# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 10:17:35 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 1-pyridin-3-ylbutan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(=O)c1cccnc1
#
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
 PBO  PBO  1-pyridin-3-ylbutan-1-one  ligand  22  11  .  2021-08-19  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PBO
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
 PBO  C10   C  CH3   0  -0.666  -0.9494   0.0128   4.2624
 PBO  C11   C  CH2   0  -0.419   0.1618   0.0032   3.2226
 PBO  C12   C  CH2   0  -0.578  -0.3950  -0.0017   1.8070
 PBO  C13   C  C     0   0.386   0.6561  -0.0151   0.7277
 PBO  C14   C  CR6   0  -0.104   0.2149  -0.0145  -0.6979
 PBO  C15   C  CR16  0  -0.148   1.1667  -0.0278  -1.7162
 PBO  C16   C  CR16  0  -0.315   0.7440  -0.0285  -3.0316
 PBO  C17   C  CR16  0  -0.052  -0.6207  -0.0156  -3.2873
 PBO  N1'   N  N     0  -0.400  -1.5416  -0.0033  -2.3312
 PBO  C18   C  CR16  0  -0.080  -1.1271  -0.0024  -1.0714
 PBO  O13   O  O     0  -0.395   1.8398  -0.0285   0.9886
 PBO  H103  H  HCH3  0   0.233  -0.5409   0.0142   5.2731
 PBO  H101  H  HCH3  0   0.220  -1.5822   0.8960   4.1606
 PBO  H102  H  HCH3  0   0.220  -1.5908  -0.8648   4.1665
 PBO  H111  H  HCH2  0   0.227   0.8047   0.8747   3.3622
 PBO  H112  H  HCH2  0   0.227   0.7965  -0.8726   3.3708
 PBO  H121  H  HCH2  0   0.270  -1.0497  -0.8689   1.6616
 PBO  H122  H  HCH2  0   0.270  -1.0428   0.8685   1.6517
 PBO  H15   H  HCR6  0   0.278   2.2225  -0.0380  -1.4803
 PBO  H16   H  HCR6  0   0.280   1.4521  -0.0391  -3.8481
 PBO  H17   H  HCR6  0   0.276  -0.9838  -0.0158  -4.3089
 PBO  H18   H  HCR6  0   0.270  -1.9103   0.0078  -0.3227

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
 PBO  C10  C11   single    1.522  0.020  1.522
 PBO  C10  H103  single    0.970  0.020  1.090
 PBO  C10  H101  single    0.970  0.020  1.090
 PBO  C10  H102  single    0.970  0.020  1.090
 PBO  C11  C12   single    1.521  0.020  1.521
 PBO  C11  H111  single    0.970  0.020  1.090
 PBO  C11  H112  single    0.970  0.020  1.090
 PBO  C12  C13   single    1.507  0.020  1.507
 PBO  C12  H121  single    0.970  0.020  1.090
 PBO  C12  H122  single    0.970  0.020  1.090
 PBO  C13  C14   single    1.492  0.020  1.492
 PBO  C13  O13   double    1.212  0.020  1.212
 PBO  C14  C15   aromatic  1.394  0.020  1.394
 PBO  C14  C18   aromatic  1.393  0.020  1.393
 PBO  C15  C16   aromatic  1.382  0.020  1.382
 PBO  C15  H15   single    0.930  0.020  1.080
 PBO  C16  C17   aromatic  1.389  0.020  1.389
 PBO  C16  H16   single    0.930  0.020  1.080
 PBO  C17  N1'   aromatic  1.328  0.020  1.328
 PBO  C17  H17   single    0.930  0.020  1.080
 PBO  N1'  C18   aromatic  1.326  0.020  1.326
