# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 05:37:20 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: (3S)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CCN(C1)Cc2onc(n2)c3ccccc3
#
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
 P6B  P6B  (3S)-1-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]pyrrolidin-3-ol  ligand  33  18  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P6B
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
 P6B  C1    C  CH2   0  -0.520   3.9038  -0.1702  -1.3965
 P6B  N1    N  NT    0  -0.436   2.5452   0.1197   0.5405
 P6B  O1    O  O     0  -0.332  -0.3051   2.1201   1.5678
 P6B  C2    C  CH2   0  -0.263   2.5419   0.3438  -0.9072
 P6B  N2    N  N     0  -0.453  -0.3210   0.2245   0.5030
 P6B  O2    O  OH1   0  -0.674   4.0171  -2.2506  -0.1082
 P6B  C3    C  CH2   0  -0.393   1.8804   1.1187   1.3204
 P6B  N3    N  N     0  -0.159  -1.6143   1.8780   1.2563
 P6B  C4    C  CR5   0   0.542   0.4080   1.1052   1.0967
 P6B  C5    C  CR5   0   0.322  -1.5795   0.7442   0.6221
 P6B  C6    C  CR6   0   0.003  -2.7703   0.0898   0.0819
 P6B  C7    C  CR16  0  -0.281  -4.0365   0.6469   0.2653
 P6B  C8    C  CR16  0  -0.240  -5.1544   0.0167  -0.2550
 P6B  C9    C  CR16  0  -0.250  -5.0211  -1.1728  -0.9624
 P6B  C10   C  CR16  0  -0.240  -3.7630  -1.7292  -1.1475
 P6B  C11   C  CR16  0  -0.289  -2.6401  -1.1022  -0.6276
 P6B  C12   C  CH2   0  -0.278   3.9155  -0.1302   0.9570
 P6B  C13   C  CH1   0   0.015   4.4882  -0.9226  -0.2002
 P6B  H1    H  HCH2  0   0.253   3.8315  -0.7938  -2.2890
 P6B  H1A   H  HCH2  0   0.241   4.5574   0.6676  -1.6453
 P6B  H2    H  HCH2  0   0.214   2.4231   1.4069  -1.1541
 P6B  H2A   H  HCH2  0   0.233   1.7069  -0.1848  -1.3697
 P6B  HO2   H  HOH1  0   0.449   4.3167  -2.7256  -0.8892
 P6B  H3    H  HCH2  0   0.296   2.0526   0.9219   2.3840
 P6B  H3A   H  HCH2  0   0.248   2.2495   2.1420   1.1352
 P6B  H7    H  HCR6  0   0.261  -4.1502   1.5714   0.8163
 P6B  H8    H  HCR6  0   0.265  -6.1329   0.4541  -0.1080
 P6B  H9    H  HCR6  0   0.265  -5.8969  -1.6633  -1.3666
 P6B  H10   H  HCR6  0   0.264  -3.6530  -2.6535  -1.6990
 P6B  H11   H  HCR6  0   0.262  -1.6610  -1.5383  -0.7744
 P6B  H12   H  HCH2  0   0.208   4.5019   0.7938   1.0796
 P6B  H12A  H  HCH2  0   0.245   3.9483  -0.6711   1.9063
 P6B  H13   H  HCH1  0   0.222   5.5841  -0.8914  -0.2007

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
 P6B  C1   C2    single    1.536  0.020  1.536
 P6B  C1   C13   single    1.529  0.020  1.529
 P6B  N1   C2    single    1.465  0.020  1.465
 P6B  N1   C3    single    1.431  0.020  1.431
 P6B  N1   C12   single    1.454  0.020  1.454
 P6B  O1   N3    aromatic  1.367  0.020  1.367
 P6B  O1   C4    aromatic  1.327  0.020  1.327
 P6B  N2   C4    aromatic  1.288  0.020  1.288
 P6B  N2   C5    aromatic  1.367  0.020  1.367
