# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 05:48:04 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (5R)-2-(3,4-dichlorobenzyl)-N-(4-methylbenzyl)-2,7-diazaspiro[4.5]decane-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(CNC(=O)N2CCC[C@]3(CCN(Cc4ccc(Cl)c(Cl)c4)C3)C2)cc1
#
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
 4K7  4K7  (5R)-2-(3,4-dichlorobenzyl)-N-(4-methylbenzyl)-2,7-diazaspiro[4.5]decane-7-carboxamide  ligand  59  30  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4K7
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
 4K7  C1   C   CR16  0  -0.290  -6.3095  -1.3615   1.4866
 4K7  C2   C   CR16  0  -0.279  -7.3352  -2.3974  -0.4015
 4K7  C3   C   CR16  0  -0.273  -5.2305  -0.9854   0.6982
 4K7  C4   C   CR16  0  -0.297  -6.2604  -2.0180  -1.1920
 4K7  C5   C   CR16  0  -0.292   2.3491  -1.2937  -0.8174
 4K7  C6   C   CR16  0  -0.205   3.1462  -2.0332  -1.6715
 4K7  C7   C   CR16  0  -0.284   3.9557  -1.5695   0.9371
 4K7  C8   C   CR6   0   0.084  -7.3807  -2.0740   0.9533
 4K7  C9   C   CR6   0   0.062  -5.1898  -1.3100  -0.6539
 4K7  C10  C   CR6   0   0.106   2.7444  -1.0579   0.4980
 4K7  C11  C   CR6   0  -0.022   4.3572  -2.5471  -1.2241
 4K7  C12  C   CR6   0   0.023   4.7602  -2.3130   0.0830
 4K7  C13  C   C     0   0.745  -2.2069   0.7077  -1.2315
 4K7  C14  C   CH2   0  -0.432  -2.3850   3.3669   1.0345
 4K7  C15  C   CH2   0  -0.444  -0.9250   3.8004   1.0966
 4K7  C16  C   CH2   0  -0.467   1.4666   3.2459   0.3834
 4K7  C17  C   CH2   0  -0.320  -2.7855   3.0043  -0.3901
 4K7  C18  C   CH2   0  -0.279  -0.5019   2.4258  -0.9412
 4K7  C19  C   CH2   0  -0.262   2.3246   2.0026   0.6769
 4K7  C20  C   CH2   0  -0.234   0.1476   1.4929   1.3029
 4K7  C21  C   CR5   0  -0.094   0.0035   2.7661   0.4671
 4K7  C22  C   CH3   0  -0.724  -8.5546  -2.4730   1.7996
 4K7  C23  C   CH2   0  -0.313  -4.0075  -0.9419  -1.5151
 4K7  N25  N   NT    0  -0.498  -1.8885   2.0033  -0.9413
 4K7  N26  N   NH1   0  -0.689  -3.5323   0.3876  -1.2254
 4K7  N27  N   NR5   0  -0.413   1.3663   0.9194   0.7860
 4K7  O28  O   O     0  -0.542  -1.3501  -0.1354  -1.4868
 4K7  CL1  CL  CL    0  -0.104   5.3411  -3.4669  -2.3004
 4K7  CL2  CL  CL    0  -0.103   6.2625  -2.9298   0.6631
 4K7  H1   H   HCR6  0   0.245  -6.3168  -1.0940   2.5369
 4K7  H2   H   HCR6  0   0.245  -8.1558  -2.9458  -0.8496
 4K7  H3   H   HCR6  0   0.243  -4.4144  -0.4300   1.1443
 4K7  H4   H   HCR6  0   0.248  -6.2570  -2.2749  -2.2452
 4K7  H6   H   HCR6  0   0.284   2.8339  -2.2165  -2.6907
 4K7  H7   H   HCR6  0   0.278   4.2860  -1.3895   1.9527
 4K7  H8   H   HCH2  0   0.227  -2.5589   2.5067   1.6882
 4K7  H9   H   HCH2  0   0.239  -3.0343   4.1691   1.3928
 4K7  H10  H   HCH2  0   0.226  -0.8113   4.7521   0.5650
 4K7  H11  H   HCH2  0   0.234  -0.6253   3.9886   2.1316
 4K7  H12  H   HCH2  0   0.242   1.6537   4.0224   1.1277
