# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:57:06 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)NC(=O)CN1CCC(CC1)CNC(=O)c2cc(F)cc(Cl)c2
#
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
 DZR  DZR  ~{N}-[[1-[2-(~{tert}-butylamino)-2-oxidanylidene-ethyl]piperidin-4-yl]methyl]-3-chloranyl-5-fluoranyl-benzamide  ligand  53  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DZR
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
 DZR  C08  C   CH1   0  -0.292   0.2419  -2.1024   0.5675
 DZR  C09  C   CH2   0  -0.426   1.2985  -3.1997   0.5151
 DZR  C10  C   CH2   0  -0.417   0.7694  -0.8632  -0.1477
 DZR  C11  C   CH2   0  -0.279   2.6274  -2.7009   1.0589
 DZR  C12  C   CH2   0  -0.283   2.1209  -0.4461   0.4087
 DZR  C13  C   CH2   0  -0.241  -1.0799  -2.5941  -0.0068
 DZR  C15  C   C     0   0.534   5.0586  -0.2190  -0.3053
 DZR  C16  C   CT    0   0.097   6.7521   1.6211  -0.5392
 DZR  C17  C   C     0   0.538  -3.1614  -1.4429  -0.6507
 DZR  C18  C   CH3   0  -0.638   5.9115   2.5809  -1.3831
 DZR  C19  C   CH3   0  -0.643   7.7399   0.8510  -1.4173
 DZR  C20  C   CH3   0  -0.680   7.5311   2.4222   0.5027
 DZR  C21  C   CR6   0  -0.029  -4.1180  -0.3511  -0.2717
 DZR  C22  C   CR16  0  -0.261  -3.6910   0.8059   0.3718
 DZR  C23  C   CR16  0  -0.431  -5.4549  -0.5098  -0.6190
 DZR  C24  C   CR6   0  -0.006  -4.6190   1.7889   0.6779
 DZR  C25  C   CR6   0   0.556  -6.3451   0.4874  -0.2807
 DZR  C26  C   CR16  0  -0.367  -5.9607   1.6475   0.3649
 DZR  F02  F   F     0  -0.305  -7.6372   0.3327  -0.5898
 DZR  N05  N   NT    0  -0.408   3.0820  -1.5312   0.3297
 DZR  N06  N   NH1   0  -0.648  -2.1233  -1.6079   0.1796
 DZR  N07  N   NH1   0  -0.648   5.8908   0.6983   0.2097
 DZR  O03  O   O     0  -0.494   4.8622  -0.3824  -1.5000
 DZR  O04  O   O     0  -0.483  -3.3491  -2.1157  -1.6539
 DZR  CL1  CL  CL    0  -0.104  -4.0899   3.2332   1.4643
 DZR  H1   H   HCH1  0   0.227   0.0812  -1.8485   1.6247
 DZR  H2   H   HCH2  0   0.236   0.9764  -4.0694   1.0936
 DZR  H3   H   HCH2  0   0.220   1.4334  -3.5339  -0.5189
 DZR  H4   H   HCH2  0   0.218   0.8714  -1.0767  -1.2169
 DZR  H5   H   HCH2  0   0.235   0.0707  -0.0285  -0.0536
 DZR  H6   H   HCH2  0   0.188   2.5193  -2.4944   2.1387
 DZR  H7   H   HCH2  0   0.238   3.3818  -3.4855   0.9640
 DZR  H8   H   HCH2  0   0.240   2.4946   0.4081  -0.1606
 DZR  H9   H   HCH2  0   0.189   1.9960  -0.0995   1.4508
 DZR  H10  H   HCH2  0   0.243  -0.9749  -2.7942  -1.0738
 DZR  H11  H   HCH2  0   0.246  -1.3637  -3.5374   0.4719
 DZR  H12  H   HCH2  0   0.273   5.0364  -1.9957   0.8356
 DZR  H13  H   HCH2  0   0.216   4.3978  -0.6247   1.7285
 DZR  H14  H   HCH3  0   0.225   5.2210   3.1443  -0.7536
 DZR  H15  H   HCH3  0   0.223   6.5617   3.2953  -1.8904
 DZR  H16  H   HCH3  0   0.238   5.3343   2.0543  -2.1407
 DZR  H17  H   HCH3  0   0.239   7.2333   0.2591  -2.1774
 DZR  H18  H   HCH3  0   0.225   8.4064   1.5492  -1.9256
 DZR  H19  H   HCH3  0   0.226   8.3544   0.1823  -0.8125
