# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:23:36 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: (2~{E})-5,6-dimethoxy-2-[[1-(phenylmethyl)piperidin-4-yl]methylidene]-3~{H}-inden-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2CC(=C/C3CCN(CC3)Cc4ccccc4)\C(=O)c2cc1OC
#
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
 DZ7  DZ7  (2~{E})-5,6-dimethoxy-2-[[1-(phenylmethyl)piperidin-4-yl]methylidene]-3~{H}-inden-1-one  ligand  55  28  .  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_DZ7
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
 DZ7  OAC  O  O     0  -0.420   2.2430  -2.8366   0.0915
 DZ7  CAU  C  CR5   0   0.322   2.3270  -1.6248   0.0024
 DZ7  CAZ  C  CR56  0  -0.021   3.5489  -0.8215   0.0522
 DZ7  CAK  C  CR16  0  -0.434   4.8672  -1.2628   0.2014
 DZ7  CAY  C  CR6   0   0.316   5.8771  -0.3267   0.2233
 DZ7  OAS  O  O2    0  -0.462   7.1867  -0.5975   0.3522
 DZ7  CAB  C  CH3   0  -0.440   7.5735  -1.9541   0.4393
 DZ7  CAX  C  CR6   0   0.341   5.5618   1.0581   0.1015
 DZ7  OAR  O  O2    0  -0.452   6.6167   1.8758   0.1426
 DZ7  CAA  C  CH3   0  -0.442   6.3993   3.2707   0.0292
 DZ7  CAJ  C  CR16  0  -0.463   4.2471   1.4749  -0.0477
 DZ7  CAW  C  CR56  0   0.089   3.2383   0.5196  -0.0747
 DZ7  CAP  C  CH2   0  -0.528   1.7603   0.7369  -0.2338
 DZ7  CAT  C  CR5   0  -0.052   1.2066  -0.6648  -0.1839
 DZ7  CAD  C  C1    0  -0.203  -0.0651  -1.0489  -0.2976
 DZ7  CBA  C  CH1   0  -0.335  -1.2305  -0.1464  -0.5141
 DZ7  CAM  C  CH2   0  -0.418  -1.9562  -0.4999  -1.8158
 DZ7  CAO  C  CH2   0  -0.280  -3.1954   0.3606  -1.9985
 DZ7  CAL  C  CH2   0  -0.415  -2.2253  -0.2335   0.6472
 DZ7  CAN  C  CH2   0  -0.279  -3.4573   0.6120   0.3699
 DZ7  NBB  N  NT    0  -0.414  -4.0977   0.2197  -0.8718
 DZ7  CAQ  C  CH2   0  -0.312  -5.3459   0.9184  -1.0813
 DZ7  CAV  C  CR6   0   0.083  -6.4257   0.4819  -0.1229
 DZ7  CAH  C  CR16  0  -0.315  -7.3214   1.4054   0.4063
 DZ7  CAF  C  CR16  0  -0.242  -8.3501   0.9985   1.2479
 DZ7  CAE  C  CR16  0  -0.272  -8.4904  -0.3423   1.5774
 DZ7  CAG  C  CR16  0  -0.242  -7.5951  -1.2715   1.0595
 DZ7  CAI  C  CR16  0  -0.284  -6.5728  -0.8620   0.2158
 DZ7  H1   H  HCR6  0   0.284   5.0692  -2.3218   0.2967
 DZ7  H2   H  HCH3  0   0.263   8.6584  -1.9630   0.5063
 DZ7  H3   H  HCH3  0   0.230   7.1612  -2.4399   1.3279
 DZ7  H4   H  HCH3  0   0.230   7.2684  -2.5199  -0.4449
 DZ7  H5   H  HCH3  0   0.266   7.3783   3.7386   0.0883
 DZ7  H6   H  HCH3  0   0.235   5.9376   3.5319  -0.9259
 DZ7  H7   H  HCH3  0   0.235   5.7751   3.6500   0.8417
 DZ7  H8   H  HCR6  0   0.286   4.0026   2.5246  -0.1445
