# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 10:54:29 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 3-[[4-[(3,4-dichlorophenyl)methyl]piperidin-4-yl]methoxy]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(CC2(CCNCC2)COc3cccnc3)cc1Cl
#
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
 8L3  8L3  3-[[4-[(3,4-dichlorophenyl)methyl]piperidin-4-yl]methoxy]pyridine  ligand  43  23  .  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_8L3
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
 8L3  CAA  C   CH2   0  -0.326  -3.5960   1.4615   1.2669
 8L3  CAC  C   CH2   0  -0.324  -4.9132   0.4805  -0.4891
 8L3  CAD  C   CH2   0  -0.431  -3.9575  -0.7055  -0.5912
 8L3  CAE  C   CT    0  -0.124  -2.5203  -0.3561  -0.1629
 8L3  CAF  C   CH2   0  -0.167  -1.7609  -1.6771  -0.0729
 8L3  CAH  C   CR6   0   0.334   0.4238  -2.4255   0.5054
 8L3  CAI  C   CR16  0  -0.238   1.7144  -2.0799   0.9027
 8L3  CAJ  C   CR16  0  -0.312   2.6997  -3.0461   0.8745
 8L3  CAK  C   CR16  0  -0.094   2.3733  -4.3274   0.4448
 8L3  CAM  C   CR16  0  -0.186   0.1950  -3.7366   0.0888
 8L3  CAN  C   CH2   0  -0.529  -1.9003   0.5641  -1.2466
 8L3  CAO  C   CR6   0   0.187  -0.4199   0.7950  -1.1468
 8L3  CAP  C   CR16  0  -0.316   0.4706   0.0245  -1.8907
 8L3  CAQ  C   CR16  0  -0.193   1.8383   0.1840  -1.7629
 8L3  CAR  C   CR6   0  -0.029   2.3456   1.1363  -0.8921
 8L3  CAT  C   CR6   0   0.019   1.4697   1.9379  -0.1714
 8L3  CAV  C   CR16  0  -0.282   0.0996   1.7716  -0.3052
 8L3  CAW  C   CH2   0  -0.428  -2.5832   0.3192   1.2161
 8L3  NAB  N   NH1   0  -0.573  -4.9329   1.0983   0.8263
 8L3  NAL  N   N     0  -0.390   1.1507  -4.6599   0.0616
 8L3  OAG  O   O2    0  -0.467  -0.5097  -1.4667   0.5561
 8L3  CLS  CL  CL    0  -0.107   4.0523   1.3084  -0.7150
 8L3  CLU  CL  CL    0  -0.106   2.0705   3.1504   0.8989
 8L3  H1   H   HCH2  0   0.240  -3.6573   1.8452   2.2873
 8L3  H2   H   HCH2  0   0.220  -3.2504   2.3006   0.6535
 8L3  H3   H   HCH2  0   0.224  -4.6582   1.2459  -1.2294
 8L3  H4   H   HCH2  0   0.241  -5.9248   0.1514  -0.7353
 8L3  H5   H   HCH2  0   0.230  -4.3358  -1.5040   0.0575
 8L3  H6   H   HCH2  0   0.234  -3.9613  -1.1051  -1.6102
 8L3  H7   H   HCH2  0   0.236  -2.3512  -2.3990   0.5047
 8L3  H8   H   HCH2  0   0.235  -1.6209  -2.0981  -1.0775
 8L3  H9   H   HCR6  0   0.273   1.9295  -1.0674   1.2207
 8L3  H10  H   HCR6  0   0.271   3.7118  -2.8106   1.1741
 8L3  H11  H   HCR6  0   0.259   3.1269  -5.1055   0.4113
 8L3  H12  H   HCR6  0   0.274  -0.7891  -4.0605  -0.2303
 8L3  H13  H   HCH2  0   0.256  -2.1193   0.1230  -2.2231
