# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 12:36:51 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (3E,5S)-5-{3-chloro-5-[5-(prop-1-yn-1-yl)pyridin-3-yl]thiophen-2-yl}-2,5-dimethyl-1,2,4-thiadiazinan-3-imine 1,1-dioxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#Cc1cncc(c1)c2sc(c(Cl)c2)[C@]3(C)C[S](=O)(=O)N(C)C(=N)N3
#
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
 66J  66J  '(3E,5S)-5-{3-chloro-5-[5-(prop-1-yn-1-yl)pyridin-3-yl]thiophen-2-yl}-2,5-dimethyl-1,2,4-thiadiazinan-3-imine 1,1-dioxide'  ligand  43  26  .  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_66J
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
 66J  C1    C   CR6   0   0.048   2.9040  -0.5187  -0.4330
 66J  C11   C   C     0   0.653  -3.6952   0.8991  -1.0423
 66J  C14   C   CH3   0  -0.624  -2.2743   1.1669   2.3741
 66J  C21   C   CR15  0  -0.160   1.3498   1.4692  -0.1712
 66J  C20   C   CR5   0  -0.223   1.6362   0.1372  -0.1311
 66J  C22   C   CR5   0   0.014   0.0069   1.7371   0.1848
 66J  C26   C   CH3   0  -0.822   8.9273   1.2308   0.1864
 66J  C13   C   CT    0   0.015  -2.1847   0.5604   0.9700
 66J  C2    C   CR16  0  -0.239   4.1127   0.1254  -0.1909
 66J  C4    C   CR16  0  -0.092   5.2291  -1.8080  -1.0405
 66J  C6    C   CR16  0  -0.098   2.9538  -1.8014  -0.9808
 66J  C7    C   CR5   0  -0.083  -0.7406   0.6330   0.4865
 66J  C8    C   CH2   0  -0.666  -2.6463  -0.9123   1.0451
 66J  C3    C   CR6   0  -0.159   5.3064  -0.5190  -0.5032
 66J  N5    N   N     0  -0.385   4.0839  -2.4279  -1.2698
 66J  S9    S   S     0   1.382  -4.3419  -1.0887   0.5423
 66J  N10   N   N     0  -0.659  -4.1664  -0.4149  -0.9829
 66J  N12   N   NH1   0  -0.660  -3.0730   1.3246   0.1035
 66J  O16   O   OS    0  -0.628  -5.2224  -0.2971   1.3805
 66J  O18   O   OS    0  -0.638  -4.6441  -2.4961   0.3569
 66J  S19   S   S2    0   0.265   0.2533  -0.7674   0.3459
 66J  CL23  CL  CL    0  -0.111  -0.5729   3.3608   0.2176
 66J  C25   C   CSP   0  -0.039   7.6381   0.6108  -0.0623
 66J  H1    H   HCH3  0   0.248  -1.5991   0.6466   3.0524
 66J  H2    H   HCH3  0   0.248  -2.0043   2.2218   2.3700
 66J  H3    H   HCH3  0   0.260  -3.2915   1.0732   2.7518
 66J  H4    H   HCH3  0   0.271  -4.1932  -0.8831  -3.0092
 66J  H5    H   HCH3  0   0.285  -4.9671  -2.0696  -1.9764
 66J  H6    H   HCH3  0   0.260  -5.8017  -0.5496  -2.3268
 66J  H7    H   HCR5  0   0.293   2.0545   2.2361  -0.4604
 66J  H8    H   HCH3  0   0.273   8.8211   2.1042   0.8295
 66J  H9    H   HCH3  0   0.273   9.6073   0.5324   0.6743
 66J  H10   H   HCH3  0   0.273   9.3920   1.5534  -0.7456
 66J  H11   H   HCR6  0   0.277   4.1323   1.1127   0.2520
 66J  H12   H   HCR6  0   0.273   6.1383  -2.3450  -1.2860
 66J  H13   H   HCR6  0   0.270   2.0370  -2.3376  -1.2059
 66J  H14   H   HCH2  0   0.330  -2.1190  -1.5754   0.3588
 66J  H15   H   HCH2  0   0.351  -2.5442  -1.3129   2.0541
 66J  H16   H   HNH1  0   0.394  -2.8823   2.3147   0.0804
 66J  H17   H   H     0   0.352  -4.4640   1.3333  -2.7355
 66J  N15   N   N     0  -0.672  -3.8490   1.6962  -2.0186
 66J  C17   C   CH3   0  -0.553  -4.8303  -1.0056  -2.1354
 66J  C24   C   CSP   0   0.204   6.5679   0.0968  -0.2689

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
 66J  N5    C6   aromatic  1.324  0.020  1.324
 66J  N5    C4   aromatic  1.322  0.020  1.322
 66J  C6    C1   aromatic  1.396  0.020  1.396
 66J  CL23  C22  single    1.724  0.020  1.724
 66J  C21   C22  aromatic  1.415  0.020  1.415
 66J  C21   C20  aromatic  1.363  0.020  1.363
 66J  C22   C7   aromatic  1.367  0.020  1.367
 66J  C4    C3   aromatic  1.399  0.020  1.399