 P6B  O2   C13   single    1.412  0.020  1.412
 P6B  C3   C4    single    1.489  0.020  1.489
 P6B  N3   C5    aromatic  1.300  0.020  1.300
 P6B  C5   C6    single    1.462  0.020  1.462
 P6B  C6   C7    aromatic  1.396  0.020  1.396
 P6B  C6   C11   aromatic  1.393  0.020  1.393
 P6B  C7   C8    aromatic  1.385  0.020  1.385
 P6B  C8   C9    aromatic  1.390  0.020  1.390
 P6B  C9   C10   aromatic  1.388  0.020  1.388
 P6B  C10  C11   aromatic  1.387  0.020  1.387
 P6B  C12  C13   single    1.515  0.020  1.515
 P6B  C1   H1    single    0.970  0.020  1.090
 P6B  C1   H1A   single    0.970  0.020  1.090
 P6B  C2   H2    single    0.970  0.020  1.090
 P6B  C2   H2A   single    0.970  0.020  1.090
 P6B  O2   HO2   single    0.850  0.020  0.980
 P6B  C3   H3    single    0.970  0.020  1.090
 P6B  C3   H3A   single    0.970  0.020  1.090
 P6B  C7   H7    single    0.930  0.020  1.080
 P6B  C8   H8    single    0.930  0.020  1.080
 P6B  C9   H9    single    0.930  0.020  1.080
 P6B  C10  H10   single    0.930  0.020  1.080
 P6B  C11  H11   single    0.930  0.020  1.080
 P6B  C12  H12   single    0.970  0.020  1.090
 P6B  C12  H12A  single    0.970  0.020  1.090
 P6B  C13  H13   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
 P6B  H1A   C1   H1   106.97  3.000
 P6B  H1A   C1   C13  109.10  3.000
 P6B  H1    C1   C13  112.58  3.000
 P6B  H1A   C1   C2   110.30  3.000
 P6B  H1    C1   C2   113.15  3.000
 P6B  C13   C1   C2   104.74  3.000
 P6B  C12   N1   C3   113.68  3.000
 P6B  C12   N1   C2   108.15  3.000
 P6B  C3    N1   C2   115.51  3.000
 P6B  C4    O1   N3   107.35  3.000
 P6B  H2A   C2   H2   106.92  3.000
 P6B  H2A   C2   N1   110.27  3.000
 P6B  H2    C2   N1   111.76  3.000
 P6B  H2A   C2   C1   112.43  3.000
 P6B  H2    C2   C1   110.39  3.000
 P6B  N1    C2   C1   105.17  3.000
 P6B  C5    N2   C4   102.77  3.000
 P6B  HO2   O2   C13  107.91  3.000
 P6B  H3A   C3   H3   106.08  3.000
 P6B  H3A   C3   C4   108.29  3.000
 P6B  H3    C3   C4   107.44  3.000
 P6B  H3A   C3   N1   113.61  3.000
 P6B  H3    C3   N1   109.31  3.000
 P6B  C4    C3   N1   111.78  3.000
 P6B  C5    N3   O1   103.89  3.000
 P6B  C3    C4   N2   129.41  3.000
 P6B  C3    C4   O1   118.10  3.000
 P6B  N2    C4   O1   112.48  3.000
 P6B  C6    C5   N3   123.30  3.000
 P6B  C6    C5   N2   123.20  3.000
 P6B  N3    C5   N2   113.51  3.000
 P6B  C11   C6   C7   119.56  3.000
 P6B  C11   C6   C5   119.67  3.000
 P6B  C7    C6   C5   120.78  3.000
 P6B  H7    C7   C8   119.69  3.000
 P6B  H7    C7   C6   120.22  3.000
 P6B  C8    C7   C6   120.09  3.000
 P6B  H8    C8   C9   120.12  3.000
 P6B  H8    C8   C7   119.67  3.000
 P6B  C9    C8   C7   120.21  3.000
 P6B  H9    C9   C10  120.14  3.000
 P6B  H9    C9   C8   120.01  3.000
 P6B  C10   C9   C8   119.85  3.000
 P6B  H10   C10  C11  119.67  3.000
 P6B  H10   C10  C9   120.17  3.000
