# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 09:23:10 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 2-[(2,2-difluoro-2-pyridinium-2-ylethyl)amino]-4-(2-{[(3-fluoro-4-methylpyridin-2-yl)methyl]amino}-2-oxoethyl)-5-methyl-3-oxo-3,4-dihydropyrazin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C[NH+]=C(NCC(F)(F)c2cccc[nH+]2)C(=O)N1CC(=O)NCc3nccc(C)c3F
#
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
 CDB  CDB  2-[(2,2-difluoro-2-pyridinium-2-ylethyl)amino]-4-(2-{[(3-fluoro-4-methylpyridin-2-yl)methyl]amino}-2-oxoethyl)-5-methyl-3-oxo-3,4-dihydropyrazin-1-ium  ligand  55  32  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_CDB
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
 CDB  N1    N  NR16  1  -0.596  -6.9186  -0.5394  -1.5533
 CDB  C2    C  CR6   0   0.279  -6.4730  -0.1326  -0.3589
 CDB  C3    C  CR16  0  -0.311  -7.2059   0.7789   0.3606
 CDB  C4    C  CR16  0  -0.034  -8.3961   1.2584  -0.1758
 CDB  C5    C  CR16  0  -0.295  -8.8264   0.8143  -1.4145
 CDB  C6    C  CR16  0   0.128  -8.0556  -0.1024  -2.0951
 CDB  C11   C  CT    0   0.755  -5.1582  -0.6846   0.1438
 CDB  C12   C  CH2   0  -0.351  -4.0363   0.3198  -0.0281
 CDB  F13   F  F     0  -0.314  -4.8672  -1.8278  -0.5215
 CDB  F1    F  F     0  -0.301  -5.2996  -1.0120   1.4457
 CDB  N18   N  NH1   0  -0.653  -2.7880  -0.2164   0.4597
 CDB  C21   C  CR6   0   0.640  -1.6736   0.4761   0.5099
 CDB  C22   C  CR6   0   0.554  -0.4750  -0.2327   1.0259
 CDB  N23   N  NR6   0  -0.539   0.6459   0.5222   1.1474
 CDB  C24   C  CR6   0   0.360   0.7270   1.8377   0.7051
 CDB  C25   C  CR16  0  -0.085  -0.3702   2.4230   0.2070
 CDB  N26   N  NR16  1  -0.629  -1.5599   1.7258   0.1267
 CDB  O28   O  OC    0  -0.428  -0.5557  -1.4070   1.3257
 CDB  C29   C  CH3   0  -0.711   2.0172   2.5739   0.8119
 CDB  C33   C  CH2   0  -0.465   1.8317  -0.1692   1.6079
 CDB  C34   C  C     0   0.576   2.5404  -0.8364   0.4301
 CDB  N37   N  NH1   0  -0.618   3.6707  -1.4637   0.7773
 CDB  O38   O  O     0  -0.466   2.0875  -0.7728  -0.6972
 CDB  C39   C  CH2   0  -0.355   4.5761  -2.0871  -0.1606
 CDB  C40   C  CR6   0   0.076   5.9096  -1.3871  -0.2165
 CDB  C43   C  CR6   0   0.471   6.0225  -0.0574  -0.5932
 CDB  C44   C  CR6   0   0.026   7.2397   0.5998  -0.6382
 CDB  C45   C  CR16  0  -0.310   8.3454  -0.1676  -0.2873
 CDB  N46   N  N     0  -0.411   6.9873  -2.0890   0.1125
 CDB  F47   F  F     0  -0.301   4.9121   0.6167  -0.9321
 CDB  C50   C  CR16  0  -0.060   8.1724  -1.4936   0.0730
 CDB  C1    C  CH3   0  -0.696   7.3429   2.0356  -1.0421
 CDB  H1    H  HNR6  0   0.451  -6.3802  -1.2203  -2.0814
 CDB  H3    H  HCR6  0   0.302  -6.8622   1.1188   1.3267
 CDB  H4    H  HCR6  0   0.301  -8.9821   1.9760   0.3805
 CDB  H5    H  HCR6  0   0.300  -9.7459   1.1677  -1.8553
 CDB  H6    H  HCR6  0   0.333  -8.3119  -0.5053  -3.0622
 CDB  H121  H  HCH2  0   0.293  -4.3016   1.2282   0.5208