 DZR  H20  H   HCH3  0   0.238   8.1422   1.7696   1.1294
 DZR  H21  H   HCH3  0   0.241   8.1973   3.1299   0.0091
 DZR  H22  H   HCH3  0   0.238   6.8604   2.9911   1.1496
 DZR  H23  H   HCR6  0   0.286  -2.6481   0.9631   0.6113
 DZR  H24  H   HCR6  0   0.290  -5.7975  -1.3995  -1.1301
 DZR  H25  H   HCR6  0   0.309  -6.6854   2.4122   0.6100
 DZR  H27  H   HNH1  0   0.408  -2.1380  -1.1314   1.0681
 DZR  H28  H   HNH1  0   0.397   5.9400   0.7556   1.2148
 DZR  C14  C   CH2   0  -0.394   4.3954  -1.1131   0.7393

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
 DZR  C19  C16  single    1.530  0.020  1.530
 DZR  C18  C16  single    1.530  0.020  1.530
 DZR  C20  C16  single    1.528  0.020  1.528
 DZR  C16  N07  single    1.468  0.020  1.468
 DZR  N07  C15  single    1.341  0.020  1.341
 DZR  C15  O03  double    1.222  0.020  1.222
 DZR  C15  C14  single    1.527  0.020  1.527
 DZR  C14  N05  single    1.438  0.020  1.438
 DZR  N05  C11  single    1.451  0.020  1.451
 DZR  N05  C12  single    1.452  0.020  1.452
 DZR  C11  C09  single    1.520  0.020  1.520
 DZR  C12  C10  single    1.520  0.020  1.520
 DZR  C09  C08  single    1.524  0.020  1.524
 DZR  C10  C08  single    1.525  0.020  1.525
 DZR  CL1  C24  single    1.728  0.020  1.728
 DZR  C08  C13  single    1.523  0.020  1.523
 DZR  C13  N06  single    1.448  0.020  1.448
 DZR  N06  C17  single    1.340  0.020  1.340
 DZR  C22  C24  aromatic  1.386  0.020  1.386
 DZR  C22  C21  aromatic  1.391  0.020  1.391
 DZR  C24  C26  aromatic  1.385  0.020  1.385
 DZR  C17  C21  single    1.500  0.020  1.500
 DZR  C17  O04  double    1.222  0.020  1.222
 DZR  C21  C23  aromatic  1.390  0.020  1.390
 DZR  C26  C25  aromatic  1.382  0.020  1.382
 DZR  C23  C25  aromatic  1.379  0.020  1.379
 DZR  C25  F02  single    1.338  0.020  1.338
 DZR  C08  H1   single    0.970  0.020  1.090
 DZR  C09  H2   single    0.970  0.020  1.090
 DZR  C09  H3   single    0.970  0.020  1.090
 DZR  C10  H4   single    0.970  0.020  1.090
 DZR  C10  H5   single    0.970  0.020  1.090
 DZR  C11  H6   single    0.970  0.020  1.090
 DZR  C11  H7   single    0.970  0.020  1.090
 DZR  C12  H8   single    0.970  0.020  1.090
 DZR  C12  H9   single    0.970  0.020  1.090
 DZR  C13  H10  single    0.970  0.020  1.090
 DZR  C13  H11  single    0.970  0.020  1.090
 DZR  C14  H12  single    0.970  0.020  1.090
 DZR  C14  H13  single    0.970  0.020  1.090
 DZR  C18  H14  single    0.970  0.020  1.090
 DZR  C18  H15  single    0.970  0.020  1.090
 DZR  C18  H16  single    0.970  0.020  1.090
 DZR  C19  H17  single    0.970  0.020  1.090
 DZR  C19  H18  single    0.970  0.020  1.090
 DZR  C19  H19  single    0.970  0.020  1.090
 DZR  C20  H20  single    0.970  0.020  1.090
 DZR  C20  H21  single    0.970  0.020  1.090
 DZR  C20  H22  single    0.970  0.020  1.090
 DZR  C22  H23  single    0.930  0.020  1.080
 DZR  C23  H24  single    0.930  0.020  1.080
 DZR  C26  H25  single    0.930  0.020  1.080
 DZR  N06  H27  single    0.860  0.020  1.020
 DZR  N07  H28  single    0.860  0.020  1.020

