# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 16:43:27 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: N-benzyl-N-(1-butylpiperidin-4-yl)-N'-(3,4-dichlorophenyl)urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCN1CCC(CC1)N(Cc2ccccc2)C(=O)Nc3ccc(Cl)c(Cl)c3
#
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
 8ZA  8ZA  N-benzyl-N-(1-butylpiperidin-4-yl)-N'-(3,4-dichlorophenyl)urea  ligand  58  29  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8ZA
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
 8ZA  C4   C   CH2   0  -0.247  -5.2377  -1.8042  -0.5361
 8ZA  C14  C   CR16  0  -0.265  -1.5714   4.6428   2.3362
 8ZA  C5   C   CH2   0  -0.287  -3.5339  -0.8617  -1.9409
 8ZA  C6   C   CH2   0  -0.433  -2.0674  -0.4647  -2.0296
 8ZA  C11  C   CR6   0   0.145  -0.7842   3.3776  -0.0252
 8ZA  C7   C   CH1   0  -0.069  -1.7823   0.6630  -1.0436
 8ZA  C8   C   CH2   0  -0.429  -2.2230   0.2661   0.3625
 8ZA  C9   C   CH2   0  -0.290  -3.6803  -0.1755   0.3385
 8ZA  C10  C   CH2   0  -0.460  -0.3718   2.6606  -1.2878
 8ZA  C12  C   CR16  0  -0.302  -1.9672   4.1045   0.0253
 8ZA  C13  C   CR16  0  -0.241  -2.3610   4.7361   1.1997
 8ZA  N1   N   NT    0  -0.421  -3.8889  -1.2695  -0.5937
 8ZA  N2   N   NT    0  -0.504  -0.4247   1.2116  -1.1416
 8ZA  C3   C   CH2   0  -0.433  -5.5237  -2.6179   0.7193
 8ZA  N3   N   NH1   0  -0.803   1.8904   0.9982  -1.0701
 8ZA  C1   C   CH3   0  -0.662  -7.1935  -4.1112   1.9096
 8ZA  C2   C   CH2   0  -0.420  -6.8964  -3.2796   0.6698
 8ZA  C15  C   CR16  0  -0.241  -0.3848   3.9183   2.2932
 8ZA  C16  C   CR16  0  -0.289   0.0048   3.2910   1.1203
 8ZA  C17  C   C     0   0.750   0.6481   0.4203  -0.8778
 8ZA  O    O   O     0  -0.509   0.5448  -0.7379  -0.5038
 8ZA  C18  C   CR6   0   0.394   3.1122   0.3777  -0.8334
 8ZA  C23  C   CR16  0  -0.264   3.3126  -0.5566   0.1820
 8ZA  C22  C   CR6   0   0.014   4.5728  -1.0968   0.3826
 8ZA  CL2  CL  CL    0  -0.099   4.7809  -2.2534   1.6446
 8ZA  C21  C   CR6   0  -0.031   5.6534  -0.7153  -0.4020
 8ZA  CL1  CL  CL    0  -0.106   7.2194  -1.3901  -0.1531
 8ZA  C20  C   CR16  0  -0.207   5.4565   0.2272  -1.3994
 8ZA  C19  C   CR16  0  -0.348   4.2025   0.7641  -1.6157
 8ZA  H1   H   HCH2  0   0.183  -5.9972  -1.0088  -0.6403
 8ZA  H2   H   HCH2  0   0.220  -5.3668  -2.4631  -1.4000
 8ZA  H4   H   HCH2  0   0.184  -4.1620  -0.0215  -2.2902
 8ZA  H5   H   HCH2  0   0.237  -3.7221  -1.6952  -2.6218
 8ZA  H6   H   HCH2  0   0.235  -1.4470  -1.3339  -1.8153
 8ZA  H7   H   HCH2  0   0.234  -1.8415  -0.1364  -3.0471
 8ZA  H8   H   HCH1  0   0.240  -2.4277   1.4954  -1.3449
 8ZA  H9   H   HCH2  0   0.234  -1.6032  -0.5455   0.7432
 8ZA  H10  H   HCH2  0   0.239  -2.1177   1.1141   1.0425