 CDB  H122  H  HCH2  0   0.305  -3.9565   0.5825  -1.0869
 CDB  H18   H  HNH1  0   0.436  -2.7094  -1.1839   0.7509
 CDB  H25   H  HCR6  0   0.300  -0.3928   3.4378  -0.1505
 CDB  H26   H  HNR6  0   0.445  -2.3598   2.2225  -0.2488
 CDB  H291  H  HCH3  0   0.266   1.8963   3.5705   0.3951
 CDB  H292  H  HCH3  0   0.261   2.3346   2.6861   1.8491
 CDB  H293  H  HCH3  0   0.265   2.8193   2.0805   0.2630
 CDB  H331  H  HCH2  0   0.307   2.4967   0.5336   2.1055
 CDB  H332  H  HCH2  0   0.328   1.5558  -0.9144   2.3534
 CDB  H37   H  HNH1  0   0.390   3.9481  -1.4606   1.7472
 CDB  H391  H  HCH2  0   0.274   4.7548  -3.1222   0.1312
 CDB  H392  H  HCH2  0   0.269   4.1005  -2.1022  -1.1407
 CDB  H45   H  HCR6  0   0.245   9.3362   0.2674  -0.2994
 CDB  H50   H  HCR6  0   0.251   9.0289  -2.0997   0.3442
 CDB  H11   H  HCH3  0   0.248   6.9548   2.1946  -2.0485
 CDB  H12   H  HCH3  0   0.250   6.7737   2.6777  -0.3691
 CDB  H13   H  HCH3  0   0.243   8.3797   2.3643  -1.0259

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
 CDB  N1   C2    aromatic  1.338  0.020  1.338
 CDB  N1   C6    aromatic  1.333  0.020  1.333
 CDB  N1   H1    single    0.860  0.020  1.020
 CDB  C2   C3    aromatic  1.373  0.020  1.373
 CDB  C2   C11   single    1.512  0.020  1.512
 CDB  C3   C4    aromatic  1.391  0.020  1.391
 CDB  C3   H3    single    0.930  0.020  1.080
 CDB  C4   C5    aromatic  1.385  0.020  1.385
 CDB  C4   H4    single    0.930  0.020  1.080
 CDB  C5   C6    aromatic  1.378  0.020  1.378
 CDB  C5   H5    single    0.930  0.020  1.080
 CDB  C6   H6    single    0.930  0.020  1.080
 CDB  C11  C12   single    1.516  0.020  1.516
 CDB  C11  F13   single    1.354  0.020  1.354
 CDB  C11  F1    single    1.350  0.020  1.350
 CDB  C12  N18   single    1.444  0.020  1.444
 CDB  C12  H121  single    0.970  0.020  1.090
 CDB  C12  H122  single    0.970  0.020  1.090
 CDB  N18  C21   single    1.313  0.020  1.313
 CDB  N18  H18   single    0.860  0.020  1.020
 CDB  C21  C22   aromatic  1.485  0.020  1.485
 CDB  C21  N26   aromatic  1.312  0.020  1.312
 CDB  C22  N23   aromatic  1.357  0.020  1.357
 CDB  C22  O28   double    1.215  0.020  1.215
 CDB  N23  C24   aromatic  1.390  0.020  1.390
 CDB  N23  C33   single    1.448  0.020  1.448
 CDB  C24  C25   aromatic  1.340  0.020  1.340
 CDB  C24  C29   single    1.489  0.020  1.489
 CDB  C25  N26   aromatic  1.381  0.020  1.381
 CDB  C25  H25   single    0.930  0.020  1.080
 CDB  N26  H26   single    0.860  0.020  1.020
 CDB  C29  H291  single    0.970  0.020  1.090
 CDB  C29  H292  single    0.970  0.020  1.090
 CDB  C29  H293  single    0.970  0.020  1.090
 CDB  C33  C34   single    1.528  0.020  1.528
 CDB  C33  H331  single    0.970  0.020  1.090
 CDB  C33  H332  single    0.970  0.020  1.090
 CDB  C34  N37   single    1.338  0.020  1.338
 CDB  C34  O38   double    1.217  0.020  1.217
 CDB  N37  C39   single    1.445  0.020  1.445
 CDB  N37  H37   single    0.860  0.020  1.020
