# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 07:09:49 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[(3~{R})-pyrrolidin-3-yl]pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)N[C@@H]3CCNC3
#
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
 EYW  EYW  5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-[(3~{R})-pyrrolidin-3-yl]pentanamide  ligand  45  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EYW
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
 EYW  C1   C  CR15  0  -0.095   5.7097   0.7206  -0.4289
 EYW  C2   C  CH1   0  -0.362  -2.8824  -0.5815   0.7533
 EYW  C3   C  CR5   0   0.643  -5.4155   1.2885  -0.7211
 EYW  C4   C  CR15  0  -0.061  -4.2051   0.1719   0.9469
 EYW  C5   C  CR15  0  -0.046  -5.3741  -0.7363   0.4597
 EYW  C6   C  CH2   0  -0.570  -4.7860  -2.0073  -0.1629
 EYW  C7   C  CH2   0  -0.422  -1.6552   0.3085   0.6789
 EYW  C9   C  CH2   0  -0.415   0.8686   0.4541   0.5687
 EYW  C11  C  C     0   0.568   3.4006   0.5509   0.4165
 EYW  C12  C  CH2   0  -0.521   6.5816  -0.0355  -1.4328
 EYW  C15  C  CH2   0  -0.321   6.5547   0.5977   0.8456
 EYW  O3   O  O     0  -0.530  -5.7639   2.1580  -1.5057
 EYW  N1   N  NR15  0  -0.661  -6.0479   0.1109  -0.4888
 EYW  N2   N  NR15  0  -0.657  -4.3270   1.3262   0.0940
 EYW  S1   S  S2    0  -0.024  -3.1354  -1.5641  -0.7618
 EYW  C8   C  CH2   0  -0.419  -0.3458  -0.4655   0.5901
 EYW  C10  C  CH2   0  -0.582   2.1692  -0.3297   0.4658
 EYW  O11  O  O     0  -0.506   3.4612   1.6300   0.9920
 EYW  N12  N  NH1   0  -0.645   4.4290   0.0502  -0.2885
 EYW  C13  C  CH2   0  -0.303   7.3717  -1.0543  -0.5706
 EYW  N14  N  NR15  0  -0.587   7.0751  -0.7610   0.8350
 EYW  H1   H  HCR5  0   0.251   5.5476   1.7596  -0.7221
 EYW  H2   H  HCH1  0   0.275  -2.7710  -1.2814   1.5886
 EYW  H4   H  HCR5  0   0.277  -6.0410  -1.0111   1.2800
 EYW  H5   H  HCH2  0   0.275  -4.7036  -2.7906   0.5920
 EYW  H6   H  HCH2  0   0.289  -5.3970  -2.3870  -0.9809
 EYW  H7   H  HCH2  0   0.232  -1.7431   0.9839  -0.1764
 EYW  H8   H  HCH2  0   0.240  -1.6398   0.9394   1.5750
 EYW  H9   H  HCH2  0   0.225   0.7840   1.1435  -0.2766
 EYW  H10  H  HCH2  0   0.226   0.8773   1.0696   1.4712
 EYW  H11  H  HCH2  0   0.251   5.9963  -0.5076  -2.2238
 EYW  H12  H  HCH2  0   0.257   7.2583   0.6666  -1.9199
 EYW  H13  H  HCH2  0   0.228   7.3818   1.3129   0.7899
 EYW  H14  H  HCH2  0   0.248   6.0000   0.8030   1.7604
 EYW  H15  H  HNR5  0   0.399  -6.7812  -0.2236  -1.0908
 EYW  H16  H  HNR5  0   0.400  -3.8690   2.1977   0.3001
 EYW  H17  H  HCH2  0   0.221  -0.2693  -1.1552   1.4374
 EYW  H18  H  HCH2  0   0.221  -0.3426  -1.0882  -0.3106
 EYW  H19  H  HCH2  0   0.267   2.2708  -0.9874   1.3367
 EYW  H20  H  HCH2  0   0.249   2.1411  -0.9901  -0.4051
 EYW  H21  H  HNH1  0   0.398   4.2923  -0.8219  -0.7738
 EYW  H22  H  HCH2  0   0.236   7.1072  -2.0866  -0.8001
 EYW  H23  H  HCH2  0   0.225   8.4422  -0.9495  -0.7599
 EYW  H24  H  HNR5  0   0.346   6.3368  -1.3798   1.1458
 EYW  H3   H  HCR5  0   0.281  -4.3145   0.4444   2.0005

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
 EYW  C13  N14  single  1.466  0.020  1.466
 EYW  C13  C12  single  1.551  0.020  1.551
 EYW  N14  C15  single  1.455  0.020  1.455
 EYW  C12  C1   single  1.530  0.020  1.530
