# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 04:56:19 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (2~{R},3~{S})-3-azanyl-2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)[C@H](C(=O)N1CCC2(CC1)Oc3ccccc3O2)c4ccc(Cl)cc4
#
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
 DNZ  DNZ  (2~{R},3~{S})-3-azanyl-2-(4-chlorophenyl)-1-spiro[1,3-benzodioxole-2,4'-piperidine]-1'-yl-butan-1-one  ligand  50  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DNZ
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
 DNZ  C10  C   CH1   0  -0.049   3.4272  -2.7193  -0.1000
 DNZ  C13  C   CR6   0   0.109   2.3772  -0.4591   0.3209
 DNZ  C15  C   CR16  0  -0.194   2.5838   1.6230  -0.8960
 DNZ  C16  C   CR6   0  -0.053   2.7702   2.2948   0.3017
 DNZ  C18  C   CR16  0  -0.200   2.7743   1.6142   1.5083
 DNZ  C19  C   CR16  0  -0.303   2.5800   0.2410   1.5063
 DNZ  C21  C   CR56  0   0.312  -4.4248   0.3407   0.3280
 DNZ  C22  C   CR56  0   0.301  -3.9476   1.4688  -0.3210
 DNZ  C24  C   CR16  0  -0.355  -4.7799   2.4849  -0.7215
 DNZ  C25  C   CR16  0  -0.271  -6.1438   2.3301  -0.4413
 DNZ  C26  C   CR16  0  -0.270  -6.6211   1.2027   0.2078
 DNZ  C27  C   CR16  0  -0.356  -5.7587   0.1739   0.6087
 DNZ  C1   C   CH2   0  -0.457  -1.0623   0.0840   0.8910
 DNZ  C2   C   CR5   0   0.447  -2.2404   0.0486  -0.0618
 DNZ  C3   C   CH2   0  -0.451  -1.9520  -0.7991  -1.2922
 DNZ  C4   C   CH2   0  -0.337  -1.4439  -2.1791  -0.8862
 DNZ  N5   N   NT    0  -0.451  -0.2751  -2.0466  -0.0315
 DNZ  C6   C   CH2   0  -0.344  -0.5668  -1.3286   1.1967
 DNZ  O8   O   O     0  -0.490   1.1113  -2.7276  -1.6682
 DNZ  C9   C   CH1   0  -0.452   2.1629  -1.9575   0.3417
 DNZ  N11  N   NH2   0  -0.801   4.5411  -2.2651   0.7251
 DNZ  C12  C   CH3   0  -0.674   3.2635  -4.2191   0.1042
 DNZ  C14  C   CR16  0  -0.289   2.3896   0.2500  -0.8783
 DNZ  CL   CL  CL    0  -0.130   3.0027   4.0128   0.2890
 DNZ  O20  O   O     0  -0.492  -3.3879  -0.4804   0.6198
 DNZ  O23  O   O     0  -0.496  -2.6016   1.3759  -0.4506
 DNZ  H1   H   HCH1  0   0.209   3.5894  -2.5243  -1.1682
 DNZ  H2   H   HCR6  0   0.281   2.5881   2.1598  -1.8349
 DNZ  H3   H   HCR6  0   0.281   2.9267   2.1424   2.4397
 DNZ  H4   H   HCR6  0   0.268   2.5826  -0.2908   2.4500
 DNZ  H6   H   HCR6  0   0.259  -6.8335   3.1067  -0.7433
 DNZ  H7   H   HCR6  0   0.259  -7.6797   1.1088   0.4095
 DNZ  H8   H   HCR6  0   0.271  -6.1281  -0.7076   1.1149
 DNZ  H9   H   HCH2  0   0.256  -0.2571   0.6602   0.4288
 DNZ  H10  H   HCH2  0   0.269  -1.3447   0.5916   1.8156
 DNZ  H11  H   HCH2  0   0.262  -2.8510  -0.8915  -1.9072
 DNZ  H12  H   HCH2  0   0.256  -1.1927  -0.2953  -1.8964
 DNZ  H13  H   HCH2  0   0.260  -2.2150  -2.7263  -0.3385
 DNZ  H14  H   HCH2  0   0.278  -1.1932  -2.7648  -1.7649
 DNZ  H15  H   HCH2  0   0.281   0.3009  -1.2832   1.8456
 DNZ  H16  H   HCH2  0   0.270  -1.3289  -1.8860   1.7477
 DNZ  H17  H   HCH1  0   0.274   1.9687  -2.2622   1.3744
 DNZ  H18  H   HNH2  0   0.348   5.3657  -2.7993   0.4781
