# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:05:52 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2~{E})-5-methoxy-2-[[1-(phenylmethyl)piperidin-4-yl]methylidene]-3~{H}-inden-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2c(CC(=C/C3CCN(CC3)Cc4ccccc4)\C2=O)c1
#
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
 DZ0  DZ0  (2~{E})-5-methoxy-2-[[1-(phenylmethyl)piperidin-4-yl]methylidene]-3~{H}-inden-1-one  ligand  51  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_DZ0
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
 DZ0  OAC  O  O     0  -0.417   2.7508  -2.9379   0.5811
 DZ0  CAU  C  CR5   0   0.326   2.8740  -1.7565   0.3142
 DZ0  CAZ  C  CR56  0  -0.047   4.1181  -0.9855   0.2793
 DZ0  CAK  C  CR16  0  -0.268   5.4178  -1.4042   0.5328
 DZ0  CAY  C  CR16  0  -0.387   6.4540  -0.4938   0.4356
 DZ0  CAX  C  CR6   0   0.415   6.1837   0.8386   0.0832
 DZ0  OAR  O  O2    0  -0.463   7.1271   1.7801  -0.0326
 DZ0  CAA  C  CH3   0  -0.441   8.4803   1.4415   0.2144
 DZ0  CAJ  C  CR16  0  -0.425   4.8727   1.2574  -0.1703
 DZ0  CAW  C  CR56  0   0.114   3.8512   0.3383  -0.0692
 DZ0  CAP  C  CH2   0  -0.534   2.3810   0.5569  -0.2935
 DZ0  CAT  C  CR5   0  -0.056   1.7866  -0.8064  -0.0429
 DZ0  CAD  C  C1    0  -0.197   0.5050  -1.1670  -0.1144
 DZ0  CBA  C  CH1   0  -0.335  -0.6332  -0.2702  -0.4605
 DZ0  CAM  C  CH2   0  -0.419  -1.3375  -0.7378  -1.7382
 DZ0  CAO  C  CH2   0  -0.280  -2.5511   0.1288  -2.0335
 DZ0  CAL  C  CH2   0  -0.417  -1.6572  -0.2204   0.6771
 DZ0  CAN  C  CH2   0  -0.279  -2.8607   0.6229   0.2890
 DZ0  NBB  N  NT    0  -0.415  -3.4846   0.1241  -0.9228
 DZ0  CAQ  C  CH2   0  -0.314  -4.6989   0.8435  -1.2410
 DZ0  CAV  C  CR6   0   0.083  -5.8043   0.5977  -0.2456
 DZ0  CAH  C  CR16  0  -0.314  -6.6197   1.6415   0.1784
 DZ0  CAF  C  CR16  0  -0.242  -7.6687   1.4134   1.0614
 DZ0  CAE  C  CR16  0  -0.272  -7.9087   0.1331   1.5398
 DZ0  CAG  C  CR16  0  -0.242  -7.0939  -0.9154   1.1276
 DZ0  CAI  C  CR16  0  -0.283  -6.0521  -0.6847   0.2412
 DZ0  H1   H  HCR6  0   0.266   5.6273  -2.4314   0.8038
 DZ0  H2   H  HCR6  0   0.287   7.4641  -0.8238   0.6339
 DZ0  H3   H  HCH3  0   0.264   9.0565   2.3486   0.0521
 DZ0  H4   H  HCH3  0   0.235   8.6331   1.1042   1.2420
 DZ0  H5   H  HCH3  0   0.235   8.8376   0.6697  -0.4708
 DZ0  H6   H  HCR6  0   0.264   4.6815   2.2896  -0.4390
 DZ0  H7   H  HCH2  0   0.278   1.9849   1.3151   0.3869
