# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 07:11:19 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  47  28  .  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_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   0.064  27.7902   2.5831  53.0265
 BIN  C2    C   CR6    0  -0.040  27.3102   3.7108  52.3719
 BIN  C3    C   CR16   0  -0.208  26.8814   4.8204  53.0790
 BIN  C4    C   CR16   0  -0.266  26.9257   4.8042  54.4665
 BIN  C5    C   CR16   0  -0.230  27.3926   3.6848  55.1374
 BIN  C6    C   CR16   0  -0.287  27.8239   2.5805  54.4159
 BIN  C7    C   CR6    0   0.311  28.2743   1.3931  52.2876
 BIN  C8    C   CR6    0  -0.159  27.4025   0.3477  51.9881
 BIN  C9    C   CR6    0   0.288  30.0379   0.1126  51.3205
 BIN  C11   C   CR6    0   0.401  27.8369  -0.7616  51.2888
 BIN  C12   C   CR6    0  -0.192  29.6135   1.2668  51.9593
 BIN  C13   C   C      0   0.367  30.6195   2.3607  52.3152
 BIN  C14   C   C      0   0.380  31.5284  -0.0757  51.0116
 BIN  C15   C   CH3    0  -0.756  26.8817  -1.8498  50.9120
 BIN  C16   C   CH3    0  -0.666  29.8336  -3.2383  51.0502
 BIN  C18   C   C      0   0.460  25.9953   0.3962  52.5015
 BIN  C19   C   CH1    0   0.005  23.9297   1.5825  52.3169
 BIN  C20   C   CH3    0  -0.678  23.9423   2.4623  53.5513
 BIN  C21   C   CH3    0  -0.670  23.2513   2.2444  51.1375
 BIN  N10   N   NR6    1  -0.525  29.1516  -0.8392  50.9583
 BIN  O3A   O   O      0  -0.577  31.5253   2.0093  53.0858
 BIN  O3B   O   OC    -1  -0.559  30.4011   3.4677  51.8095
 BIN  O4A   O   O      0  -0.562  31.9532   0.6649  50.1184
 BIN  O4B   O   OC    -1  -0.551  32.1054  -0.9317  51.6898
 BIN  O8A   O   O      0  -0.417  25.6083  -0.3306  53.3801
 BIN  O8    O   O2     0  -0.433  25.2912   1.3147  51.8869
 BIN  CL2   CL  CL     0  -0.126  27.2285   3.7271  50.6481
 BIN  H3    H   HCR6   0   0.281  26.5108   5.6901  52.5538
 BIN  H4    H   HCR6   0   0.269  26.5886   5.6720  55.0176
 BIN  H5    H   HCR6   0   0.265  27.4251   3.6682  56.2183
 BIN  H6    H   HCR6   0   0.267  28.1974   1.7058  54.9333
 BIN  H151  H   HCH3   0   0.288  27.1396  -2.3499  49.9841
 BIN  H152  H   HCH3   0   0.294  26.8271  -2.6048  51.6968
 BIN  H153  H   HCH3   0   0.287  25.8817  -1.4464  50.7754
 BIN  H161  H   HCH3   0   0.256  30.2557  -4.0302  50.4326
 BIN  H162  H   HCH3   0   0.253  30.5277  -3.0348  51.8618
 BIN  H163  H   HCH3   0   0.244  28.8990  -3.6081  51.4673
 BIN  H171  H   HCH2   0   0.305  30.5735  -1.7231  49.7122
 BIN  H172  H   HCH2   0   0.293  28.9443  -2.1856  49.3757
 BIN  H19   H   HCH1   0   0.249  23.4440   0.6295  52.5388
 BIN  H201  H   HCH3   0   0.244  24.4757   2.0038  54.3828
 BIN  H202  H   HCH3   0   0.238  24.4012   3.4275  53.3371
 BIN  H203  H   HCH3   0   0.244  22.9162   2.6404  53.8739
 BIN  H211  H   HCH3   0   0.244  23.2354   1.5909  50.2654
 BIN  H212  H   HCH3   0   0.239  22.2198   2.4795  51.3975
 BIN  H213  H   HCH3   0   0.233  23.7538   3.1746  50.8685
 BIN  C17   C   CH2    0  -0.370  29.6422  -2.0075  50.1880

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  1.390  0.020  1.390
 BIN  C1   C7    single    1.482  0.020  1.482
 BIN  C2   C3    aromatic  1.384  0.020  1.384
 BIN  C2   CL2   single    1.726  0.020  1.726
 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  1.394  0.020  1.394
 BIN  C7   C12   aromatic  1.385  0.020  1.385
 BIN  C8   C11   aromatic  1.381  0.020  1.381
 BIN  C8   C18   single    1.499  0.020  1.499
 BIN  C9   C12   aromatic  1.386  0.020  1.386
 BIN  C9   C14   single    1.534  0.020  1.534
 BIN  C9   N10   aromatic  1.350  0.020  1.350
 BIN  C11  C15   single    1.496  0.020  1.496
 BIN  C11  N10   aromatic  1.358  0.020  1.358
 BIN  C12  C13   single    1.528  0.020  1.528
 BIN  C13  O3A   deloc     1.240  0.020  1.240
 BIN  C13  O3B   deloc     1.237  0.020  1.237
 BIN  C14  O4A   deloc     1.236  0.020  1.236
 BIN  C14  O4B   deloc     1.235  0.020  1.235
 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    1.515  0.020  1.515
 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    1.483  0.020  1.483
 BIN  C17  H171  single    0.970  0.020  1.090