 DNZ  H19  H   HNH2  0   0.349   4.7678  -1.3029   0.5053
 DNZ  H21  H   HCH3  0   0.236   2.4654  -4.6285  -0.5110
 DNZ  H22  H   HCH3  0   0.233   4.1831  -4.7436  -0.1629
 DNZ  H23  H   HCH3  0   0.220   3.0432  -4.4413   1.1501
 DNZ  H24  H   HCR6  0   0.263   2.2429  -0.2637  -1.8203
 DNZ  C7   C   C     0   0.590   0.9587  -2.2873  -0.5368
 DNZ  H5   H   HCR6  0   0.271  -4.4031   3.3644  -1.2259

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
 DNZ  C27  C26  aromatic  1.401  0.020  1.401
 DNZ  C27  C21  aromatic  1.373  0.020  1.373
 DNZ  C6   N5   single    1.452  0.020  1.452
 DNZ  C6   C1   single    1.528  0.020  1.528
 DNZ  O20  C21  single    1.354  0.020  1.354
 DNZ  O20  C2   single    1.436  0.020  1.436
 DNZ  C26  C25  aromatic  1.386  0.020  1.386
 DNZ  C12  C10  single    1.522  0.020  1.522
 DNZ  C21  C22  aromatic  1.386  0.020  1.386
 DNZ  N5   C4   single    1.454  0.020  1.454
 DNZ  N5   C7   single    1.355  0.020  1.355
 DNZ  N11  C10  single    1.459  0.020  1.459
 DNZ  C1   C2   single    1.516  0.020  1.516
 DNZ  C9   C10  single    1.541  0.020  1.541
 DNZ  C9   C7   single    1.527  0.020  1.527
 DNZ  C9   C13  single    1.514  0.020  1.514
 DNZ  C4   C3   single    1.526  0.020  1.526
 DNZ  C2   C3   single    1.522  0.020  1.522
 DNZ  C2   O23  single    1.430  0.020  1.430
 DNZ  C14  C13  aromatic  1.393  0.020  1.393
 DNZ  C14  C15  aromatic  1.387  0.020  1.387
 DNZ  C7   O8   double    1.224  0.020  1.224
 DNZ  C25  C24  aromatic  1.401  0.020  1.401
 DNZ  C22  O23  single    1.355  0.020  1.355
 DNZ  C22  C24  aromatic  1.373  0.020  1.373
 DNZ  C13  C19  aromatic  1.392  0.020  1.392
 DNZ  C15  C16  aromatic  1.386  0.020  1.386
 DNZ  C19  C18  aromatic  1.387  0.020  1.387
 DNZ  C16  C18  aromatic  1.385  0.020  1.385
 DNZ  C16  CL   single    1.734  0.020  1.734
 DNZ  C10  H1   single    0.970  0.020  1.090
 DNZ  C15  H2   single    0.930  0.020  1.080
 DNZ  C18  H3   single    0.930  0.020  1.080
 DNZ  C19  H4   single    0.930  0.020  1.080
 DNZ  C24  H5   single    0.930  0.020  1.080
 DNZ  C25  H6   single    0.930  0.020  1.080
 DNZ  C26  H7   single    0.930  0.020  1.080
 DNZ  C27  H8   single    0.930  0.020  1.080
 DNZ  C1   H9   single    0.970  0.020  1.090
 DNZ  C1   H10  single    0.970  0.020  1.090
 DNZ  C3   H11  single    0.970  0.020  1.090
 DNZ  C3   H12  single    0.970  0.020  1.090
 DNZ  C4   H13  single    0.970  0.020  1.090
 DNZ  C4   H14  single    0.970  0.020  1.090
 DNZ  C6   H15  single    0.970  0.020  1.090
 DNZ  C6   H16  single    0.970  0.020  1.090
 DNZ  C9   H17  single    0.970  0.020  1.090
 DNZ  N11  H18  single    0.890  0.020  1.040
 DNZ  N11  H19  single    0.890  0.020  1.040
 DNZ  C12  H21  single    0.970  0.020  1.090
 DNZ  C12  H22  single    0.970  0.020  1.090
 DNZ  C12  H23  single    0.970  0.020  1.090
 DNZ  C14  H24  single    0.930  0.020  1.080

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
 DNZ  H1   C10  C12  108.74  3.000
 DNZ  H1   C10  N11  112.47  3.000
 DNZ  C12  C10  N11  108.24  3.000