 CDB  C39  C40   single    1.507  0.020  1.507
 CDB  C39  H391  single    0.970  0.020  1.090
 CDB  C39  H392  single    0.970  0.020  1.090
 CDB  C40  C43   aromatic  1.387  0.020  1.387
 CDB  C40  N46   aromatic  1.328  0.020  1.328
 CDB  C43  C44   aromatic  1.384  0.020  1.384
 CDB  C43  F47   single    1.343  0.020  1.343
 CDB  C44  C45   aromatic  1.391  0.020  1.391
 CDB  C44  C1    single    1.495  0.020  1.495
 CDB  C45  C50   aromatic  1.385  0.020  1.385
 CDB  C45  H45   single    0.930  0.020  1.080
 CDB  N46  C50   aromatic  1.327  0.020  1.327
 CDB  C50  H50   single    0.930  0.020  1.080
 CDB  C1   H11   single    0.970  0.020  1.090
 CDB  C1   H12   single    0.970  0.020  1.090
 CDB  C1   H13   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
 CDB  H1    N1   C6    117.41  3.000
 CDB  H1    N1   C2    119.42  3.000
 CDB  C6    N1   C2    123.17  3.000
 CDB  C11   C2   C3    122.15  3.000
 CDB  C11   C2   N1    118.38  3.000
 CDB  C3    C2   N1    119.46  3.000
 CDB  H3    C3   C4    120.58  3.000
 CDB  H3    C3   C2    120.51  3.000
 CDB  C4    C3   C2    118.91  3.000
 CDB  H4    C4   C5    120.33  3.000
 CDB  H4    C4   C3    119.63  3.000
 CDB  C5    C4   C3    120.04  3.000
 CDB  H5    C5   C6    119.53  3.000
 CDB  H5    C5   C4    121.68  3.000
 CDB  C6    C5   C4    118.78  3.000
 CDB  H6    C6   C5    123.96  3.000
 CDB  H6    C6   N1    116.40  3.000
 CDB  C5    C6   N1    119.64  3.000
 CDB  F1    C11  F13   106.95  3.000
 CDB  F1    C11  C12   110.34  3.000
 CDB  F13   C11  C12   110.16  3.000
 CDB  F1    C11  C2    108.55  3.000
 CDB  F13   C11  C2    109.37  3.000
 CDB  C12   C11  C2    111.35  3.000
 CDB  H122  C12  H121  107.70  3.000
 CDB  H122  C12  N18   110.68  3.000
 CDB  H121  C12  N18   110.40  3.000
 CDB  H122  C12  C11   108.84  3.000
 CDB  H121  C12  C11   108.29  3.000
 CDB  N18   C12  C11   110.83  3.000
 CDB  H18   N18  C21   115.26  3.000
 CDB  H18   N18  C12   121.25  3.000
 CDB  C21   N18  C12   123.43  3.000
 CDB  N26   C21  C22   119.09  3.000
 CDB  N26   C21  N18   124.38  3.000
 CDB  C22   C21  N18   116.53  3.000
 CDB  O28   C22  N23   124.80  3.000
 CDB  O28   C22  C21   119.57  3.000
 CDB  N23   C22  C21   115.62  3.000
 CDB  C33   N23  C24   120.35  3.000
 CDB  C33   N23  C22   116.07  3.000
 CDB  C24   N23  C22   123.10  3.000
 CDB  C29   C24  C25   121.35  3.000
 CDB  C29   C24  N23   119.70  3.000
 CDB  C25   C24  N23   118.94  3.000
 CDB  H25   C25  N26   116.01  3.000
 CDB  H25   C25  C24   123.56  3.000
 CDB  N26   C25  C24   120.44  3.000
 CDB  H26   N26  C25   116.99  3.000
 CDB  H26   N26  C21   120.43  3.000
 CDB  C25   N26  C21   122.57  3.000
 CDB  H293  C29  H292  108.14  3.000
 CDB  H293  C29  H291  107.68  3.000
 CDB  H292  C29  H291  107.62  3.000
 CDB  H293  C29  C24   112.19  3.000
 CDB  H292  C29  C24   111.79  3.000
 CDB  H291  C29  C24   109.23  3.000
 CDB  H332  C33  H331  106.48  3.000