 4K7  H13  H   HCH2  0   0.239   1.6898   3.6830  -0.5925
 4K7  H14  H   HCH2  0   0.247  -3.8217   2.6771  -0.4034
 4K7  H15  H   HCH2  0   0.236  -2.7387   3.8973  -1.0229
 4K7  H16  H   HCH2  0   0.232  -0.4149   3.3211  -1.5693
 4K7  H17  H   HCH2  0   0.274   0.1163   1.6482  -1.3806
 4K7  H18  H   HCH2  0   0.227   3.0587   1.7988  -0.1062
 4K7  H19  H   HCH2  0   0.195   2.8861   2.1399   1.6147
 4K7  H20  H   HCH2  0   0.194   0.2146   1.7578   2.3740
 4K7  H21  H   HCH2  0   0.236  -0.6819   0.7925   1.1908
 4K7  H22  H   HCH3  0   0.245  -8.7224  -3.5504   1.7642
 4K7  H23  H   HCH3  0   0.243  -8.4106  -2.1922   2.8422
 4K7  H24  H   HCH3  0   0.246  -9.4729  -1.9965   1.4521
 4K7  H25  H   HCH2  0   0.263  -3.1911  -1.6418  -1.3362
 4K7  H26  H   HCH2  0   0.242  -4.2799  -1.0507  -2.5706
 4K7  H29  H   HNH1  0   0.393  -4.2238   1.1146  -1.2747
 4K7  C24  C   CH2   0  -0.331   1.8466  -0.2741   1.4209
 4K7  H5   H   HCR6  0   0.279   1.4075  -0.8906  -1.1692
 4K7  H27  H   HCH2  0   0.256   0.9849  -0.8979   1.6780
 4K7  H28  H   HCH2  0   0.215   2.3731  -0.0723   2.3687

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
 4K7  C23  C9   single    1.508  0.020  1.508
 4K7  C23  N26  single    1.441  0.020  1.441
 4K7  C4   C9   aromatic  1.392  0.020  1.392
 4K7  C4   C2   aromatic  1.387  0.020  1.387
 4K7  CL2  C12  single    1.725  0.020  1.725
 4K7  C9   C3   aromatic  1.391  0.020  1.391
 4K7  C2   C8   aromatic  1.394  0.020  1.394
 4K7  C3   C1   aromatic  1.388  0.020  1.388
 4K7  N26  C13  single    1.364  0.020  1.364
 4K7  C8   C1   aromatic  1.393  0.020  1.393
 4K7  C8   C22  single    1.501  0.020  1.501
 4K7  C12  C7   aromatic  1.389  0.020  1.389
 4K7  C12  C11  aromatic  1.388  0.020  1.388
 4K7  C7   C10  aromatic  1.386  0.020  1.386
 4K7  C13  O28  double    1.229  0.020  1.229
 4K7  C13  N25  single    1.365  0.020  1.365
 4K7  C18  N25  single    1.450  0.020  1.450
 4K7  C18  C21  single    1.534  0.020  1.534
 4K7  N27  C19  single    1.450  0.020  1.450
 4K7  N27  C24  single    1.435  0.020  1.435
 4K7  N27  C20  single    1.443  0.020  1.443
 4K7  CL1  C11  single    1.724  0.020  1.724
 4K7  C19  C16  single    1.539  0.020  1.539
 4K7  C11  C6   aromatic  1.389  0.020  1.389
 4K7  C16  C21  single    1.542  0.020  1.542
 4K7  C10  C24  single    1.507  0.020  1.507
 4K7  C10  C5   aromatic  1.394  0.020  1.394
 4K7  N25  C17  single    1.453  0.020  1.453
 4K7  C21  C20  single    1.530  0.020  1.530
 4K7  C21  C15  single    1.526  0.020  1.526
 4K7  C6   C5   aromatic  1.383  0.020  1.383
 4K7  C17  C14  single    1.524  0.020  1.524
 4K7  C15  C14  single    1.524  0.020  1.524
 4K7  C1   H1   single    0.930  0.020  1.080
 4K7  C2   H2   single    0.930  0.020  1.080
 4K7  C3   H3   single    0.930  0.020  1.080
 4K7  C4   H4   single    0.930  0.020  1.080
