# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 05:07:29 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: (5-tert-butyl-1,3,4-oxadiazol-2-yl)[(2S)-pyrrolidin-2-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1oc(nn1)C(=O)[C@@H]2CCCN2
#
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
 PTB  PTB  (5-tert-butyl-1,3,4-oxadiazol-2-yl)[(2S)-pyrrolidin-2-yl]methanone  ligand  33  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PTB
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
 PTB  N    N  NH1   0  -0.601   0.1460  -1.3555  -3.6180
 PTB  CA   C  CH1   0  -0.216   0.6998  -0.6502  -2.4796
 PTB  C    C  C     0   0.330  -0.2275  -0.7270  -1.2862
 PTB  O    O  O     0  -0.350  -1.3956  -1.0174  -1.3307
 PTB  CB   C  CH2   0  -0.483   0.8333   0.8275  -2.9197
 PTB  CG   C  CH2   0  -0.463  -0.1844   0.9276  -4.0495
 PTB  CD   C  CH2   0  -0.269  -0.0490  -0.4264  -4.7290
 PTB  C2   C  CR5   0   0.382   0.3791  -0.3674   0.0188
 PTB  N3   N  N     0  -0.277   1.6030  -0.0790   0.2839
 PTB  N4   N  N     0  -0.305   1.6642   0.1799   1.6198
 PTB  C5   C  CR5   0   0.548   0.4679   0.0307   2.0848
 PTB  O1   O  O     0  -0.396  -0.3880  -0.3171   1.1155
 PTB  C6   C  CT    0  -0.247  -0.0318   0.1955   3.4815
 PTB  C7   C  CH3   0  -0.637   1.1298   0.6046   4.3854
 PTB  C8   C  CH3   0  -0.640  -0.6215  -1.1373   3.9620
 PTB  C9   C  CH3   0  -0.638  -1.1160   1.2817   3.4964
 PTB  HN   H  HNH1  0   0.359   0.7188  -2.1444  -3.8766
 PTB  HA   H  HCH1  0   0.283   1.6756  -1.0414  -2.1784
 PTB  HB1  H  HCH2  0   0.259   0.6647   1.5455  -2.1163
 PTB  HB2  H  HCH2  0   0.257   1.8437   0.9947  -3.2957
 PTB  HG1  H  HCH2  0   0.236  -1.1930   1.0611  -3.6517
 PTB  HG2  H  HCH2  0   0.249   0.0150   1.7565  -4.7282
 PTB  HD1  H  HCH2  0   0.225  -0.9337  -0.6894  -5.3134
 PTB  HD2  H  HCH2  0   0.207   0.8055  -0.4115  -5.4157
 PTB  H71  H  HCH3  0   0.242   0.7616   0.7252   5.4047
 PTB  H72  H  HCH3  0   0.240   1.9172  -0.1492   4.4019
 PTB  H73  H  HCH3  0   0.240   1.5715   1.5517   4.0748
 PTB  H81  H  HCH3  0   0.244   0.1223  -1.9346   3.9369
 PTB  H82  H  HCH3  0   0.246  -0.9616  -1.0290   4.9925
 PTB  H83  H  HCH3  0   0.243  -1.4787  -1.4463   3.3634
 PTB  H91  H  HCH3  0   0.243  -0.7356   2.2329   3.1220
 PTB  H92  H  HCH3  0   0.242  -1.9836   0.9991   2.8997
 PTB  H93  H  HCH3  0   0.246  -1.4560   1.4370   4.5206

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
 PTB  N   CA   single    1.449  0.020  1.449
 PTB  N   CD   single    1.461  0.020  1.461
 PTB  N   HN   single    0.890  0.020  1.040
 PTB  CA  C    single    1.513  0.020  1.513
 PTB  CA  CB   single    1.548  0.020  1.548
 PTB  CA  HA   single    0.970  0.020  1.090
 PTB  C   O    double    1.204  0.020  1.204
 PTB  C   C2   single    1.483  0.020  1.483
 PTB  CB  CG   single    1.524  0.020  1.524
 PTB  CB  HB1  single    0.970  0.020  1.090
 PTB  CB  HB2  single    0.970  0.020  1.090
 PTB  CG  CD   single    1.521  0.020  1.521
 PTB  CG  HG1  single    0.970  0.020  1.090
 PTB  CG  HG2  single    0.970  0.020  1.090
 PTB  CD  HD1  single    0.970  0.020  1.090
 PTB  CD  HD2  single    0.970  0.020  1.090
 PTB  C2  N3   aromatic  1.285  0.020  1.285
 PTB  C2  O1   aromatic  1.339  0.020  1.339
 PTB  N3  N4   aromatic  1.362  0.020  1.362
 PTB  N4  C5   aromatic  1.292  0.020  1.292
 PTB  C5  O1   aromatic  1.339  0.020  1.339
 PTB  C5  C6   single    1.492  0.020  1.492
 PTB  C6  C7   single    1.528  0.020  1.528
 PTB  C6  C8   single    1.535  0.020  1.535
 PTB  C6  C9   single    1.535  0.020  1.535
 PTB  C7  H71  single    0.970  0.020  1.090
 PTB  C7  H72  single    0.970  0.020  1.090
 PTB  C7  H73  single    0.970  0.020  1.090
