# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 23:31:01 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: [(2~{R})-butan-2-yl] (2~{S})-2-(2-hydroxyethyl)piperidine-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](C)OC(=O)N1CCCC[C@H]1CCO
#
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
 KBR  KBR  '[(2~{R})-butan-2-yl] (2~{S})-2-(2-hydroxyethyl)piperidine-1-carboxylate'  ligand  39  16  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KBR
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
 KBR  C4   C  CH2   0  -0.426   2.0566   0.8855   1.0379
 KBR  C5   C  CH1   0  -0.083   1.8068   0.0942  -0.2465
 KBR  C6   C  C     0   0.758  -0.5681  -0.5086  -0.0731
 KBR  C11  C  CH2   0  -0.469   2.3290  -1.3414  -0.2240
 KBR  C7   C  CH1   0   0.033  -2.9339  -0.7726   0.1343
 KBR  C8   C  CH2   0  -0.434  -4.0598   0.2445   0.2208
 KBR  C9   C  CH3   0  -0.671  -3.7635   1.4146   1.1487
 KBR  C10  C  CH3   0  -0.677  -3.2786  -1.9451  -0.7650
 KBR  C12  C  CH2   0  -0.143   3.8318  -1.3626  -0.4503
 KBR  N1   N  NT    0  -0.490   0.4006   0.2604  -0.6381
 KBR  C3   C  CH2   0  -0.440   1.7164   2.3605   0.8233
 KBR  O2   O  O2    0  -0.488  -1.7904  -0.0722  -0.3840
 KBR  O1   O  O     0  -0.513  -0.3714  -1.4964   0.6070
 KBR  C1   C  CH2   0  -0.337   0.1253   1.6520  -0.9950
 KBR  C2   C  CH2   0  -0.439   0.3264   2.5532   0.2190
 KBR  O3   O  OH1   0  -0.674   4.2744  -2.7015  -0.3935
 KBR  H1   H  HCH2  0   0.226   1.4567   0.4585   1.8475
 KBR  H2   H  HCH2  0   0.235   3.1019   0.7921   1.3420
 KBR  H3   H  HCH1  0   0.234   2.3574   0.6017  -1.0494
 KBR  H4   H  HCH2  0   0.235   2.0958  -1.8288   0.7219
 KBR  H5   H  HCH2  0   0.234   1.8506  -1.9195  -1.0188
 KBR  H6   H  HCH1  0   0.230  -2.7052  -1.1350   1.1406
 KBR  H8   H  HCH2  0   0.230  -4.9455  -0.2860   0.5785
 KBR  H9   H  HCH3  0   0.219  -3.5242   1.0681   2.1559
 KBR  H10  H  HCH3  0   0.229  -2.9232   2.0112   0.7936
 KBR  H11  H  HCH3  0   0.232  -4.6274   2.0749   1.2239
 KBR  H12  H  HCH3  0   0.241  -2.4678  -2.6715  -0.8086
 KBR  H13  H  HCH3  0   0.234  -4.1615  -2.4579  -0.3818
 KBR  H14  H  HCH3  0   0.227  -3.4996  -1.6094  -1.7795
 KBR  H15  H  HCH2  0   0.191   4.0572  -0.9083  -1.4248
 KBR  H16  H  HCH2  0   0.192   4.3353  -0.7477   0.3071
 KBR  H17  H  HCH2  0   0.237   1.7991   2.9112   1.7624
 KBR  H18  H  HCH2  0   0.219   2.4592   2.7925   0.1442
 KBR  H19  H  HCH2  0   0.242   0.8261   1.9300  -1.7870
 KBR  H20  H  HCH2  0   0.268  -0.8728   1.7563  -1.4095
 KBR  H21  H  HCH2  0   0.224  -0.4455   2.3304   0.9629
 KBR  H22  H  HCH2  0   0.238   0.1823   3.5959  -0.0736
 KBR  H23  H  HOH1  0   0.453   5.2306  -2.7046  -0.4916
 KBR  H7   H  HCH2  0   0.224  -4.3048   0.6067  -0.7822

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
 KBR  C9   C8   single  1.522  0.020  1.522
 KBR  C8   C7   single  1.520  0.020  1.520
 KBR  C7   C10  single  1.517  0.020  1.517
 KBR  C7   O2   single  1.438  0.020  1.438
 KBR  O2   C6   single  1.335  0.020  1.335
 KBR  C6   O1   double  1.215  0.020  1.215
 KBR  C6   N1   single  1.360  0.020  1.360
 KBR  C1   N1   single  1.463  0.020  1.463
 KBR  C1   C2   single  1.525  0.020  1.525
 KBR  N1   C5   single  1.469  0.020  1.469
 KBR  C2   C3   single  1.528  0.020  1.528
 KBR  C5   C4   single  1.529  0.020  1.529
 KBR  C5   C11  single  1.528  0.020  1.528
 KBR  C3   C4   single  1.529  0.020  1.529
 KBR  C11  C12  single  1.520  0.020  1.520
 KBR  C12  O3   single  1.411  0.020  1.411
 KBR  C4   H1   single  0.970  0.020  1.090
 KBR  C4   H2   single  0.970  0.020  1.090
 KBR  C5   H3   single  0.970  0.020  1.090
 KBR  C11  H4   single  0.970  0.020  1.090
 KBR  C11  H5   single  0.970  0.020  1.090
 KBR  C7   H6   single  0.970  0.020  1.090
 KBR  C8   H7   single  0.970  0.020  1.090
 KBR  C8   H8   single  0.970  0.020  1.090
 KBR  C9   H9   single  0.970  0.020  1.090