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
 DZR  H1   C08  C13  108.08  3.000
 DZR  H1   C08  C10  108.30  3.000
 DZR  C13  C08  C10  112.69  3.000
 DZR  H1   C08  C09  107.50  3.000
 DZR  C13  C08  C09  110.88  3.000
 DZR  C10  C08  C09  109.22  3.000
 DZR  H3   C09  H2   107.05  3.000
 DZR  H3   C09  C11  109.29  3.000
 DZR  H2   C09  C11  109.23  3.000
 DZR  H3   C09  C08  109.73  3.000
 DZR  H2   C09  C08  110.51  3.000
 DZR  C11  C09  C08  110.95  3.000
 DZR  H5   C10  H4   107.01  3.000
 DZR  H5   C10  C12  109.11  3.000
 DZR  H4   C10  C12  109.15  3.000
 DZR  H5   C10  C08  111.06  3.000
 DZR  H4   C10  C08  109.38  3.000
 DZR  C12  C10  C08  111.03  3.000
 DZR  H7   C11  H6   106.66  3.000
 DZR  H7   C11  N05  108.59  3.000
 DZR  H6   C11  N05  111.78  3.000
 DZR  H7   C11  C09  109.69  3.000
 DZR  H6   C11  C09  109.00  3.000
 DZR  N05  C11  C09  111.01  3.000
 DZR  H9   C12  H8   106.54  3.000
 DZR  H9   C12  N05  111.13  3.000
 DZR  H8   C12  N05  109.24  3.000
 DZR  H9   C12  C10  109.32  3.000
 DZR  H8   C12  C10  109.15  3.000
 DZR  N05  C12  C10  111.33  3.000
 DZR  H11  C13  H10  107.13  3.000
 DZR  H11  C13  N06  110.10  3.000
 DZR  H10  C13  N06  108.69  3.000
 DZR  H11  C13  C08  109.76  3.000
 DZR  H10  C13  C08  110.16  3.000
 DZR  N06  C13  C08  110.92  3.000
 DZR  O03  C15  N07  124.52  3.000
 DZR  O03  C15  C14  121.40  3.000
 DZR  N07  C15  C14  114.04  3.000
 DZR  N07  C16  C20  106.31  3.000
 DZR  N07  C16  C19  110.82  3.000
 DZR  C20  C16  C19  109.04  3.000
 DZR  N07  C16  C18  110.71  3.000
 DZR  C20  C16  C18  109.11  3.000
 DZR  C19  C16  C18  110.73  3.000
 DZR  O04  C17  N06  124.05  3.000
 DZR  O04  C17  C21  120.66  3.000
 DZR  N06  C17  C21  115.29  3.000
 DZR  H16  C18  H15  108.01  3.000
 DZR  H16  C18  H14  108.41  3.000
 DZR  H15  C18  H14  107.90  3.000
 DZR  H16  C18  C16  111.83  3.000
 DZR  H15  C18  C16  109.87  3.000
 DZR  H14  C18  C16  110.70  3.000
 DZR  H19  C19  H18  107.84  3.000
 DZR  H19  C19  H17  108.42  3.000
 DZR  H18  C19  H17  107.88  3.000
 DZR  H19  C19  C16  110.73  3.000
 DZR  H18  C19  C16  109.87  3.000
 DZR  H17  C19  C16  111.97  3.000
 DZR  H22  C20  H21  107.79  3.000
 DZR  H22  C20  H20  108.37  3.000
 DZR  H21  C20  H20  107.82  3.000
 DZR  H22  C20  C16  111.35  3.000
 DZR  H21  C20  C16  110.07  3.000
 DZR  H20  C20  C16  111.31  3.000
 DZR  C23  C21  C22  120.38  3.000
 DZR  C23  C21  C17  117.84  3.000
 DZR  C22  C21  C17  121.76  3.000
 DZR  H23  C22  C24  119.58  3.000
 DZR  H23  C22  C21  121.29  3.000
 DZR  C24  C22  C21  119.11  3.000
 DZR  H24  C23  C25  120.42  3.000
 DZR  H24  C23  C21  121.09  3.000
 DZR  C25  C23  C21  118.48  3.000
 DZR  CL1  C24  C26  119.01  3.000
 DZR  C26  C24  C22  121.76  3.000
 DZR  CL1  C24  C22  119.24  3.000
 DZR  F02  C25  C26  118.27  3.000
 DZR  F02  C25  C23  118.90  3.000
 DZR  C26  C25  C23  122.83  3.000
 DZR  H25  C26  C25  120.85  3.000
 DZR  H25  C26  C24  121.72  3.000
 DZR  C25  C26  C24  117.43  3.000
 DZR  C14  N05  C12  111.83  3.000
