# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:53:03 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 2,3-dicarboxy-4-(2-chlorophenyl)-1-ethyl-6-methyl-5-[(1-methylethoxy)carbonyl]pyridinium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[n+]1c(C)c(C(=O)OC(C)C)c(c2ccccc2Cl)c(C(O)=O)c1C(O)=O
#
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
 BIN  BIN  2,3-dicarboxy-4-(2-chlorophenyl)-1-ethyl-6-methyl-5-[(1-methylethoxy)carbonyl]pyridinium  ligand  49  28  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BIN
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
 BIN  C1    C   CR6   0   0.034  27.7620   2.6568  52.9895
 BIN  C2    C   CR6   0  -0.041  27.2133   3.7637  52.3529
 BIN  C3    C   CR16  0  -0.203  26.7514   4.8446  53.0811
 BIN  C4    C   CR16  0  -0.256  26.8292   4.8140  54.4669
 BIN  C5    C   CR16  0  -0.227  27.3629   3.7118  55.1165
 BIN  C6    C   CR16  0  -0.275  27.8286   2.6341  54.3769
 BIN  C7    C   CR6   0   0.383  28.2581   1.4905  52.2216
 BIN  C8    C   CR6   0  -0.151  27.4057   0.4245  51.9855
 BIN  C9    C   CR6   0   0.395  29.9810   0.2239  51.1512
 BIN  C11   C   CR6   0   0.448  27.8225  -0.7004  51.2881
 BIN  C12   C   CR6   0  -0.186  29.5817   1.3759  51.7941
 BIN  C13   C   C     0   0.487  30.6271   2.4121  52.0763
 BIN  C14   C   C     0   0.447  31.4059   0.0974  50.6508
 BIN  C15   C   CH3   0  -0.766  26.8642  -1.8085  51.0118
 BIN  C16   C   CH3   0  -0.663  29.8120  -3.1588  51.0418
 BIN  C18   C   C     0   0.469  26.0163   0.4562  52.5623
 BIN  C19   C   CH1   0  -0.001  23.8812   1.5116  52.3376
 BIN  C20   C   CH3   0  -0.680  23.8650   2.4485  53.5284
 BIN  C21   C   CH3   0  -0.669  23.1669   2.0874  51.1349
 BIN  N10   N   NR6   1  -0.537  29.1109  -0.7677  50.8807
 BIN  O3A   O   O     0  -0.405  31.7502   2.1040  52.3764
 BIN  O3B   O   OH1   0  -0.557  30.1743   3.6325  51.9454
 BIN  O4A   O   O     0  -0.372  31.7687   0.7021  49.6837
 BIN  O4B   O   OH1   0  -0.550  32.1007  -0.7302  51.3887
 BIN  O8A   O   O     0  -0.401  25.7139  -0.2176  53.5101
 BIN  O8    O   O2    0  -0.429  25.2541   1.2850  51.9012
 BIN  CL2   CL  CL    0  -0.108  27.1185   3.7877  50.6306
 BIN  H3    H   HCR6  0   0.290  26.3303   5.7017  52.5740
 BIN  H4    H   HCR6  0   0.277  26.4652   5.6591  55.0353
 BIN  H5    H   HCR6  0   0.274  27.4203   3.6868  56.1958
 BIN  H6    H   HCR6  0   0.280  28.2529   1.7727  54.8766
 BIN  H151  H   HCH3  0   0.304  27.1044  -2.3901  50.1290
 BIN  H152  H   HCH3  0   0.315  26.8231  -2.4861  51.8655
 BIN  H153  H   HCH3  0   0.303  25.8646  -1.4086  50.8598
 BIN  H161  H   HCH3  0   0.273  30.2043  -3.9717  50.4330
 BIN  H162  H   HCH3  0   0.258  30.5409  -2.9371  51.8179
 BIN  H163  H   HCH3  0   0.257  28.8981  -3.5125  51.5140
 BIN  H171  H   HCH2  0   0.324  30.4806  -1.7083  49.5926
 BIN  H172  H   HCH2  0   0.320  28.8411  -2.1774  49.3654
 BIN  H19   H   HCH1  0   0.256  23.4454   0.5469  52.6062
 BIN  H201  H   HCH3  0   0.246  24.4045   2.0463  54.3844
 BIN  H202  H   HCH3  0   0.240  24.2950   3.4156  53.2688
 BIN  H203  H   HCH3  0   0.250  22.8324   2.6109  53.8377
