# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 11:22:27 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 4-[2-(4-cyclohexylpiperazin-4-ium-1-yl)-2-oxidanylidene-ethyl]sulfanyl-1-ethyl-quinolin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1C(=O)C=C(SCC(=O)N2CC[NH+](CC2)C3CCCCC3)c4ccccc14
#
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
 EGN  EGN  4-[2-(4-cyclohexylpiperazin-4-ium-1-yl)-2-oxidanylidene-ethyl]sulfanyl-1-ethyl-quinolin-2-one  ligand  61  29  .  2021-08-08  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EGN
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
 EGN  CAN  C  CH2   0  -0.471  -6.3183   1.7643   0.2471
 EGN  CAJ  C  CH2   0  -0.436  -7.5147   2.3794  -0.4759
 EGN  CAI  C  CH2   0  -0.435  -8.6984   1.4264  -0.5275
 EGN  CAK  C  CH2   0  -0.437  -8.2838   0.1115  -1.1687
 EGN  CAO  C  CH2   0  -0.474  -7.0951  -0.5255  -0.4535
 EGN  CAZ  C  CH1   0  -0.074  -5.9131   0.4379  -0.3921
 EGN  NBB  N  NT1   1  -0.554  -4.7541  -0.1854   0.3715
 EGN  CAS  C  CH2   0  -0.318  -3.5558   0.7087   0.4044
 EGN  CAQ  C  CH2   0  -0.338  -2.4024   0.0793   1.1597
 EGN  CAR  C  CH2   0  -0.326  -4.3611  -1.5261  -0.1645
 EGN  CAP  C  CH2   0  -0.333  -3.2020  -2.1184   0.6088
 EGN  NBA  N  NT    0  -0.466  -2.0712  -1.2186   0.6203
 EGN  CAU  C  C     0   0.624  -0.8430  -1.6367   0.2541
 EGN  OAB  O  O     0  -0.472  -0.6169  -2.7705  -0.1330
 EGN  CAM  C  CH2   0  -0.771   0.2774  -0.6159   0.3328
 EGN  SAT  S  S2    0   0.114   1.7929  -1.4937  -0.1014
 EGN  CAV  C  CR6   0   0.043   3.0005  -0.2342   0.0315
 EGN  CAX  C  CR66  0   0.025   4.3749  -0.6427  -0.1689
 EGN  CAF  C  CR16  0  -0.330   4.7316  -1.9694  -0.4476
 EGN  CAD  C  CR16  0  -0.255   6.0436  -2.3381  -0.6355
 EGN  CAE  C  CR16  0  -0.254   7.0374  -1.3665  -0.5448
 EGN  CAG  C  CR16  0  -0.325   6.7186  -0.0542  -0.2702
 EGN  CAY  C  CR66  0   0.392   5.3848   0.3370  -0.0735
 EGN  NBC  N  NR6   0  -0.612   5.0618   1.6514   0.2104
 EGN  CAL  C  CH2   0  -0.351   6.1076   2.6717   0.2801
 EGN  CAA  C  CH3   0  -0.665   6.5076   3.1946  -1.0894
 EGN  CAW  C  CR6   0   0.578   3.7579   2.0759   0.3649
 EGN  OAC  O  O     0  -0.503   3.4904   3.2570   0.5588
 EGN  CAH  C  CR16  0  -0.493   2.7293   1.0638   0.2911
 EGN  H1   H  HCH2  0   0.267  -5.5004   2.4838   0.2224
 EGN  H2   H  HCH2  0   0.245  -6.5722   1.5964   1.2995
 EGN  H3   H  HCH2  0   0.248  -7.7848   3.3095   0.0269
 EGN  H4   H  HCH2  0   0.228  -7.2180   2.6516  -1.4935
 EGN  H5   H  HCH2  0   0.219  -9.0684   1.2422   0.4866
 EGN  H6   H  HCH2  0   0.240  -9.5219   1.8755  -1.0863
 EGN  H7   H  HCH2  0   0.248  -9.1114  -0.5995  -1.1690
 EGN  H8   H  HCH2  0   0.227  -8.0200   0.2816  -2.2172
