# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 03:26:30 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: (phenylmethyl) 4-oxidanylpiperidine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1CCN(CC1)C(=O)OCc2ccccc2
#
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
 B0G  B0G  '(phenylmethyl) 4-oxidanylpiperidine-1-carboxylate'  ligand  34  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B0G
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
 B0G  N1   N  NT    0  -0.480   1.6821   0.8092   0.5457
 B0G  C4   C  CR6   0   0.077  -2.7784   0.3239  -0.3352
 B0G  C5   C  CR16  0  -0.283  -3.3713   0.2753   0.9245
 B0G  C6   C  CR16  0  -0.243  -4.4076  -0.6098   1.1818
 B0G  C7   C  CH2   0  -0.232  -1.6463   1.2692  -0.6015
 B0G  C8   C  C     0   0.770   0.6546   1.4028  -0.0956
 B0G  C10  C  CH2   0  -0.456   2.4861  -1.4930   0.2923
 B0G  C13  C  CH2   0  -0.326   3.0232   1.3539   0.4318
 B0G  C1   C  CR16  0  -0.262  -4.8648  -1.4566   0.1784
 B0G  C2   C  CR16  0  -0.241  -4.2801  -1.4141  -1.0794
 B0G  C3   C  CR16  0  -0.299  -3.2397  -0.5287  -1.3322
 B0G  O1   O  O2    0  -0.478  -0.4791   0.7004  -0.0004
 B0G  O2   O  O     0  -0.531   0.7241   2.4668  -0.6827
 B0G  C9   C  CH2   0  -0.330   1.6449  -0.5268   1.1192
 B0G  C11  C  CH1   0   0.068   3.9072  -0.9732   0.1441
 B0G  C12  C  CH2   0  -0.473   3.8973   0.4432  -0.4227
 B0G  O3   O  OH1   0  -0.673   4.6253  -1.8741  -0.6705
 B0G  H1   H  HCR6  0   0.254  -3.0247   0.9385   1.7085
 B0G  H2   H  HCR6  0   0.258  -4.8626  -0.6369   2.1634
 B0G  H3   H  HCH2  0   0.246  -1.4961   1.3985  -1.6752
 B0G  H4   H  HCH2  0   0.245  -1.8516   2.2502  -0.1673
 B0G  H5   H  HCH2  0   0.246   2.4910  -2.4709   0.7799
 B0G  H6   H  HCH2  0   0.230   2.0312  -1.6196  -0.6954
 B0G  H7   H  HCH2  0   0.269   2.9799   2.3566   0.0172
 B0G  H8   H  HCH2  0   0.243   3.4455   1.4380   1.4384
 B0G  H9   H  HCR6  0   0.259  -5.6772  -2.1438   0.3756
 B0G  H10  H  HCR6  0   0.258  -4.6329  -2.0697  -1.8649
 B0G  H11  H  HCR6  0   0.255  -2.7865  -0.4990  -2.3159
 B0G  H12  H  HCH2  0   0.243   2.0444  -0.4667   2.1366
 B0G  H13  H  HCH2  0   0.276   0.6230  -0.8818   1.2036
 B0G  H14  H  HCH1  0   0.191   4.3541  -0.9254   1.1502
 B0G  H15  H  HCH2  0   0.230   3.5196   0.4265  -1.4498
 B0G  H16  H  HCH2  0   0.243   4.9140   0.8458  -0.4540
 B0G  H17  H  HOH1  0   0.448   5.5357  -1.5670  -0.7282

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
 B0G  O3   C11  single    1.411  0.020  1.411
 B0G  C12  C11  single    1.526  0.020  1.526
 B0G  C12  C13  single    1.524  0.020  1.524
 B0G  C11  C10  single    1.520  0.020  1.520
 B0G  C13  N1   single    1.452  0.020  1.452
 B0G  C10  C9   single    1.525  0.020  1.525
 B0G  C9   N1   single    1.454  0.020  1.454
 B0G  N1   C8   single    1.349  0.020  1.349
 B0G  C2   C3   aromatic  1.389  0.020  1.389
 B0G  C2   C1   aromatic  1.388  0.020  1.388
 B0G  O1   C8   single    1.337  0.020  1.337
 B0G  O1   C7   single    1.431  0.020  1.431
 B0G  C8   O2   double    1.217  0.020  1.217
 B0G  C3   C4   aromatic  1.391  0.020  1.391
 B0G  C1   C6   aromatic  1.390  0.020  1.390
 B0G  C4   C7   single    1.499  0.020  1.499
 B0G  C4   C5   aromatic  1.393  0.020  1.393
 B0G  C6   C5   aromatic  1.387  0.020  1.387
 B0G  C5   H1   single    0.930  0.020  1.080
 B0G  C6   H2   single    0.930  0.020  1.080
 B0G  C7   H3   single    0.970  0.020  1.090
 B0G  C7   H4   single    0.970  0.020  1.090
 B0G  C10  H5   single    0.970  0.020  1.090
 B0G  C10  H6   single    0.970  0.020  1.090
 B0G  C13  H7   single    0.970  0.020  1.090
 B0G  C13  H8   single    0.970  0.020  1.090
 B0G  C1   H9   single    0.930  0.020  1.080
 B0G  C2   H10  single    0.930  0.020  1.080
 B0G  C3   H11  single    0.930  0.020  1.080
 B0G  C9   H12  single    0.970  0.020  1.090
 B0G  C9   H13  single    0.970  0.020  1.090
 B0G  C11  H14  single    0.970  0.020  1.090
 B0G  C12  H15  single    0.970  0.020  1.090
 B0G  C12  H16  single    0.970  0.020  1.090
 B0G  O3   H17  single    0.850  0.020  0.980