 BIN  H211  H   HCH3  0   0.247  23.1846   1.4003  50.2892
 BIN  H212  H   HCH3  0   0.242  22.1247   2.2745  51.3905
 BIN  H213  H   HCH3  0   0.234  23.6164   3.0332  50.8296
 BIN  HOB3  H   HOH1  0   0.507  30.8600   4.2831  52.1686
 BIN  HOB4  H   HOH1  0   0.511  33.0096  -0.8226  51.0560
 BIN  C17   C   CH2   0  -0.396  29.5783  -1.9698  50.1346

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
 BIN  C1   C2    aromatic  1.390  0.020  1.390
 BIN  C1   C6    aromatic  1.389  0.020  1.389
 BIN  C1   C7    single    1.482  0.020  1.482
 BIN  C2   C3    aromatic  1.383  0.020  1.383
 BIN  C2   CL2   single    1.725  0.020  1.725
 BIN  C3   C4    aromatic  1.388  0.020  1.388
 BIN  C3   H3    single    0.930  0.020  1.080
 BIN  C4   C5    aromatic  1.386  0.020  1.386
 BIN  C4   H4    single    0.930  0.020  1.080
 BIN  C5   C6    aromatic  1.388  0.020  1.388
 BIN  C5   H5    single    0.930  0.020  1.080
 BIN  C6   H6    single    0.930  0.020  1.080
 BIN  C7   C8    aromatic  1.385  0.020  1.385
 BIN  C7   C12   aromatic  1.396  0.020  1.396
 BIN  C8   C11   aromatic  1.388  0.020  1.388
 BIN  C8   C18   single    1.505  0.020  1.505
 BIN  C9   C12   aromatic  1.378  0.020  1.378
 BIN  C9   C14   single    1.516  0.020  1.516
 BIN  C9   N10   aromatic  1.347  0.020  1.347
 BIN  C11  C15   single    1.491  0.020  1.491
 BIN  C11  N10   aromatic  1.353  0.020  1.353
 BIN  C12  C13   single    1.499  0.020  1.499
 BIN  C13  O3A   double    1.203  0.020  1.203
 BIN  C13  O3B   single    1.308  0.020  1.308
 BIN  C14  O4A   double    1.197  0.020  1.197
 BIN  C14  O4B   single    1.309  0.020  1.309
 BIN  C15  H151  single    0.970  0.020  1.090
 BIN  C15  H152  single    0.970  0.020  1.090
 BIN  C15  H153  single    0.970  0.020  1.090
 BIN  C16  C17   single    1.514  0.020  1.514
 BIN  C16  H161  single    0.970  0.020  1.090
 BIN  C16  H162  single    0.970  0.020  1.090
 BIN  C16  H163  single    0.970  0.020  1.090
 BIN  C17  N10   single    1.490  0.020  1.490
 BIN  C17  H171  single    0.970  0.020  1.090
 BIN  C17  H172  single    0.970  0.020  1.090
 BIN  C18  O8A   double    1.202  0.020  1.202
 BIN  C18  O8    single    1.306  0.020  1.306
 BIN  C19  C20   single    1.515  0.020  1.515
 BIN  C19  C21   single    1.513  0.020  1.513
 BIN  C19  O8    single    1.458  0.020  1.458
 BIN  C19  H19   single    0.970  0.020  1.090
 BIN  C20  H201  single    0.970  0.020  1.090
 BIN  C20  H202  single    0.970  0.020  1.090
 BIN  C20  H203  single    0.970  0.020  1.090
 BIN  C21  H211  single    0.970  0.020  1.090
 BIN  C21  H212  single    0.970  0.020  1.090
 BIN  C21  H213  single    0.970  0.020  1.090
 BIN  O3B  HOB3  single    0.850  0.020  0.980
 BIN  O4B  HOB4  single    0.850  0.020  0.980

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
 BIN  C7    C1   C6    119.25  3.000
 BIN  C7    C1   C2    121.44  3.000
 BIN  C6    C1   C2    119.30  3.000
 BIN  CL2   C2   C3    119.78  3.000
 BIN  CL2   C2   C1    119.35  3.000
 BIN  C3    C2   C1    120.88  3.000
 BIN  H3    C3   C4    120.49  3.000
 BIN  H3    C3   C2    120.18  3.000
 BIN  C4    C3   C2    119.33  3.000
 BIN  H4    C4   C5    120.31  3.000