 66J  C1    C20  single    1.459  0.020  1.459
 66J  C1    C2   aromatic  1.391  0.020  1.391
 66J  C20   S19  aromatic  1.720  0.020  1.720
 66J  C14   C13  single    1.532  0.020  1.532
 66J  C7    S19  aromatic  1.723  0.020  1.723
 66J  C7    C13  single    1.525  0.020  1.525
 66J  C3    C2   aromatic  1.392  0.020  1.392
 66J  C3    C24  single    1.423  0.020  1.423
 66J  C13   C8   single    1.545  0.020  1.545
 66J  C13   N12  single    1.457  0.020  1.457
 66J  C24   C25  triple    1.205  0.020  1.205
 66J  C8    S9   single    1.777  0.020  1.777
 66J  O18   S9   double    1.451  0.020  1.451
 66J  N12   C11  single    1.371  0.020  1.371
 66J  C25   C26  single    1.452  0.020  1.452
 66J  S9    N10  single    1.677  0.020  1.677
 66J  S9    O16  double    1.451  0.020  1.451
 66J  C11   N10  single    1.397  0.020  1.397
 66J  C11   N15  double    1.270  0.020  1.270
 66J  N10   C17  single    1.455  0.020  1.455
 66J  C14   H1   single    0.970  0.020  1.090
 66J  C14   H2   single    0.970  0.020  1.090
 66J  C14   H3   single    0.970  0.020  1.090
 66J  C17   H4   single    0.970  0.020  1.090
 66J  C17   H5   single    0.970  0.020  1.090
 66J  C17   H6   single    0.970  0.020  1.090
 66J  C21   H7   single    0.930  0.020  1.080
 66J  C26   H8   single    0.970  0.020  1.090
 66J  C26   H9   single    0.970  0.020  1.090
 66J  C26   H10  single    0.970  0.020  1.090
 66J  C2    H11  single    0.930  0.020  1.080
 66J  C4    H12  single    0.930  0.020  1.080
 66J  C6    H13  single    0.930  0.020  1.080
 66J  C8    H14  single    0.970  0.020  1.090
 66J  C8    H15  single    0.970  0.020  1.090
 66J  N12   H16  single    0.890  0.020  1.040
 66J  N15   H17  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
 66J  C6    C1   C2   117.58  3.000
 66J  C2    C1   C20  120.73  3.000
 66J  C6    C1   C20  121.70  3.000
 66J  N15   C11  N12  120.17  3.000
 66J  N15   C11  N10  125.61  3.000
 66J  N12   C11  N10  114.16  3.000
 66J  H3    C14  H2   108.44  3.000
 66J  H3    C14  H1   108.78  3.000
 66J  H2    C14  H1   108.15  3.000
 66J  H3    C14  C13  109.78  3.000
 66J  H2    C14  C13  111.44  3.000
 66J  H1    C14  C13  110.20  3.000
 66J  H7    C21  C22  123.48  3.000
 66J  H7    C21  C20  124.36  3.000
 66J  C22   C21  C20  112.15  3.000
 66J  S19   C20  C21  110.69  3.000
 66J  S19   C20  C1   121.31  3.000
 66J  C21   C20  C1   128.01  3.000
 66J  CL23  C22  C7   124.92  3.000
 66J  C7    C22  C21  114.93  3.000
 66J  CL23  C22  C21  120.15  3.000
 66J  H10   C26  H9   107.83  3.000
 66J  H10   C26  H8   107.99  3.000
 66J  H9    C26  H8   108.07  3.000
 66J  H10   C26  C25  111.00  3.000
 66J  H9    C26  C25  110.92  3.000
 66J  H8    C26  C25  110.90  3.000
 66J  N12   C13  C8   110.28  3.000
 66J  N12   C13  C7   111.33  3.000
 66J  C8    C13  C7   110.11  3.000
 66J  N12   C13  C14  107.56  3.000
 66J  C8    C13  C14  108.38  3.000
 66J  C7    C13  C14  109.09  3.000
 66J  H11   C2   C3   119.90  3.000
 66J  H11   C2   C1   120.63  3.000
 66J  C3    C2   C1   119.46  3.000
 66J  H12   C4   N5   117.06  3.000
 66J  H12   C4   C3   119.81  3.000
 66J  N5    C4   C3   123.13  3.000
 66J  H13   C6   N5   116.22  3.000
 66J  H13   C6   C1   120.34  3.000
 66J  N5    C6   C1   123.44  3.000
 66J  S19   C7   C13  122.24  3.000
 66J  C13   C7   C22  128.78  3.000
 66J  S19   C7   C22  108.85  3.000
 66J  H15   C8   H14  108.29  3.000
 66J  H15   C8   S9   108.34  3.000
 66J  H14   C8   S9   102.89  3.000
 66J  H15   C8   C13  111.54  3.000
 66J  H14   C8   C13  113.86  3.000
 66J  S9    C8   C13  111.46  3.000
 66J  C4    C3   C2   117.74  3.000
 66J  C2    C3   C24  121.53  3.000