 DZ7  H9   H  HCH2  0   0.273   1.3587   1.3685   0.5631
 DZ7  H10  H  H     0   0.254  -0.2842  -2.1137  -0.2382
 DZ7  H12  H  HCH1  0   0.250  -0.8814   0.8898  -0.5877
 DZ7  H13  H  HCH2  0   0.241  -1.2893  -0.3643  -2.6700
 DZ7  H14  H  HCH2  0   0.223  -2.2478  -1.5547  -1.7967
 DZ7  H15  H  HCH2  0   0.188  -2.8889   1.4111  -2.1498
 DZ7  H16  H  HCH2  0   0.239  -3.7194   0.0530  -2.9066
 DZ7  H17  H  HCH2  0   0.223  -2.5278  -1.2745   0.7972
 DZ7  H18  H  HCH2  0   0.239  -1.7561   0.1030   1.5743
 DZ7  H19  H  HCH2  0   0.243  -4.1681   0.4934   1.1903
 DZ7  H20  H  HCH2  0   0.191  -3.1737   1.6801   0.3508
 DZ7  H22  H  HCH2  0   0.209  -5.2284   2.0140  -1.0236
 DZ7  H23  H  HCH2  0   0.251  -5.6824   0.7055  -2.1014
 DZ7  H24  H  HCR6  0   0.246  -7.2138   2.4558   0.1601
 DZ7  H25  H  HCR6  0   0.252  -9.0384   1.7312   1.6498
 DZ7  H26  H  HCR6  0   0.252  -9.2892  -0.6618   2.2345
 DZ7  H27  H  HCR6  0   0.251  -7.6946  -2.3191   1.3143
 DZ7  H28  H  HCR6  0   0.244  -5.8702  -1.5854  -0.1786
 DZ7  H29  H  HCH2  0   0.273   1.5282   1.2373  -1.1776

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
 DZ7  CAE  CAF  aromatic  1.388  0.020  1.388
 DZ7  CAE  CAG  aromatic  1.390  0.020  1.390
 DZ7  CAF  CAH  aromatic  1.390  0.020  1.390
 DZ7  CAG  CAI  aromatic  1.387  0.020  1.387
 DZ7  CAH  CAV  aromatic  1.391  0.020  1.391
 DZ7  CAI  CAV  aromatic  1.394  0.020  1.394
 DZ7  CAV  CAQ  single    1.508  0.020  1.508
 DZ7  CAQ  NBB  single    1.446  0.020  1.446
 DZ7  CAO  NBB  single    1.450  0.020  1.450
 DZ7  CAO  CAM  single    1.520  0.020  1.520
 DZ7  NBB  CAN  single    1.451  0.020  1.451
 DZ7  CAM  CBA  single    1.532  0.020  1.532
 DZ7  CAN  CAL  single    1.520  0.020  1.520
 DZ7  CBA  CAL  single    1.532  0.020  1.532
 DZ7  CBA  CAD  single    1.490  0.020  1.490
 DZ7  CAD  CAT  double    1.333  0.020  1.333
 DZ7  CAT  CAP  single    1.508  0.020  1.508
 DZ7  CAT  CAU  single    1.487  0.020  1.487
 DZ7  OAC  CAU  double    1.218  0.020  1.218
 DZ7  CAP  CAW  single    1.502  0.020  1.502
 DZ7  CAU  CAZ  single    1.463  0.020  1.463
 DZ7  CAW  CAZ  aromatic  1.382  0.020  1.382
 DZ7  CAW  CAJ  aromatic  1.390  0.020  1.390
 DZ7  CAZ  CAK  aromatic  1.398  0.020  1.398
 DZ7  CAJ  CAX  aromatic  1.387  0.020  1.387
 DZ7  CAK  CAY  aromatic  1.377  0.020  1.377
 DZ7  CAX  CAY  aromatic  1.426  0.020  1.426
 DZ7  CAX  OAR  single    1.335  0.020  1.335
 DZ7  CAY  OAS  single    1.343  0.020  1.343
 DZ7  CAB  OAS  single    1.413  0.020  1.413
 DZ7  OAR  CAA  single    1.416  0.020  1.416
 DZ7  CAK  H1   single    0.930  0.020  1.080