 CDB  H332  C33  C34   110.26  3.000
 CDB  H331  C33  C34   110.56  3.000
 CDB  H332  C33  N23   109.68  3.000
 CDB  H331  C33  N23   109.73  3.000
 CDB  C34   C33  N23   110.07  3.000
 CDB  O38   C34  N37   125.39  3.000
 CDB  O38   C34  C33   121.25  3.000
 CDB  N37   C34  C33   113.35  3.000
 CDB  H37   N37  C39   116.94  3.000
 CDB  H37   N37  C34   118.70  3.000
 CDB  C39   N37  C34   124.26  3.000
 CDB  H392  C39  H391  107.41  3.000
 CDB  H392  C39  C40   111.06  3.000
 CDB  H391  C39  C40   107.81  3.000
 CDB  H392  C39  N37   108.44  3.000
 CDB  H391  C39  N37   109.79  3.000
 CDB  C40   C39  N37   112.22  3.000
 CDB  N46   C40  C43   120.54  3.000
 CDB  N46   C40  C39   117.61  3.000
 CDB  C43   C40  C39   121.84  3.000
 CDB  F47   C43  C44   118.74  3.000
 CDB  F47   C43  C40   118.86  3.000
 CDB  C44   C43  C40   122.40  3.000
 CDB  C1    C44  C45   122.89  3.000
 CDB  C1    C44  C43   121.70  3.000
 CDB  C45   C44  C43   115.40  3.000
 CDB  H45   C45  C50   120.14  3.000
 CDB  H45   C45  C44   120.22  3.000
 CDB  C50   C45  C44   119.64  3.000
 CDB  C50   N46  C40   118.71  3.000
 CDB  H50   C50  N46   116.58  3.000
 CDB  H50   C50  C45   120.12  3.000
 CDB  N46   C50  C45   123.30  3.000
 CDB  H13   C1   H12   108.08  3.000
 CDB  H13   C1   H11   108.00  3.000
 CDB  H12   C1   H11   107.34  3.000
 CDB  H13   C1   C44   110.61  3.000
 CDB  H12   C1   C44   111.26  3.000
 CDB  H11   C1   C44   111.40  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
 CDB  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 CDB  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 CDB  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 CDB  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 CDB  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 CDB  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 CDB  CONST_07  C24   N23  C22  C21     0.00   0.0  0
 CDB  CONST_08  C24   C25  N26  C21     0.00   0.0  0
 CDB  CONST_09  C25   N26  C21  C22     0.00   0.0  0
 CDB  CONST_10  C25   C24  N23  C22     0.00   0.0  0
 CDB  CONST_11  N26   C21  C22  N23     0.00   0.0  0
 CDB  CONST_12  N26   C25  C24  N23     0.00   0.0  0
 CDB  CONST_13  C45   C44  C43  C40     0.00   0.0  0
 CDB  CONST_14  C45   C50  N46  C40     0.00   0.0  0
 CDB  CONST_15  C50   N46  C40  C43     0.00   0.0  0
 CDB  CONST_16  C50   C45  C44  C43     0.00   0.0  0
 CDB  CONST_17  N46   C40  C43  C44     0.00   0.0  0
 CDB  CONST_18  N46   C50  C45  C44     0.00   0.0  0
 CDB  CONST_19  C11   C2   C3   C4    180.00   0.0  0
 CDB  CONST_20  C11   C2   N1   C6    180.00   0.0  0
 CDB  CONST_21  N23   C22  C21  N18   180.00   0.0  0
 CDB  CONST_22  C25   N26  C21  N18   180.00   0.0  0
 CDB  CONST_23  C33   N23  C22  C21   180.00   0.0  0
 CDB  CONST_24  C29   C24  N23  C22   180.00   0.0  0
 CDB  CONST_25  O28   C22  N23  C24   180.00   0.0  0
 CDB  CONST_26  C33   N23  C24  C25   180.00   0.0  0