 8ZA  H11  H   HCH2  0   0.241  -3.9673  -0.4908   1.3427
 8ZA  H12  H   HCH2  0   0.183  -4.3242   0.6880   0.0864
 8ZA  H13  H   HCH2  0   0.283  -1.0309   2.9452  -2.1101
 8ZA  H14  H   HCH2  0   0.274   0.6192   2.9965  -1.5848
 8ZA  H15  H   HCR6  0   0.253  -2.5899   4.1748  -0.8592
 8ZA  H16  H   HCR6  0   0.256  -3.2856   5.2986   1.2242
 8ZA  H18  H   HCH2  0   0.212  -4.7488  -3.3832   0.8269
 8ZA  H19  H   HCH2  0   0.216  -5.4676  -1.9896   1.6131
 8ZA  H20  H   HNH1  0   0.417   1.9507   1.8010  -1.6743
 8ZA  H21  H   HCH3  0   0.217  -6.4533  -4.9027   2.0403
 8ZA  H22  H   HCH3  0   0.217  -7.1803  -3.4962   2.8115
 8ZA  H23  H   HCH3  0   0.227  -8.1744  -4.5842   1.8485
 8ZA  H24  H   HCH2  0   0.213  -7.6673  -2.5118   0.5520
 8ZA  H25  H   HCH2  0   0.212  -6.9609  -3.9142  -0.2197
 8ZA  H26  H   HCR6  0   0.256   0.2376   3.8437   3.1755
 8ZA  H27  H   HCR6  0   0.248   0.9322   2.7302   1.0977
 8ZA  H28  H   HCR6  0   0.295   2.5044  -0.8618   0.8268
 8ZA  H29  H   HCR6  0   0.290   6.2872   0.5368  -2.0186
 8ZA  H30  H   HCR6  0   0.283   4.0707   1.4927  -2.4058
 8ZA  H3   H   HCR6  0   0.257  -1.8751   5.1336   3.2518

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
 8ZA  C2   C1   single    1.522  0.020  1.522
 8ZA  C2   C3   single    1.525  0.020  1.525
 8ZA  C4   C3   single    1.523  0.020  1.523
 8ZA  C4   N1   single    1.452  0.020  1.452
 8ZA  N1   C5   single    1.452  0.020  1.452
 8ZA  N1   C9   single    1.452  0.020  1.452
 8ZA  C5   C6   single    1.522  0.020  1.522
 8ZA  C13  C12  aromatic  1.390  0.020  1.390
 8ZA  C13  C14  aromatic  1.387  0.020  1.387
 8ZA  C9   C8   single    1.523  0.020  1.523
 8ZA  C6   C7   single    1.525  0.020  1.525
 8ZA  C12  C11  aromatic  1.389  0.020  1.389
 8ZA  C14  C15  aromatic  1.391  0.020  1.391
 8ZA  C8   C7   single    1.526  0.020  1.526
 8ZA  C7   N2   single    1.468  0.020  1.468
 8ZA  C11  C10  single    1.509  0.020  1.509
 8ZA  C11  C16  aromatic  1.394  0.020  1.394
 8ZA  C15  C16  aromatic  1.386  0.020  1.386
 8ZA  C10  N2   single    1.457  0.020  1.457
 8ZA  N2   C17  single    1.359  0.020  1.359
 8ZA  C17  O    double    1.221  0.020  1.221
 8ZA  C17  N3   single    1.384  0.020  1.384
 8ZA  N3   C18  single    1.391  0.020  1.391
 8ZA  C18  C23  aromatic  1.394  0.020  1.394
 8ZA  C18  C19  aromatic  1.396  0.020  1.396
 8ZA  C23  C22  aromatic  1.386  0.020  1.386
 8ZA  C19  C20  aromatic  1.381  0.020  1.381
 8ZA  C22  CL2  single    1.724  0.020  1.724
 8ZA  C22  C21  aromatic  1.389  0.020  1.389
 8ZA  C20  C21  aromatic  1.386  0.020  1.386
 8ZA  C21  CL1  single    1.723  0.020  1.723
 8ZA  C4   H1   single    0.970  0.020  1.090
 8ZA  C4   H2   single    0.970  0.020  1.090
 8ZA  C14  H3   single    0.930  0.020  1.080