 DZ7  CAB  H2   single    0.970  0.020  1.090
 DZ7  CAB  H3   single    0.970  0.020  1.090
 DZ7  CAB  H4   single    0.970  0.020  1.090
 DZ7  CAA  H5   single    0.970  0.020  1.090
 DZ7  CAA  H6   single    0.970  0.020  1.090
 DZ7  CAA  H7   single    0.970  0.020  1.090
 DZ7  CAJ  H8   single    0.930  0.020  1.080
 DZ7  CAP  H9   single    0.970  0.020  1.090
 DZ7  CAD  H10  single    0.930  0.020  1.080
 DZ7  CBA  H12  single    0.970  0.020  1.090
 DZ7  CAM  H13  single    0.970  0.020  1.090
 DZ7  CAM  H14  single    0.970  0.020  1.090
 DZ7  CAO  H15  single    0.970  0.020  1.090
 DZ7  CAO  H16  single    0.970  0.020  1.090
 DZ7  CAL  H17  single    0.970  0.020  1.090
 DZ7  CAL  H18  single    0.970  0.020  1.090
 DZ7  CAN  H19  single    0.970  0.020  1.090
 DZ7  CAN  H20  single    0.970  0.020  1.090
 DZ7  CAQ  H22  single    0.970  0.020  1.090
 DZ7  CAQ  H23  single    0.970  0.020  1.090
 DZ7  CAH  H24  single    0.930  0.020  1.080
 DZ7  CAF  H25  single    0.930  0.020  1.080
 DZ7  CAE  H26  single    0.930  0.020  1.080
 DZ7  CAG  H27  single    0.930  0.020  1.080
 DZ7  CAI  H28  single    0.930  0.020  1.080
 DZ7  CAP  H29  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
 DZ7  CAT  CAU  CAZ  106.20  3.000
 DZ7  CAZ  CAU  OAC  126.96  3.000
 DZ7  CAT  CAU  OAC  126.84  3.000
 DZ7  CAW  CAZ  CAK  121.86  3.000
 DZ7  CAK  CAZ  CAU  128.15  3.000
 DZ7  CAW  CAZ  CAU  109.99  3.000
 DZ7  H1   CAK  CAY  121.79  3.000
 DZ7  H1   CAK  CAZ  119.61  3.000
 DZ7  CAY  CAK  CAZ  118.59  3.000
 DZ7  CAX  CAY  OAS  114.81  3.000
 DZ7  OAS  CAY  CAK  125.41  3.000
 DZ7  CAX  CAY  CAK  119.78  3.000
 DZ7  CAB  OAS  CAY  117.78  3.000
 DZ7  H4   CAB  H3   108.79  3.000
 DZ7  H4   CAB  H2   108.92  3.000
 DZ7  H3   CAB  H2   108.82  3.000
 DZ7  H4   CAB  OAS  111.75  3.000
 DZ7  H3   CAB  OAS  111.92  3.000
 DZ7  H2   CAB  OAS  106.55  3.000
 DZ7  CAJ  CAX  OAR  124.62  3.000
 DZ7  OAR  CAX  CAY  114.68  3.000
 DZ7  CAJ  CAX  CAY  120.71  3.000
 DZ7  CAA  OAR  CAX  118.64  3.000
 DZ7  H7   CAA  H6   109.00  3.000
 DZ7  H7   CAA  H5   108.95  3.000
 DZ7  H6   CAA  H5   108.99  3.000
 DZ7  H7   CAA  OAR  111.72  3.000
 DZ7  H6   CAA  OAR  111.74  3.000
 DZ7  H5   CAA  OAR  106.35  3.000
 DZ7  H8   CAJ  CAW  120.07  3.000
 DZ7  H8   CAJ  CAX  121.01  3.000
 DZ7  CAW  CAJ  CAX  118.92  3.000
 DZ7  CAP  CAW  CAJ  128.08  3.000
 DZ7  CAJ  CAW  CAZ  120.13  3.000
 DZ7  CAP  CAW  CAZ  111.79  3.000
 DZ7  H29  CAP  H9   106.67  3.000
 DZ7  H29  CAP  CAT  112.09  3.000
 DZ7  H9   CAP  CAT  112.21  3.000
 DZ7  H29  CAP  CAW  111.51  3.000
 DZ7  H9   CAP  CAW  111.58  3.000
