# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:55:42 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (5-bromopyridin-3-yl)[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1cncc(c1)C(=O)N2CCC(CC2)N3CCCC3
#
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
 P8H  P8H  (5-bromopyridin-3-yl)[4-(pyrrolidin-1-yl)piperidin-1-yl]methanone  ligand  40  20  .  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_P8H
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
 P8H  C1    C   CR6   0  -0.181   3.5326   0.3772  -0.2479
 P8H  C2    C   CR16  0  -0.035   3.6776   0.5394  -1.6197
 P8H  N3    N   N     0  -0.391   2.7419   1.1116  -2.3622
 P8H  C4    C   CR16  0  -0.051   1.6383   1.5479  -1.7735
 P8H  C5    C   CR6   0  -0.168   1.3986   1.4102  -0.4112
 P8H  C6    C   CR16  0  -0.120   2.3746   0.8113   0.3739
 P8H  C7    C   C     0   0.523   0.1650   2.0190   0.1826
 P8H  BR8   BR  BR    0  -0.010   4.9059  -0.4298   0.7484
 P8H  O9    O   O     0  -0.477  -0.0343   3.2131   0.0082
 P8H  N10   N   NT    0  -0.436  -0.6357   1.2205   0.9112
 P8H  C11   C   CH2   0  -0.326  -0.6704  -0.2303   0.8108
 P8H  C12   C   CH2   0  -0.449  -1.8756  -0.6857  -0.0029
 P8H  C13   C   CH2   0  -0.325  -1.8378   1.7597   1.5267
 P8H  C14   C   CH2   0  -0.451  -3.0773   1.3759   0.7307
 P8H  C15   C   CH1   0  -0.032  -3.1883  -0.1401   0.5580
 P8H  N16   N   NT    0  -0.436  -4.3090  -0.4792  -0.2981
 P8H  C17   C   CH2   0  -0.281  -4.4684  -1.8998  -0.5673
 P8H  C18   C   CH2   0  -0.455  -5.8326  -1.9760  -1.2390
 P8H  C19   C   CH2   0  -0.473  -6.6422  -0.8638  -0.5501
 P8H  C20   C   CH2   0  -0.280  -5.5988  -0.0558   0.2352
 P8H  H2    H   HCR6  0   0.289   4.5714   0.1995  -2.1302
 P8H  H4    H   HCR6  0   0.281   0.9009   2.0195  -2.4133
 P8H  H6    H   HCR6  0   0.305   2.2326   0.6950   1.4412
 P8H  H11   H   HCH2  0   0.277   0.2401  -0.6117   0.3574
 P8H  H11A  H   HCH2  0   0.252  -0.7194  -0.6410   1.8226
 P8H  H12   H   HCH2  0   0.229  -1.7592  -0.3568  -1.0408
 P8H  H12A  H   HCH2  0   0.254  -1.8771  -1.7771  -0.0084
 P8H  H13   H   HCH2  0   0.250  -1.9014   1.3556   2.5412
 P8H  H13A  H   HCH2  0   0.269  -1.7535   2.8396   1.6133
 P8H  H14   H   HCH2  0   0.251  -3.9518   1.7741   1.2489
 P8H  H14A  H   HCH2  0   0.229  -3.0408   1.8514  -0.2541
 P8H  H15   H   HCH1  0   0.185  -3.3351  -0.5812   1.5656
 P8H  H17   H   HCH2  0   0.235  -3.6705  -2.2822  -1.2051
 P8H  H17A  H   HCH2  0   0.188  -4.4631  -2.4968   0.3617
 P8H  H18   H   HCH2  0   0.230  -5.7333  -1.7737  -2.3064
 P8H  H18A  H   HCH2  0   0.233  -6.2845  -2.9619  -1.1343
 P8H  H19   H   HCH2  0   0.237  -7.1649  -0.2435  -1.2779
 P8H  H19A  H   HCH2  0   0.233  -7.3979  -1.2703   0.1216
 P8H  H20   H   HCH2  0   0.193  -5.6736  -0.2818   1.3121
 P8H  H20A  H   HCH2  0   0.233  -5.7388   1.0202   0.1237

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
 P8H  C2   C1    aromatic  1.389  0.020  1.389
 P8H  C1   C6    aromatic  1.384  0.020  1.384
 P8H  C1   BR8   single    1.879  0.020  1.879
 P8H  N3   C2    aromatic  1.324  0.020  1.324
 P8H  C2   H2    single    0.930  0.020  1.080
 P8H  N3   C4    aromatic  1.325  0.020  1.325
 P8H  C4   C5    aromatic  1.390  0.020  1.390