 8ZA  C5   H4   single    0.970  0.020  1.090
 8ZA  C5   H5   single    0.970  0.020  1.090
 8ZA  C6   H6   single    0.970  0.020  1.090
 8ZA  C6   H7   single    0.970  0.020  1.090
 8ZA  C7   H8   single    0.970  0.020  1.090
 8ZA  C8   H9   single    0.970  0.020  1.090
 8ZA  C8   H10  single    0.970  0.020  1.090
 8ZA  C9   H11  single    0.970  0.020  1.090
 8ZA  C9   H12  single    0.970  0.020  1.090
 8ZA  C10  H13  single    0.970  0.020  1.090
 8ZA  C10  H14  single    0.970  0.020  1.090
 8ZA  C12  H15  single    0.930  0.020  1.080
 8ZA  C13  H16  single    0.930  0.020  1.080
 8ZA  C3   H18  single    0.970  0.020  1.090
 8ZA  C3   H19  single    0.970  0.020  1.090
 8ZA  N3   H20  single    0.860  0.020  1.020
 8ZA  C1   H21  single    0.970  0.020  1.090
 8ZA  C1   H22  single    0.970  0.020  1.090
 8ZA  C1   H23  single    0.970  0.020  1.090
 8ZA  C2   H24  single    0.970  0.020  1.090
 8ZA  C2   H25  single    0.970  0.020  1.090
 8ZA  C15  H26  single    0.930  0.020  1.080
 8ZA  C16  H27  single    0.930  0.020  1.080
 8ZA  C23  H28  single    0.930  0.020  1.080
 8ZA  C20  H29  single    0.930  0.020  1.080
 8ZA  C19  H30  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
 8ZA  H2   C4   H1   106.14  3.000
 8ZA  H2   C4   C3   107.88  3.000
 8ZA  H1   C4   C3   109.47  3.000
 8ZA  H2   C4   N1   107.46  3.000
 8ZA  H1   C4   N1   111.70  3.000
 8ZA  C3   C4   N1   113.82  3.000
 8ZA  H3   C14  C15  120.11  3.000
 8ZA  H3   C14  C13  120.19  3.000
 8ZA  C15  C14  C13  119.69  3.000
 8ZA  H5   C5   H4   106.56  3.000
 8ZA  H5   C5   N1   108.78  3.000
 8ZA  H4   C5   N1   111.58  3.000
 8ZA  H5   C5   C6   109.19  3.000
 8ZA  H4   C5   C6   109.32  3.000
 8ZA  N1   C5   C6   111.28  3.000
 8ZA  H7   C6   H6   107.77  3.000
 8ZA  H7   C6   C7   109.96  3.000
 8ZA  H6   C6   C7   110.89  3.000
 8ZA  H7   C6   C5   109.38  3.000
 8ZA  H6   C6   C5   109.22  3.000
 8ZA  C7   C6   C5   109.59  3.000
 8ZA  C16  C11  C12  118.99  3.000
 8ZA  C16  C11  C10  120.22  3.000
 8ZA  C12  C11  C10  120.76  3.000
 8ZA  H8   C7   N2   104.04  3.000
 8ZA  H8   C7   C8   106.31  3.000
 8ZA  N2   C7   C8   115.21  3.000
 8ZA  H8   C7   C6   105.90  3.000
 8ZA  N2   C7   C6   113.97  3.000
 8ZA  C8   C7   C6   110.45  3.000
 8ZA  H10  C8   H9   107.81  3.000
 8ZA  H10  C8   C9   109.10  3.000
 8ZA  H9   C8   C9   109.49  3.000
 8ZA  H10  C8   C7   110.12  3.000
 8ZA  H9   C8   C7   110.57  3.000
 8ZA  C9   C8   C7   109.71  3.000
 8ZA  H12  C9   H11  106.39  3.000
 8ZA  H12  C9   N1   110.99  3.000
 8ZA  H11  C9   N1   109.60  3.000
 8ZA  H12  C9   C8   109.52  3.000
 8ZA  H11  C9   C8   108.72  3.000
 8ZA  N1   C9   C8   111.47  3.000
 8ZA  H14  C10  H13  105.30  3.000
 8ZA  H14  C10  N2   111.56  3.000
 8ZA  H13  C10  N2   108.24  3.000
