# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:52:28 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: tert-butyl {(3S,5R)-5-[cyclopropyl(2,3-dichlorobenzyl)carbamoyl]piperidin-3-yl}carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)OC(=O)N[C@@H]1CNC[C@@H](C1)C(=O)N(Cc2cccc(Cl)c2Cl)C3CC3
#
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
 2XF  2XF  'tert-butyl {(3S,5R)-5-[cyclopropyl(2,3-dichlorobenzyl)carbamoyl]piperidin-3-yl}carbamate'  ligand  58  29  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2XF
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
 2XF  C1   C   CH1   0  -0.058  -2.7367   0.2560  -0.4488
 2XF  C2   C   CH2   0  -0.282  -2.2892  -0.3193  -1.7908
 2XF  N3   N   NH1   0  -0.599  -1.0630   0.3331  -2.2049
 2XF  C4   C   CH2   0  -0.269   0.0269   0.0771  -1.2868
 2XF  C5   C   CH1   0  -0.424  -0.3269   0.6585   0.0903
 2XF  C6   C   CH2   0  -0.433  -1.6396   0.0663   0.5927
 2XF  C7   C   C     0   0.598   0.8223   0.3710   1.0377
 2XF  N8   N   NT    0  -0.471   1.9043   1.1916   0.9838
 2XF  O9   O   O     0  -0.475   0.8192  -0.6140   1.7600
 2XF  N10  N   NH1   0  -0.671  -3.9596  -0.3554   0.0207
 2XF  C11  C   CH1   0  -0.113   1.8763   2.4725   0.3374
 2XF  C12  C   CH2   0  -0.382   3.1223   0.7407   1.6455
 2XF  C13  C   CH2   0  -0.488   0.9707   3.5482   0.8559
 2XF  C14  C   CH2   0  -0.502   2.4470   3.6551   1.0539
 2XF  C15  C   CR6   0   0.211   3.6529  -0.5735   1.1266
 2XF  C16  C   CR16  0  -0.296   3.6966  -1.6814   1.9652
 2XF  C17  C   CR16  0  -0.243   4.2063  -2.8946   1.5341
 2XF  C18  C   CR16  0  -0.240   4.6758  -3.0306   0.2378
 2XF  C19  C   CR6   0   0.017   4.6421  -1.9374  -0.6124
 2XF  C20  C   CR6   0  -0.075   4.1389  -0.7164  -0.1708
 2XF  CL1  CL  CL    0  -0.090   4.1466   0.6354  -1.2422
 2XF  CL2  CL  CL    0  -0.101   5.2399  -2.1064  -2.2214
 2XF  C23  C   C     0   0.760  -5.1811   0.0642  -0.3671
 2XF  O24  O   O     0  -0.522  -5.3766   1.0145  -1.0994
 2XF  O25  O   O2    0  -0.507  -6.1264  -0.7008   0.1818
 2XF  C26  C   CT    0   0.190  -7.5424  -0.4888  -0.0560
 2XF  C27  C   CH3   0  -0.660  -8.1999  -1.5842   0.7751
 2XF  C28  C   CH3   0  -0.671  -7.9889   0.8764   0.4538
 2XF  C29  C   CH3   0  -0.670  -7.8855  -0.6854  -1.5282
 2XF  H1   H   HCH1  0   0.242  -2.9190   1.3252  -0.5800
 2XF  H2   H   HCH2  0   0.189  -2.1801  -1.4117  -1.6832
 2XF  H3   H   HCH2  0   0.241  -3.0594  -0.1421  -2.5439
 2XF  H4   H   HNH1  0   0.360  -0.8065   0.0257  -3.1333
 2XF  H6   H   HCH2  0   0.201   0.2473  -0.9970  -1.1705
 2XF  H7   H   HCH2  0   0.241   0.9315   0.5483  -1.6774