 8L3  H14  H   HCH2  0   0.261  -2.4152   1.5267  -1.2337
 8L3  H15  H   HCR6  0   0.261   0.0921  -0.7269  -2.5727
 8L3  H16  H   HCR6  0   0.284   2.5167  -0.4345  -2.3346
 8L3  H17  H   HCR6  0   0.276  -0.5638   2.4144   0.2593
 8L3  H18  H   HCH2  0   0.241  -1.6013   0.6880   1.5200
 8L3  H19  H   HCH2  0   0.229  -2.8670  -0.4341   1.9604
 8L3  H20  H   HNH1  0   0.338  -5.3221   0.4345   1.4867

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
 8L3  CLU  CAT  single    1.725  0.020  1.725
 8L3  CLS  CAR  single    1.724  0.020  1.724
 8L3  CAT  CAR  aromatic  1.389  0.020  1.389
 8L3  CAT  CAV  aromatic  1.387  0.020  1.387
 8L3  CAR  CAQ  aromatic  1.387  0.020  1.387
 8L3  CAV  CAO  aromatic  1.390  0.020  1.390
 8L3  CAQ  CAP  aromatic  1.383  0.020  1.383
 8L3  CAO  CAP  aromatic  1.393  0.020  1.393
 8L3  CAO  CAN  single    1.502  0.020  1.502
 8L3  CAN  CAE  single    1.551  0.020  1.551
 8L3  CAW  CAE  single    1.537  0.020  1.537
 8L3  CAW  CAA  single    1.527  0.020  1.527
 8L3  CAE  CAD  single    1.540  0.020  1.540
 8L3  CAE  CAF  single    1.526  0.020  1.526
 8L3  CAA  NAB  single    1.454  0.020  1.454
 8L3  CAD  CAC  single    1.527  0.020  1.527
 8L3  CAF  OAG  single    1.416  0.020  1.416
 8L3  NAB  CAC  single    1.453  0.020  1.453
 8L3  OAG  CAH  single    1.339  0.020  1.339
 8L3  CAH  CAI  aromatic  1.394  0.020  1.394
 8L3  CAH  CAM  aromatic  1.395  0.020  1.395
 8L3  CAI  CAJ  aromatic  1.380  0.020  1.380
 8L3  CAM  NAL  aromatic  1.329  0.020  1.329
 8L3  CAJ  CAK  aromatic  1.390  0.020  1.390
 8L3  NAL  CAK  aromatic  1.324  0.020  1.324
 8L3  CAA  H1   single    0.970  0.020  1.090
 8L3  CAA  H2   single    0.970  0.020  1.090
 8L3  CAC  H3   single    0.970  0.020  1.090
 8L3  CAC  H4   single    0.970  0.020  1.090
 8L3  CAD  H5   single    0.970  0.020  1.090
 8L3  CAD  H6   single    0.970  0.020  1.090
 8L3  CAF  H7   single    0.970  0.020  1.090
 8L3  CAF  H8   single    0.970  0.020  1.090
 8L3  CAI  H9   single    0.930  0.020  1.080
 8L3  CAJ  H10  single    0.930  0.020  1.080
 8L3  CAK  H11  single    0.930  0.020  1.080
 8L3  CAM  H12  single    0.930  0.020  1.080
 8L3  CAN  H13  single    0.970  0.020  1.090
 8L3  CAN  H14  single    0.970  0.020  1.090
 8L3  CAP  H15  single    0.930  0.020  1.080
 8L3  CAQ  H16  single    0.930  0.020  1.080
 8L3  CAV  H17  single    0.930  0.020  1.080
 8L3  CAW  H18  single    0.970  0.020  1.090
 8L3  CAW  H19  single    0.970  0.020  1.090
 8L3  NAB  H20  single    0.890  0.020  1.040

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
 8L3  H2   CAA  H1   105.77  3.000
 8L3  H2   CAA  NAB  108.17  3.000