 EYW  C15  C1   single  1.534  0.020  1.534
 EYW  C1   N12  single  1.452  0.020  1.452
 EYW  N12  C11  single  1.344  0.020  1.344
 EYW  O11  C11  double  1.224  0.020  1.224
 EYW  C11  C10  single  1.515  0.020  1.515
 EYW  C10  C9   single  1.522  0.020  1.522
 EYW  C9   C8   single  1.523  0.020  1.523
 EYW  C8   C7   single  1.524  0.020  1.524
 EYW  C7   C2   single  1.518  0.020  1.518
 EYW  C2   C4   single  1.535  0.020  1.535
 EYW  C2   S1   single  1.823  0.020  1.823
 EYW  C4   C5   single  1.558  0.020  1.558
 EYW  C4   N2   single  1.440  0.020  1.440
 EYW  C6   S1   single  1.811  0.020  1.811
 EYW  C6   C5   single  1.533  0.020  1.533
 EYW  C5   N1   single  1.439  0.020  1.439
 EYW  N2   C3   single  1.360  0.020  1.360
 EYW  N1   C3   single  1.357  0.020  1.357
 EYW  C3   O3   double  1.222  0.020  1.222
 EYW  C1   H1   single  0.970  0.020  1.090
 EYW  C2   H2   single  0.970  0.020  1.090
 EYW  C4   H3   single  0.970  0.020  1.090
 EYW  C5   H4   single  0.970  0.020  1.090
 EYW  C6   H5   single  0.970  0.020  1.090
 EYW  C6   H6   single  0.970  0.020  1.090
 EYW  C7   H7   single  0.970  0.020  1.090
 EYW  C7   H8   single  0.970  0.020  1.090
 EYW  C9   H9   single  0.970  0.020  1.090
 EYW  C9   H10  single  0.970  0.020  1.090
 EYW  C12  H11  single  0.970  0.020  1.090
 EYW  C12  H12  single  0.970  0.020  1.090
 EYW  C15  H13  single  0.970  0.020  1.090
 EYW  C15  H14  single  0.970  0.020  1.090
 EYW  N1   H15  single  0.860  0.020  1.020
 EYW  N2   H16  single  0.860  0.020  1.020
 EYW  C8   H17  single  0.970  0.020  1.090
 EYW  C8   H18  single  0.970  0.020  1.090
 EYW  C10  H19  single  0.970  0.020  1.090
 EYW  C10  H20  single  0.970  0.020  1.090
 EYW  N12  H21  single  0.860  0.020  1.020
 EYW  C13  H22  single  0.970  0.020  1.090
 EYW  C13  H23  single  0.970  0.020  1.090
 EYW  N14  H24  single  0.890  0.020  1.040

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
 EYW  H1   C1   N12  109.53  3.000
 EYW  H1   C1   C15  112.41  3.000
 EYW  N12  C1   C15  111.62  3.000
 EYW  H1   C1   C12  112.26  3.000
 EYW  N12  C1   C12  109.75  3.000
 EYW  C15  C1   C12  101.06  3.000
 EYW  H2   C2   S1   107.66  3.000
 EYW  H2   C2   C7   109.26  3.000
 EYW  S1   C2   C7   112.80  3.000
 EYW  H2   C2   C4   107.77  3.000
 EYW  S1   C2   C4   104.47  3.000
 EYW  C7   C2   C4   114.53  3.000
 EYW  N2   C3   N1   107.12  3.000
 EYW  N1   C3   O3   126.49  3.000
 EYW  N2   C3   O3   126.39  3.000
 EYW  H3   C4   N2   111.24  3.000
 EYW  H3   C4   C5   111.80  3.000
 EYW  N2   C4   C5   102.62  3.000
 EYW  H3   C4   C2   109.27  3.000
 EYW  N2   C4   C2   113.06  3.000
 EYW  C5   C4   C2   108.72  3.000
 EYW  H4   C5   N1   110.93  3.000
 EYW  H4   C5   C6   109.32  3.000
 EYW  N1   C5   C6   113.58  3.000
 EYW  H4   C5   C4   111.70  3.000
 EYW  N1   C5   C4   102.36  3.000
 EYW  C6   C5   C4   108.81  3.000
 EYW  H6   C6   H5   108.16  3.000
 EYW  H6   C6   S1   110.38  3.000
 EYW  H5   C6   S1   109.61  3.000
 EYW  H6   C6   C5   112.27  3.000
 EYW  H5   C6   C5   110.08  3.000
 EYW  S1   C6   C5   106.33  3.000
 EYW  H8   C7   H7   106.57  3.000
 EYW  H8   C7   C8   109.15  3.000
 EYW  H7   C7   C8   109.71  3.000
 EYW  H8   C7   C2   107.99  3.000
 EYW  H7   C7   C2   109.61  3.000
 EYW  C8   C7   C2   113.56  3.000