 DZ0  H8   H  H     0   0.255   0.2536  -2.2041   0.1002
 DZ0  H10  H  HCH1  0   0.250  -0.2596   0.7459  -0.6309
 DZ0  H11  H  HCH2  0   0.242  -0.6507  -0.6991  -2.5863
 DZ0  H12  H  HCH2  0   0.224  -1.6539  -1.7794  -1.6246
 DZ0  H13  H  HCH2  0   0.189  -2.2136   1.1521  -2.2768
 DZ0  H14  H  HCH2  0   0.239  -3.0616  -0.2523  -2.9213
 DZ0  H15  H  HCH2  0   0.224  -1.9897  -1.2353   0.9160
 DZ0  H16  H  HCH2  0   0.241  -1.2024   0.1922   1.5803
 DZ0  H17  H  HCH2  0   0.244  -3.5905   0.6009   1.1007
 DZ0  H18  H  HCH2  0   0.191  -2.5479   1.6764   0.1717
 DZ0  H20  H  HCH2  0   0.209  -4.5286   1.9300  -1.3325
 DZ0  H21  H  HCH2  0   0.250  -5.0394   0.5090  -2.2268
 DZ0  H22  H  HCR6  0   0.246  -6.4319   2.6464  -0.1823
 DZ0  H23  H  HCR6  0   0.253  -8.2939   2.2382   1.3792
 DZ0  H24  H  HCR6  0   0.253  -8.7223  -0.0465   2.2308
 DZ0  H25  H  HCR6  0   0.252  -7.2717  -1.9169   1.4988
 DZ0  H26  H  HCR6  0   0.243  -5.4139  -1.5024  -0.0698
 DZ0  H27  H  HCH2  0   0.278   2.1834   0.9136  -1.3077

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
 DZ0  CAE  CAF  aromatic  1.388  0.020  1.388
 DZ0  CAE  CAG  aromatic  1.390  0.020  1.390
 DZ0  CAF  CAH  aromatic  1.390  0.020  1.390
 DZ0  CAG  CAI  aromatic  1.387  0.020  1.387
 DZ0  CAH  CAV  aromatic  1.391  0.020  1.391
 DZ0  CAI  CAV  aromatic  1.394  0.020  1.394
 DZ0  CAV  CAQ  single    1.508  0.020  1.508
 DZ0  CAQ  NBB  single    1.447  0.020  1.447
 DZ0  NBB  CAO  single    1.451  0.020  1.451
 DZ0  NBB  CAN  single    1.451  0.020  1.451
 DZ0  CAO  CAM  single    1.520  0.020  1.520
 DZ0  CAM  CBA  single    1.532  0.020  1.532
 DZ0  CAN  CAL  single    1.520  0.020  1.520
 DZ0  CAL  CBA  single    1.531  0.020  1.531
 DZ0  CBA  CAD  single    1.490  0.020  1.490
 DZ0  CAD  CAT  double    1.333  0.020  1.333
 DZ0  CAT  CAP  single    1.508  0.020  1.508
 DZ0  CAT  CAU  single    1.487  0.020  1.487
 DZ0  CAP  CAW  single    1.503  0.020  1.503
 DZ0  OAC  CAU  double    1.217  0.020  1.217
 DZ0  CAU  CAZ  single    1.464  0.020  1.464
 DZ0  CAW  CAZ  aromatic  1.395  0.020  1.395
 DZ0  CAW  CAJ  aromatic  1.378  0.020  1.378
 DZ0  CAZ  CAK  aromatic  1.389  0.020  1.389
 DZ0  CAJ  CAX  aromatic  1.399  0.020  1.399
 DZ0  CAK  CAY  aromatic  1.383  0.020  1.383
 DZ0  CAX  CAY  aromatic  1.404  0.020  1.404
 DZ0  CAX  OAR  single    1.338  0.020  1.338
 DZ0  OAR  CAA  single    1.417  0.020  1.417
 DZ0  CAK  H1   single    0.930  0.020  1.080