 8L3  H1   CAA  NAB  108.62  3.000
 8L3  H2   CAA  CAW  110.19  3.000
 8L3  H1   CAA  CAW  109.33  3.000
 8L3  NAB  CAA  CAW  114.39  3.000
 8L3  H4   CAC  H3   105.90  3.000
 8L3  H4   CAC  NAB  108.65  3.000
 8L3  H3   CAC  NAB  108.54  3.000
 8L3  H4   CAC  CAD  109.31  3.000
 8L3  H3   CAC  CAD  110.61  3.000
 8L3  NAB  CAC  CAD  113.53  3.000
 8L3  H6   CAD  H5   106.49  3.000
 8L3  H6   CAD  CAE  110.18  3.000
 8L3  H5   CAD  CAE  108.83  3.000
 8L3  H6   CAD  CAC  110.10  3.000
 8L3  H5   CAD  CAC  108.07  3.000
 8L3  CAE  CAD  CAC  112.92  3.000
 8L3  CAW  CAE  CAN  112.50  3.000
 8L3  CAW  CAE  CAF  110.35  3.000
 8L3  CAN  CAE  CAF  110.84  3.000
 8L3  CAF  CAE  CAD  106.52  3.000
 8L3  CAW  CAE  CAD  108.12  3.000
 8L3  CAN  CAE  CAD  108.26  3.000
 8L3  H8   CAF  H7   107.34  3.000
 8L3  H8   CAF  OAG  110.53  3.000
 8L3  H7   CAF  OAG  109.84  3.000
 8L3  H8   CAF  CAE  109.95  3.000
 8L3  H7   CAF  CAE  109.44  3.000
 8L3  OAG  CAF  CAE  109.70  3.000
 8L3  OAG  CAH  CAM  124.76  3.000
 8L3  CAM  CAH  CAI  118.04  3.000
 8L3  OAG  CAH  CAI  117.20  3.000
 8L3  H9   CAI  CAJ  121.25  3.000
 8L3  H9   CAI  CAH  119.96  3.000
 8L3  CAJ  CAI  CAH  118.79  3.000
 8L3  H10  CAJ  CAK  120.40  3.000
 8L3  H10  CAJ  CAI  120.66  3.000
 8L3  CAK  CAJ  CAI  118.93  3.000
 8L3  H11  CAK  NAL  116.94  3.000
 8L3  H11  CAK  CAJ  120.52  3.000
 8L3  NAL  CAK  CAJ  122.54  3.000
 8L3  H12  CAM  NAL  116.05  3.000
 8L3  H12  CAM  CAH  121.18  3.000
 8L3  NAL  CAM  CAH  122.77  3.000
 8L3  H14  CAN  H13  105.77  3.000
 8L3  H14  CAN  CAO  109.18  3.000
 8L3  H13  CAN  CAO  108.59  3.000
 8L3  H14  CAN  CAE  109.04  3.000
 8L3  H13  CAN  CAE  107.73  3.000
 8L3  CAO  CAN  CAE  116.03  3.000
 8L3  CAV  CAO  CAP  118.23  3.000
 8L3  CAP  CAO  CAN  120.64  3.000
 8L3  CAV  CAO  CAN  121.12  3.000
 8L3  H15  CAP  CAQ  118.93  3.000
 8L3  H15  CAP  CAO  119.78  3.000
 8L3  CAQ  CAP  CAO  121.28  3.000
 8L3  H16  CAQ  CAR  119.69  3.000
 8L3  H16  CAQ  CAP  120.37  3.000
 8L3  CAR  CAQ  CAP  119.94  3.000
 8L3  CLS  CAR  CAT  120.88  3.000
 8L3  CAT  CAR  CAQ  119.44  3.000
 8L3  CLS  CAR  CAQ  119.68  3.000
 8L3  CLU  CAT  CAV  119.22  3.000
 8L3  CAV  CAT  CAR  120.25  3.000
 8L3  CLU  CAT  CAR  120.53  3.000
 8L3  H17  CAV  CAT  118.94  3.000
 8L3  H17  CAV  CAO  120.26  3.000
 8L3  CAT  CAV  CAO  120.80  3.000
 8L3  H19  CAW  H18  106.02  3.000
 8L3  H19  CAW  CAE  108.53  3.000
 8L3  H18  CAW  CAE  111.18  3.000
 8L3  H19  CAW  CAA  108.64  3.000
 8L3  H18  CAW  CAA  109.53  3.000
 8L3  CAE  CAW  CAA  112.68  3.000
 8L3  H20  NAB  CAC  108.44  3.000
 8L3  H20  NAB  CAA  108.61  3.000