 BIN  H4    C4   C3    119.24  3.000
 BIN  C5    C4   C3    120.45  3.000
 BIN  H5    C5   C6    119.76  3.000
 BIN  H5    C5   C4    120.44  3.000
 BIN  C6    C5   C4    119.80  3.000
 BIN  H6    C6   C5    120.24  3.000
 BIN  H6    C6   C1    119.53  3.000
 BIN  C5    C6   C1    120.23  3.000
 BIN  C12   C7   C8    117.92  3.000
 BIN  C12   C7   C1    122.74  3.000
 BIN  C8    C7   C1    119.21  3.000
 BIN  C18   C8   C11   119.15  3.000
 BIN  C18   C8   C7    119.13  3.000
 BIN  C11   C8   C7    121.64  3.000
 BIN  N10   C9   C14   118.66  3.000
 BIN  N10   C9   C12   121.46  3.000
 BIN  C14   C9   C12   119.75  3.000
 BIN  N10   C11  C15   121.29  3.000
 BIN  N10   C11  C8    118.53  3.000
 BIN  C15   C11  C8    120.17  3.000
 BIN  C13   C12  C9    117.62  3.000
 BIN  C13   C12  C7    123.17  3.000
 BIN  C9    C12  C7    119.09  3.000
 BIN  O3B   C13  O3A   125.95  3.000
 BIN  O3B   C13  C12   112.63  3.000
 BIN  O3A   C13  C12   121.41  3.000
 BIN  O4B   C14  O4A   127.90  3.000
 BIN  O4B   C14  C9    111.46  3.000
 BIN  O4A   C14  C9    120.64  3.000
 BIN  H153  C15  H152  107.66  3.000
 BIN  H153  C15  H151  106.69  3.000
 BIN  H152  C15  H151  108.20  3.000
 BIN  H153  C15  C11   110.09  3.000
 BIN  H152  C15  C11   109.93  3.000
 BIN  H151  C15  C11   114.03  3.000
 BIN  H163  C16  H162  108.64  3.000
 BIN  H163  C16  H161  107.62  3.000
 BIN  H162  C16  H161  108.04  3.000
 BIN  H163  C16  C17   112.70  3.000
 BIN  H162  C16  C17   111.77  3.000
 BIN  H161  C16  C17   107.88  3.000
 BIN  O8    C18  O8A   127.47  3.000
 BIN  O8    C18  C8    111.00  3.000
 BIN  O8A   C18  C8    121.53  3.000
 BIN  H19   C19  O8    108.18  3.000
 BIN  H19   C19  C21   110.08  3.000
 BIN  O8    C19  C21   105.42  3.000
 BIN  H19   C19  C20   110.40  3.000
 BIN  O8    C19  C20   109.96  3.000
 BIN  C21   C19  C20   112.61  3.000
 BIN  H203  C20  H202  108.01  3.000
 BIN  H203  C20  H201  107.53  3.000
 BIN  H202  C20  H201  108.63  3.000
 BIN  H203  C20  C19   108.98  3.000
 BIN  H202  C20  C19   110.94  3.000
 BIN  H201  C20  C19   112.59  3.000
 BIN  H213  C21  H212  108.12  3.000
 BIN  H213  C21  H211  108.83  3.000
 BIN  H212  C21  H211  107.81  3.000
 BIN  H213  C21  C19   110.98  3.000
 BIN  H212  C21  C19   109.31  3.000
 BIN  H211  C21  C19   111.68  3.000
 BIN  C17   N10  C11   119.31  3.000
 BIN  C17   N10  C9    119.47  3.000
 BIN  C11   N10  C9    121.21  3.000
 BIN  HOB3  O3B  C13   110.95  3.000
 BIN  HOB4  O4B  C14   111.31  3.000
 BIN  C19   O8   C18   119.79  3.000
 BIN  H172  C17  H171  104.90  3.000
 BIN  H172  C17  N10   107.22  3.000
 BIN  H171  C17  N10   108.47  3.000
 BIN  H172  C17  C16   112.29  3.000
 BIN  H171  C17  C16   111.13  3.000
 BIN  N10   C17  C16   112.46  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
 BIN  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 BIN  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 BIN  CONST_03  C11   C8   C7   C1    180.00   0.0  0
 BIN  CONST_04  C9    C12  C7   C1    180.00   0.0  0
 BIN  CONST_05  C5    C6   C1   C2      0.00   0.0  0
 BIN  CONST_08  C5    C4   C3   C2      0.00   0.0  0
 BIN  CONST_09  C6    C1   C2   C3      0.00   0.0  0
