# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 07:46:45 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: 2-methyl-N-{5-[(2S)-oxolan-2-yl]-1,3,4-thiadiazol-2(3H)-ylidene}propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C(=O)N=C1NN=C(S1)[C@@H]2CCCO2
#
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
 LDJ  LDJ  2-methyl-N-{5-[(2S)-oxolan-2-yl]-1,3,4-thiadiazol-2(3H)-ylidene}propanamide  ligand  31  16  .  2022-07-25  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_LDJ
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
 LDJ  N1   N  N     0  -0.519  -2.0649   0.8668   0.6115
 LDJ  N3   N  N     0  -0.186   1.2505   1.6921   1.4631
 LDJ  C4   C  C     0   0.495  -2.6490  -0.2218   0.0302
 LDJ  C5   C  CR5   0   0.378  -0.7773   0.8227   0.7741
 LDJ  C6   C  CR5   0   0.035   1.6289   0.5662   0.9917
 LDJ  C7   C  CR15  0   0.018   3.0494   0.0977   0.9300
 LDJ  C8   C  CH2   0  -0.497   3.8998   0.9009  -0.0699
 LDJ  C10  C  CH2   0  -0.170   3.7402  -1.3445  -0.7549
 LDJ  C1   C  CH3   0  -0.655  -4.3937   0.9157  -1.3155
 LDJ  C2   C  CH1   0  -0.357  -4.1404  -0.0812  -0.1790
 LDJ  C3   C  CH3   0  -0.650  -4.8178  -1.4154  -0.4490
 LDJ  C9   C  CH2   0  -0.490   4.7221  -0.1880  -0.7498
 LDJ  N2   N  NR15  0  -0.471  -0.0820   1.8202   1.3356
 LDJ  O1   O  O     0  -0.472  -2.0288  -1.2208  -0.3169
 LDJ  O2   O  O     0  -0.501   3.0499  -1.2455   0.4886
 LDJ  S1   S  S2    0   0.211   0.3571  -0.4448   0.3584
 LDJ  H3   H  HCR5  0   0.279   3.4790   0.1471   1.9359
 LDJ  H4   H  HCH2  0   0.254   3.2638   1.4075  -0.7983
 LDJ  H5   H  HCH2  0   0.270   4.4997   1.6581   0.4316
 LDJ  H6   H  HCH2  0   0.215   3.0372  -1.2560  -1.5913
 LDJ  H7   H  HCH2  0   0.242   4.2133  -2.3252  -0.8076
 LDJ  H8   H  HCH3  0   0.225  -3.9737   0.5530  -2.2554
 LDJ  H9   H  HCH3  0   0.237  -5.4655   1.0531  -1.4611
 LDJ  H10  H  HCH3  0   0.237  -3.9572   1.8905  -1.1010
 LDJ  H11  H  HCH1  0   0.250  -4.5500   0.3525   0.7387
 LDJ  H12  H  HCH3  0   0.231  -4.6555  -2.1255   0.3622
 LDJ  H13  H  HCH3  0   0.229  -5.8939  -1.2720  -0.5512
 LDJ  H14  H  HCH3  0   0.221  -4.4559  -1.8703  -1.3718
 LDJ  H15  H  HCH2  0   0.258   5.0441   0.0916  -1.7520
 LDJ  H16  H  HCH2  0   0.247   5.6084  -0.4376  -0.1632
 LDJ  H17  H  HNR5  0   0.437  -0.5193   2.6671   1.6699

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
 LDJ  C9   C8   single  1.525  0.020  1.525
 LDJ  C9   C10  single  1.517  0.020  1.517
 LDJ  C8   C7   single  1.539  0.020  1.539
 LDJ  C10  O2   single  1.426  0.020  1.426
 LDJ  C7   O2   single  1.414  0.020  1.414
 LDJ  C7   C6   single  1.497  0.020  1.497
 LDJ  S1   C6   single  1.744  0.020  1.744
 LDJ  S1   C5   single  1.751  0.020  1.751
 LDJ  C6   N3   double  1.278  0.020  1.278
 LDJ  O1   C4   double  1.226  0.020  1.226
 LDJ  N3   N2   single  1.345  0.020  1.345
 LDJ  C5   N2   single  1.339  0.020  1.339
 LDJ  C5   N1   double  1.299  0.020  1.299
 LDJ  C4   N1   single  1.365  0.020  1.365
 LDJ  C4   C2   single  1.513  0.020  1.513
 LDJ  C3   C2   single  1.520  0.020  1.520
 LDJ  C2   C1   single  1.533  0.020  1.533
 LDJ  C7   H3   single  0.970  0.020  1.090
 LDJ  C8   H4   single  0.970  0.020  1.090
 LDJ  C8   H5   single  0.970  0.020  1.090
 LDJ  C10  H6   single  0.970  0.020  1.090
 LDJ  C10  H7   single  0.970  0.020  1.090
 LDJ  C1   H8   single  0.970  0.020  1.090
 LDJ  C1   H9   single  0.970  0.020  1.090
 LDJ  C1   H10  single  0.970  0.020  1.090