 EGN  H9   H  HCH2  0   0.246  -7.3856  -0.8123   0.5627
 EGN  H10  H  HCH2  0   0.269  -6.8310  -1.4381  -0.9859
 EGN  H11  H  HCH1  0   0.298  -5.5222   0.6124  -1.3992
 EGN  H12  H  HNT1  0   0.453  -5.0696  -0.3195   1.3368
 EGN  H13  H  HCH2  0   0.309  -3.2895   0.9226  -0.6297
 EGN  H14  H  HCH2  0   0.320  -3.8272   1.6339   0.9013
 EGN  H15  H  HCH2  0   0.312  -1.5668   0.7702   1.0945
 EGN  H16  H  HCH2  0   0.285  -2.6596  -0.0161   2.2194
 EGN  H17  H  HCH2  0   0.321  -5.2099  -2.1964  -0.0795
 EGN  H18  H  HCH2  0   0.307  -4.1169  -1.3906  -1.2178
 EGN  H19  H  HCH2  0   0.280  -3.5098  -2.3377   1.6362
 EGN  H20  H  HCH2  0   0.308  -2.9328  -3.0606   0.1396
 EGN  H21  H  HCH2  0   0.330   0.0926   0.2014  -0.3681
 EGN  H22  H  HCH2  0   0.329   0.3661  -0.1979   1.3373
 EGN  H23  H  HCR6  0   0.268   3.9659  -2.7310  -0.5160
 EGN  H24  H  HCR6  0   0.266   6.2958  -3.3672  -0.8498
 EGN  H25  H  HCR6  0   0.270   8.0751  -1.6343  -0.6922
 EGN  H26  H  HCR6  0   0.286   7.5233   0.6620  -0.2148
 EGN  H27  H  HCH2  0   0.279   5.7291   3.4845   0.8925
 EGN  H28  H  HCH2  0   0.263   6.9632   2.2637   0.8151
 EGN  H29  H  HCH3  0   0.233   6.9117   2.4087  -1.7277
 EGN  H30  H  HCH3  0   0.239   5.6546   3.6405  -1.5996
 EGN  H31  H  HCH3  0   0.243   7.2738   3.9615  -0.9797
 EGN  H32  H  HCR6  0   0.280   1.7252   1.4299   0.4451

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
 EGN  CAP  CAR  single    1.514  0.020  1.514
 EGN  CAP  NBA  single    1.445  0.020  1.445
 EGN  CAR  NBB  single    1.496  0.020  1.496
 EGN  OAB  CAU  double    1.219  0.020  1.219
 EGN  NBB  CAZ  single    1.521  0.020  1.521
 EGN  NBB  CAS  single    1.495  0.020  1.495
 EGN  NBA  CAU  single    1.348  0.020  1.348
 EGN  NBA  CAQ  single    1.444  0.020  1.444
 EGN  CAU  CAM  single    1.518  0.020  1.518
 EGN  CAZ  CAO  single    1.526  0.020  1.526
 EGN  CAZ  CAN  single    1.527  0.020  1.527
 EGN  CAO  CAK  single    1.527  0.020  1.527
 EGN  CAQ  CAS  single    1.516  0.020  1.516
 EGN  CAK  CAI  single    1.521  0.020  1.521
 EGN  CAM  SAT  single    1.804  0.020  1.804
 EGN  CAN  CAJ  single    1.527  0.020  1.527
 EGN  SAT  CAV  single    1.750  0.020  1.750
 EGN  CAJ  CAI  single    1.521  0.020  1.521
 EGN  CAV  CAH  double    1.351  0.020  1.351
 EGN  CAV  CAX  single    1.448  0.020  1.448
 EGN  CAF  CAX  aromatic  1.402  0.020  1.402
 EGN  CAF  CAD  aromatic  1.376  0.020  1.376
 EGN  CAH  CAW  single    1.445  0.020  1.445
 EGN  CAX  CAY  aromatic  1.410  0.020  1.410
 EGN  CAD  CAE  aromatic  1.393  0.020  1.393
 EGN  CAW  OAC  double    1.226  0.020  1.226
 EGN  CAW  NBC  single    1.380  0.020  1.380
 EGN  CAY  NBC  single    1.383  0.020  1.383
 EGN  CAY  CAG  aromatic  1.404  0.020  1.404