 4K7  C5   H5   single    0.930  0.020  1.080
 4K7  C6   H6   single    0.930  0.020  1.080
 4K7  C7   H7   single    0.930  0.020  1.080
 4K7  C14  H8   single    0.970  0.020  1.090
 4K7  C14  H9   single    0.970  0.020  1.090
 4K7  C15  H10  single    0.970  0.020  1.090
 4K7  C15  H11  single    0.970  0.020  1.090
 4K7  C16  H12  single    0.970  0.020  1.090
 4K7  C16  H13  single    0.970  0.020  1.090
 4K7  C17  H14  single    0.970  0.020  1.090
 4K7  C17  H15  single    0.970  0.020  1.090
 4K7  C18  H16  single    0.970  0.020  1.090
 4K7  C18  H17  single    0.970  0.020  1.090
 4K7  C19  H18  single    0.970  0.020  1.090
 4K7  C19  H19  single    0.970  0.020  1.090
 4K7  C20  H20  single    0.970  0.020  1.090
 4K7  C20  H21  single    0.970  0.020  1.090
 4K7  C22  H22  single    0.970  0.020  1.090
 4K7  C22  H23  single    0.970  0.020  1.090
 4K7  C22  H24  single    0.970  0.020  1.090
 4K7  C23  H25  single    0.970  0.020  1.090
 4K7  C23  H26  single    0.970  0.020  1.090
 4K7  C24  H27  single    0.970  0.020  1.090
 4K7  C24  H28  single    0.970  0.020  1.090
 4K7  N26  H29  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
 4K7  H1   C1   C8   119.48  3.000
 4K7  H1   C1   C3   119.26  3.000
 4K7  C8   C1   C3   121.26  3.000
 4K7  H2   C2   C8   119.64  3.000
 4K7  H2   C2   C4   119.30  3.000
 4K7  C8   C2   C4   121.05  3.000
 4K7  H3   C3   C9   119.85  3.000
 4K7  H3   C3   C1   119.38  3.000
 4K7  C9   C3   C1   120.77  3.000
 4K7  H4   C4   C9   119.59  3.000
 4K7  H4   C4   C2   119.42  3.000
 4K7  C9   C4   C2   120.99  3.000
 4K7  H5   C5   C10  119.36  3.000
 4K7  H5   C5   C6   119.98  3.000
 4K7  C10  C5   C6   120.66  3.000
 4K7  H6   C6   C11  119.50  3.000
 4K7  H6   C6   C5   120.41  3.000
 4K7  C11  C6   C5   120.09  3.000
 4K7  H7   C7   C12  119.27  3.000
 4K7  H7   C7   C10  120.14  3.000
 4K7  C12  C7   C10  120.59  3.000
 4K7  C22  C8   C2   120.79  3.000
 4K7  C22  C8   C1   121.44  3.000
 4K7  C2   C8   C1   117.77  3.000
 4K7  C23  C9   C4   120.42  3.000
 4K7  C4   C9   C3   118.16  3.000
 4K7  C23  C9   C3   121.40  3.000
 4K7  C24  C10  C7   121.23  3.000
 4K7  C24  C10  C5   119.80  3.000
 4K7  C7   C10  C5   118.97  3.000
 4K7  CL1  C11  C12  120.81  3.000
 4K7  CL1  C11  C6   119.59  3.000
 4K7  C12  C11  C6   119.60  3.000
 4K7  CL2  C12  C11  120.63  3.000
 4K7  C11  C12  C7   120.09  3.000
 4K7  CL2  C12  C7   119.28  3.000
 4K7  O28  C13  N26  121.17  3.000
 4K7  O28  C13  N25  122.18  3.000
 4K7  N26  C13  N25  116.65  3.000
 4K7  H9   C14  H8   106.67  3.000
 4K7  H9   C14  C17  108.98  3.000
 4K7  H8   C14  C17  109.25  3.000
 4K7  H9   C14  C15  110.31  3.000
 4K7  H8   C14  C15  110.57  3.000
 4K7  C17  C14  C15  110.95  3.000
 4K7  H11  C15  H10  106.33  3.000
 4K7  H11  C15  C21  109.90  3.000
 4K7  H10  C15  C21  108.99  3.000
 4K7  H11  C15  C14  110.48  3.000