 BIN  C17  H172  single    0.970  0.020  1.090
 BIN  C18  O8A   double    1.204  0.020  1.204
 BIN  C18  O8    single    1.310  0.020  1.310
 BIN  C19  C20   single    1.516  0.020  1.516
 BIN  C19  C21   single    1.513  0.020  1.513
 BIN  C19  O8    single    1.453  0.020  1.453
 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

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    119.27  3.000
 BIN  C7    C1   C2    121.98  3.000
 BIN  C6    C1   C2    118.75  3.000
 BIN  CL2   C2   C3    119.22  3.000
 BIN  CL2   C2   C1    119.64  3.000
 BIN  C3    C2   C1    121.13  3.000
 BIN  H3    C3   C4    120.37  3.000
 BIN  H3    C3   C2    120.19  3.000
 BIN  C4    C3   C2    119.44  3.000
 BIN  H4    C4   C5    120.41  3.000
 BIN  H4    C4   C3    119.33  3.000
 BIN  C5    C4   C3    120.26  3.000
 BIN  H5    C5   C6    119.87  3.000
 BIN  H5    C5   C4    120.42  3.000
 BIN  C6    C5   C4    119.72  3.000
 BIN  H6    C6   C5    120.11  3.000
 BIN  H6    C6   C1    119.18  3.000
 BIN  C5    C6   C1    120.71  3.000
 BIN  C12   C7   C8    119.05  3.000
 BIN  C12   C7   C1    120.49  3.000
 BIN  C8    C7   C1    120.33  3.000
 BIN  C18   C8   C11   119.65  3.000
 BIN  C18   C8   C7    119.30  3.000
 BIN  C11   C8   C7    120.95  3.000
 BIN  N10   C9   C14   119.83  3.000
 BIN  N10   C9   C12   120.65  3.000
 BIN  C14   C9   C12   119.52  3.000
 BIN  N10   C11  C15   121.02  3.000
 BIN  N10   C11  C8    118.27  3.000
 BIN  C15   C11  C8    120.71  3.000
 BIN  C13   C12  C9    120.13  3.000
 BIN  C13   C12  C7    121.08  3.000
 BIN  C9    C12  C7    118.78  3.000
 BIN  O3B   C13  O3A   129.56  3.000
 BIN  O3B   C13  C12   115.42  3.000
 BIN  O3A   C13  C12   115.01  3.000
 BIN  O4B   C14  O4A   130.67  3.000
 BIN  O4B   C14  C9    115.37  3.000
 BIN  O4A   C14  C9    113.96  3.000
 BIN  H153  C15  H152  107.54  3.000
 BIN  H153  C15  H151  106.39  3.000
 BIN  H152  C15  H151  107.95  3.000
 BIN  H153  C15  C11   110.44  3.000
 BIN  H152  C15  C11   110.75  3.000
 BIN  H151  C15  C11   113.50  3.000
 BIN  H163  C16  H162  109.01  3.000
 BIN  H163  C16  H161  107.64  3.000
 BIN  H162  C16  H161  108.18  3.000
 BIN  H163  C16  C17   112.69  3.000
 BIN  H162  C16  C17   110.70  3.000
 BIN  H161  C16  C17   108.47  3.000
 BIN  O8    C18  O8A   126.34  3.000
 BIN  O8    C18  C8    111.50  3.000
 BIN  O8A   C18  C8    122.15  3.000
 BIN  H19   C19  O8    108.43  3.000
 BIN  H19   C19  C21   109.91  3.000
 BIN  O8    C19  C21   105.67  3.000
 BIN  H19   C19  C20   110.16  3.000
 BIN  O8    C19  C20   109.89  3.000
 BIN  C21   C19  C20   112.61  3.000
 BIN  H203  C20  H202  108.05  3.000
 BIN  H203  C20  H201  107.69  3.000
 BIN  H202  C20  H201  108.46  3.000
 BIN  H203  C20  C19   109.15  3.000
 BIN  H202  C20  C19   110.94  3.000
 BIN  H201  C20  C19   112.42  3.000
 BIN  H213  C21  H212  108.12  3.000
 BIN  H213  C21  H211  108.70  3.000
 BIN  H212  C21  H211  107.85  3.000
 BIN  H213  C21  C19   111.02  3.000
 BIN  H212  C21  C19   109.45  3.000
 BIN  H211  C21  C19   111.59  3.000
 BIN  C17   N10  C11   119.46  3.000
 BIN  C17   N10  C9    118.53  3.000
 BIN  C11   N10  C9    122.01  3.000
 BIN  C19   O8   C18   119.60  3.000
 BIN  H172  C17  H171  105.48  3.000
 BIN  H172  C17  N10   107.77  3.000
 BIN  H171  C17  N10   107.79  3.000
 BIN  H172  C17  C16   111.95  3.000
 BIN  H171  C17  C16   110.76  3.000
 BIN  N10   C17  C16   112.72  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  Var_01    O8A   C18  C8   C7   -108.68  30.0  2
 BIN  Var_02    O3A   C13  C12  C7    118.19  30.0  2
 BIN  Var_03    C16   C17  N10  C9    100.86  30.0  2
 BIN  Var_04    O4A   C14  C9   C12   -70.86  30.0  2
 BIN  Var_05    H151  C15  C11  C8    148.74  30.0  2
 BIN  Var_06    H161  C16  C17  N10  -176.28  30.0  3
 BIN  Var_07    C20   C19  O8   C18    79.60  30.0  1
 BIN  Var_08    H211  C21  C19  C20  -178.95  30.0  3
 BIN  Var_09    H201  C20  C19  C21  -177.07  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-4  C9   0.020
 BIN  plan-4  C14  0.020
 BIN  plan-4  O4A  0.020
 BIN  plan-4  O4B  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