 P6B  C11   C10  C9   120.17  3.000
 P6B  H11   C11  C10  119.97  3.000
 P6B  H11   C11  C6   119.91  3.000
 P6B  C10   C11  C6   120.13  3.000
 P6B  H12A  C12  H12  107.61  3.000
 P6B  H12A  C12  C13  113.16  3.000
 P6B  H12   C12  C13  108.82  3.000
 P6B  H12A  C12  N1   111.23  3.000
 P6B  H12   C12  N1   112.93  3.000
 P6B  C13   C12  N1   103.15  3.000
 P6B  H13   C13  C12  111.30  3.000
 P6B  H13   C13  O2   111.12  3.000
 P6B  C12   C13  O2   108.42  3.000
 P6B  H13   C13  C1   111.57  3.000
 P6B  C12   C13  C1   101.28  3.000
 P6B  O2    C13  C1   112.72  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
 P6B  CONST_01  N2   C5   N3   O1     0.00   0.0  0
 P6B  CONST_02  C6   C5   N3   O1   180.00   0.0  0
 P6B  CONST_03  C5   N2   C4   O1     0.00   0.0  0
 P6B  CONST_04  N3   O1   C4   N2     0.00   0.0  0
 P6B  CONST_05  C7   C6   C5   N2   180.00   0.0  0
 P6B  CONST_06  C11  C6   C5   N2     0.00   0.0  0
 P6B  CONST_07  C4   N2   C5   N3     0.00   0.0  0
 P6B  CONST_08  C7   C6   C5   N3     0.00   0.0  0
 P6B  CONST_09  C11  C6   C5   N3   180.00   0.0  0
 P6B  CONST_10  C5   N3   O1   C4     0.00   0.0  0
 P6B  CONST_11  C6   C5   N2   C4   180.00   0.0  0
 P6B  CONST_12  C8   C7   C6   C5   180.00   0.0  0
 P6B  CONST_13  C10  C11  C6   C5   180.00   0.0  0
 P6B  CONST_14  C9   C8   C7   C6     0.00   0.0  0
 P6B  CONST_15  C9   C10  C11  C6     0.00   0.0  0
 P6B  CONST_16  C10  C11  C6   C7     0.00   0.0  0
 P6B  CONST_17  C10  C9   C8   C7     0.00   0.0  0
 P6B  CONST_18  C11  C6   C7   C8     0.00   0.0  0
 P6B  CONST_19  C11  C10  C9   C8     0.00   0.0  0
 P6B  CONST_20  N3   O1   C4   C3   180.00   0.0  0
 P6B  CONST_21  C5   N2   C4   C3   180.00   0.0  0
 P6B  CONST_22  H7   C7   C6   C5     0.00   0.0  0
 P6B  CONST_23  H11  C11  C6   C5     0.00   0.0  0
 P6B  CONST_24  H8   C8   C7   C6   180.00   0.0  0
 P6B  CONST_25  H10  C10  C11  C6   180.00   0.0  0
 P6B  CONST_26  H9   C9   C8   C7   180.00   0.0  0
 P6B  Var_01    C12  N1   C2   C1    15.53  30.0  1
 P6B  Var_02    C13  C1   C2   N1    11.18  30.0  1
 P6B  Var_03    C13  C12  N1   C2   -36.40  30.0  1
 P6B  Var_04    O1   C4   C3   N1  -168.37  30.0  2
 P6B  Var_05    C4   C3   N1   C2    68.36  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
 P6B  chir_01  C13  C1  O2  C12  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
 P6B  plan-1  O1   0.020
 P6B  plan-1  N2   0.020
 P6B  plan-1  C3   0.020
 P6B  plan-1  N3   0.020
 P6B  plan-1  C4   0.020
 P6B  plan-1  C5   0.020
 P6B  plan-1  C6   0.020
 P6B  plan-2  C5   0.020
 P6B  plan-2  C6   0.020
 P6B  plan-2  C7   0.020
 P6B  plan-2  C8   0.020
 P6B  plan-2  C9   0.020
 P6B  plan-2  C10  0.020
 P6B  plan-2  C11  0.020
 P6B  plan-2  H7   0.020
 P6B  plan-2  H8   0.020
 P6B  plan-2  H9   0.020
 P6B  plan-2  H10  0.020
 P6B  plan-2  H11  0.020