 PTB  C8  H81  single    0.970  0.020  1.090
 PTB  C8  H82  single    0.970  0.020  1.090
 PTB  C8  H83  single    0.970  0.020  1.090
 PTB  C9  H91  single    0.970  0.020  1.090
 PTB  C9  H92  single    0.970  0.020  1.090
 PTB  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
 PTB  HN   N   CD   112.22  3.000
 PTB  HN   N   CA   111.41  3.000
 PTB  CD   N   CA   109.80  3.000
 PTB  HA   CA  CB   110.05  3.000
 PTB  HA   CA  C    108.14  3.000
 PTB  CB   CA  C    109.00  3.000
 PTB  HA   CA  N    112.54  3.000
 PTB  CB   CA  N    105.92  3.000
 PTB  C    CA  N    111.14  3.000
 PTB  C2   C   O    119.18  3.000
 PTB  C2   C   CA   115.53  3.000
 PTB  O    C   CA   125.26  3.000
 PTB  HB2  CB  HB1  107.23  3.000
 PTB  HB2  CB  CG   110.66  3.000
 PTB  HB1  CB  CG   113.56  3.000
 PTB  HB2  CB  CA   108.92  3.000
 PTB  HB1  CB  CA   113.94  3.000
 PTB  CG   CB  CA   102.47  3.000
 PTB  HG2  CG  HG1  107.62  3.000
 PTB  HG2  CG  CD   112.50  3.000
 PTB  HG1  CG  CD   110.71  3.000
 PTB  HG2  CG  CB   112.92  3.000
 PTB  HG1  CG  CB   110.77  3.000
 PTB  CD   CG  CB   102.32  3.000
 PTB  HD2  CD  HD1  107.42  3.000
 PTB  HD2  CD  CG   109.70  3.000
 PTB  HD1  CD  CG   112.41  3.000
 PTB  HD2  CD  N    112.38  3.000
 PTB  HD1  CD  N    111.21  3.000
 PTB  CG   CD  N    103.78  3.000
 PTB  O1   C2  N3   111.60  3.000
 PTB  O1   C2  C    119.69  3.000
 PTB  N3   C2  C    128.71  3.000
 PTB  N4   N3  C2   106.72  3.000
 PTB  C5   N4  N3   106.82  3.000
 PTB  C6   C5  O1   119.47  3.000
 PTB  C6   C5  N4   129.35  3.000
 PTB  O1   C5  N4   111.18  3.000
 PTB  C5   O1  C2   103.67  3.000
 PTB  C9   C6  C8   109.89  3.000
 PTB  C9   C6  C7   109.99  3.000
 PTB  C8   C6  C7   109.85  3.000
 PTB  C9   C6  C5   108.89  3.000
 PTB  C8   C6  C5   109.02  3.000
 PTB  C7   C6  C5   109.19  3.000
 PTB  H73  C7  H72  108.20  3.000
 PTB  H73  C7  H71  107.88  3.000
 PTB  H72  C7  H71  107.83  3.000
 PTB  H73  C7  C6   111.84  3.000
 PTB  H72  C7  C6   111.90  3.000
 PTB  H71  C7  C6   109.02  3.000
 PTB  H83  C8  H82  107.56  3.000
 PTB  H83  C8  H81  108.44  3.000
 PTB  H82  C8  H81  107.88  3.000
 PTB  H83  C8  C6   112.11  3.000
 PTB  H82  C8  C6   109.24  3.000
 PTB  H81  C8  C6   111.45  3.000
 PTB  H93  C9  H92  107.63  3.000
 PTB  H93  C9  H91  107.88  3.000
 PTB  H92  C9  H91  108.41  3.000
 PTB  H93  C9  C6   109.28  3.000
 PTB  H92  C9  C6   111.93  3.000
 PTB  H91  C9  C6   111.56  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
 PTB  CONST_01  C5   N4  N3  C2    0.00   0.0  0
 PTB  CONST_02  N4   C5  O1  C2    0.00   0.0  0
 PTB  CONST_03  C5   O1  C2  N3    0.00   0.0  0
 PTB  CONST_04  O1   C5  N4  N3    0.00   0.0  0
 PTB  CONST_05  O1   C2  N3  N4    0.00   0.0  0
 PTB  CONST_06  N4   N3  C2  C   180.00   0.0  0
 PTB  CONST_07  C5   O1  C2  C   180.00   0.0  0
 PTB  CONST_08  C6   C5  O1  C2  180.00   0.0  0
 PTB  CONST_09  C6   C5  N4  N3  180.00   0.0  0
 PTB  Var_01    CB   CG  CD  N    38.23  30.0  1
 PTB  Var_02    CG   CD  N   CA  -24.59  30.0  1
 PTB  Var_03    CD   CG  CB  CA  -37.05  30.0  1
 PTB  Var_04    N3   C2  C   CA   -4.69  30.0  2
 PTB  Var_05    C7   C6  C5  N4    0.32  30.0  2
 PTB  Var_06    H71  C7  C6  C5  179.94  30.0  3
 PTB  Var_07    H81  C8  C6  C5   59.27  30.0  3
 PTB  Var_08    H91  C9  C6  C5  -58.43  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
 PTB  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
 PTB  plan-1  C   0.020
 PTB  plan-1  C2  0.020
 PTB  plan-1  N3  0.020
 PTB  plan-1  N4  0.020
 PTB  plan-1  C5  0.020
 PTB  plan-1  O1  0.020
 PTB  plan-1  C6  0.020
 PTB  plan-2  CA  0.020
 PTB  plan-2  C   0.020
 PTB  plan-2  O   0.020
 PTB  plan-2  C2  0.020