 2XF  H8   H   HCH1  0   0.285  -0.4583   1.7336  -0.0411
 2XF  H9   H   HCH2  0   0.254  -1.9349   0.5366   1.5336
 2XF  H10  H   HCH2  0   0.229  -1.5126  -1.0025   0.7894
 2XF  H11  H   HNH1  0   0.393  -3.8923  -1.1950   0.5750
 2XF  H12  H   HCH1  0   0.268   2.0288   2.4545  -0.7368
 2XF  H13  H   HCH2  0   0.282   3.8756   1.5143   1.5039
 2XF  H14  H   HCH2  0   0.274   2.9624   0.6481   2.7217
 2XF  H15  H   HCH2  0   0.262   0.4849   4.1876   0.1303
 2XF  H16  H   HCH2  0   0.262   0.3695   3.3204   1.7273
 2XF  H17  H   HCH2  0   0.264   2.8225   3.5126   2.0595
 2XF  H18  H   HCH2  0   0.265   3.0096   4.3673   0.4653
 2XF  H19  H   HCR6  0   0.263   3.3209  -1.5834   2.9749
 2XF  H20  H   HCR6  0   0.272   4.2302  -3.7430   2.2040
 2XF  H21  H   HCR6  0   0.288   5.0692  -3.9744  -0.1137
 2XF  H22  H   HCH3  0   0.237  -7.9669  -1.4737   1.8354
 2XF  H23  H   HCH3  0   0.230  -9.2829  -1.5291   0.6653
 2XF  H24  H   HCH3  0   0.237  -7.8799  -2.5760   0.4525
 2XF  H25  H   HCH3  0   0.246  -7.5734   1.6954  -0.1281
 2XF  H26  H   HCH3  0   0.233  -9.0762   0.9414   0.3946
 2XF  H27  H   HCH3  0   0.234  -7.7086   1.0127   1.4996
 2XF  H28  H   HCH3  0   0.234  -7.5180  -1.6473  -1.8902
 2XF  H29  H   HCH3  0   0.233  -8.9699  -0.6841  -1.6449
 2XF  H30  H   HCH3  0   0.245  -7.4813   0.1028  -2.1593

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
 2XF  N3   C2   single    1.449  0.020  1.449
 2XF  N3   C4   single    1.448  0.020  1.448
 2XF  C2   C1   single    1.527  0.020  1.527
 2XF  C4   C5   single    1.536  0.020  1.536
 2XF  C1   N10  single    1.446  0.020  1.446
 2XF  C1   C6   single    1.525  0.020  1.525
 2XF  C5   C6   single    1.525  0.020  1.525
 2XF  C5   C7   single    1.517  0.020  1.517
 2XF  N10  C23  single    1.349  0.020  1.349
 2XF  C28  C26  single    1.524  0.020  1.524
 2XF  C23  O25  single    1.334  0.020  1.334
 2XF  C23  O24  double    1.216  0.020  1.216
 2XF  O9   C7   double    1.221  0.020  1.221
 2XF  O25  C26  single    1.451  0.020  1.451
 2XF  C7   N8   single    1.359  0.020  1.359
 2XF  C14  C11  single    1.496  0.020  1.496
 2XF  C14  C13  single    1.493  0.020  1.493
 2XF  C17  C16  aromatic  1.385  0.020  1.385
 2XF  C17  C18  aromatic  1.385  0.020  1.385
 2XF  C16  C15  aromatic  1.390  0.020  1.390
 2XF  C26  C29  single    1.524  0.020  1.524
 2XF  C26  C27  single    1.524  0.020  1.524
 2XF  N8   C11  single    1.435  0.020  1.435
 2XF  N8   C12  single    1.458  0.020  1.458
 2XF  C11  C13  single    1.499  0.020  1.499
 2XF  C18  C19  aromatic  1.385  0.020  1.385
 2XF  C15  C12  single    1.509  0.020  1.509