 KBR  C9   H10  single  0.970  0.020  1.090
 KBR  C9   H11  single  0.970  0.020  1.090
 KBR  C10  H12  single  0.970  0.020  1.090
 KBR  C10  H13  single  0.970  0.020  1.090
 KBR  C10  H14  single  0.970  0.020  1.090
 KBR  C12  H15  single  0.970  0.020  1.090
 KBR  C12  H16  single  0.970  0.020  1.090
 KBR  C3   H17  single  0.970  0.020  1.090
 KBR  C3   H18  single  0.970  0.020  1.090
 KBR  C1   H19  single  0.970  0.020  1.090
 KBR  C1   H20  single  0.970  0.020  1.090
 KBR  C2   H21  single  0.970  0.020  1.090
 KBR  C2   H22  single  0.970  0.020  1.090
 KBR  O3   H23  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
 KBR  H2   C4   H1   106.57  3.000
 KBR  H2   C4   C3   109.53  3.000
 KBR  H1   C4   C3   110.99  3.000
 KBR  H2   C4   C5   110.24  3.000
 KBR  H1   C4   C5   109.26  3.000
 KBR  C3   C4   C5   110.19  3.000
 KBR  H3   C5   N1   103.46  3.000
 KBR  H3   C5   C11  105.89  3.000
 KBR  N1   C5   C11  115.94  3.000
 KBR  H3   C5   C4   107.04  3.000
 KBR  C11  C5   C4   114.71  3.000
 KBR  N1   C5   C4   108.76  3.000
 KBR  O1   C6   O2   122.98  3.000
 KBR  O1   C6   N1   125.23  3.000
 KBR  O2   C6   N1   111.76  3.000
 KBR  H5   C11  H4   107.52  3.000
 KBR  H5   C11  C12  108.49  3.000
 KBR  H4   C11  C12  109.55  3.000
 KBR  H5   C11  C5   109.67  3.000
 KBR  H4   C11  C5   111.11  3.000
 KBR  C12  C11  C5   110.42  3.000
 KBR  H6   C7   O2   109.07  3.000
 KBR  H6   C7   C10  109.68  3.000
 KBR  O2   C7   C10  110.09  3.000
 KBR  H6   C7   C8   108.93  3.000
 KBR  O2   C7   C8   106.48  3.000
 KBR  C10  C7   C8   112.50  3.000
 KBR  H8   C8   H7   106.22  3.000
 KBR  H8   C8   C9   109.35  3.000
 KBR  H7   C8   C9   110.36  3.000
 KBR  H8   C8   C7   107.11  3.000
 KBR  H7   C8   C7   109.59  3.000
 KBR  C9   C8   C7   113.88  3.000
 KBR  H11  C9   H10  107.58  3.000
 KBR  H11  C9   H9   107.60  3.000
 KBR  H10  C9   H9   107.78  3.000
 KBR  H11  C9   C8   110.69  3.000
 KBR  H10  C9   C8   111.85  3.000
 KBR  H9   C9   C8   111.16  3.000
 KBR  H14  C10  H13  107.90  3.000
 KBR  H14  C10  H12  108.59  3.000
 KBR  H13  C10  H12  107.64  3.000
 KBR  H14  C10  C7   111.05  3.000
 KBR  H13  C10  C7   109.81  3.000
 KBR  H12  C10  C7   111.71  3.000
 KBR  H16  C12  H15  106.63  3.000
 KBR  H16  C12  O3   111.09  3.000
 KBR  H15  C12  O3   111.32  3.000
 KBR  H16  C12  C11  110.06  3.000
 KBR  H15  C12  C11  109.22  3.000
 KBR  O3   C12  C11  108.50  3.000
 KBR  C1   N1   C6   120.36  3.000
 KBR  C1   N1   C5   110.66  3.000
 KBR  C6   N1   C5   120.47  3.000
 KBR  H18  C3   H17  106.44  3.000
 KBR  H18  C3   C2   108.79  3.000
 KBR  H17  C3   C2   110.21  3.000
 KBR  H18  C3   C4   108.46  3.000
 KBR  H17  C3   C4   110.43  3.000
 KBR  C2   C3   C4   112.31  3.000
 KBR  C7   O2   C6   119.03  3.000
 KBR  H20  C1   H19  106.75  3.000
 KBR  H20  C1   C2   111.61  3.000
 KBR  H19  C1   C2   109.99  3.000
 KBR  H20  C1   N1   110.95  3.000
 KBR  H19  C1   N1   107.34  3.000
 KBR  C2   C1   N1   110.06  3.000
 KBR  H22  C2   H21  106.45  3.000
 KBR  H22  C2   C1   109.47  3.000
 KBR  H21  C2   C1   109.13  3.000
 KBR  H22  C2   C3   110.26  3.000
 KBR  H21  C2   C3   110.30  3.000
 KBR  C1   C2   C3   111.11  3.000
 KBR  H23  O3   C12  108.12  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
 KBR  Var_01  C1  C2   C3   C4   -49.04  30.0  1
 KBR  Var_02  C2  C3   C4   C5    50.99  30.0  1
 KBR  Var_03  C3  C2   C1   N1    54.31  30.0  1
 KBR  Var_04  O2  C6   N1   C5   169.76  30.0  2
 KBR  Var_05  O3  C12  C11  C5   178.78  30.0  3
 KBR  Var_06  N1  C6   O2   C7  -179.91  30.0  3
 KBR  Var_07  H9  C9   C8   C7   -56.67  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
 KBR  chir_01  C5  N1  C4  C11  negativ
 KBR  chir_02  C7  O2  C8  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
 KBR  plan-1  C6  0.020
 KBR  plan-1  N1  0.020
 KBR  plan-1  O2  0.020
 KBR  plan-1  O1  0.020