 DNZ  H1   C10  C9   108.20  3.000
 DNZ  N11  C10  C9   108.09  3.000
 DNZ  C12  C10  C9   111.12  3.000
 DNZ  C14  C13  C9   121.12  3.000
 DNZ  C14  C13  C19  118.42  3.000
 DNZ  C9   C13  C19  120.46  3.000
 DNZ  H2   C15  C14  120.20  3.000
 DNZ  H2   C15  C16  120.60  3.000
 DNZ  C14  C15  C16  119.19  3.000
 DNZ  CL   C16  C18  119.53  3.000
 DNZ  CL   C16  C15  119.48  3.000
 DNZ  C18  C16  C15  120.99  3.000
 DNZ  H3   C18  C19  120.30  3.000
 DNZ  H3   C18  C16  120.70  3.000
 DNZ  C19  C18  C16  119.00  3.000
 DNZ  H4   C19  C18  118.98  3.000
 DNZ  H4   C19  C13  119.70  3.000
 DNZ  C18  C19  C13  121.32  3.000
 DNZ  O20  C21  C27  128.75  3.000
 DNZ  O20  C21  C22  109.31  3.000
 DNZ  C27  C21  C22  121.93  3.000
 DNZ  O23  C22  C24  128.66  3.000
 DNZ  C24  C22  C21  122.01  3.000
 DNZ  O23  C22  C21  109.32  3.000
 DNZ  H5   C24  C25  121.48  3.000
 DNZ  H5   C24  C22  121.77  3.000
 DNZ  C25  C24  C22  116.74  3.000
 DNZ  H6   C25  C26  119.69  3.000
 DNZ  H6   C25  C24  119.05  3.000
 DNZ  C26  C25  C24  121.26  3.000
 DNZ  H7   C26  C27  119.03  3.000
 DNZ  H7   C26  C25  119.68  3.000
 DNZ  C27  C26  C25  121.29  3.000
 DNZ  H8   C27  C26  121.48  3.000
 DNZ  H8   C27  C21  121.76  3.000
 DNZ  C26  C27  C21  116.76  3.000
 DNZ  H10  C1   H9   107.67  3.000
 DNZ  H10  C1   C6   110.13  3.000
 DNZ  H9   C1   C6   109.46  3.000
 DNZ  H10  C1   C2   110.01  3.000
 DNZ  H9   C1   C2   108.62  3.000
 DNZ  C6   C1   C2   110.87  3.000
 DNZ  O23  C2   O20  105.62  3.000
 DNZ  O23  C2   C3   110.20  3.000
 DNZ  O20  C2   C3   109.28  3.000
 DNZ  O23  C2   C1   110.22  3.000
 DNZ  C3   C2   C1   111.97  3.000
 DNZ  O20  C2   C1   109.36  3.000
 DNZ  H12  C3   H11  107.42  3.000
 DNZ  H12  C3   C4   109.42  3.000
 DNZ  H11  C3   C4   110.31  3.000
 DNZ  H12  C3   C2   108.77  3.000
 DNZ  H11  C3   C2   110.25  3.000
 DNZ  C4   C3   C2   110.60  3.000
 DNZ  H14  C4   H13  107.37  3.000
 DNZ  H14  C4   N5   109.84  3.000
 DNZ  H13  C4   N5   108.55  3.000
 DNZ  H14  C4   C3   110.47  3.000
 DNZ  H13  C4   C3   110.57  3.000
 DNZ  N5   C4   C3   109.99  3.000
 DNZ  C7   N5   C6   125.89  3.000
 DNZ  C7   N5   C4   119.77  3.000
 DNZ  C6   N5   C4   112.38  3.000
 DNZ  H16  C6   H15  106.12  3.000
 DNZ  H16  C6   N5   108.32  3.000
 DNZ  H15  C6   N5   111.47  3.000
 DNZ  H16  C6   C1   110.25  3.000
 DNZ  H15  C6   C1   109.90  3.000
 DNZ  N5   C6   C1   110.67  3.000
 DNZ  H17  C9   C7   110.06  3.000
 DNZ  H17  C9   C13  108.28  3.000
 DNZ  C7   C9   C13  108.51  3.000
 DNZ  H17  C9   C10  106.18  3.000
 DNZ  C13  C9   C10  111.67  3.000
 DNZ  C7   C9   C10  112.06  3.000
 DNZ  H19  N11  H18  105.42  3.000
 DNZ  H19  N11  C10  110.12  3.000
 DNZ  H18  N11  C10  108.64  3.000
 DNZ  H23  C12  H22  107.85  3.000
 DNZ  H23  C12  H21  108.50  3.000
 DNZ  H22  C12  H21  107.38  3.000
 DNZ  H23  C12  C10  110.53  3.000
 DNZ  H22  C12  C10  110.48  3.000
 DNZ  H21  C12  C10  111.96  3.000
 DNZ  H24  C14  C15  118.52  3.000
 DNZ  H24  C14  C13  120.41  3.000
 DNZ  C15  C14  C13  121.07  3.000