 BIN  CONST_10  C7    C1   C2   C3    180.00   0.0  0
 BIN  CONST_11  C6    C5   C4   C3      0.00   0.0  0
 BIN  CONST_12  C7    C1   C6   C5    180.00   0.0  0
 BIN  CONST_15  N10   C11  C8   C7      0.00   0.0  0
 BIN  CONST_16  N10   C9   C12  C7      0.00   0.0  0
 BIN  CONST_17  C9    C12  C7   C8      0.00   0.0  0
 BIN  CONST_18  C9    N10  C11  C8      0.00   0.0  0
 BIN  CONST_19  C12   C7   C8   C11     0.00   0.0  0
 BIN  CONST_20  C12   C9   N10  C11     0.00   0.0  0
 BIN  CONST_21  C18   C8   C7   C1      0.00   0.0  0
 BIN  CONST_22  C13   C12  C7   C1      0.00   0.0  0
 BIN  CONST_23  CL2   C2   C3   C4    180.00   0.0  0
 BIN  CONST_24  CL2   C2   C1   C6    180.00   0.0  0
 BIN  CONST_25  CL2   C2   C1   C7      0.00   0.0  0
 BIN  CONST_26  C15   C11  C8   C7    180.00   0.0  0
 BIN  CONST_27  C14   C9   C12  C7    180.00   0.0  0
 BIN  CONST_28  C13   C12  C7   C8    180.00   0.0  0
 BIN  CONST_29  C17   N10  C11  C8    180.00   0.0  0
 BIN  CONST_30  C15   C11  N10  C9    180.00   0.0  0
 BIN  CONST_31  C14   C9   N10  C11   180.00   0.0  0
 BIN  CONST_32  C18   C8   C7   C12   180.00   0.0  0
 BIN  CONST_33  C17   N10  C9   C12   180.00   0.0  0
 BIN  CONST_34  N10   C9   C12  C13   180.00   0.0  0
 BIN  CONST_35  N10   C11  C8   C18   180.00   0.0  0
 BIN  CONST_36  H3    C3   C2   C1    180.00   0.0  0
 BIN  CONST_37  H5    C5   C6   C1    180.00   0.0  0
 BIN  CONST_38  H6    C6   C1   C2    180.00   0.0  0
 BIN  CONST_39  H4    C4   C3   C2    180.00   0.0  0
 BIN  CONST_40  HOB4  O4B  C14  C9    180.00   0.0  0
 BIN  CONST_41  HOB3  O3B  C13  C12   180.00   0.0  0
 BIN  Var_01    O8A   C18  C8   C7   -105.38  30.0  2
 BIN  Var_02    O3A   C13  C12  C7    139.74  30.0  2
 BIN  Var_03    C16   C17  N10  C9    102.22  30.0  2
 BIN  Var_04    O4A   C14  C9   C12   -73.64  30.0  2
 BIN  Var_05    H151  C15  C11  C8    153.40  30.0  2
 BIN  Var_06    H161  C16  C17  N10  -176.76  30.0  3
 BIN  Var_07    C20   C19  O8   C18    78.06  30.0  1
 BIN  Var_08    H211  C21  C19  C20  -179.79  30.0  3
 BIN  Var_09    H201  C20  C19  C21  -178.30  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
 BIN  plan-1  C1    0.020
 BIN  plan-1  C2    0.020
 BIN  plan-1  C3    0.020
 BIN  plan-1  C4    0.020
 BIN  plan-1  C5    0.020
 BIN  plan-1  C6    0.020
 BIN  plan-1  C7    0.020
 BIN  plan-1  CL2   0.020
 BIN  plan-1  H3    0.020
 BIN  plan-1  H4    0.020
 BIN  plan-1  H5    0.020
 BIN  plan-1  H6    0.020
 BIN  plan-2  C1    0.020
 BIN  plan-2  C7    0.020
 BIN  plan-2  C8    0.020
 BIN  plan-2  C9    0.020
 BIN  plan-2  C11   0.020
 BIN  plan-2  C12   0.020
 BIN  plan-2  C13   0.020
 BIN  plan-2  C14   0.020
 BIN  plan-2  C15   0.020
 BIN  plan-2  C18   0.020
 BIN  plan-2  N10   0.020
 BIN  plan-2  C17   0.020
 BIN  plan-3  C12   0.020
 BIN  plan-3  C13   0.020
 BIN  plan-3  O3A   0.020
 BIN  plan-3  O3B   0.020
 BIN  plan-3  HOB3  0.020
 BIN  plan-4  C9    0.020
 BIN  plan-4  C14   0.020
 BIN  plan-4  O4A   0.020
 BIN  plan-4  O4B   0.020
 BIN  plan-4  HOB4  0.020
 BIN  plan-5  C8    0.020
 BIN  plan-5  C18   0.020
 BIN  plan-5  O8A   0.020
 BIN  plan-5  O8    0.020

