# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:56:02 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 1-(5-tert-butyl-1,3,4-oxadiazol-2-yl)-2-(methylamino)ethanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNCC(=O)c1oc(nn1)C(C)(C)C
#
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
 STX  STX  1-(5-tert-butyl-1,3,4-oxadiazol-2-yl)-2-(methylamino)ethanone  ligand  29  14  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_STX
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
 STX  N    N  NH1   0  -0.595   4.1518   0.0368  -0.5115
 STX  CA   C  CH2   0  -0.368   2.9333  -0.4185   0.0975
 STX  C    C  C     0   0.304   1.7256   0.2646  -0.4776
 STX  O    O  O     0  -0.354   1.7589   1.1455  -1.2995
 STX  CD   C  CH3   0  -0.519   5.3098  -0.6691   0.0011
 STX  C5   C  CR5   0   0.382   0.4205  -0.1971   0.0485
 STX  N4   N  N     0  -0.278   0.1846  -1.1239   0.9057
 STX  N3   N  N     0  -0.305  -1.1679  -1.1803   1.0565
 STX  C2   C  CR5   0   0.550  -1.6695  -0.2799   0.2770
 STX  O1   O  O     0  -0.395  -0.7081   0.3751  -0.3870
 STX  C6   C  CT    0  -0.249  -3.0994   0.0840   0.0509
 STX  C7   C  CH3   0  -0.636  -3.9843  -0.8139   0.9134
 STX  C8   C  CH3   0  -0.639  -3.3096   1.5530   0.4420
 STX  C9   C  CH3   0  -0.639  -3.4401  -0.1181  -1.4319
 STX  HN   H  HNH1  0   0.354   4.2664   1.0284  -0.3460
 STX  HA1  H  HCH2  0   0.278   2.8209  -1.4958  -0.0677
 STX  HA2  H  HCH2  0   0.253   2.8929  -0.2947   1.1934
 STX  HD1  H  HCH3  0   0.238   6.2131  -0.2665  -0.4556
 STX  HD2  H  HCH3  0   0.201   5.4259  -0.6110   1.0917
 STX  HD3  H  HCH3  0   0.228   5.2471  -1.7256  -0.2653
 STX  H71  H  HCH3  0   0.240  -3.7818  -0.6813   1.9762
 STX  H72  H  HCH3  0   0.243  -5.0297  -0.5596   0.7372
 STX  H73  H  HCH3  0   0.240  -3.8502  -1.8681   0.6708
 STX  H81  H  HCH3  0   0.243  -2.7067   2.2299  -0.1634
 STX  H82  H  HCH3  0   0.246  -4.3570   1.8183   0.2919
 STX  H83  H  HCH3  0   0.243  -3.0677   1.7224   1.4919
 STX  H91  H  HCH3  0   0.244  -3.2837  -1.1528  -1.7400
 STX  H92  H  HCH3  0   0.246  -4.4910   0.1241  -1.5923
 STX  H93  H  HCH3  0   0.243  -2.8487   0.5267  -2.0819

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
 STX  N   CA   single    1.436  0.020  1.436
 STX  N   CD   single    1.450  0.020  1.450
 STX  N   HN   single    0.890  0.020  1.040
 STX  CA  C    single    1.502  0.020  1.502
 STX  CA  HA1  single    0.970  0.020  1.090
 STX  CA  HA2  single    0.970  0.020  1.090
 STX  C   O    double    1.205  0.020  1.205
 STX  C   C5   single    1.481  0.020  1.481
 STX  CD  HD1  single    0.970  0.020  1.090
 STX  CD  HD2  single    0.970  0.020  1.090
 STX  CD  HD3  single    0.970  0.020  1.090
 STX  C5  N4   aromatic  1.284  0.020  1.284
 STX  C5  O1   aromatic  1.338  0.020  1.338
 STX  N4  N3   aromatic  1.362  0.020  1.362
 STX  N3  C2   aromatic  1.292  0.020  1.292
 STX  C2  O1   aromatic  1.339  0.020  1.339
 STX  C2  C6   single    1.493  0.020  1.493
 STX  C6  C7   single    1.528  0.020  1.528
 STX  C6  C8   single    1.535  0.020  1.535
 STX  C6  C9   single    1.535  0.020  1.535
 STX  C7  H71  single    0.970  0.020  1.090
 STX  C7  H72  single    0.970  0.020  1.090
 STX  C7  H73  single    0.970  0.020  1.090