 8L3  CAC  NAB  CAA  111.59  3.000
 8L3  CAM  NAL  CAK  118.93  3.000
 8L3  CAH  OAG  CAF  119.52  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
 8L3  CONST_01  CAK  CAJ  CAI  CAH    0.00   0.0  0
 8L3  CONST_02  CAK  NAL  CAM  CAH    0.00   0.0  0
 8L3  CONST_03  NAL  CAM  CAH  CAI    0.00   0.0  0
 8L3  CONST_04  NAL  CAK  CAJ  CAI    0.00   0.0  0
 8L3  CONST_05  CAM  CAH  CAI  CAJ    0.00   0.0  0
 8L3  CONST_06  CAM  NAL  CAK  CAJ    0.00   0.0  0
 8L3  CONST_07  CAR  CAT  CAV  CAO    0.00   0.0  0
 8L3  CONST_08  CAR  CAQ  CAP  CAO    0.00   0.0  0
 8L3  CONST_09  CAT  CAR  CAQ  CAP    0.00   0.0  0
 8L3  CONST_10  CAT  CAV  CAO  CAP    0.00   0.0  0
 8L3  CONST_11  CAV  CAT  CAR  CAQ    0.00   0.0  0
 8L3  CONST_12  CAV  CAO  CAP  CAQ    0.00   0.0  0
 8L3  CONST_13  OAG  CAH  CAI  CAJ  180.00   0.0  0
 8L3  CONST_14  CAT  CAV  CAO  CAN  180.00   0.0  0
 8L3  CONST_15  CAQ  CAP  CAO  CAN  180.00   0.0  0
 8L3  CONST_16  CLU  CAT  CAV  CAO  180.00   0.0  0
 8L3  CONST_17  CLS  CAR  CAQ  CAP  180.00   0.0  0
 8L3  CONST_18  CLU  CAT  CAR  CAQ  180.00   0.0  0
 8L3  CONST_19  CLS  CAR  CAT  CAV  180.00   0.0  0
 8L3  CONST_20  OAG  CAH  CAM  NAL  180.00   0.0  0
 8L3  CONST_21  H10  CAJ  CAI  CAH  180.00   0.0  0
 8L3  CONST_22  H12  CAM  CAH  CAI  180.00   0.0  0
 8L3  CONST_23  H11  CAK  CAJ  CAI  180.00   0.0  0
 8L3  CONST_24  H9   CAI  CAJ  CAK  180.00   0.0  0
 8L3  CONST_25  H16  CAQ  CAP  CAO  180.00   0.0  0
 8L3  CONST_26  H17  CAV  CAO  CAP  180.00   0.0  0
 8L3  CONST_27  H15  CAP  CAQ  CAR  180.00   0.0  0
 8L3  Var_01    CAD  CAC  NAB  CAA   53.39  30.0  1
 8L3  Var_02    CAW  CAA  NAB  CAC  -53.07  30.0  1
 8L3  Var_03    NAB  CAA  CAW  CAE   53.21  30.0  1
 8L3  Var_04    NAB  CAC  CAD  CAE  -54.44  30.0  1
 8L3  Var_05    CAV  CAO  CAN  CAE  -83.76  30.0  2
 8L3  Var_06    CAI  CAH  OAG  CAF  167.73  30.0  2
 8L3  Var_07    H7   CAF  OAG  CAH   72.71  30.0  1

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
 8L3  chir_01  CAE  CAW  CAD  CAF  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
 8L3  plan-1  CAH  0.020
 8L3  plan-1  CAI  0.020
 8L3  plan-1  CAJ  0.020
 8L3  plan-1  CAK  0.020
 8L3  plan-1  CAM  0.020
 8L3  plan-1  NAL  0.020
 8L3  plan-1  OAG  0.020
 8L3  plan-1  H9   0.020
 8L3  plan-1  H10  0.020
 8L3  plan-1  H11  0.020
 8L3  plan-1  H12  0.020
 8L3  plan-2  CAN  0.020
 8L3  plan-2  CAO  0.020
 8L3  plan-2  CAP  0.020
 8L3  plan-2  CAQ  0.020
 8L3  plan-2  CAR  0.020
 8L3  plan-2  CAT  0.020
 8L3  plan-2  CAV  0.020
 8L3  plan-2  CLS  0.020
 8L3  plan-2  CLU  0.020
 8L3  plan-2  H15  0.020
 8L3  plan-2  H16  0.020
 8L3  plan-2  H17  0.020