 2XF  C15  C20  aromatic  1.393  0.020  1.393
 2XF  C19  C20  aromatic  1.392  0.020  1.392
 2XF  C19  CL2  single    1.725  0.020  1.725
 2XF  C20  CL1  single    1.725  0.020  1.725
 2XF  C1   H1   single    0.970  0.020  1.090
 2XF  C2   H2   single    0.970  0.020  1.090
 2XF  C2   H3   single    0.970  0.020  1.090
 2XF  N3   H4   single    0.890  0.020  1.040
 2XF  C4   H6   single    0.970  0.020  1.090
 2XF  C4   H7   single    0.970  0.020  1.090
 2XF  C5   H8   single    0.970  0.020  1.090
 2XF  C6   H9   single    0.970  0.020  1.090
 2XF  C6   H10  single    0.970  0.020  1.090
 2XF  N10  H11  single    0.860  0.020  1.020
 2XF  C11  H12  single    0.970  0.020  1.090
 2XF  C12  H13  single    0.970  0.020  1.090
 2XF  C12  H14  single    0.970  0.020  1.090
 2XF  C13  H15  single    0.970  0.020  1.090
 2XF  C13  H16  single    0.970  0.020  1.090
 2XF  C14  H17  single    0.970  0.020  1.090
 2XF  C14  H18  single    0.970  0.020  1.090
 2XF  C16  H19  single    0.930  0.020  1.080
 2XF  C17  H20  single    0.930  0.020  1.080
 2XF  C18  H21  single    0.930  0.020  1.080
 2XF  C27  H22  single    0.970  0.020  1.090
 2XF  C27  H23  single    0.970  0.020  1.090
 2XF  C27  H24  single    0.970  0.020  1.090
 2XF  C28  H25  single    0.970  0.020  1.090
 2XF  C28  H26  single    0.970  0.020  1.090
 2XF  C28  H27  single    0.970  0.020  1.090
 2XF  C29  H28  single    0.970  0.020  1.090
 2XF  C29  H29  single    0.970  0.020  1.090
 2XF  C29  H30  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
 2XF  H1   C1   N10  108.16  3.000
 2XF  H1   C1   C6   108.90  3.000
 2XF  N10  C1   C6   109.52  3.000
 2XF  H1   C1   C2   108.19  3.000
 2XF  C6   C1   C2   110.04  3.000
 2XF  N10  C1   C2   111.96  3.000
 2XF  H3   C2   H2   107.33  3.000
 2XF  H3   C2   N3   109.07  3.000
 2XF  H2   C2   N3   112.95  3.000
 2XF  H3   C2   C1   109.77  3.000
 2XF  H2   C2   C1   108.44  3.000
 2XF  N3   C2   C1   109.23  3.000
 2XF  H4   N3   C4   109.73  3.000
 2XF  H4   N3   C2   109.89  3.000
 2XF  C4   N3   C2   112.09  3.000
 2XF  H7   C4   H6   107.01  3.000
 2XF  H7   C4   C5   110.37  3.000
 2XF  H6   C4   C5   108.68  3.000
 2XF  H7   C4   N3   108.68  3.000
 2XF  H6   C4   N3   112.93  3.000
 2XF  C5   C4   N3   109.16  3.000
 2XF  H8   C5   C7   110.69  3.000
 2XF  H8   C5   C6   108.58  3.000
 2XF  C7   C5   C6   111.89  3.000
 2XF  H8   C5   C4   107.02  3.000
 2XF  C7   C5   C4   108.28  3.000
 2XF  C6   C5   C4   110.27  3.000
 2XF  H10  C6   H9   107.28  3.000
 2XF  H10  C6   C5   109.79  3.000
 2XF  H9   C6   C5   110.44  3.000
 2XF  H10  C6   C1   109.14  3.000