 PBO  C18  H18   single    0.930  0.020  1.080

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
 PBO  H102  C10  H101  107.57  3.000
 PBO  H102  C10  H103  107.62  3.000
 PBO  H101  C10  H103  107.62  3.000
 PBO  H102  C10  C11   111.35  3.000
 PBO  H101  C10  C11   111.40  3.000
 PBO  H103  C10  C11   111.09  3.000
 PBO  H112  C11  H111  106.29  3.000
 PBO  H112  C11  C12   109.67  3.000
 PBO  H111  C11  C12   109.70  3.000
 PBO  H112  C11  C10   109.68  3.000
 PBO  H111  C11  C10   109.73  3.000
 PBO  C12   C11  C10   111.63  3.000
 PBO  H122  C12  H121  104.85  3.000
 PBO  H122  C12  C13   108.54  3.000
 PBO  H121  C12  C13   108.33  3.000
 PBO  H122  C12  C11   110.22  3.000
 PBO  H121  C12  C11   110.16  3.000
 PBO  C13   C12  C11   114.29  3.000
 PBO  O13   C13  C14   119.62  3.000
 PBO  O13   C13  C12   121.81  3.000
 PBO  C14   C13  C12   118.56  3.000
 PBO  C18   C14  C15   117.52  3.000
 PBO  C18   C14  C13   122.75  3.000
 PBO  C15   C14  C13   119.73  3.000
 PBO  H15   C15  C16   120.41  3.000
 PBO  H15   C15  C14   120.48  3.000
 PBO  C16   C15  C14   119.11  3.000
 PBO  H16   C16  C17   120.32  3.000
 PBO  H16   C16  C15   121.25  3.000
 PBO  C17   C16  C15   118.43  3.000
 PBO  H17   C17  N1'   116.51  3.000
 PBO  H17   C17  C16   120.18  3.000
 PBO  N1'   C17  C16   123.31  3.000
 PBO  C18   N1'  C17   117.86  3.000
 PBO  H18   C18  N1'   115.50  3.000
 PBO  H18   C18  C14   120.74  3.000
 PBO  N1'   C18  C14   123.76  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
 PBO  CONST_01  C17   C16  C15  C14     0.00   0.0  0
 PBO  CONST_02  C17   N1'  C18  C14     0.00   0.0  0
 PBO  CONST_03  N1'   C18  C14  C15     0.00   0.0  0
 PBO  CONST_04  N1'   C17  C16  C15     0.00   0.0  0
 PBO  CONST_05  C18   C14  C15  C16     0.00   0.0  0
 PBO  CONST_06  C18   N1'  C17  C16     0.00   0.0  0
 PBO  CONST_07  C16   C15  C14  C13   180.00   0.0  0
 PBO  CONST_08  N1'   C18  C14  C13   180.00   0.0  0
 PBO  CONST_09  H16   C16  C15  C14   180.00   0.0  0
 PBO  CONST_10  H18   C18  C14  C15   180.00   0.0  0
 PBO  CONST_11  H17   C17  C16  C15   180.00   0.0  0
 PBO  CONST_12  H15   C15  C16  C17   180.00   0.0  0
 PBO  Var_01    C15   C14  C13  C12  -179.95  30.0  2
 PBO  Var_02    C14   C13  C12  C11  -179.72  30.0  3
 PBO  Var_03    C13   C12  C11  C10  -179.84  30.0  3
 PBO  Var_04    H103  C10  C11  C12   179.88  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
 PBO  plan-1  C13  0.020
 PBO  plan-1  C14  0.020
 PBO  plan-1  C15  0.020
 PBO  plan-1  C16  0.020
 PBO  plan-1  C17  0.020
 PBO  plan-1  N1'  0.020
 PBO  plan-1  C18  0.020
 PBO  plan-1  H15  0.020
 PBO  plan-1  H16  0.020
 PBO  plan-1  H17  0.020
 PBO  plan-1  H18  0.020
 PBO  plan-2  C12  0.020
 PBO  plan-2  C13  0.020
 PBO  plan-2  C14  0.020
 PBO  plan-2  O13  0.020