 DZ0  CAY  H2   single    0.930  0.020  1.080
 DZ0  CAA  H3   single    0.970  0.020  1.090
 DZ0  CAA  H4   single    0.970  0.020  1.090
 DZ0  CAA  H5   single    0.970  0.020  1.090
 DZ0  CAJ  H6   single    0.930  0.020  1.080
 DZ0  CAP  H7   single    0.970  0.020  1.090
 DZ0  CAD  H8   single    0.930  0.020  1.080
 DZ0  CBA  H10  single    0.970  0.020  1.090
 DZ0  CAM  H11  single    0.970  0.020  1.090
 DZ0  CAM  H12  single    0.970  0.020  1.090
 DZ0  CAO  H13  single    0.970  0.020  1.090
 DZ0  CAO  H14  single    0.970  0.020  1.090
 DZ0  CAL  H15  single    0.970  0.020  1.090
 DZ0  CAL  H16  single    0.970  0.020  1.090
 DZ0  CAN  H17  single    0.970  0.020  1.090
 DZ0  CAN  H18  single    0.970  0.020  1.090
 DZ0  CAQ  H20  single    0.970  0.020  1.090
 DZ0  CAQ  H21  single    0.970  0.020  1.090
 DZ0  CAH  H22  single    0.930  0.020  1.080
 DZ0  CAF  H23  single    0.930  0.020  1.080
 DZ0  CAE  H24  single    0.930  0.020  1.080
 DZ0  CAG  H25  single    0.930  0.020  1.080
 DZ0  CAI  H26  single    0.930  0.020  1.080
 DZ0  CAP  H27  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
 DZ0  CAT  CAU  CAZ  106.20  3.000
 DZ0  CAZ  CAU  OAC  127.03  3.000
 DZ0  CAT  CAU  OAC  126.76  3.000
 DZ0  CAW  CAZ  CAK  120.73  3.000
 DZ0  CAK  CAZ  CAU  129.20  3.000
 DZ0  CAW  CAZ  CAU  110.07  3.000
 DZ0  H1   CAK  CAY  119.81  3.000
 DZ0  H1   CAK  CAZ  120.85  3.000
 DZ0  CAY  CAK  CAZ  119.34  3.000
 DZ0  H2   CAY  CAX  121.03  3.000
 DZ0  H2   CAY  CAK  119.10  3.000
 DZ0  CAX  CAY  CAK  119.87  3.000
 DZ0  CAJ  CAX  OAR  115.74  3.000
 DZ0  OAR  CAX  CAY  123.62  3.000
 DZ0  CAJ  CAX  CAY  120.64  3.000
 DZ0  CAA  OAR  CAX  119.36  3.000
 DZ0  H5   CAA  H4   109.04  3.000
 DZ0  H5   CAA  H3   108.82  3.000
 DZ0  H4   CAA  H3   108.91  3.000
 DZ0  H5   CAA  OAR  111.84  3.000
 DZ0  H4   CAA  OAR  111.81  3.000
 DZ0  H3   CAA  OAR  106.31  3.000
 DZ0  H6   CAJ  CAW  121.52  3.000
 DZ0  H6   CAJ  CAX  119.69  3.000
 DZ0  CAW  CAJ  CAX  118.79  3.000
 DZ0  CAP  CAW  CAJ  128.11  3.000
 DZ0  CAJ  CAW  CAZ  120.64  3.000
 DZ0  CAP  CAW  CAZ  111.25  3.000
 DZ0  H27  CAP  H7   106.60  3.000
 DZ0  H27  CAP  CAT  112.20  3.000
 DZ0  H7   CAP  CAT  112.38  3.000
 DZ0  H27  CAP  CAW  111.27  3.000
 DZ0  H7   CAP  CAW  111.25  3.000
 DZ0  CAT  CAP  CAW  103.25  3.000
 DZ0  CAD  CAT  CAP  127.91  3.000
 DZ0  CAP  CAT  CAU  109.22  3.000
 DZ0  CAD  CAT  CAU  122.87  3.000
 DZ0  H8   CAD  CBA  116.29  3.000