 STX  C8  H81  single    0.970  0.020  1.090
 STX  C8  H82  single    0.970  0.020  1.090
 STX  C8  H83  single    0.970  0.020  1.090
 STX  C9  H91  single    0.970  0.020  1.090
 STX  C9  H92  single    0.970  0.020  1.090
 STX  C9  H93  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
 STX  HN   N   CD   109.21  3.000
 STX  HN   N   CA   109.72  3.000
 STX  CD   N   CA   111.93  3.000
 STX  HA2  CA  HA1  104.84  3.000
 STX  HA2  CA  C    107.45  3.000
 STX  HA1  CA  C    107.88  3.000
 STX  HA2  CA  N    114.61  3.000
 STX  HA1  CA  N    109.56  3.000
 STX  C    CA  N    112.07  3.000
 STX  C5   C   O    119.63  3.000
 STX  C5   C   CA   115.52  3.000
 STX  O    C   CA   124.84  3.000
 STX  HD3  CD  HD2  107.43  3.000
 STX  HD3  CD  HD1  107.64  3.000
 STX  HD2  CD  HD1  108.01  3.000
 STX  HD3  CD  N    109.83  3.000
 STX  HD2  CD  N    114.19  3.000
 STX  HD1  CD  N    109.52  3.000
 STX  O1   C5  N4   111.77  3.000
 STX  O1   C5  C    119.63  3.000
 STX  N4   C5  C    128.60  3.000
 STX  N3   N4  C5   106.63  3.000
 STX  C2   N3  N4   106.85  3.000
 STX  C6   C2  O1   119.55  3.000
 STX  C6   C2  N3   129.28  3.000
 STX  O1   C2  N3   111.17  3.000
 STX  C2   O1  C5   103.59  3.000
 STX  C9   C6  C8   109.99  3.000
 STX  C9   C6  C7   109.85  3.000
 STX  C8   C6  C7   109.84  3.000
 STX  C9   C6  C2   109.08  3.000
 STX  C8   C6  C2   109.03  3.000
 STX  C7   C6  C2   109.03  3.000
 STX  H73  C7  H72  107.91  3.000
 STX  H73  C7  H71  108.17  3.000
 STX  H72  C7  H71  107.89  3.000
 STX  H73  C7  C6   111.81  3.000
 STX  H72  C7  C6   109.09  3.000
 STX  H71  C7  C6   111.80  3.000
 STX  H83  C8  H82  107.92  3.000
 STX  H83  C8  H81  108.39  3.000
 STX  H82  C8  H81  107.67  3.000
 STX  H83  C8  C6   111.32  3.000
 STX  H82  C8  C6   109.23  3.000
 STX  H81  C8  C6   112.15  3.000
 STX  H93  C9  H92  107.69  3.000
 STX  H93  C9  H91  108.35  3.000
 STX  H92  C9  H91  107.90  3.000
 STX  H93  C9  C6   112.20  3.000
 STX  H92  C9  C6   109.08  3.000
 STX  H91  C9  C6   111.47  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
 STX  CONST_01  C2   N3  N4  C5     0.00   0.0  0
 STX  CONST_02  N3   C2  O1  C5     0.00   0.0  0
 STX  CONST_03  C2   O1  C5  N4     0.00   0.0  0
 STX  CONST_04  O1   C2  N3  N4     0.00   0.0  0
 STX  CONST_05  O1   C5  N4  N3     0.00   0.0  0
 STX  CONST_06  N3   N4  C5  C    180.00   0.0  0
 STX  CONST_07  C2   O1  C5  C    180.00   0.0  0
 STX  CONST_08  C6   C2  O1  C5   180.00   0.0  0
 STX  CONST_09  C6   C2  N3  N4   180.00   0.0  0
 STX  Var_01    N4   C5  C   CA    -1.83  30.0  2
 STX  Var_02    C7   C6  C2  N3    -0.45  30.0  2
 STX  Var_03    C5   C   CA  N    177.06  30.0  3
 STX  Var_04    H71  C7  C6  C2    61.63  30.0  3
 STX  Var_05    H81  C8  C6  C2    61.54  30.0  3
 STX  Var_06    H91  C9  C6  C2    59.57  30.0  3
 STX  Var_07    CD   N   CA  C   -177.30  30.0  2
 STX  Var_08    HD1  CD  N   CA  -177.72  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
 STX  plan-1  C   0.020
 STX  plan-1  C5  0.020
 STX  plan-1  N4  0.020
 STX  plan-1  N3  0.020
 STX  plan-1  C2  0.020
 STX  plan-1  O1  0.020
 STX  plan-1  C6  0.020
 STX  plan-2  CA  0.020
 STX  plan-2  C   0.020
 STX  plan-2  O   0.020
 STX  plan-2  C5  0.020