 DZR  C12  N05  C11  111.57  3.000
 DZR  C14  N05  C11  112.17  3.000
 DZR  H27  N06  C17  118.47  3.000
 DZR  H27  N06  C13  116.48  3.000
 DZR  C17  N06  C13  124.24  3.000
 DZR  H28  N07  C16  116.38  3.000
 DZR  H28  N07  C15  116.88  3.000
 DZR  C16  N07  C15  126.73  3.000
 DZR  H13  C14  H12  106.06  3.000
 DZR  H13  C14  N05  112.72  3.000
 DZR  H12  C14  N05  108.99  3.000
 DZR  H13  C14  C15  110.69  3.000
 DZR  H12  C14  C15  106.14  3.000
 DZR  N05  C14  C15  111.85  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
 DZR  CONST_01  C26  C24  C22  C21     0.00   0.0  0
 DZR  CONST_02  C26  C25  C23  C21     0.00   0.0  0
 DZR  CONST_03  C25  C26  C24  C22     0.00   0.0  0
 DZR  CONST_04  C25  C23  C21  C22     0.00   0.0  0
 DZR  CONST_05  C24  C22  C21  C23     0.00   0.0  0
 DZR  CONST_06  C24  C26  C25  C23     0.00   0.0  0
 DZR  CONST_07  C24  C22  C21  C17   180.00   0.0  0
 DZR  CONST_08  C25  C23  C21  C17   180.00   0.0  0
 DZR  CONST_09  CL1  C24  C22  C21   180.00   0.0  0
 DZR  CONST_10  F02  C25  C23  C21   180.00   0.0  0
 DZR  CONST_11  F02  C25  C26  C24   180.00   0.0  0
 DZR  CONST_12  CL1  C24  C26  C25   180.00   0.0  0
 DZR  CONST_13  H25  C26  C24  C22   180.00   0.0  0
 DZR  CONST_14  H24  C23  C21  C22   180.00   0.0  0
 DZR  CONST_15  H23  C22  C21  C23   180.00   0.0  0
 DZR  CONST_16  C21  C17  N06  C13   180.00   0.0  0
 DZR  CONST_17  H27  N06  C17  C21     0.00   0.0  0
 DZR  CONST_18  O04  C17  N06  C13     0.00   0.0  0
 DZR  CONST_19  C16  N07  C15  C14   180.00   0.0  0
 DZR  CONST_20  O03  C15  N07  C16     0.00   0.0  0
 DZR  CONST_21  H28  N07  C15  C14     0.00   0.0  0
 DZR  Var_01    N05  C11  C09  C08   -57.07  30.0  1
 DZR  Var_02    N05  C12  C10  C08    56.22  30.0  1
 DZR  Var_03    C12  N05  C11  C09    59.10  30.0  1
 DZR  Var_04    C11  N05  C12  C10   -58.75  30.0  1
 DZR  Var_05    C15  C14  N05  C11   160.74  30.0  1
 DZR  Var_06    N06  C17  C21  C22    32.68  30.0  2
 DZR  Var_07    C17  N06  C13  C08   149.57  30.0  3
 DZR  Var_08    N07  C15  C14  N05   148.57  30.0  1
 DZR  Var_09    C19  C16  N07  C15   -59.82  30.0  3
 DZR  Var_10    H17  C19  C16  C18   -60.11  30.0  3
 DZR  Var_11    H20  C20  C16  C18   179.77  30.0  3
 DZR  Var_12    H14  C18  C16  C19  -178.87  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
 DZR  chir_01  C08  C09  C10  C13  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
 DZR  plan-1  C17  0.020
 DZR  plan-1  C21  0.020
 DZR  plan-1  C22  0.020
 DZR  plan-1  C23  0.020
 DZR  plan-1  C24  0.020
 DZR  plan-1  C25  0.020
 DZR  plan-1  C26  0.020
 DZR  plan-1  F02  0.020
 DZR  plan-1  CL1  0.020
 DZR  plan-1  H23  0.020
 DZR  plan-1  H24  0.020
 DZR  plan-1  H25  0.020
 DZR  plan-2  C15  0.020
 DZR  plan-2  C16  0.020
 DZR  plan-2  N07  0.020
 DZR  plan-2  O03  0.020
 DZR  plan-2  H28  0.020
 DZR  plan-2  C14  0.020
 DZR  plan-3  C13  0.020
 DZR  plan-3  C17  0.020
 DZR  plan-3  C21  0.020
 DZR  plan-3  N06  0.020
 DZR  plan-3  O04  0.020
 DZR  plan-3  H27  0.020