 DZ0  H8   CAD  CAT  117.98  3.000
 DZ0  CBA  CAD  CAT  125.73  3.000
 DZ0  H10  CBA  CAL  108.26  3.000
 DZ0  H10  CBA  CAM  108.06  3.000
 DZ0  CAL  CBA  CAM  108.79  3.000
 DZ0  H10  CBA  CAD  109.50  3.000
 DZ0  CAL  CBA  CAD  110.97  3.000
 DZ0  CAM  CBA  CAD  111.18  3.000
 DZ0  H12  CAM  H11  107.23  3.000
 DZ0  H12  CAM  CAO  109.38  3.000
 DZ0  H11  CAM  CAO  109.33  3.000
 DZ0  H12  CAM  CBA  109.68  3.000
 DZ0  H11  CAM  CBA  110.35  3.000
 DZ0  CAO  CAM  CBA  110.80  3.000
 DZ0  H14  CAO  H13  106.67  3.000
 DZ0  H14  CAO  NBB  108.68  3.000
 DZ0  H13  CAO  NBB  111.60  3.000
 DZ0  H14  CAO  CAM  109.39  3.000
 DZ0  H13  CAO  CAM  109.09  3.000
 DZ0  NBB  CAO  CAM  111.29  3.000
 DZ0  H16  CAL  H15  107.23  3.000
 DZ0  H16  CAL  CAN  109.35  3.000
 DZ0  H15  CAL  CAN  109.25  3.000
 DZ0  H16  CAL  CBA  110.38  3.000
 DZ0  H15  CAL  CBA  109.58  3.000
 DZ0  CAN  CAL  CBA  110.97  3.000
 DZ0  H18  CAN  H17  106.70  3.000
 DZ0  H18  CAN  NBB  111.14  3.000
 DZ0  H17  CAN  NBB  109.06  3.000
 DZ0  H18  CAN  CAL  109.38  3.000
 DZ0  H17  CAN  CAL  109.16  3.000
 DZ0  NBB  CAN  CAL  111.28  3.000
 DZ0  CAQ  NBB  CAN  111.93  3.000
 DZ0  CAN  NBB  CAO  111.19  3.000
 DZ0  CAQ  NBB  CAO  111.72  3.000
 DZ0  H21  CAQ  H20  105.91  3.000
 DZ0  H21  CAQ  CAV  108.45  3.000
 DZ0  H20  CAQ  CAV  109.17  3.000
 DZ0  H21  CAQ  NBB  107.88  3.000
 DZ0  H20  CAQ  NBB  112.23  3.000
 DZ0  CAV  CAQ  NBB  112.89  3.000
 DZ0  CAI  CAV  CAH  118.67  3.000
 DZ0  CAI  CAV  CAQ  120.73  3.000
 DZ0  CAH  CAV  CAQ  120.58  3.000
 DZ0  H22  CAH  CAF  119.62  3.000
 DZ0  H22  CAH  CAV  119.52  3.000
 DZ0  CAF  CAH  CAV  120.87  3.000
 DZ0  H23  CAF  CAE  120.12  3.000
 DZ0  H23  CAF  CAH  119.82  3.000
 DZ0  CAE  CAF  CAH  120.06  3.000
 DZ0  H24  CAE  CAG  120.30  3.000
 DZ0  H24  CAE  CAF  120.21  3.000
 DZ0  CAG  CAE  CAF  119.49  3.000
 DZ0  H25  CAG  CAI  119.75  3.000
 DZ0  H25  CAG  CAE  119.98  3.000
 DZ0  CAI  CAG  CAE  120.27  3.000
 DZ0  H26  CAI  CAG  120.03  3.000
 DZ0  H26  CAI  CAV  119.32  3.000
 DZ0  CAG  CAI  CAV  120.65  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
 DZ0  CONST_01  CAX  CAJ  CAW  CAZ     0.00   0.0  0
 DZ0  CONST_02  CAX  CAY  CAK  CAZ     0.00   0.0  0
 DZ0  CONST_03  CAJ  CAW  CAZ  CAK     0.00   0.0  0
 DZ0  CONST_04  CAJ  CAX  CAY  CAK     0.00   0.0  0
 DZ0  CONST_05  CAW  CAZ  CAK  CAY     0.00   0.0  0
 DZ0  CONST_06  CAW  CAJ  CAX  CAY     0.00   0.0  0