 CDB  CONST_27  O28   C22  C21  N26   180.00   0.0  0
 CDB  CONST_28  C29   C24  C25  N26   180.00   0.0  0
 CDB  CONST_29  C44   C43  C40  C39   180.00   0.0  0
 CDB  CONST_30  C50   N46  C40  C39   180.00   0.0  0
 CDB  CONST_31  C1    C44  C43  C40   180.00   0.0  0
 CDB  CONST_32  F47   C43  C44  C45   180.00   0.0  0
 CDB  CONST_33  F47   C43  C40  N46   180.00   0.0  0
 CDB  CONST_34  C1    C44  C45  C50   180.00   0.0  0
 CDB  CONST_35  H3    C3   C2   N1    180.00   0.0  0
 CDB  CONST_36  H5    C5   C6   N1    180.00   0.0  0
 CDB  CONST_37  H6    C6   N1   C2    180.00   0.0  0
 CDB  CONST_38  H4    C4   C3   C2    180.00   0.0  0
 CDB  CONST_39  H1    N1   C2   C3    180.00   0.0  0
 CDB  CONST_40  H25   C25  N26  C21   180.00   0.0  0
 CDB  CONST_41  H26   N26  C21  C22   180.00   0.0  0
 CDB  CONST_42  H50   C50  N46  C40   180.00   0.0  0
 CDB  CONST_43  H45   C45  C44  C43   180.00   0.0  0
 CDB  CONST_44  C33   N23  C22  O28     0.00   0.0  0
 CDB  CONST_45  C22   C21  N18  C12   180.00   0.0  0
 CDB  CONST_46  N26   C21  N18  C12     0.00   0.0  0
 CDB  CONST_47  H18   N18  C21  C22     0.00   0.0  0
 CDB  CONST_48  C39   N37  C34  C33   180.00   0.0  0
 CDB  CONST_49  C39   N37  C34  O38     0.00   0.0  0
 CDB  CONST_50  H37   N37  C34  C33     0.00   0.0  0
 CDB  Var_01    C12   C11  C2   N1    102.23  30.0  2
 CDB  Var_02    C34   C33  N23  C22    84.59  30.0  2
 CDB  Var_03    C43   C40  C39  N37   -60.62  30.0  2
 CDB  Var_04    H291  C29  C24  N23   178.48  30.0  2
 CDB  Var_05    H11   C1   C44  C43   -59.20  30.0  2
 CDB  Var_06    N18   C12  C11  C2    179.78  30.0  3
 CDB  Var_07    C21   N18  C12  C11  -175.46  30.0  3
 CDB  Var_08    N37   C34  C33  N23   178.15  30.0  3
 CDB  Var_09    C40   C39  N37  C34   113.66  30.0  3

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
 CDB  plan-1  N1   0.020
 CDB  plan-1  C2   0.020
 CDB  plan-1  C3   0.020
 CDB  plan-1  C4   0.020
 CDB  plan-1  C5   0.020
 CDB  plan-1  C6   0.020
 CDB  plan-1  C11  0.020
 CDB  plan-1  H1   0.020
 CDB  plan-1  H3   0.020
 CDB  plan-1  H4   0.020
 CDB  plan-1  H5   0.020
 CDB  plan-1  H6   0.020
 CDB  plan-2  N18  0.020
 CDB  plan-2  C21  0.020
 CDB  plan-2  C22  0.020
 CDB  plan-2  N23  0.020
 CDB  plan-2  C24  0.020
 CDB  plan-2  C25  0.020
 CDB  plan-2  N26  0.020
 CDB  plan-2  O28  0.020
 CDB  plan-2  C29  0.020
 CDB  plan-2  C33  0.020
 CDB  plan-2  H25  0.020
 CDB  plan-2  H26  0.020
 CDB  plan-3  C39  0.020
 CDB  plan-3  C40  0.020
 CDB  plan-3  C43  0.020
 CDB  plan-3  C44  0.020
 CDB  plan-3  C45  0.020
 CDB  plan-3  N46  0.020
 CDB  plan-3  F47  0.020
 CDB  plan-3  C50  0.020
 CDB  plan-3  C1   0.020
 CDB  plan-3  H45  0.020
 CDB  plan-3  H50  0.020
 CDB  plan-4  C33  0.020
 CDB  plan-4  C34  0.020
 CDB  plan-4  N37  0.020
 CDB  plan-4  O38  0.020
 CDB  plan-4  C39  0.020
 CDB  plan-4  H37  0.020
 CDB  plan-5  C12  0.020
 CDB  plan-5  N18  0.020
 CDB  plan-5  C21  0.020
 CDB  plan-5  H18  0.020

