3   C4   C5   125.48  3.000
 7EY  CAS  C5   C6   133.35  3.000
 7EY  CAS  C5   C4   112.22  3.000
 7EY  C6   C5   C4   114.37  3.000
 7EY  SAN  C6   N1   118.81  3.000
 7EY  SAN  C6   C5   120.91  3.000
 7EY  N1   C6   C5   120.26  3.000
 7EY  C2   N1   C6   118.93  3.000
 7EY  C2   N3   C4   114.09  3.000
 7EY  CAK  CAP  OAC  115.55  3.000
 7EY  CAK  CAP  OAB  117.47  3.000
 7EY  OAC  CAP  OAB  126.98  3.000
 7EY  H3   CAK  H2   105.67  3.000
 7EY  H3   CAK  CAJ  110.45  3.000
 7EY  H2   CAK  CAJ  110.15  3.000
 7EY  H3   CAK  CAP  108.47  3.000
 7EY  H2   CAK  CAP  108.26  3.000
 7EY  CAJ  CAK  CAP  113.53  3.000
 7EY  H5   CAJ  H4   108.21  3.000
 7EY  H5   CAJ  SAN  109.00  3.000
 7EY  H4   CAJ  SAN  109.08  3.000
 7EY  H5   CAJ  CAK  111.45  3.000
 7EY  H4   CAJ  CAK  111.58  3.000
 7EY  SAN  CAJ  CAK  107.46  3.000
 7EY  CAJ  SAN  C6   102.55  3.000
 7EY  H6   C2   N3   116.97  3.000
 7EY  H6   C2   N1   116.20  3.000
 7EY  N3   C2   N1   126.83  3.000
 7EY  CAI  SAO  C4    90.70  3.000
 7EY  H7   CAI  CAS  126.34  3.000
 7EY  H7   CAI  SAO  119.37  3.000
 7EY  CAS  CAI  SAO  114.28  3.000
 7EY  CAR  CAS  CAI  122.44  3.000
 7EY  CAR  CAS  C5   126.46  3.000
 7EY  CAI  CAS  C5   111.10  3.000
 7EY  CAH  CAR  CAG  118.68  3.000
 7EY  CAH  CAR  CAS  120.69  3.000
 7EY  CAG  CAR  CAS  120.60  3.000
 7EY  H9   CAG  CAE  119.80  3.000
 7EY  H9   CAG  CAR  119.66  3.000
 7EY  CAE  CAG  CAR  120.54  3.000
 7EY  H10  CAE  CAQ  119.56  3.000
 7EY  H10  CAE  CAG  119.37  3.000
 7EY  CAQ  CAE  CAG  121.07  3.000
 7EY  CAF  CAQ  CAA  121.09  3.000
 7EY  CAF  CAQ  CAE  118.06  3.000
 7EY  CAA  CAQ  CAE  120.84  3.000
 7EY  H13  CAA  H12  108.11  3.000
 7EY  H13  CAA  H11  107.16  3.000
 7EY  H12  CAA  H11  107.35  3.000
 7EY  H13  CAA  CAQ  111.53  3.000
 7EY  H12  CAA  CAQ  111.69  3.000
 7EY  H11  CAA  CAQ  110.79  3.000
 7EY  H14  CAF  CAH  119.29  3.000
 7EY  H14  CAF  CAQ  119.58  3.000
 7EY  CAH  CAF  CAQ  121.13  3.000
 7EY  H15  CAH  CAF  119.70  3.000
 7EY  H15  CAH  CAR  119.78  3.000
 7EY  CAF  CAH  CAR  120.52  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
 7EY  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 7EY  CONST_02  CAI  CAS  C5   C4      0.00   0.0  0
 7EY  CONST_03  CAR  CAS  C5   C4    180.00   0.0  0
 7EY  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 7EY  CONST_05  CAS  CAI  SAO  C4      0.00   0.0  0
 7EY  CONST_06  C2   N3   C4   C5      0.00   0.0  0
 7EY  CONST_07  CAI  SAO  C4   C5      0.00   0.0  0
 7EY  CONST_08  C2   N1   C6   C5      0.00   0.0  0
 7EY  CONST_09  SAO  CAI  CAS  C5      0.00   0.0  0