 EGN  NBC  CAL  single    1.463  0.020  1.463
 EGN  CAE  CAG  aromatic  1.378  0.020  1.378
 EGN  CAA  CAL  single    1.520  0.020  1.520
 EGN  CAN  H1   single    0.970  0.020  1.090
 EGN  CAN  H2   single    0.970  0.020  1.090
 EGN  CAJ  H3   single    0.970  0.020  1.090
 EGN  CAJ  H4   single    0.970  0.020  1.090
 EGN  CAI  H5   single    0.970  0.020  1.090
 EGN  CAI  H6   single    0.970  0.020  1.090
 EGN  CAK  H7   single    0.970  0.020  1.090
 EGN  CAK  H8   single    0.970  0.020  1.090
 EGN  CAO  H9   single    0.970  0.020  1.090
 EGN  CAO  H10  single    0.970  0.020  1.090
 EGN  CAZ  H11  single    0.970  0.020  1.090
 EGN  NBB  H12  single    0.890  0.020  1.040
 EGN  CAS  H13  single    0.970  0.020  1.090
 EGN  CAS  H14  single    0.970  0.020  1.090
 EGN  CAQ  H15  single    0.970  0.020  1.090
 EGN  CAQ  H16  single    0.970  0.020  1.090
 EGN  CAR  H17  single    0.970  0.020  1.090
 EGN  CAR  H18  single    0.970  0.020  1.090
 EGN  CAP  H19  single    0.970  0.020  1.090
 EGN  CAP  H20  single    0.970  0.020  1.090
 EGN  CAM  H21  single    0.970  0.020  1.090
 EGN  CAM  H22  single    0.970  0.020  1.090
 EGN  CAF  H23  single    0.930  0.020  1.080
 EGN  CAD  H24  single    0.930  0.020  1.080
 EGN  CAE  H25  single    0.930  0.020  1.080
 EGN  CAG  H26  single    0.930  0.020  1.080
 EGN  CAL  H27  single    0.970  0.020  1.090
 EGN  CAL  H28  single    0.970  0.020  1.090
 EGN  CAA  H29  single    0.970  0.020  1.090
 EGN  CAA  H30  single    0.970  0.020  1.090
 EGN  CAA  H31  single    0.970  0.020  1.090
 EGN  CAH  H32  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
 EGN  H2   CAN  H1   107.28  3.000
 EGN  H2   CAN  CAZ  109.29  3.000
 EGN  H1   CAN  CAZ  111.40  3.000
 EGN  H2   CAN  CAJ  109.57  3.000
 EGN  H1   CAN  CAJ  108.14  3.000
 EGN  CAZ  CAN  CAJ  111.07  3.000
 EGN  H4   CAJ  H3   106.47  3.000
 EGN  H4   CAJ  CAI  109.60  3.000
 EGN  H3   CAJ  CAI  110.92  3.000
 EGN  H4   CAJ  CAN  109.15  3.000
 EGN  H3   CAJ  CAN  108.60  3.000
 EGN  CAI  CAJ  CAN  111.93  3.000
 EGN  H6   CAI  H5   106.76  3.000
 EGN  H6   CAI  CAK  110.21  3.000
 EGN  H5   CAI  CAK  109.70  3.000
 EGN  H6   CAI  CAJ  110.29  3.000
 EGN  H5   CAI  CAJ  109.70  3.000
 EGN  CAK  CAI  CAJ  110.12  3.000
 EGN  H8   CAK  H7   106.49  3.000
 EGN  H8   CAK  CAO  109.02  3.000
 EGN  H7   CAK  CAO  108.59  3.000
 EGN  H8   CAK  CAI  109.59  3.000
 EGN  H7   CAK  CAI  110.91  3.000
 EGN  CAO  CAK  CAI  112.06  3.000
 EGN  H10  CAO  H9   107.37  3.000
 EGN  H10  CAO  CAZ  111.15  3.000
 EGN  H9   CAO  CAZ  109.47  3.000
 EGN  H10  CAO  CAK  108.03  3.000
 EGN  H9   CAO  CAK  109.72  3.000
 EGN  CAZ  CAO  CAK  111.01  3.000
 EGN  H11  CAZ  NBB  104.78  3.000
 EGN  H11  CAZ  CAO  109.89  3.000