 2XF  H9   C6   C1   109.89  3.000
 2XF  C5   C6   C1   110.24  3.000
 2XF  O9   C7   N8   120.83  3.000
 2XF  N8   C7   C5   117.64  3.000
 2XF  O9   C7   C5   121.35  3.000
 2XF  C12  N8   C11  119.80  3.000
 2XF  C12  N8   C7   117.42  3.000
 2XF  C11  N8   C7   122.77  3.000
 2XF  H11  N10  C23  118.53  3.000
 2XF  H11  N10  C1   118.31  3.000
 2XF  C23  N10  C1   122.77  3.000
 2XF  H12  C11  C14  115.70  3.000
 2XF  H12  C11  C13  116.06  3.000
 2XF  C14  C11  C13   59.83  3.000
 2XF  H12  C11  N8   115.37  3.000
 2XF  C13  C11  N8   119.78  3.000
 2XF  C14  C11  N8   118.85  3.000
 2XF  H14  C12  H13  106.84  3.000
 2XF  H14  C12  C15  108.45  3.000
 2XF  H13  C12  C15  109.31  3.000
 2XF  H14  C12  N8   110.56  3.000
 2XF  H13  C12  N8   107.41  3.000
 2XF  C15  C12  N8   114.02  3.000
 2XF  H16  C13  H15  114.49  3.000
 2XF  H16  C13  C14  117.21  3.000
 2XF  H15  C13  C14  119.36  3.000
 2XF  H16  C13  C11  117.57  3.000
 2XF  H15  C13  C11  117.60  3.000
 2XF  C14  C13  C11   59.99  3.000
 2XF  H18  C14  H17  114.31  3.000
 2XF  H18  C14  C13  119.28  3.000
 2XF  H17  C14  C13  117.16  3.000
 2XF  H18  C14  C11  117.28  3.000
 2XF  H17  C14  C11  118.23  3.000
 2XF  C13  C14  C11   60.18  3.000
 2XF  C20  C15  C16  117.98  3.000
 2XF  C20  C15  C12  122.16  3.000
 2XF  C16  C15  C12  119.84  3.000
 2XF  H19  C16  C17  119.85  3.000
 2XF  H19  C16  C15  118.68  3.000
 2XF  C17  C16  C15  121.46  3.000
 2XF  H20  C17  C18  119.68  3.000
 2XF  H20  C17  C16  120.18  3.000
 2XF  C18  C17  C16  120.14  3.000
 2XF  H21  C18  C19  119.88  3.000
 2XF  H21  C18  C17  120.88  3.000
 2XF  C19  C18  C17  119.25  3.000
 2XF  CL2  C19  C20  120.46  3.000
 2XF  CL2  C19  C18  119.13  3.000
 2XF  C20  C19  C18  120.40  3.000
 2XF  CL1  C20  C19  119.25  3.000
 2XF  CL1  C20  C15  119.98  3.000
 2XF  C19  C20  C15  120.76  3.000
 2XF  O25  C23  O24  125.60  3.000
 2XF  O24  C23  N10  124.21  3.000
 2XF  O25  C23  N10  110.19  3.000
 2XF  C26  O25  C23  122.69  3.000
 2XF  C29  C26  C28  111.88  3.000
 2XF  C29  C26  C27  109.69  3.000
 2XF  C28  C26  C27  109.57  3.000
 2XF  C27  C26  O25  103.09  3.000
 2XF  C29  C26  O25  111.04  3.000
 2XF  C28  C26  O25  111.22  3.000
 2XF  H24  C27  H23  107.91  3.000
 2XF  H24  C27  H22  108.47  3.000
 2XF  H23  C27  H22  107.76  3.000
 2XF  H24  C27  C26  111.44  3.000
 2XF  H23  C27  C26  109.72  3.000
 2XF  H22  C27  C26  111.41  3.000
 2XF  H27  C28  H26  107.49  3.000
 2XF  H27  C28  H25  108.70  3.000
 2XF  H26  C28  H25  107.88  3.000
 2XF  H27  C28  C26  110.93  3.000
 2XF  H26  C28  C26  109.10  3.000
 2XF  H25  C28  C26  112.57  3.000