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
 B0G  C9   N1   C13  113.53  3.000
 B0G  C9   N1   C8   124.91  3.000
 B0G  C13  N1   C8   120.08  3.000
 B0G  C3   C4   C7   120.66  3.000
 B0G  C7   C4   C5   120.27  3.000
 B0G  C3   C4   C5   119.06  3.000
 B0G  H1   C5   C6   119.69  3.000
 B0G  H1   C5   C4   119.78  3.000
 B0G  C6   C5   C4   120.53  3.000
 B0G  H2   C6   C1   120.07  3.000
 B0G  H2   C6   C5   119.89  3.000
 B0G  C1   C6   C5   120.04  3.000
 B0G  H4   C7   H3   108.08  3.000
 B0G  H4   C7   O1   110.08  3.000
 B0G  H3   C7   O1   110.36  3.000
 B0G  H4   C7   C4   110.73  3.000
 B0G  H3   C7   C4   110.69  3.000
 B0G  O1   C7   C4   106.91  3.000
 B0G  O2   C8   O1   122.82  3.000
 B0G  O2   C8   N1   124.78  3.000
 B0G  O1   C8   N1   112.39  3.000
 B0G  H6   C10  H5   107.52  3.000
 B0G  H6   C10  C11  109.88  3.000
 B0G  H5   C10  C11  110.20  3.000
 B0G  H6   C10  C9   109.47  3.000
 B0G  H5   C10  C9   109.12  3.000
 B0G  C11  C10  C9   110.60  3.000
 B0G  H8   C13  H7   107.19  3.000
 B0G  H8   C13  C12  109.88  3.000
 B0G  H7   C13  C12  111.13  3.000
 B0G  H8   C13  N1   108.23  3.000
 B0G  H7   C13  N1   109.85  3.000
 B0G  C12  C13  N1   110.46  3.000
 B0G  H9   C1   C2   120.06  3.000
 B0G  H9   C1   C6   120.14  3.000
 B0G  C2   C1   C6   119.80  3.000
 B0G  H10  C2   C3   119.87  3.000
 B0G  H10  C2   C1   120.13  3.000
 B0G  C3   C2   C1   119.99  3.000
 B0G  H11  C3   C2   119.73  3.000
 B0G  H11  C3   C4   119.70  3.000
 B0G  C2   C3   C4   120.58  3.000
 B0G  C8   O1   C7   116.93  3.000
 B0G  H13  C9   H12  106.82  3.000
 B0G  H13  C9   C10  110.76  3.000
 B0G  H12  C9   C10  109.72  3.000
 B0G  H13  C9   N1   110.81  3.000
 B0G  H12  C9   N1   107.87  3.000
 B0G  C10  C9   N1   110.74  3.000
 B0G  H14  C11  O3   110.39  3.000
 B0G  H14  C11  C12  107.55  3.000
 B0G  O3   C11  C12  112.43  3.000
 B0G  H14  C11  C10  107.76  3.000
 B0G  C12  C11  C10  110.34  3.000
 B0G  O3   C11  C10  108.28  3.000
 B0G  H16  C12  H15  107.42  3.000
 B0G  H16  C12  C11  110.26  3.000
 B0G  H15  C12  C11  109.68  3.000
 B0G  H16  C12  C13  109.22  3.000
 B0G  H15  C12  C13  109.71  3.000
 B0G  C11  C12  C13  110.50  3.000
 B0G  H17  O3   C11  108.19  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
 B0G  CONST_01  C1   C2   C3   C4     0.00   0.0  0
 B0G  CONST_02  C1   C6   C5   C4     0.00   0.0  0
 B0G  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 B0G  CONST_04  C2   C1   C6   C5     0.00   0.0  0
 B0G  CONST_05  C3   C2   C1   C6     0.00   0.0  0
 B0G  CONST_06  C3   C4   C5   C6     0.00   0.0  0
 B0G  CONST_07  C7   C4   C5   C6   180.00   0.0  0
 B0G  CONST_08  C2   C3   C4   C7   180.00   0.0  0
 B0G  CONST_09  H10  C2   C3   C4   180.00   0.0  0
 B0G  CONST_10  H2   C6   C5   C4   180.00   0.0  0
 B0G  CONST_11  H11  C3   C4   C5   180.00   0.0  0
 B0G  CONST_12  H9   C1   C6   C5   180.00   0.0  0
 B0G  CONST_13  H1   C5   C6   C1   180.00   0.0  0
 B0G  Var_01    C11  C12  C13  N1   -55.76  30.0  1
 B0G  Var_02    C11  C10  C9   N1    55.09  30.0  1
 B0G  Var_03    C13  N1   C9   C10  -57.89  30.0  1
 B0G  Var_04    C12  C13  N1   C9    58.20  30.0  1
 B0G  Var_05    O1   C7   C4   C5    76.49  30.0  2
 B0G  Var_06    O1   C8   N1   C13  173.48  30.0  2

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
 B0G  chir_01  C11  O3  C12  C10  negativ

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
 B0G  plan-1  C4   0.020
 B0G  plan-1  C5   0.020
 B0G  plan-1  C6   0.020
 B0G  plan-1  C7   0.020
 B0G  plan-1  C1   0.020
 B0G  plan-1  C2   0.020
 B0G  plan-1  C3   0.020
 B0G  plan-1  H1   0.020
 B0G  plan-1  H2   0.020
 B0G  plan-1  H9   0.020
 B0G  plan-1  H10  0.020
 B0G  plan-1  H11  0.020
 B0G  plan-2  N1   0.020
 B0G  plan-2  C8   0.020
 B0G  plan-2  O1   0.020
 B0G  plan-2  O2   0.020