 P8H  C4   H4    single    0.930  0.020  1.080
 P8H  C7   C5    single    1.498  0.020  1.498
 P8H  C5   C6    aromatic  1.388  0.020  1.388
 P8H  C6   H6    single    0.930  0.020  1.080
 P8H  N10  C7    single    1.345  0.020  1.345
 P8H  C7   O9    double    1.223  0.020  1.223
 P8H  C11  N10   single    1.455  0.020  1.455
 P8H  C13  N10   single    1.454  0.020  1.454
 P8H  C11  C12   single    1.524  0.020  1.524
 P8H  C11  H11   single    0.970  0.020  1.090
 P8H  C11  H11A  single    0.970  0.020  1.090
 P8H  C15  C12   single    1.528  0.020  1.528
 P8H  C12  H12   single    0.970  0.020  1.090
 P8H  C12  H12A  single    0.970  0.020  1.090
 P8H  C13  C14   single    1.522  0.020  1.522
 P8H  C13  H13   single    0.970  0.020  1.090
 P8H  C13  H13A  single    0.970  0.020  1.090
 P8H  C15  C14   single    1.530  0.020  1.530
 P8H  C14  H14   single    0.970  0.020  1.090
 P8H  C14  H14A  single    0.970  0.020  1.090
 P8H  C15  N16   single    1.450  0.020  1.450
 P8H  C15  H15   single    0.970  0.020  1.090
 P8H  C17  N16   single    1.455  0.020  1.455
 P8H  N16  C20   single    1.459  0.020  1.459
 P8H  C17  C18   single    1.523  0.020  1.523
 P8H  C17  H17   single    0.970  0.020  1.090
 P8H  C17  H17A  single    0.970  0.020  1.090
 P8H  C18  C19   single    1.538  0.020  1.538
 P8H  C18  H18   single    0.970  0.020  1.090
 P8H  C18  H18A  single    0.970  0.020  1.090
 P8H  C20  C19   single    1.536  0.020  1.536
 P8H  C19  H19   single    0.970  0.020  1.090
 P8H  C19  H19A  single    0.970  0.020  1.090
 P8H  C20  H20   single    0.970  0.020  1.090
 P8H  C20  H20A  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
 P8H  BR8   C1   C6   120.53  3.000
 P8H  BR8   C1   C2   119.84  3.000
 P8H  C6    C1   C2   119.63  3.000
 P8H  H2    C2   N3   117.00  3.000
 P8H  H2    C2   C1   120.97  3.000
 P8H  N3    C2   C1   122.03  3.000
 P8H  C4    N3   C2   118.79  3.000
 P8H  H4    C4   C5   120.27  3.000
 P8H  H4    C4   N3   116.60  3.000
 P8H  C5    C4   N3   123.13  3.000
 P8H  C7    C5   C6   122.00  3.000
 P8H  C6    C5   C4   118.41  3.000
 P8H  C7    C5   C4   119.35  3.000
 P8H  H6    C6   C5   120.76  3.000
 P8H  H6    C6   C1   121.24  3.000
 P8H  C5    C6   C1   117.99  3.000
 P8H  N10   C7   O9   124.04  3.000
 P8H  O9    C7   C5   118.31  3.000
 P8H  N10   C7   C5   117.61  3.000
 P8H  C13   N10  C11  112.29  3.000
 P8H  C13   N10  C7   120.07  3.000
 P8H  C11   N10  C7   124.67  3.000
 P8H  H11A  C11  H11  106.98  3.000
 P8H  H11A  C11  C12  110.28  3.000
 P8H  H11   C11  C12  109.58  3.000
 P8H  H11A  C11  N10  108.18  3.000
 P8H  H11   C11  N10  111.03  3.000
 P8H  C12   C11  N10  110.72  3.000
 P8H  H12A  C12  H12  107.20  3.000
 P8H  H12A  C12  C15  110.96  3.000
 P8H  H12   C12  C15  109.39  3.000
 P8H  H12A  C12  C11  107.61  3.000
 P8H  H12   C12  C11  109.41  3.000
 P8H  C15   C12  C11  112.13  3.000
 P8H  H13A  C13  H13  107.32  3.000
 P8H  H13A  C13  C14  110.82  3.000
 P8H  H13   C13  C14  110.14  3.000
 P8H  H13A  C13  N10  109.77  3.000
 P8H  H13   C13  N10  107.68  3.000
 P8H  C14   C13  N10  110.99  3.000
 P8H  H14A  C14  H14  107.18  3.000
 P8H  H14A  C14  C15  109.36  3.000
 P8H  H14   C14  C15  110.91  3.000