 2XF  H30  C29  H29  107.85  3.000
 2XF  H30  C29  H28  108.73  3.000
 2XF  H29  C29  H28  107.48  3.000
 2XF  H30  C29  C26  112.54  3.000
 2XF  H29  C29  C26  109.09  3.000
 2XF  H28  C29  C26  110.99  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
 2XF  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 2XF  CONST_02  C18  C19  C20  C15     0.00   0.0  0
 2XF  CONST_03  C19  C18  C17  C16     0.00   0.0  0
 2XF  CONST_04  C19  C20  C15  C16     0.00   0.0  0
 2XF  CONST_05  C20  C15  C16  C17     0.00   0.0  0
 2XF  CONST_06  C20  C19  C18  C17     0.00   0.0  0
 2XF  CONST_07  C17  C16  C15  C12   180.00   0.0  0
 2XF  CONST_08  C19  C20  C15  C12   180.00   0.0  0
 2XF  CONST_09  CL2  C19  C20  C15   180.00   0.0  0
 2XF  CONST_10  CL1  C20  C15  C16   180.00   0.0  0
 2XF  CONST_11  CL2  C19  C18  C17   180.00   0.0  0
 2XF  CONST_12  CL1  C20  C19  C18   180.00   0.0  0
 2XF  CONST_13  H20  C17  C16  C15   180.00   0.0  0
 2XF  CONST_14  H21  C18  C17  C16   180.00   0.0  0
 2XF  CONST_15  H19  C16  C17  C18   180.00   0.0  0
 2XF  CONST_17  C12  N8   C7   C5    180.00   0.0  0
 2XF  CONST_18  C11  N8   C7   O9    180.00   0.0  0
 2XF  CONST_19  C12  N8   C7   O9      0.00   0.0  0
 2XF  Var_01    C4   N3   C2   C1     63.24  30.0  1
 2XF  Var_02    C5   C4   N3   C2    -62.51  30.0  1
 2XF  Var_03    C13  C14  C11  N8   -109.61  30.0  1
 2XF  Var_04    H15  C13  C14  C11  -106.80  30.0  1
 2XF  Var_05    C14  C11  N8   C7    132.86  30.0  3
 2XF  Var_06    C16  C15  C12  N8   -115.74  30.0  2
 2XF  Var_07    C15  C12  N8   C11  -122.59  30.0  3
 2XF  Var_08    O25  C23  N10  C1    177.99  30.0  2
 2XF  Var_09    C28  C26  O25  C23   -62.37  30.0  3
 2XF  Var_10    H25  C28  C26  O25    68.61  30.0  3
 2XF  Var_11    H28  C29  C26  O25    52.42  30.0  3
 2XF  Var_12    H22  C27  C26  O25    61.30  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
 2XF  chir_01  C1   C2   N10  C6   negativ
 2XF  chir_02  C5   C7   C6   C4   positiv
 2XF  chir_03  C11  C14  N8   C13  both

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
 2XF  plan-1  C5   0.020
 2XF  plan-1  C7   0.020
 2XF  plan-1  N8   0.020
 2XF  plan-1  O9   0.020
 2XF  plan-1  C11  0.020
 2XF  plan-1  C12  0.020
 2XF  plan-2  C12  0.020
 2XF  plan-2  C15  0.020
 2XF  plan-2  C16  0.020
 2XF  plan-2  C17  0.020
 2XF  plan-2  C18  0.020
 2XF  plan-2  C19  0.020
 2XF  plan-2  C20  0.020
 2XF  plan-2  CL1  0.020
 2XF  plan-2  CL2  0.020
 2XF  plan-2  H19  0.020
 2XF  plan-2  H20  0.020
 2XF  plan-2  H21  0.020
 2XF  plan-3  N10  0.020
 2XF  plan-3  C23  0.020
 2XF  plan-3  O24  0.020
 2XF  plan-3  O25  0.020

