# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 17:29:20 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: (3~{R})-~{N}-(5-bromanylpyridin-2-yl)piperidine-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccc(NC(=O)[C@@H]2CCCNC2)nc1
#
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
 AVB  AVB  (3~{R})-~{N}-(5-bromanylpyridin-2-yl)piperidine-3-carboxamide  ligand  30  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AVB
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
 AVB  BR1  BR  BR    0  -0.028  -4.8390  -0.0369   0.2894
 AVB  C02  C   CR6   0  -0.201  -2.9688  -0.2265   0.3272
 AVB  C03  C   CR16  0  -0.110  -2.3670  -1.2100   1.1035
 AVB  C04  C   CR16  0  -0.395  -0.9931  -1.3036   1.0935
 AVB  C05  C   CR6   0   0.534  -0.2625  -0.4052   0.3055
 AVB  N06  N   N     0  -0.417  -0.8425   0.5280  -0.4278
 AVB  C07  C   CR16  0  -0.042  -2.1662   0.6163  -0.4204
 AVB  N08  N   NH1   0  -0.730   1.1208  -0.5130   0.3245
 AVB  C09  C   C     0   0.566   2.0589   0.1504  -0.4201
 AVB  O10  O   O     0  -0.442   1.7953   0.9657  -1.2785
 AVB  C11  C   CH1   0  -0.413   3.4860  -0.2177  -0.0695
 AVB  C12  C   CH2   0  -0.424   4.2190   0.9991   0.5069
 AVB  C13  C   CH2   0  -0.437   5.6812   0.6584   0.7694
 AVB  C14  C   CH2   0  -0.292   6.3314   0.0953  -0.4846
 AVB  N15  N   NH1   0  -0.599   5.5904  -1.0677  -0.9425
 AVB  C16  C   CH2   0  -0.265   4.2265  -0.7359  -1.3054
 AVB  H1   H   HCR6  0   0.297  -2.9519  -1.8941   1.7033
 AVB  H2   H   HCR6  0   0.292  -0.4943  -2.0621   1.6827
 AVB  H3   H   HCR6  0   0.282  -2.5988   1.3971  -1.0361
 AVB  H4   H   HNH1  0   0.424   1.4823  -1.1970   0.9709
 AVB  H5   H   HCH1  0   0.257   3.4973  -1.0142   0.6822
 AVB  H6   H   HCH2  0   0.226   4.1603   1.8250  -0.2089
 AVB  H7   H   HCH2  0   0.246   3.7300   1.3335   1.4248
 AVB  H8   H   HCH2  0   0.235   6.2202   1.5494   1.0979
 AVB  H9   H   HCH2  0   0.219   5.7528  -0.0770   1.5763
 AVB  H10  H   HCH2  0   0.188   6.3784   0.8910  -1.2474
 AVB  H11  H   HCH2  0   0.233   7.3597  -0.2053  -0.2749
 AVB  H12  H   HNH1  0   0.355   6.0571  -1.4742  -1.7424
 AVB  H14  H   HCH2  0   0.243   3.7341  -1.6350  -1.6829
 AVB  H15  H   HCH2  0   0.198   4.1688   0.0253  -2.0993

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
 AVB  C14  C13  single    1.521  0.020  1.521
 AVB  C14  N15  single    1.453  0.020  1.453
 AVB  C13  C12  single    1.524  0.020  1.524
 AVB  C12  C11  single    1.533  0.020  1.533
 AVB  N06  C07  aromatic  1.327  0.020  1.327
 AVB  N06  C05  aromatic  1.321  0.020  1.321
 AVB  C07  C02  aromatic  1.383  0.020  1.383
 AVB  N15  C16  single    1.450  0.020  1.450
 AVB  N08  C05  single    1.388  0.020  1.388
 AVB  N08  C09  single    1.369  0.020  1.369
 AVB  C16  C11  single    1.531  0.020  1.531
 AVB  C11  C09  single    1.515  0.020  1.515
 AVB  C05  C04  aromatic  1.401  0.020  1.401
 AVB  C09  O10  double    1.213  0.020  1.213
 AVB  C02  BR1  single    1.880  0.020  1.880
 AVB  C02  C03  aromatic  1.390  0.020  1.390
 AVB  C04  C03  aromatic  1.377  0.020  1.377
 AVB  C03  H1   single    0.930  0.020  1.080
 AVB  C04  H2   single    0.930  0.020  1.080
 AVB  C07  H3   single    0.930  0.020  1.080
 AVB  N08  H4   single    0.860  0.020  1.020
 AVB  C11  H5   single    0.970  0.020  1.090
 AVB  C12  H6   single    0.970  0.020  1.090
 AVB  C12  H7   single    0.970  0.020  1.090
 AVB  C13  H8   single    0.970  0.020  1.090
 AVB  C13  H9   single    0.970  0.020  1.090
 AVB  C14  H10  single    0.970  0.020  1.090
 AVB  C14  H11  single    0.970  0.020  1.090
 AVB  N15  H12  single    0.890  0.020  1.040
 AVB  C16  H14  single    0.970  0.020  1.090
 AVB  C16  H15  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