 7EY  CONST_12  N3   C4   C5   C6      0.00   0.0  0
 7EY  CONST_13  SAO  C4   C5   C6    180.00   0.0  0
 7EY  CONST_14  CAI  CAS  C5   C6    180.00   0.0  0
 7EY  CONST_15  CAR  CAS  C5   C6      0.00   0.0  0
 7EY  CONST_16  N3   C2   N1   C6      0.00   0.0  0
 7EY  CONST_17  CAS  C5   C6   N1    180.00   0.0  0
 7EY  CONST_18  CAS  C5   C4   N3    180.00   0.0  0
 7EY  CONST_19  CAI  SAO  C4   N3    180.00   0.0  0
 7EY  CONST_20  SAO  C4   N3   C2    180.00   0.0  0
 7EY  CONST_21  CAS  C5   C4   SAO     0.00   0.0  0
 7EY  CONST_22  CAR  CAS  CAI  SAO   180.00   0.0  0
 7EY  CONST_25  CAE  CAG  CAR  CAS   180.00   0.0  0
 7EY  CONST_26  CAF  CAH  CAR  CAS   180.00   0.0  0
 7EY  CONST_27  CAQ  CAE  CAG  CAR     0.00   0.0  0
 7EY  CONST_28  CAQ  CAF  CAH  CAR     0.00   0.0  0
 7EY  CONST_29  CAF  CAH  CAR  CAG     0.00   0.0  0
 7EY  CONST_30  CAF  CAQ  CAE  CAG     0.00   0.0  0
 7EY  CONST_31  CAH  CAR  CAG  CAE     0.00   0.0  0
 7EY  CONST_32  CAH  CAF  CAQ  CAE     0.00   0.0  0
 7EY  CONST_33  SAN  C6   C5   C4    180.00   0.0  0
 7EY  CONST_34  CAS  C5   C6   SAN     0.00   0.0  0
 7EY  CONST_35  C2   N1   C6   SAN   180.00   0.0  0
 7EY  CONST_36  CAA  CAQ  CAE  CAG   180.00   0.0  0
 7EY  CONST_37  CAH  CAF  CAQ  CAA   180.00   0.0  0
 7EY  CONST_38  H6   C2   N3   C4    180.00   0.0  0
 7EY  CONST_39  H7   CAI  SAO  C4    180.00   0.0  0
 7EY  CONST_40  H9   CAG  CAR  CAS     0.00   0.0  0
 7EY  CONST_41  H15  CAH  CAR  CAS     0.00   0.0  0
 7EY  CONST_42  H10  CAE  CAG  CAR   180.00   0.0  0
 7EY  CONST_43  H14  CAF  CAH  CAR   180.00   0.0  0
 7EY  Var_01    H11  CAA  CAQ  CAE    85.04  30.0  2
 7EY  Var_02    CAK  CAJ  SAN  C6   -178.32  30.0  2
 7EY  Var_03    CAJ  CAK  CAP  OAB    -2.06  30.0  3
 7EY  Var_04    SAN  CAJ  CAK  CAP   179.65  30.0  3

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
 7EY  plan-1  CAS  0.020
 7EY  plan-1  CAR  0.020
 7EY  plan-1  CAG  0.020
 7EY  plan-1  CAE  0.020
 7EY  plan-1  CAQ  0.020
 7EY  plan-1  CAA  0.020
 7EY  plan-1  CAF  0.020
 7EY  plan-1  CAH  0.020
 7EY  plan-1  H9   0.020
 7EY  plan-1  H10  0.020
 7EY  plan-1  H14  0.020
 7EY  plan-1  H15  0.020
 7EY  plan-2  C4   0.020
 7EY  plan-2  C5   0.020
 7EY  plan-2  C6   0.020
 7EY  plan-2  N1   0.020
 7EY  plan-2  N3   0.020
 7EY  plan-2  SAN  0.020
 7EY  plan-2  C2   0.020
 7EY  plan-2  SAO  0.020
 7EY  plan-2  CAI  0.020
 7EY  plan-2  CAS  0.020
 7EY  plan-2  CAR  0.020
 7EY  plan-2  H6   0.020
 7EY  plan-2  H7   0.020
 7EY  plan-3  OAB  0.020
 7EY  plan-3  CAP  0.020
 7EY  plan-3  OAC  0.020
 7EY  plan-3  CAK  0.020