 DNZ  C2   O20  C21  106.63  3.000
 DNZ  C2   O23  C22  106.77  3.000
 DNZ  C9   C7   O8   120.76  3.000
 DNZ  O8   C7   N5   121.49  3.000
 DNZ  C9   C7   N5   117.73  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
 DNZ  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 DNZ  CONST_02  C16  C18  C19  C13    0.00   0.0  0
 DNZ  CONST_03  C19  C13  C14  C15    0.00   0.0  0
 DNZ  CONST_04  C19  C18  C16  C15    0.00   0.0  0
 DNZ  CONST_05  C14  C13  C19  C18    0.00   0.0  0
 DNZ  CONST_06  C14  C15  C16  C18    0.00   0.0  0
 DNZ  CONST_07  C25  C26  C27  C21    0.00   0.0  0
 DNZ  CONST_08  C25  C24  C22  C21    0.00   0.0  0
 DNZ  CONST_09  C26  C27  C21  C22    0.00   0.0  0
 DNZ  CONST_10  C26  C25  C24  C22    0.00   0.0  0
 DNZ  CONST_11  C27  C26  C25  C24    0.00   0.0  0
 DNZ  CONST_12  C27  C21  C22  C24    0.00   0.0  0
 DNZ  CONST_13  C9   C13  C14  C15  180.00   0.0  0
 DNZ  CONST_14  C9   C13  C19  C18  180.00   0.0  0
 DNZ  CONST_15  CL   C16  C18  C19  180.00   0.0  0
 DNZ  CONST_16  CL   C16  C15  C14  180.00   0.0  0
 DNZ  CONST_17  H2   C15  C14  C13  180.00   0.0  0
 DNZ  CONST_18  H3   C18  C19  C13  180.00   0.0  0
 DNZ  CONST_19  H24  C14  C15  C16  180.00   0.0  0
 DNZ  CONST_20  H4   C19  C18  C16  180.00   0.0  0
 DNZ  CONST_21  H7   C26  C27  C21  180.00   0.0  0
 DNZ  CONST_22  H5   C24  C22  C21  180.00   0.0  0
 DNZ  CONST_23  H8   C27  C21  C22  180.00   0.0  0
 DNZ  CONST_24  H6   C25  C24  C22  180.00   0.0  0
 DNZ  CONST_25  C9   C7   N5   C4   180.00   0.0  0
 DNZ  CONST_26  O8   C7   N5   C4     0.00   0.0  0
 DNZ  CONST_27  C9   C7   N5   C6     0.00   0.0  0
 DNZ  CONST_28  O8   C7   N5   C6   180.00   0.0  0
 DNZ  Var_01    C1   C2   O20  C21  133.43  30.0  1
 DNZ  Var_02    O20  C2   O23  C22  -14.78  30.0  1
 DNZ  Var_03    C4   N5   C6   C1   -60.31  30.0  1
 DNZ  Var_04    C4   C3   C2   C1    51.82  30.0  3
 DNZ  Var_05    N5   C6   C1   C2    54.08  30.0  1
 DNZ  Var_06    N5   C4   C3   C2   -55.84  30.0  1
 DNZ  Var_07    C6   N5   C4   C3    61.16  30.0  1
 DNZ  Var_08    C6   C1   C2   C3   -50.78  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
 DNZ  chir_01  C10  C12  N11  C9   positiv
 DNZ  chir_02  C9   C10  C7   C13  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
 DNZ  plan-1  C13  0.020
 DNZ  plan-1  C15  0.020
 DNZ  plan-1  C16  0.020
 DNZ  plan-1  C18  0.020
 DNZ  plan-1  C19  0.020
 DNZ  plan-1  C9   0.020
 DNZ  plan-1  C14  0.020
 DNZ  plan-1  CL   0.020
 DNZ  plan-1  H2   0.020
 DNZ  plan-1  H3   0.020
 DNZ  plan-1  H4   0.020
 DNZ  plan-1  H24  0.020
 DNZ  plan-2  C21  0.020
 DNZ  plan-2  C22  0.020
 DNZ  plan-2  C24  0.020
 DNZ  plan-2  C25  0.020
 DNZ  plan-2  C26  0.020
 DNZ  plan-2  C27  0.020
 DNZ  plan-2  O20  0.020
 DNZ  plan-2  O23  0.020
 DNZ  plan-2  H6   0.020
 DNZ  plan-2  H7   0.020
 DNZ  plan-2  H8   0.020
 DNZ  plan-2  H5   0.020
 DNZ  plan-3  C4   0.020
 DNZ  plan-3  N5   0.020
 DNZ  plan-3  C6   0.020
 DNZ  plan-3  O8   0.020
 DNZ  plan-3  C9   0.020
 DNZ  plan-3  C7   0.020