 8ZA  H14  C10  C11  109.30  3.000
 8ZA  H13  C10  C11  109.96  3.000
 8ZA  N2   C10  C11  112.24  3.000
 8ZA  H15  C12  C13  119.80  3.000
 8ZA  H15  C12  C11  119.57  3.000
 8ZA  C13  C12  C11  120.63  3.000
 8ZA  H16  C13  C12  119.81  3.000
 8ZA  H16  C13  C14  120.17  3.000
 8ZA  C12  C13  C14  120.02  3.000
 8ZA  C9   N1   C5   110.42  3.000
 8ZA  C9   N1   C4   112.67  3.000
 8ZA  C5   N1   C4   111.55  3.000
 8ZA  C17  N2   C10  124.74  3.000
 8ZA  C17  N2   C7   119.98  3.000
 8ZA  C10  N2   C7   114.32  3.000
 8ZA  H19  C3   H18  106.56  3.000
 8ZA  H19  C3   C2   108.78  3.000
 8ZA  H18  C3   C2   109.70  3.000
 8ZA  H19  C3   C4   110.92  3.000
 8ZA  H18  C3   C4   108.77  3.000
 8ZA  C2   C3   C4   111.97  3.000
 8ZA  H20  N3   C18  113.92  3.000
 8ZA  H20  N3   C17  118.06  3.000
 8ZA  C18  N3   C17  125.37  3.000
 8ZA  H23  C1   H22  107.55  3.000
 8ZA  H23  C1   H21  107.59  3.000
 8ZA  H22  C1   H21  107.54  3.000
 8ZA  H23  C1   C2   111.52  3.000
 8ZA  H22  C1   C2   111.27  3.000
 8ZA  H21  C1   C2   111.18  3.000
 8ZA  H25  C2   H24  106.13  3.000
 8ZA  H25  C2   C1   109.49  3.000
 8ZA  H24  C2   C1   109.48  3.000
 8ZA  H25  C2   C3   109.33  3.000
 8ZA  H24  C2   C3   109.46  3.000
 8ZA  C1   C2   C3   112.73  3.000
 8ZA  H26  C15  C16  119.80  3.000
 8ZA  H26  C15  C14  120.09  3.000
 8ZA  C16  C15  C14  120.12  3.000
 8ZA  H27  C16  C15  119.50  3.000
 8ZA  H27  C16  C11  119.96  3.000
 8ZA  C15  C16  C11  120.55  3.000
 8ZA  O    C17  N3   120.97  3.000
 8ZA  N3   C17  N2   116.01  3.000
 8ZA  O    C17  N2   123.01  3.000
 8ZA  C19  C18  C23  118.76  3.000
 8ZA  C19  C18  N3   117.85  3.000
 8ZA  C23  C18  N3   123.32  3.000
 8ZA  H28  C23  C22  119.00  3.000
 8ZA  H28  C23  C18  121.17  3.000
 8ZA  C22  C23  C18  119.83  3.000
 8ZA  C21  C22  CL2  120.25  3.000
 8ZA  C21  C22  C23  121.24  3.000
 8ZA  CL2  C22  C23  118.50  3.000
 8ZA  C20  C21  CL1  119.95  3.000
 8ZA  CL1  C21  C22  121.19  3.000
 8ZA  C20  C21  C22  118.86  3.000
 8ZA  H29  C20  C19  119.77  3.000
 8ZA  H29  C20  C21  119.84  3.000
 8ZA  C19  C20  C21  120.39  3.000
 8ZA  H30  C19  C20  119.10  3.000
 8ZA  H30  C19  C18  119.99  3.000
 8ZA  C20  C19  C18  120.90  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
 8ZA  CONST_01  C11  C12  C13  C14     0.00   0.0  0
 8ZA  CONST_02  C11  C16  C15  C14     0.00   0.0  0
 8ZA  CONST_03  C15  C14  C13  C12     0.00   0.0  0
 8ZA  CONST_04  C15  C16  C11  C12     0.00   0.0  0
 8ZA  CONST_05  C16  C11  C12  C13     0.00   0.0  0
 8ZA  CONST_06  C16  C15  C14  C13     0.00   0.0  0
 8ZA  CONST_07  C21  C22  C23  C18     0.00   0.0  0
 8ZA  CONST_08  C21  C20  C19  C18     0.00   0.0  0
 8ZA  CONST_09  C20  C19  C18  C23     0.00   0.0  0