 AVB  C07  C02  C03  118.80  3.000
 AVB  C03  C02  BR1  120.88  3.000
 AVB  C07  C02  BR1  120.32  3.000
 AVB  H1   C03  C04  120.04  3.000
 AVB  H1   C03  C02  121.54  3.000
 AVB  C04  C03  C02  118.42  3.000
 AVB  H2   C04  C05  121.02  3.000
 AVB  H2   C04  C03  120.23  3.000
 AVB  C05  C04  C03  118.74  3.000
 AVB  N08  C05  N06  120.01  3.000
 AVB  N08  C05  C04  117.55  3.000
 AVB  N06  C05  C04  122.44  3.000
 AVB  C07  N06  C05  118.82  3.000
 AVB  H3   C07  N06  116.28  3.000
 AVB  H3   C07  C02  120.94  3.000
 AVB  N06  C07  C02  122.77  3.000
 AVB  H4   N08  C09  115.58  3.000
 AVB  H4   N08  C05  114.77  3.000
 AVB  C09  N08  C05  129.64  3.000
 AVB  C11  C09  O10  122.14  3.000
 AVB  O10  C09  N08  124.17  3.000
 AVB  C11  C09  N08  113.69  3.000
 AVB  H5   C11  C16  107.63  3.000
 AVB  H5   C11  C12  108.31  3.000
 AVB  C16  C11  C12  109.93  3.000
 AVB  H5   C11  C09  110.20  3.000
 AVB  C16  C11  C09  110.55  3.000
 AVB  C12  C11  C09  110.15  3.000
 AVB  H7   C12  H6   107.13  3.000
 AVB  H7   C12  C13  110.68  3.000
 AVB  H6   C12  C13  109.44  3.000
 AVB  H7   C12  C11  110.17  3.000
 AVB  H6   C12  C11  109.11  3.000
 AVB  C13  C12  C11  110.24  3.000
 AVB  H9   C13  H8   107.12  3.000
 AVB  H9   C13  C14  109.35  3.000
 AVB  H8   C13  C14  109.83  3.000
 AVB  H9   C13  C12  109.88  3.000
 AVB  H8   C13  C12  110.05  3.000
 AVB  C14  C13  C12  110.54  3.000
 AVB  H11  C14  H10  106.93  3.000
 AVB  H11  C14  N15  108.69  3.000
 AVB  H10  C14  N15  112.40  3.000
 AVB  H11  C14  C13  110.26  3.000
 AVB  H10  C14  C13  108.75  3.000
 AVB  N15  C14  C13  109.77  3.000
 AVB  H12  N15  C16  109.16  3.000
 AVB  H12  N15  C14  109.61  3.000
 AVB  C16  N15  C14  112.05  3.000
 AVB  H15  C16  H14  107.22  3.000
 AVB  H15  C16  N15  112.83  3.000
 AVB  H14  C16  N15  108.79  3.000
 AVB  H15  C16  C11  108.82  3.000
 AVB  H14  C16  C11  109.85  3.000
 AVB  N15  C16  C11  109.29  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
 AVB  CONST_01  C05  N06  C07  C02    0.00   0.0  0
 AVB  CONST_02  C05  C04  C03  C02    0.00   0.0  0
 AVB  CONST_03  N06  C07  C02  C03    0.00   0.0  0
 AVB  CONST_04  N06  C05  C04  C03    0.00   0.0  0
 AVB  CONST_05  C07  N06  C05  C04    0.00   0.0  0
 AVB  CONST_06  C07  C02  C03  C04    0.00   0.0  0
 AVB  CONST_07  N06  C07  C02  BR1  180.00   0.0  0
 AVB  CONST_08  C04  C03  C02  BR1  180.00   0.0  0
 AVB  CONST_09  N08  C05  C04  C03  180.00   0.0  0
 AVB  CONST_10  N08  C05  N06  C07  180.00   0.0  0
 AVB  CONST_11  H2   C04  C03  C02  180.00   0.0  0
 AVB  CONST_12  H3   C07  C02  C03  180.00   0.0  0
 AVB  CONST_13  H1   C03  C04  C05  180.00   0.0  0
 AVB  CONST_14  C11  C09  N08  C05  180.00   0.0  0
 AVB  CONST_15  C09  N08  C05  C04  180.00   0.0  0
 AVB  CONST_16  C09  N08  C05  N06    0.00   0.0  0
 AVB  CONST_17  H4   N08  C05  C04    0.00   0.0  0
 AVB  CONST_18  O10  C09  N08  C05    0.00   0.0  0
 AVB  Var_01    C14  C13  C12  C11   53.63  30.0  1
 AVB  Var_02    C14  N15  C16  C11  -62.60  30.0  1
 AVB  Var_03    N15  C14  C13  C12  -56.74  30.0  1
 AVB  Var_04    C16  N15  C14  C13   62.15  30.0  1

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
 AVB  chir_01  C11  C12  C16  C09  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
 AVB  plan-1  BR1  0.020
 AVB  plan-1  C02  0.020
 AVB  plan-1  C03  0.020
 AVB  plan-1  C04  0.020
 AVB  plan-1  C05  0.020
 AVB  plan-1  N06  0.020
 AVB  plan-1  C07  0.020
 AVB  plan-1  N08  0.020
 AVB  plan-1  H1   0.020
 AVB  plan-1  H2   0.020
 AVB  plan-1  H3   0.020
 AVB  plan-2  C05  0.020
 AVB  plan-2  N08  0.020
 AVB  plan-2  C09  0.020
 AVB  plan-2  O10  0.020
 AVB  plan-2  C11  0.020
 AVB  plan-2  H4   0.020