 DZ7  CAT  CAP  CAW  102.90  3.000
 DZ7  CAD  CAT  CAP  127.97  3.000
 DZ7  CAP  CAT  CAU  109.12  3.000
 DZ7  CAD  CAT  CAU  122.91  3.000
 DZ7  H10  CAD  CBA  116.30  3.000
 DZ7  H10  CAD  CAT  117.97  3.000
 DZ7  CBA  CAD  CAT  125.73  3.000
 DZ7  H12  CBA  CAL  108.16  3.000
 DZ7  H12  CBA  CAM  108.19  3.000
 DZ7  CAL  CBA  CAM  108.87  3.000
 DZ7  H12  CBA  CAD  109.47  3.000
 DZ7  CAL  CBA  CAD  111.31  3.000
 DZ7  CAM  CBA  CAD  110.75  3.000
 DZ7  H14  CAM  H13  107.22  3.000
 DZ7  H14  CAM  CAO  109.31  3.000
 DZ7  H13  CAM  CAO  109.49  3.000
 DZ7  H14  CAM  CBA  109.50  3.000
 DZ7  H13  CAM  CBA  110.28  3.000
 DZ7  CAO  CAM  CBA  110.97  3.000
 DZ7  H16  CAO  H15  106.67  3.000
 DZ7  H16  CAO  NBB  108.66  3.000
 DZ7  H15  CAO  NBB  111.80  3.000
 DZ7  H16  CAO  CAM  109.36  3.000
 DZ7  H15  CAO  CAM  109.19  3.000
 DZ7  NBB  CAO  CAM  111.03  3.000
 DZ7  H18  CAL  H17  107.18  3.000
 DZ7  H18  CAL  CAN  109.38  3.000
 DZ7  H17  CAL  CAN  109.28  3.000
 DZ7  H18  CAL  CBA  110.31  3.000
 DZ7  H17  CAL  CBA  109.72  3.000
 DZ7  CAN  CAL  CBA  110.89  3.000
 DZ7  H20  CAN  H19  106.56  3.000
 DZ7  H20  CAN  NBB  111.09  3.000
 DZ7  H19  CAN  NBB  109.04  3.000
 DZ7  H20  CAN  CAL  109.44  3.000
 DZ7  H19  CAN  CAL  109.28  3.000
 DZ7  NBB  CAN  CAL  111.31  3.000
 DZ7  CAQ  NBB  CAN  111.98  3.000
 DZ7  CAN  NBB  CAO  111.34  3.000
 DZ7  CAQ  NBB  CAO  112.18  3.000
 DZ7  H23  CAQ  H22  105.93  3.000
 DZ7  H23  CAQ  CAV  108.40  3.000
 DZ7  H22  CAQ  CAV  109.29  3.000
 DZ7  H23  CAQ  NBB  107.84  3.000
 DZ7  H22  CAQ  NBB  112.36  3.000
 DZ7  CAV  CAQ  NBB  112.71  3.000
 DZ7  CAI  CAV  CAH  118.67  3.000
 DZ7  CAI  CAV  CAQ  120.60  3.000
 DZ7  CAH  CAV  CAQ  120.70  3.000
 DZ7  H24  CAH  CAF  119.64  3.000
 DZ7  H24  CAH  CAV  119.53  3.000
 DZ7  CAF  CAH  CAV  120.84  3.000
 DZ7  H25  CAF  CAE  120.09  3.000
 DZ7  H25  CAF  CAH  119.82  3.000
 DZ7  CAE  CAF  CAH  120.09  3.000
 DZ7  H26  CAE  CAG  120.27  3.000
 DZ7  H26  CAE  CAF  120.25  3.000
 DZ7  CAG  CAE  CAF  119.48  3.000
 DZ7  H27  CAG  CAI  119.76  3.000
 DZ7  H27  CAG  CAE  119.98  3.000
 DZ7  CAI  CAG  CAE  120.25  3.000
 DZ7  H28  CAI  CAG  120.17  3.000
 DZ7  H28  CAI  CAV  119.16  3.000
 DZ7  CAG  CAI  CAV  120.67  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
 DZ7  CONST_01  CAX  CAJ  CAW  CAZ     0.00   0.0  0
 DZ7  CONST_02  CAX  CAY  CAK  CAZ     0.00   0.0  0
 DZ7  CONST_03  CAJ  CAW  CAZ  CAK     0.00   0.0  0
 DZ7  CONST_04  CAJ  CAX  CAY  CAK     0.00   0.0  0
 DZ7  CONST_05  CAW  CAZ  CAK  CAY     0.00   0.0  0
 DZ7  CONST_06  CAW  CAJ  CAX  CAY     0.00   0.0  0