 8ZA  CONST_10  C20  C21  C22  C23     0.00   0.0  0
 8ZA  CONST_11  C19  C18  C23  C22     0.00   0.0  0
 8ZA  CONST_12  C19  C20  C21  C22     0.00   0.0  0
 8ZA  CONST_13  C13  C12  C11  C10   180.00   0.0  0
 8ZA  CONST_14  C15  C16  C11  C10   180.00   0.0  0
 8ZA  CONST_15  C22  C23  C18  N3    180.00   0.0  0
 8ZA  CONST_16  C20  C19  C18  N3    180.00   0.0  0
 8ZA  CONST_17  CL2  C22  C23  C18   180.00   0.0  0
 8ZA  CONST_18  CL1  C21  C22  C23   180.00   0.0  0
 8ZA  CONST_19  C20  C21  C22  CL2   180.00   0.0  0
 8ZA  CONST_20  C19  C20  C21  CL1   180.00   0.0  0
 8ZA  CONST_21  H15  C12  C13  C14   180.00   0.0  0
 8ZA  CONST_22  H27  C16  C15  C14   180.00   0.0  0
 8ZA  CONST_23  H16  C13  C12  C11   180.00   0.0  0
 8ZA  CONST_24  H26  C15  C16  C11   180.00   0.0  0
 8ZA  CONST_25  H3   C14  C13  C12   180.00   0.0  0
 8ZA  CONST_26  H29  C20  C19  C18   180.00   0.0  0
 8ZA  CONST_27  H30  C19  C18  C23   180.00   0.0  0
 8ZA  CONST_28  H28  C23  C22  C21   180.00   0.0  0
 8ZA  CONST_31  H20  N3   C18  C23   180.00   0.0  0
 8ZA  CONST_32  O    C17  N2   C7      0.00   0.0  0
 8ZA  CONST_33  C18  N3   C17  O       0.00   0.0  0
 8ZA  CONST_34  C18  N3   C17  N2    180.00   0.0  0
 8ZA  CONST_35  N3   C17  N2   C7    180.00   0.0  0
 8ZA  CONST_36  O    C17  N2   C10   180.00   0.0  0
 8ZA  Var_01    C8   C9   N1   C5    -60.57  30.0  1
 8ZA  Var_02    C9   N1   C5   C6     60.94  30.0  1
 8ZA  Var_03    N1   C5   C6   C7    -57.75  30.0  1
 8ZA  Var_04    N1   C9   C8   C7     56.98  30.0  1
 8ZA  Var_05    C3   C4   N1   C5    162.74  30.0  1
 8ZA  Var_06    C7   N2   C10  C11    70.11  30.0  3
 8ZA  Var_07    N2   C10  C11  C12  -111.54  30.0  2
 8ZA  Var_08    C2   C3   C4   N1   -174.00  30.0  3
 8ZA  Var_09    C1   C2   C3   C4    179.32  30.0  1
 8ZA  Var_10    H21  C1   C2   C3    -59.28  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
 8ZA  chir_01  C7  C6  C8  N2  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
 8ZA  plan-1  C14  0.020
 8ZA  plan-1  C11  0.020
 8ZA  plan-1  C10  0.020
 8ZA  plan-1  C12  0.020
 8ZA  plan-1  C13  0.020
 8ZA  plan-1  C15  0.020
 8ZA  plan-1  C16  0.020
 8ZA  plan-1  H15  0.020
 8ZA  plan-1  H16  0.020
 8ZA  plan-1  H26  0.020
 8ZA  plan-1  H27  0.020
 8ZA  plan-1  H3   0.020
 8ZA  plan-2  N3   0.020
 8ZA  plan-2  C18  0.020
 8ZA  plan-2  C23  0.020
 8ZA  plan-2  C22  0.020
 8ZA  plan-2  CL2  0.020
 8ZA  plan-2  C21  0.020
 8ZA  plan-2  CL1  0.020
 8ZA  plan-2  C20  0.020
 8ZA  plan-2  C19  0.020
 8ZA  plan-2  H28  0.020
 8ZA  plan-2  H29  0.020
 8ZA  plan-2  H30  0.020
 8ZA  plan-3  C7   0.020
 8ZA  plan-3  C10  0.020
 8ZA  plan-3  N2   0.020
 8ZA  plan-3  N3   0.020
 8ZA  plan-3  C17  0.020
 8ZA  plan-3  O    0.020
 8ZA  plan-3  C18  0.020
 8ZA  plan-3  H20  0.020