 DZ0  CONST_07  CAE  CAF  CAH  CAV     0.00   0.0  0
 DZ0  CONST_08  CAE  CAG  CAI  CAV     0.00   0.0  0
 DZ0  CONST_09  CAG  CAE  CAF  CAH     0.00   0.0  0
 DZ0  CONST_10  CAG  CAI  CAV  CAH     0.00   0.0  0
 DZ0  CONST_11  CAI  CAG  CAE  CAF     0.00   0.0  0
 DZ0  CONST_12  CAI  CAV  CAH  CAF     0.00   0.0  0
 DZ0  CONST_13  OAR  CAX  CAY  CAK   180.00   0.0  0
 DZ0  CONST_14  CAW  CAJ  CAX  OAR   180.00   0.0  0
 DZ0  CONST_15  CAF  CAH  CAV  CAQ   180.00   0.0  0
 DZ0  CONST_16  CAG  CAI  CAV  CAQ   180.00   0.0  0
 DZ0  CONST_17  H1   CAK  CAZ  CAU     0.00   0.0  0
 DZ0  CONST_18  H6   CAJ  CAW  CAZ   180.00   0.0  0
 DZ0  CONST_19  H2   CAY  CAK  CAZ   180.00   0.0  0
 DZ0  CONST_20  H23  CAF  CAH  CAV   180.00   0.0  0
 DZ0  CONST_21  H25  CAG  CAI  CAV   180.00   0.0  0
 DZ0  CONST_22  H24  CAE  CAF  CAH   180.00   0.0  0
 DZ0  CONST_23  H26  CAI  CAV  CAH   180.00   0.0  0
 DZ0  CONST_24  H22  CAH  CAF  CAE   180.00   0.0  0
 DZ0  Var_01    CAW  CAP  CAT  CAU     0.23  30.0  1
 DZ0  Var_02    CAP  CAT  CAU  CAZ    -0.13  30.0  1
 DZ0  Var_03    CAT  CAP  CAW  CAZ    -0.25  30.0  1
 DZ0  Var_04    CAT  CAU  CAZ  CAK  -179.89  30.0  1
 DZ0  Var_05    NBB  CAO  CAM  CBA   -57.30  30.0  1
 DZ0  Var_06    NBB  CAN  CAL  CBA    57.01  30.0  1
 DZ0  Var_07    CAN  NBB  CAO  CAM    59.52  30.0  1
 DZ0  Var_08    CAL  CAN  NBB  CAO   -59.32  30.0  1
 DZ0  Var_09    CBA  CAD  CAT  CAU   179.79  30.0  2
 DZ0  Var_10    CAV  CAQ  NBB  CAO   166.94  30.0  1
 DZ0  Var_11    CAH  CAV  CAQ  NBB   139.20  30.0  2
 DZ0  Var_12    CAJ  CAX  OAR  CAA   179.65  30.0  2
 DZ0  Var_13    H3   CAA  OAR  CAX   179.45  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
 DZ0  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
 DZ0  plan-1  CAQ  0.020
 DZ0  plan-1  CAV  0.020
 DZ0  plan-1  CAH  0.020
 DZ0  plan-1  CAF  0.020
 DZ0  plan-1  CAE  0.020
 DZ0  plan-1  CAG  0.020
 DZ0  plan-1  CAI  0.020
 DZ0  plan-1  H22  0.020
 DZ0  plan-1  H23  0.020
 DZ0  plan-1  H24  0.020
 DZ0  plan-1  H25  0.020
 DZ0  plan-1  H26  0.020
 DZ0  plan-2  CAU  0.020
 DZ0  plan-2  CAZ  0.020
 DZ0  plan-2  CAK  0.020
 DZ0  plan-2  CAY  0.020
 DZ0  plan-2  CAX  0.020
 DZ0  plan-2  OAR  0.020
 DZ0  plan-2  CAJ  0.020
 DZ0  plan-2  CAW  0.020
 DZ0  plan-2  CAP  0.020
 DZ0  plan-2  H1   0.020
 DZ0  plan-2  H2   0.020
 DZ0  plan-2  H6   0.020
 DZ0  plan-3  OAC  0.020
 DZ0  plan-3  CAU  0.020
 DZ0  plan-3  CAZ  0.020
 DZ0  plan-3  CAT  0.020