 DZ7  CONST_07  CAE  CAF  CAH  CAV     0.00   0.0  0
 DZ7  CONST_08  CAE  CAG  CAI  CAV     0.00   0.0  0
 DZ7  CONST_09  CAG  CAE  CAF  CAH     0.00   0.0  0
 DZ7  CONST_10  CAG  CAI  CAV  CAH     0.00   0.0  0
 DZ7  CONST_11  CAI  CAG  CAE  CAF     0.00   0.0  0
 DZ7  CONST_12  CAI  CAV  CAH  CAF     0.00   0.0  0
 DZ7  CONST_13  OAS  CAY  CAK  CAZ   180.00   0.0  0
 DZ7  CONST_14  OAR  CAX  CAY  CAK   180.00   0.0  0
 DZ7  CONST_15  CAJ  CAX  CAY  OAS   180.00   0.0  0
 DZ7  CONST_16  CAW  CAJ  CAX  OAR   180.00   0.0  0
 DZ7  CONST_17  CAF  CAH  CAV  CAQ   180.00   0.0  0
 DZ7  CONST_18  CAG  CAI  CAV  CAQ   180.00   0.0  0
 DZ7  CONST_19  H1   CAK  CAZ  CAU     0.00   0.0  0
 DZ7  CONST_20  H8   CAJ  CAW  CAZ   180.00   0.0  0
 DZ7  CONST_21  H25  CAF  CAH  CAV   180.00   0.0  0
 DZ7  CONST_22  H27  CAG  CAI  CAV   180.00   0.0  0
 DZ7  CONST_23  H26  CAE  CAF  CAH   180.00   0.0  0
 DZ7  CONST_24  H28  CAI  CAV  CAH   180.00   0.0  0
 DZ7  CONST_25  H24  CAH  CAF  CAE   180.00   0.0  0
 DZ7  Var_01    CAW  CAP  CAT  CAU     0.29  30.0  1
 DZ7  Var_02    CAP  CAT  CAU  CAZ    -0.55  30.0  1
 DZ7  Var_03    CAT  CAP  CAW  CAZ     0.10  30.0  1
 DZ7  Var_04    CAT  CAU  CAZ  CAK  -179.33  30.0  1
 DZ7  Var_05    NBB  CAO  CAM  CBA   -57.26  30.0  1
 DZ7  Var_06    NBB  CAN  CAL  CBA    56.82  30.0  1
 DZ7  Var_07    CAN  NBB  CAO  CAM    59.58  30.0  1
 DZ7  Var_08    CAL  CAN  NBB  CAO   -59.47  30.0  1
 DZ7  Var_09    CBA  CAD  CAT  CAU  -178.64  30.0  2
 DZ7  Var_10    CAV  CAQ  NBB  CAO   164.06  30.0  1
 DZ7  Var_11    CAH  CAV  CAQ  NBB   141.93  30.0  2
 DZ7  Var_12    CAX  CAY  OAS  CAB  -178.23  30.0  2
 DZ7  Var_13    CAJ  CAX  OAR  CAA     0.08  30.0  2
 DZ7  Var_14    H2   CAB  OAS  CAY   178.28  30.0  3
 DZ7  Var_15    H5   CAA  OAR  CAX   179.92  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
 DZ7  chir_01  CBA  CAM  CAL  CAD  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
 DZ7  plan-1  CAQ  0.020
 DZ7  plan-1  CAV  0.020
 DZ7  plan-1  CAH  0.020
 DZ7  plan-1  CAF  0.020
 DZ7  plan-1  CAE  0.020
 DZ7  plan-1  CAG  0.020
 DZ7  plan-1  CAI  0.020
 DZ7  plan-1  H24  0.020
 DZ7  plan-1  H25  0.020
 DZ7  plan-1  H26  0.020
 DZ7  plan-1  H27  0.020
 DZ7  plan-1  H28  0.020
 DZ7  plan-2  CAU  0.020
 DZ7  plan-2  CAZ  0.020
 DZ7  plan-2  CAK  0.020
 DZ7  plan-2  CAY  0.020
 DZ7  plan-2  OAS  0.020
 DZ7  plan-2  CAX  0.020
 DZ7  plan-2  OAR  0.020
 DZ7  plan-2  CAJ  0.020
 DZ7  plan-2  CAW  0.020
 DZ7  plan-2  CAP  0.020
 DZ7  plan-2  H1   0.020
 DZ7  plan-2  H8   0.020
 DZ7  plan-3  OAC  0.020
 DZ7  plan-3  CAU  0.020
 DZ7  plan-3  CAZ  0.020
 DZ7  plan-3  CAT  0.020