 4K7  H10  C15  C14  109.06  3.000
 4K7  C21  C15  C14  111.92  3.000
 4K7  H13  C16  H12  106.83  3.000
 4K7  H13  C16  C21  111.52  3.000
 4K7  H12  C16  C21  110.29  3.000
 4K7  H13  C16  C19  112.32  3.000
 4K7  H12  C16  C19  110.43  3.000
 4K7  C21  C16  C19  105.50  3.000
 4K7  H15  C17  H14  106.21  3.000
 4K7  H15  C17  N25  108.43  3.000
 4K7  H14  C17  N25  112.13  3.000
 4K7  H15  C17  C14  109.56  3.000
 4K7  H14  C17  C14  109.50  3.000
 4K7  N25  C17  C14  110.88  3.000
 4K7  H17  C18  H16  107.90  3.000
 4K7  H17  C18  N25  109.62  3.000
 4K7  H16  C18  N25  108.28  3.000
 4K7  H17  C18  C21  110.03  3.000
 4K7  H16  C18  C21  108.57  3.000
 4K7  N25  C18  C21  112.32  3.000
 4K7  H19  C19  H18  106.91  3.000
 4K7  H19  C19  N27  111.46  3.000
 4K7  H18  C19  N27  111.01  3.000
 4K7  H19  C19  C16  110.24  3.000
 4K7  H18  C19  C16  112.87  3.000
 4K7  N27  C19  C16  104.44  3.000
 4K7  H21  C20  H20  107.42  3.000
 4K7  H21  C20  N27  110.50  3.000
 4K7  H20  C20  N27  113.03  3.000
 4K7  H21  C20  C21  113.98  3.000
 4K7  H20  C20  C21  109.61  3.000
 4K7  N27  C20  C21  102.40  3.000
 4K7  C20  C21  C18  110.36  3.000
 4K7  C20  C21  C16  101.49  3.000
 4K7  C18  C21  C16  109.37  3.000
 4K7  C20  C21  C15  113.34  3.000
 4K7  C16  C21  C15  112.88  3.000
 4K7  C18  C21  C15  109.18  3.000
 4K7  H24  C22  H23  107.66  3.000
 4K7  H24  C22  H22  106.94  3.000
 4K7  H23  C22  H22  107.82  3.000
 4K7  H24  C22  C8   111.25  3.000
 4K7  H23  C22  C8   111.57  3.000
 4K7  H22  C22  C8   111.37  3.000
 4K7  H26  C23  H25  106.29  3.000
 4K7  H26  C23  N26  111.54  3.000
 4K7  H25  C23  N26  108.20  3.000
 4K7  H26  C23  C9   109.33  3.000
 4K7  H25  C23  C9   109.68  3.000
 4K7  N26  C23  C9   111.64  3.000
 4K7  C18  N25  C17  112.94  3.000
 4K7  C17  N25  C13  126.19  3.000
 4K7  C18  N25  C13  119.98  3.000
 4K7  H29  N26  C23  115.52  3.000
 4K7  H29  N26  C13  119.93  3.000
 4K7  C23  N26  C13  122.42  3.000
 4K7  C24  N27  C20  117.06  3.000
 4K7  C20  N27  C19  106.75  3.000
 4K7  C24  N27  C19  115.69  3.000
 4K7  H28  C24  H27  106.16  3.000
 4K7  H28  C24  N27  112.82  3.000
 4K7  H27  C24  N27  108.34  3.000
 4K7  H28  C24  C10  109.69  3.000
 4K7  H27  C24  C10  108.44  3.000
 4K7  N27  C24  C10  111.16  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
 4K7  CONST_01  C4   C9   C3   C1      0.00   0.0  0
 4K7  CONST_02  C4   C2   C8   C1      0.00   0.0  0
 4K7  CONST_03  C3   C9   C4   C2      0.00   0.0  0
 4K7  CONST_04  C3   C1   C8   C2      0.00   0.0  0
 4K7  CONST_05  C12  C7   C10  C5      0.00   0.0  0
 4K7  CONST_06  C12  C11  C6   C5      0.00   0.0  0
 4K7  CONST_07  C7   C12  C11  C6      0.00   0.0  0
 4K7  CONST_08  C7   C10  C5   C6      0.00   0.0  0
 4K7  CONST_09  C9   C4   C2   C8      0.00   0.0  0
 4K7  CONST_10  C9   C3   C1   C8      0.00   0.0  0