 P8H  H14A  C14  C13  109.50  3.000
 P8H  H14   C14  C13  108.19  3.000
 P8H  C15   C14  C13  111.59  3.000
 P8H  H15   C15  N16  109.93  3.000
 P8H  H15   C15  C14  107.52  3.000
 P8H  N16   C15  C14  110.76  3.000
 P8H  H15   C15  C12  107.75  3.000
 P8H  N16   C15  C12  111.32  3.000
 P8H  C14   C15  C12  109.44  3.000
 P8H  C20   N16  C17  104.73  3.000
 P8H  C20   N16  C15  113.55  3.000
 P8H  C17   N16  C15  114.97  3.000
 P8H  H17A  C17  H17  107.39  3.000
 P8H  H17A  C17  C18  110.39  3.000
 P8H  H17   C17  C18  112.33  3.000
 P8H  H17A  C17  N16  111.82  3.000
 P8H  H17   C17  N16  111.74  3.000
 P8H  C18   C17  N16  103.22  3.000
 P8H  H18A  C18  H18  107.43  3.000
 P8H  H18A  C18  C19  113.13  3.000
 P8H  H18   C18  C19  110.61  3.000
 P8H  H18A  C18  C17  111.99  3.000
 P8H  H18   C18  C17  109.92  3.000
 P8H  C19   C18  C17  103.76  3.000
 P8H  H19A  C19  H19  106.94  3.000
 P8H  H19A  C19  C20  110.63  3.000
 P8H  H19   C19  C20  111.58  3.000
 P8H  H19A  C19  C18  111.80  3.000
 P8H  H19   C19  C18  111.40  3.000
 P8H  C20   C19  C18  104.58  3.000
 P8H  H20A  C20  H20  107.05  3.000
 P8H  H20A  C20  C19  112.31  3.000
 P8H  H20   C20  C19  110.21  3.000
 P8H  H20A  C20  N16  111.25  3.000
 P8H  H20   C20  N16  110.94  3.000
 P8H  C19   C20  N16  105.14  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
 P8H  CONST_01  C4   N3   C2   C1      0.00   0.0  0
 P8H  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 P8H  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 P8H  CONST_04  C5   C4   N3   C2      0.00   0.0  0
 P8H  CONST_05  C6   C1   C2   N3      0.00   0.0  0
 P8H  CONST_06  C6   C5   C4   N3      0.00   0.0  0
 P8H  CONST_07  C7   C5   C6   C1    180.00   0.0  0
 P8H  CONST_08  BR8  C1   C2   N3    180.00   0.0  0
 P8H  CONST_09  C7   C5   C4   N3    180.00   0.0  0
 P8H  CONST_10  BR8  C1   C6   C5    180.00   0.0  0
 P8H  CONST_12  C13  N10  C7   C5    180.00   0.0  0
 P8H  CONST_13  H6   C6   C1   C2    180.00   0.0  0
 P8H  CONST_14  H4   C4   N3   C2    180.00   0.0  0
 P8H  CONST_15  H2   C2   N3   C4    180.00   0.0  0
 P8H  CONST_17  C13  N10  C7   O9      0.00   0.0  0
 P8H  Var_01    C15  C12  C11  N10   -55.23  30.0  1
 P8H  Var_02    C15  C14  C13  N10    55.87  30.0  1
 P8H  Var_03    C14  C13  N10  C11   -59.16  30.0  1
 P8H  Var_04    C13  N10  C11  C12    58.58  30.0  1
 P8H  Var_05    C18  C17  N16  C15   169.55  30.0  1
 P8H  Var_06    C19  C20  N16  C15  -162.83  30.0  1
 P8H  Var_07    C19  C18  C17  N16   -33.82  30.0  1
 P8H  Var_08    C18  C19  C20  N16    14.44  30.0  1
 P8H  Var_09    C20  C19  C18  C17    11.67  30.0  1
 P8H  Var_10    N10  C7   C5   C4    127.02  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
 P8H  chir_01  C15  C12  C14  N16  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
 P8H  plan-1  C1   0.020
 P8H  plan-1  C2   0.020
 P8H  plan-1  N3   0.020
 P8H  plan-1  C4   0.020
 P8H  plan-1  C5   0.020
 P8H  plan-1  C6   0.020
 P8H  plan-1  C7   0.020
 P8H  plan-1  BR8  0.020
 P8H  plan-1  H2   0.020
 P8H  plan-1  H4   0.020
 P8H  plan-1  H6   0.020
 P8H  plan-2  C5   0.020
 P8H  plan-2  C7   0.020
 P8H  plan-2  O9   0.020
 P8H  plan-2  N10  0.020
 P8H  plan-2  C11  0.020
 P8H  plan-2  C13  0.020