 66J  C4    C3   C24  120.73  3.000
 66J  C6    N5   C4   118.66  3.000
 66J  O18   S9   O16  118.47  3.000
 66J  O16   S9   N10  111.71  3.000
 66J  O18   S9   N10  107.17  3.000
 66J  O16   S9   C8   111.19  3.000
 66J  N10   S9   C8    96.75  3.000
 66J  O18   S9   C8   109.33  3.000
 66J  S9    N10  C17  120.64  3.000
 66J  C17   N10  C11  120.13  3.000
 66J  S9    N10  C11  116.86  3.000
 66J  H16   N12  C13  114.40  3.000
 66J  H16   N12  C11  111.79  3.000
 66J  C13   N12  C11  127.63  3.000
 66J  C7    S19  C20   93.38  3.000
 66J  C26   C25  C24  180.00  3.000
 66J  H17   N15  C11  113.16  3.000
 66J  H6    C17  H5   108.89  3.000
 66J  H6    C17  H4   109.49  3.000
 66J  H5    C17  H4   107.57  3.000
 66J  H6    C17  N10  112.08  3.000
 66J  H5    C17  N10  109.86  3.000
 66J  H4    C17  N10  108.85  3.000
 66J  C25   C24  C3   180.00  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
 66J  CONST_01  C4    N5   C6   C1     0.00   0.0  0
 66J  CONST_02  C22   C21  C20  C1   180.00   0.0  0
 66J  CONST_03  C7    S19  C20  C1   180.00   0.0  0
 66J  CONST_04  C4    C3   C2   C1     0.00   0.0  0
 66J  CONST_05  S19   C7   C22  C21    0.00   0.0  0
 66J  CONST_08  C7    S19  C20  C21    0.00   0.0  0
 66J  CONST_09  C7    C22  C21  C20    0.00   0.0  0
 66J  CONST_10  N5    C6   C1   C20  180.00   0.0  0
 66J  CONST_11  C3    C2   C1   C20  180.00   0.0  0
 66J  CONST_12  C22   C7   S19  C20    0.00   0.0  0
 66J  CONST_13  S19   C20  C21  C22    0.00   0.0  0
 66J  CONST_14  N5    C6   C1   C2     0.00   0.0  0
 66J  CONST_16  N5    C4   C3   C2     0.00   0.0  0
 66J  CONST_17  C3    C4   N5   C6     0.00   0.0  0
 66J  CONST_19  C3    C2   C1   C6     0.00   0.0  0
 66J  CONST_20  C13   C7   C22  C21  180.00   0.0  0
 66J  CONST_21  C13   C7   S19  C20  180.00   0.0  0
 66J  CONST_24  C24   C3   C2   C1   180.00   0.0  0
 66J  CONST_25  CL23  C22  C21  C20  180.00   0.0  0
 66J  CONST_26  N5    C4   C3   C24  180.00   0.0  0
 66J  CONST_27  CL23  C22  C7   C13    0.00   0.0  0
 66J  CONST_28  CL23  C22  C7   S19  180.00   0.0  0
 66J  CONST_29  N12   C11  N10  C17  180.00   0.0  0
 66J  CONST_32  H7    C21  C20  C1     0.00   0.0  0
 66J  CONST_33  H13   C6   C1   C20    0.00   0.0  0
 66J  CONST_34  H11   C2   C1   C20    0.00   0.0  0
 66J  CONST_35  H12   C4   C3   C2   180.00   0.0  0
 66J  CONST_36  H16   N12  C11  N10  180.00   0.0  0
 66J  CONST_37  N15   C11  N10  C17    0.00   0.0  0
 66J  CONST_38  H17   N15  C11  N10    0.00   0.0  0
 66J  Var_01    C8    S9   N10  C11  -59.01  30.0  1
 66J  Var_02    N10   S9   C8   C13   57.14  30.0  1
 66J  Var_03    H4    C17  N10  C11   52.39  30.0  3
 66J  Var_04    H8    C26  C25  C24   51.96  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
 66J  chir_01  C13  C7  C8  N12  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
 66J  plan-1  C1    0.020
 66J  plan-1  C21   0.020
 66J  plan-1  C20   0.020
 66J  plan-1  C22   0.020
 66J  plan-1  C13   0.020
 66J  plan-1  C7    0.020
 66J  plan-1  S19   0.020
 66J  plan-1  CL23  0.020
 66J  plan-1  H7    0.020
 66J  plan-2  C1    0.020
 66J  plan-2  C20   0.020
 66J  plan-2  C2    0.020
 66J  plan-2  C4    0.020
 66J  plan-2  C6    0.020
 66J  plan-2  C3    0.020
 66J  plan-2  N5    0.020
 66J  plan-2  C25   0.020
 66J  plan-2  H11   0.020
 66J  plan-2  H12   0.020
 66J  plan-2  H13   0.020
 66J  plan-2  C24   0.020
 66J  plan-3  C11   0.020
 66J  plan-3  C13   0.020
 66J  plan-3  S9    0.020
 66J  plan-3  N10   0.020
 66J  plan-3  N12   0.020
 66J  plan-3  H16   0.020
 66J  plan-3  H17   0.020
 66J  plan-3  N15   0.020
 66J  plan-3  C17   0.020

