# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:39:39 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (2S)-2-amino-1-(5-tert-butyl-1,3,4-oxadiazol-2-yl)propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)C(=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
 ATX  ATX  (2S)-2-amino-1-(5-tert-butyl-1,3,4-oxadiazol-2-yl)propan-1-one  ligand  29  14  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ATX
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
 ATX  N    N  NH2   0  -0.781   4.1995  -0.2320  -1.0967
 ATX  CA   C  CH1   0  -0.224   3.1025  -0.5805  -0.2201
 ATX  C    C  C     0   0.338   1.8757   0.2076  -0.6117
 ATX  O    O  O     0  -0.355   1.9050   1.2566  -1.2053
 ATX  CB   C  CH3   0  -0.675   3.3729  -0.3464   1.2752
 ATX  C5   C  CR5   0   0.385   0.5718  -0.3520  -0.1884
 ATX  N4   N  N     0  -0.275   0.3186  -1.5028   0.3242
 ATX  N3   N  N     0  -0.304  -1.0285  -1.5586   0.5138
 ATX  C2   C  CR5   0   0.549  -1.5114  -0.4320   0.1038
 ATX  O1   O  O     0  -0.395  -0.5426   0.3710  -0.3544
 ATX  C6   C  CT    0  -0.246  -2.9248   0.0474   0.1065
 ATX  C7   C  CH3   0  -0.636  -3.8341  -1.0783   0.5959
 ATX  C8   C  CH3   0  -0.639  -3.0319   1.2528   1.0522
 ATX  C9   C  CH3   0  -0.641  -3.3239   0.4621  -1.3157
 ATX  HN1  H  HNH2  0   0.347   4.5019   0.7183  -0.9176
 ATX  HN2  H  HNH2  0   0.359   4.9906  -0.8204  -0.8680
 ATX  HA   H  HCH1  0   0.274   2.8796  -1.6418  -0.3610
 ATX  HB1  H  HCH3  0   0.236   3.5877   0.7057   1.4686
 ATX  HB2  H  HCH3  0   0.239   2.5383  -0.6493   1.9072
 ATX  HB3  H  HCH3  0   0.253   4.2431  -0.9308   1.5740
 ATX  H71  H  HCH3  0   0.240  -3.5650  -1.4113   1.5983
 ATX  H72  H  HCH3  0   0.242  -4.8625  -0.7172   0.6269
 ATX  H73  H  HCH3  0   0.240  -3.8035  -1.9414  -0.0698
 ATX  H81  H  HCH3  0   0.243  -2.4112   2.0873   0.7246
 ATX  H82  H  HCH3  0   0.246  -4.0653   1.5999   1.0749
 ATX  H83  H  HCH3  0   0.244  -2.7430   0.9877   2.0700
 ATX  H91  H  HCH3  0   0.244  -3.2279  -0.3692  -2.0149
 ATX  H92  H  HCH3  0   0.246  -4.3662   0.7826  -1.3152
 ATX  H93  H  HCH3  0   0.243  -2.7232   1.2936  -1.6842

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
 ATX  N   CA   single    1.447  0.020  1.447
 ATX  N   HN1  single    0.890  0.020  1.040
 ATX  N   HN2  single    0.890  0.020  1.040
 ATX  CA  C    single    1.510  0.020  1.510
 ATX  CA  CB   single    1.537  0.020  1.537
 ATX  CA  HA   single    0.970  0.020  1.090
 ATX  C   O    double    1.206  0.020  1.206
 ATX  C   C5   single    1.481  0.020  1.481
 ATX  CB  HB1  single    0.970  0.020  1.090
 ATX  CB  HB2  single    0.970  0.020  1.090
 ATX  CB  HB3  single    0.970  0.020  1.090
 ATX  C5  N4   aromatic  1.285  0.020  1.285
 ATX  C5  O1   aromatic  1.339  0.020  1.339
 ATX  N4  N3   aromatic  1.362  0.020  1.362
 ATX  N3  C2   aromatic  1.292  0.020  1.292
 ATX  C2  O1   aromatic  1.339  0.020  1.339
 ATX  C2  C6   single    1.492  0.020  1.492
 ATX  C6  C7   single    1.528  0.020  1.528
 ATX  C6  C8   single    1.536  0.020  1.536
 ATX  C6  C9   single    1.534  0.020  1.534
 ATX  C7  H71  single    0.970  0.020  1.090
 ATX  C7  H72  single    0.970  0.020  1.090