 EYW  H10  C9   H9   106.49  3.000
 EYW  H10  C9   C10  109.83  3.000
 EYW  H9   C9   C10  109.78  3.000
 EYW  H10  C9   C8   109.57  3.000
 EYW  H9   C9   C8   109.24  3.000
 EYW  C10  C9   C8   111.79  3.000
 EYW  N12  C11  O11  122.49  3.000
 EYW  O11  C11  C10  122.50  3.000
 EYW  N12  C11  C10  115.00  3.000
 EYW  H12  C12  H11  106.72  3.000
 EYW  H12  C12  C13  110.81  3.000
 EYW  H11  C12  C13  113.07  3.000
 EYW  H12  C12  C1   109.20  3.000
 EYW  H11  C12  C1   112.57  3.000
 EYW  C13  C12  C1   104.49  3.000
 EYW  H14  C15  H13  107.71  3.000
 EYW  H14  C15  N14  111.36  3.000
 EYW  H13  C15  N14  109.84  3.000
 EYW  H14  C15  C1   113.71  3.000
 EYW  H13  C15  C1   108.75  3.000
 EYW  N14  C15  C1   105.41  3.000
 EYW  H15  N1   C5   122.67  3.000
 EYW  H15  N1   C3   121.73  3.000
 EYW  C5   N1   C3   113.93  3.000
 EYW  H16  N2   C4   122.30  3.000
 EYW  H16  N2   C3   120.74  3.000
 EYW  C4   N2   C3   113.60  3.000
 EYW  C6   S1   C2    89.06  3.000
 EYW  H18  C8   H17  106.15  3.000
 EYW  H18  C8   C9   109.23  3.000
 EYW  H17  C8   C9   109.59  3.000
 EYW  H18  C8   C7   109.83  3.000
 EYW  H17  C8   C7   109.56  3.000
 EYW  C9   C8   C7   112.28  3.000
 EYW  H20  C10  H19  105.84  3.000
 EYW  H20  C10  C11  110.25  3.000
 EYW  H19  C10  C11  107.42  3.000
 EYW  H20  C10  C9   110.05  3.000
 EYW  H19  C10  C9   109.54  3.000
 EYW  C11  C10  C9   113.42  3.000
 EYW  H21  N12  C11  118.14  3.000
 EYW  H21  N12  C1   118.21  3.000
 EYW  C11  N12  C1   123.61  3.000
 EYW  H23  C13  H22  106.99  3.000
 EYW  H23  C13  N14  110.19  3.000
 EYW  H22  C13  N14  110.01  3.000
 EYW  H23  C13  C12  109.88  3.000
 EYW  H22  C13  C12  112.42  3.000
 EYW  N14  C13  C12  107.37  3.000
 EYW  H24  N14  C13  108.64  3.000
 EYW  H24  N14  C15  107.92  3.000
 EYW  C13  N14  C15  105.43  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
 EYW  CONST_01  N1   C3   N2   C4      0.00   0.0  0
 EYW  CONST_02  N2   C3   N1   C5      0.00   0.0  0
 EYW  CONST_03  O3   C3   N2   C4    180.00   0.0  0
 EYW  CONST_04  O3   C3   N1   C5    180.00   0.0  0
 EYW  CONST_06  H15  N1   C3   N2    180.00   0.0  0
 EYW  CONST_07  O11  C11  N12  C1      0.00   0.0  0
 EYW  CONST_08  C10  C11  N12  C1    180.00   0.0  0
 EYW  CONST_09  H21  N12  C11  C10     0.00   0.0  0
 EYW  Var_01    N14  C13  C12  C1     -6.52  30.0  1
 EYW  Var_02    C13  N14  C15  C1     37.24  30.0  1
 EYW  Var_03    C5   C6   S1   C2     40.78  30.0  1
 EYW  Var_04    C15  N14  C13  C12   -18.78  30.0  1
 EYW  Var_05    C9   C8   C7   C2   -177.89  30.0  1
 EYW  Var_06    C10  C9   C8   C7   -179.43  30.0  2
 EYW  Var_07    N12  C11  C10  C9   -149.08  30.0  2
 EYW  Var_08    C8   C9   C10  C11   178.96  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
 EYW  chir_01  C1  C12  C15  N12  positiv
 EYW  chir_02  C2  C7   C4   S1   negativ
 EYW  chir_03  C4  N2   C5   C2   negativ
 EYW  chir_04  C5  N1   C4   C6   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
 EYW  plan-1  C1   0.020
 EYW  plan-1  C11  0.020
 EYW  plan-1  C10  0.020
 EYW  plan-1  O11  0.020
 EYW  plan-1  N12  0.020
 EYW  plan-1  H21  0.020
 EYW  plan-2  C3   0.020
 EYW  plan-2  C4   0.020
 EYW  plan-2  C5   0.020
 EYW  plan-2  O3   0.020
 EYW  plan-2  N1   0.020
 EYW  plan-2  N2   0.020
 EYW  plan-2  H15  0.020
 EYW  plan-2  H16  0.020