 LDJ  C2   H11  single  0.970  0.020  1.090
 LDJ  C3   H12  single  0.970  0.020  1.090
 LDJ  C3   H13  single  0.970  0.020  1.090
 LDJ  C3   H14  single  0.970  0.020  1.090
 LDJ  C9   H15  single  0.970  0.020  1.090
 LDJ  C9   H16  single  0.970  0.020  1.090
 LDJ  N2   H17  single  0.860  0.020  1.020

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
 LDJ  C5   N1   C4   116.77  3.000
 LDJ  N2   N3   C6   110.02  3.000
 LDJ  O1   C4   C2   122.37  3.000
 LDJ  C2   C4   N1   113.99  3.000
 LDJ  O1   C4   N1   123.63  3.000
 LDJ  S1   C5   N2   107.59  3.000
 LDJ  N2   C5   N1   122.82  3.000
 LDJ  S1   C5   N1   129.59  3.000
 LDJ  S1   C6   C7   119.71  3.000
 LDJ  S1   C6   N3   115.39  3.000
 LDJ  C7   C6   N3   124.88  3.000
 LDJ  H3   C7   O2   109.24  3.000
 LDJ  H3   C7   C8   110.89  3.000
 LDJ  O2   C7   C8   107.03  3.000
 LDJ  H3   C7   C6   108.68  3.000
 LDJ  O2   C7   C6   108.09  3.000
 LDJ  C8   C7   C6   112.82  3.000
 LDJ  H5   C8   H4   107.81  3.000
 LDJ  H5   C8   C9   113.90  3.000
 LDJ  H4   C8   C9   110.37  3.000
 LDJ  H5   C8   C7   111.61  3.000
 LDJ  H4   C8   C7   110.72  3.000
 LDJ  C9   C8   C7   102.41  3.000
 LDJ  H7   C10  H6   108.31  3.000
 LDJ  H7   C10  O2   108.35  3.000
 LDJ  H6   C10  O2   110.46  3.000
 LDJ  H7   C10  C9   113.89  3.000
 LDJ  H6   C10  C9   110.86  3.000
 LDJ  O2   C10  C9   104.92  3.000
 LDJ  H10  C1   H9   107.90  3.000
 LDJ  H10  C1   H8   108.23  3.000
 LDJ  H9   C1   H8   107.77  3.000
 LDJ  H10  C1   C2   111.70  3.000
 LDJ  H9   C1   C2   110.09  3.000
 LDJ  H8   C1   C2   111.02  3.000
 LDJ  H11  C2   C3   109.26  3.000
 LDJ  H11  C2   C1   107.58  3.000
 LDJ  C3   C2   C1   111.43  3.000
 LDJ  H11  C2   C4   106.85  3.000
 LDJ  C1   C2   C4   109.02  3.000
 LDJ  C3   C2   C4   112.48  3.000
 LDJ  H14  C3   H13  107.63  3.000
 LDJ  H14  C3   H12  107.97  3.000
 LDJ  H13  C3   H12  107.59  3.000
 LDJ  H14  C3   C2   111.62  3.000
 LDJ  H13  C3   C2   109.94  3.000
 LDJ  H12  C3   C2   111.91  3.000
 LDJ  H16  C9   H15  108.25  3.000
 LDJ  H16  C9   C10  110.67  3.000
 LDJ  H15  C9   C10  112.58  3.000
 LDJ  H16  C9   C8   111.20  3.000
 LDJ  H15  C9   C8   112.73  3.000
 LDJ  C10  C9   C8   101.36  3.000
 LDJ  H17  N2   C5   122.58  3.000
 LDJ  H17  N2   N3   118.52  3.000
 LDJ  C5   N2   N3   118.90  3.000
 LDJ  C10  O2   C7   109.78  3.000
 LDJ  C6   S1   C5    88.09  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
 LDJ  CONST_01  S1   C5   N2  N3     0.00   0.0  0
 LDJ  CONST_02  N3   N2   C5  N1   180.00   0.0  0
 LDJ  CONST_03  H17  N2   C5  S1   180.00   0.0  0
 LDJ  CONST_04  S1   C5   N1  C4     0.00   0.0  0
 LDJ  CONST_05  N2   C5   N1  C4   180.00   0.0  0
 LDJ  CONST_06  O1   C4   N1  C5     0.00   0.0  0
 LDJ  CONST_07  C2   C4   N1  C5   180.00   0.0  0
 LDJ  Var_01    C10  C9   C8  C7    33.80  30.0  1
 LDJ  Var_02    C9   C10  O2  C7    26.73  30.0  1
 LDJ  Var_03    O2   C10  C9  C8   -37.62  30.0  1
 LDJ  Var_04    C3   C2   C4  N1  -163.73  30.0  3
 LDJ  Var_05    H12  C3   C2  C4    58.12  30.0  3
 LDJ  Var_06    H8   C1   C2  C4    62.45  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
 LDJ  chir_01  C7  C8  O2  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
 LDJ  plan-1  N1   0.020
 LDJ  plan-1  N3   0.020
 LDJ  plan-1  C4   0.020
 LDJ  plan-1  C5   0.020
 LDJ  plan-1  C6   0.020
 LDJ  plan-1  C7   0.020
 LDJ  plan-1  C2   0.020
 LDJ  plan-1  N2   0.020
 LDJ  plan-1  O1   0.020
 LDJ  plan-1  S1   0.020
 LDJ  plan-1  H17  0.020