 ATX  C7  H73  single    0.970  0.020  1.090
 ATX  C8  H81  single    0.970  0.020  1.090
 ATX  C8  H82  single    0.970  0.020  1.090
 ATX  C8  H83  single    0.970  0.020  1.090
 ATX  C9  H91  single    0.970  0.020  1.090
 ATX  C9  H92  single    0.970  0.020  1.090
 ATX  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
 ATX  HN2  N   HN1  105.78  3.000
 ATX  HN2  N   CA   108.40  3.000
 ATX  HN1  N   CA   110.19  3.000
 ATX  HA   CA  CB   108.00  3.000
 ATX  HA   CA  C    107.91  3.000
 ATX  CB   CA  C    108.40  3.000
 ATX  HA   CA  N    108.08  3.000
 ATX  CB   CA  N    114.79  3.000
 ATX  C    CA  N    109.46  3.000
 ATX  C5   C   O    119.40  3.000
 ATX  C5   C   CA   116.37  3.000
 ATX  O    C   CA   124.21  3.000
 ATX  HB3  CB  HB2  107.66  3.000
 ATX  HB3  CB  HB1  108.13  3.000
 ATX  HB2  CB  HB1  108.41  3.000
 ATX  HB3  CB  CA   109.00  3.000
 ATX  HB2  CB  CA   112.77  3.000
 ATX  HB1  CB  CA   110.72  3.000
 ATX  O1   C5  N4   111.66  3.000
 ATX  O1   C5  C    119.57  3.000
 ATX  N4   C5  C    128.76  3.000
 ATX  N3   N4  C5   106.69  3.000
 ATX  C2   N3  N4   106.85  3.000
 ATX  C6   C2  O1   119.54  3.000
 ATX  C6   C2  N3   129.29  3.000
 ATX  O1   C2  N3   111.16  3.000
 ATX  C2   O1  C5   103.64  3.000
 ATX  C9   C6  C8   109.91  3.000
 ATX  C9   C6  C7   109.95  3.000
 ATX  C8   C6  C7   109.85  3.000
 ATX  C9   C6  C2   109.36  3.000
 ATX  C8   C6  C2   108.62  3.000
 ATX  C7   C6  C2   109.12  3.000
 ATX  H73  C7  H72  107.81  3.000
 ATX  H73  C7  H71  108.22  3.000
 ATX  H72  C7  H71  107.93  3.000
 ATX  H73  C7  C6   111.78  3.000
 ATX  H72  C7  C6   109.06  3.000
 ATX  H71  C7  C6   111.89  3.000
 ATX  H83  C8  H82  107.99  3.000
 ATX  H83  C8  H81  108.40  3.000
 ATX  H82  C8  H81  107.58  3.000
 ATX  H83  C8  C6   111.44  3.000
 ATX  H82  C8  C6   109.19  3.000
 ATX  H81  C8  C6   112.09  3.000
 ATX  H93  C9  H92  107.62  3.000
 ATX  H93  C9  H91  108.43  3.000
 ATX  H92  C9  H91  107.97  3.000
 ATX  H93  C9  C6   112.10  3.000
 ATX  H92  C9  C6   109.13  3.000
 ATX  H91  C9  C6   111.44  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
 ATX  CONST_01  C2   N3  N4  C5    0.00   0.0  0
 ATX  CONST_02  N3   C2  O1  C5    0.00   0.0  0
 ATX  CONST_03  C2   O1  C5  N4    0.00   0.0  0
 ATX  CONST_04  O1   C2  N3  N4    0.00   0.0  0
 ATX  CONST_05  O1   C5  N4  N3    0.00   0.0  0
 ATX  CONST_06  N3   N4  C5  C   180.00   0.0  0
 ATX  CONST_07  C2   O1  C5  C   180.00   0.0  0
 ATX  CONST_08  C6   C2  O1  C5  180.00   0.0  0
 ATX  CONST_09  C6   C2  N3  N4  180.00   0.0  0
 ATX  Var_01    N4   C5  C   CA   -9.62  30.0  2
 ATX  Var_02    C7   C6  C2  N3   -4.51  30.0  2
 ATX  Var_03    H71  C7  C6  C2   58.94  30.0  3
 ATX  Var_04    H81  C8  C6  C2   61.89  30.0  3
 ATX  Var_05    H91  C9  C6  C2   59.13  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
 ATX  chir_01  CA  N  C  CB  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
 ATX  plan-1  C   0.020
 ATX  plan-1  C5  0.020
 ATX  plan-1  N4  0.020
 ATX  plan-1  N3  0.020
 ATX  plan-1  C2  0.020
 ATX  plan-1  O1  0.020
 ATX  plan-1  C6  0.020
 ATX  plan-2  CA  0.020
 ATX  plan-2  C   0.020
 ATX  plan-2  O   0.020
 ATX  plan-2  C5  0.020