 EGN  NBB  CAZ  CAO  110.58  3.000
 EGN  H11  CAZ  CAN  109.97  3.000
 EGN  CAO  CAZ  CAN  111.08  3.000
 EGN  NBB  CAZ  CAN  110.36  3.000
 EGN  H12  NBB  CAR  107.53  3.000
 EGN  H12  NBB  CAS  107.72  3.000
 EGN  CAR  NBB  CAS  109.46  3.000
 EGN  H12  NBB  CAZ  106.98  3.000
 EGN  CAS  NBB  CAZ  112.12  3.000
 EGN  CAR  NBB  CAZ  112.79  3.000
 EGN  H14  CAS  H13  109.19  3.000
 EGN  H14  CAS  CAQ  108.44  3.000
 EGN  H13  CAS  CAQ  111.63  3.000
 EGN  H14  CAS  NBB  108.63  3.000
 EGN  H13  CAS  NBB  107.01  3.000
 EGN  CAQ  CAS  NBB  111.87  3.000
 EGN  H16  CAQ  H15  107.11  3.000
 EGN  H16  CAQ  NBA  109.70  3.000
 EGN  H15  CAQ  NBA  111.89  3.000
 EGN  H16  CAQ  CAS  109.87  3.000
 EGN  H15  CAQ  CAS  106.94  3.000
 EGN  NBA  CAQ  CAS  111.21  3.000
 EGN  H18  CAR  H17  109.15  3.000
 EGN  H18  CAR  CAP  111.76  3.000
 EGN  H17  CAR  CAP  108.50  3.000
 EGN  H18  CAR  NBB  107.08  3.000
 EGN  H17  CAR  NBB  108.66  3.000
 EGN  CAP  CAR  NBB  111.63  3.000
 EGN  H20  CAP  H19  107.53  3.000
 EGN  H20  CAP  NBA  110.45  3.000
 EGN  H19  CAP  NBA  109.71  3.000
 EGN  H20  CAP  CAR  107.96  3.000
 EGN  H19  CAP  CAR  110.03  3.000
 EGN  NBA  CAP  CAR  111.08  3.000
 EGN  CAU  NBA  CAP  121.18  3.000
 EGN  CAU  NBA  CAQ  126.10  3.000
 EGN  CAP  NBA  CAQ  112.52  3.000
 EGN  CAM  CAU  OAB  120.33  3.000
 EGN  CAM  CAU  NBA  116.73  3.000
 EGN  OAB  CAU  NBA  122.93  3.000
 EGN  H22  CAM  H21  108.52  3.000
 EGN  H22  CAM  SAT  109.84  3.000
 EGN  H21  CAM  SAT  110.58  3.000
 EGN  H22  CAM  CAU  111.43  3.000
 EGN  H21  CAM  CAU  110.19  3.000
 EGN  SAT  CAM  CAU  106.28  3.000
 EGN  CAV  SAT  CAM  102.19  3.000
 EGN  CAH  CAV  CAX  119.22  3.000
 EGN  CAX  CAV  SAT  116.20  3.000
 EGN  CAH  CAV  SAT  124.58  3.000
 EGN  CAY  CAX  CAF  119.26  3.000
 EGN  CAY  CAX  CAV  118.32  3.000
 EGN  CAF  CAX  CAV  122.42  3.000
 EGN  H23  CAF  CAD  118.53  3.000
 EGN  H23  CAF  CAX  119.91  3.000
 EGN  CAD  CAF  CAX  121.56  3.000
 EGN  H24  CAD  CAE  120.70  3.000
 EGN  H24  CAD  CAF  120.31  3.000
 EGN  CAE  CAD  CAF  118.99  3.000
 EGN  H25  CAE  CAG  119.00  3.000
 EGN  H25  CAE  CAD  120.19  3.000
 EGN  CAG  CAE  CAD  120.81  3.000
 EGN  H26  CAG  CAY  121.11  3.000
 EGN  H26  CAG  CAE  118.02  3.000
 EGN  CAY  CAG  CAE  120.87  3.000
 EGN  NBC  CAY  CAG  121.03  3.000
 EGN  CAG  CAY  CAX  118.51  3.000
 EGN  NBC  CAY  CAX  120.46  3.000
 EGN  CAW  NBC  CAL  117.11  3.000
 EGN  CAL  NBC  CAY  120.38  3.000
 EGN  CAW  NBC  CAY  122.42  3.000
 EGN  H28  CAL  H27  106.10  3.000
 EGN  H28  CAL  CAA  111.41  3.000
 EGN  H27  CAL  CAA  110.03  3.000
 EGN  H28  CAL  NBC  108.91  3.000
 EGN  H27  CAL  NBC  107.45  3.000
 EGN  CAA  CAL  NBC  112.66  3.000
 EGN  H31  CAA  H30  108.04  3.000
 EGN  H31  CAA  H29  107.80  3.000