 4K7  CONST_11  C11  C12  C7   C10     0.00   0.0  0
 4K7  CONST_12  C11  C6   C5   C10     0.00   0.0  0
 4K7  CONST_13  C23  C9   C3   C1    180.00   0.0  0
 4K7  CONST_14  C23  C9   C4   C2    180.00   0.0  0
 4K7  CONST_15  C22  C8   C1   C3    180.00   0.0  0
 4K7  CONST_16  C22  C8   C2   C4    180.00   0.0  0
 4K7  CONST_17  CL1  C11  C6   C5    180.00   0.0  0
 4K7  CONST_18  CL2  C12  C11  C6    180.00   0.0  0
 4K7  CONST_19  C24  C10  C5   C6    180.00   0.0  0
 4K7  CONST_20  CL1  C11  C12  C7    180.00   0.0  0
 4K7  CONST_21  CL2  C12  C7   C10   180.00   0.0  0
 4K7  CONST_22  C24  C10  C7   C12   180.00   0.0  0
 4K7  CONST_23  H2   C2   C8   C1    180.00   0.0  0
 4K7  CONST_24  H1   C1   C8   C2    180.00   0.0  0
 4K7  CONST_25  H4   C4   C9   C3    180.00   0.0  0
 4K7  CONST_26  H3   C3   C9   C4    180.00   0.0  0
 4K7  CONST_27  H7   C7   C10  C5    180.00   0.0  0
 4K7  CONST_28  H5   C5   C10  C7    180.00   0.0  0
 4K7  CONST_29  H6   C6   C5   C10   180.00   0.0  0
 4K7  CONST_30  O28  C13  N25  C17   180.00   0.0  0
 4K7  CONST_31  O28  C13  N25  C18     0.00   0.0  0
 4K7  CONST_32  N26  C13  N25  C17     0.00   0.0  0
 4K7  CONST_33  N26  C13  N25  C18   180.00   0.0  0
 4K7  CONST_34  N25  C13  N26  C23   180.00   0.0  0
 4K7  CONST_36  O28  C13  N26  C23     0.00   0.0  0
 4K7  Var_01    C18  N25  C17  C14   -57.69  30.0  1
 4K7  Var_02    N25  C17  C14  C15    54.43  30.0  1
 4K7  Var_03    C20  N27  C19  C16   -30.90  30.0  1
 4K7  Var_04    C21  C18  N25  C17    58.46  30.0  1
 4K7  Var_05    C21  C15  C14  C17   -53.07  30.0  1
 4K7  Var_06    C21  C20  N27  C19    44.91  30.0  1
 4K7  Var_07    N27  C19  C16  C21     4.73  30.0  1
 4K7  Var_08    N27  C24  C10  C5    -47.06  30.0  2
 4K7  Var_09    C19  N27  C24  C10   -75.69  30.0  1
 4K7  Var_10    N26  C23  C9   C3    -41.62  30.0  1
 4K7  Var_11    H22  C22  C8   C1   -124.14  30.0  2
 4K7  Var_12    C13  N26  C23  C9    142.69  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
 4K7  chir_01  C21  C16  C20  C15  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
 4K7  plan-1  C1   0.020
 4K7  plan-1  C2   0.020
 4K7  plan-1  C3   0.020
 4K7  plan-1  C4   0.020
 4K7  plan-1  C8   0.020
 4K7  plan-1  C9   0.020
 4K7  plan-1  C22  0.020
 4K7  plan-1  C23  0.020
 4K7  plan-1  H1   0.020
 4K7  plan-1  H2   0.020
 4K7  plan-1  H3   0.020
 4K7  plan-1  H4   0.020
 4K7  plan-2  C5   0.020
 4K7  plan-2  C6   0.020
 4K7  plan-2  C7   0.020
 4K7  plan-2  C10  0.020
 4K7  plan-2  C11  0.020
 4K7  plan-2  C12  0.020
 4K7  plan-2  CL1  0.020
 4K7  plan-2  CL2  0.020
 4K7  plan-2  H6   0.020
 4K7  plan-2  H7   0.020
 4K7  plan-2  C24  0.020
 4K7  plan-2  H5   0.020
 4K7  plan-3  C13  0.020
 4K7  plan-3  C17  0.020
 4K7  plan-3  C18  0.020
 4K7  plan-3  C23  0.020
 4K7  plan-3  N25  0.020
 4K7  plan-3  N26  0.020
 4K7  plan-3  O28  0.020
 4K7  plan-3  H29  0.020