 EGN  H30  CAA  H29  108.13  3.000
 EGN  H31  CAA  CAL  109.67  3.000
 EGN  H30  CAA  CAL  110.90  3.000
 EGN  H29  CAA  CAL  112.16  3.000
 EGN  CAH  CAW  OAC  121.82  3.000
 EGN  OAC  CAW  NBC  121.34  3.000
 EGN  CAH  CAW  NBC  116.83  3.000
 EGN  H32  CAH  CAW  114.66  3.000
 EGN  H32  CAH  CAV  122.66  3.000
 EGN  CAW  CAH  CAV  122.67  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
 EGN  CONST_01  CAE  CAD  CAF  CAX    0.00   0.0  0
 EGN  CONST_02  CAE  CAG  CAY  CAX    0.00   0.0  0
 EGN  CONST_03  CAG  CAY  CAX  CAF    0.00   0.0  0
 EGN  CONST_04  CAG  CAE  CAD  CAF    0.00   0.0  0
 EGN  CONST_05  CAY  CAX  CAF  CAD    0.00   0.0  0
 EGN  CONST_06  CAY  CAG  CAE  CAD    0.00   0.0  0
 EGN  CONST_07  CAH  CAW  NBC  CAY    0.00   0.0  0
 EGN  CONST_08  OAC  CAW  NBC  CAY  180.00   0.0  0
 EGN  CONST_09  CAH  CAW  NBC  CAL  180.00   0.0  0
 EGN  CONST_10  H23  CAF  CAX  CAV    0.00   0.0  0
 EGN  CONST_11  H24  CAD  CAF  CAX  180.00   0.0  0
 EGN  CONST_12  H26  CAG  CAY  CAX  180.00   0.0  0
 EGN  CONST_13  H25  CAE  CAD  CAF  180.00   0.0  0
 EGN  CONST_14  OAB  CAU  NBA  CAQ  180.00   0.0  0
 EGN  CONST_15  CAM  CAU  NBA  CAQ    0.00   0.0  0
 EGN  CONST_16  OAB  CAU  NBA  CAP    0.00   0.0  0
 EGN  CONST_17  CAM  CAU  NBA  CAP  180.00   0.0  0
 EGN  CONST_18  OAC  CAW  NBC  CAL    0.00   0.0  0
 EGN  Var_01    CAK  CAI  CAJ  CAN  -55.71  30.0  1
 EGN  Var_02    CAO  CAK  CAI  CAJ   55.74  30.0  1
 EGN  Var_03    CAZ  CAO  CAK  CAI  -55.79  30.0  1
 EGN  Var_04    CAZ  CAN  CAJ  CAI   55.82  30.0  1
 EGN  Var_05    NBA  CAP  CAR  NBB  -55.79  30.0  1
 EGN  Var_06    NBA  CAQ  CAS  NBB   54.98  30.0  1
 EGN  Var_07    CAP  NBA  CAQ  CAS  -56.17  30.0  1
 EGN  Var_08    CAR  CAP  NBA  CAQ   56.63  30.0  1
 EGN  Var_09    CAH  CAV  SAT  CAM   -4.81  30.0  3
 EGN  Var_10    CAA  CAL  NBC  CAY   81.74  30.0  3
 EGN  Var_11    SAT  CAM  CAU  NBA  176.13  30.0  3
 EGN  Var_12    H29  CAA  CAL  NBC  -61.25  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
 EGN  chir_01  CAZ  NBB  CAO  CAN  negativ
 EGN  chir_02  NBB  CAR  CAZ  CAS  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
 EGN  plan-1  CAQ  0.020
 EGN  plan-1  CAP  0.020
 EGN  plan-1  NBA  0.020
 EGN  plan-1  CAU  0.020
 EGN  plan-1  OAB  0.020
 EGN  plan-1  CAM  0.020
 EGN  plan-2  SAT  0.020
 EGN  plan-2  CAV  0.020
 EGN  plan-2  CAX  0.020
 EGN  plan-2  CAF  0.020
 EGN  plan-2  CAD  0.020
 EGN  plan-2  CAE  0.020
 EGN  plan-2  CAG  0.020
 EGN  plan-2  CAY  0.020
 EGN  plan-2  NBC  0.020
 EGN  plan-2  CAL  0.020
 EGN  plan-2  CAW  0.020
 EGN  plan-2  OAC  0.020
 EGN  plan-2  CAH  0.020
 EGN  plan-2  H23  0.020
 EGN  plan-2  H24  0.020
 EGN  plan-2  H25  0.020
 EGN  plan-2  H26  0.020
 EGN  plan-2  H32  0.020

