# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:55:00 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 2,2'-[(1,4-dioxobutane-1,4-diyl)bis(oxy)]bis(N,N,N-trimethylethanaminium)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCOC(=O)CCC(=O)OCC[N+](C)(C)C
#
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
 SCK  SCK  2,2'-[(1,4-dioxobutane-1,4-diyl)bis(oxy)]bis(N,N,N-trimethylethanaminium)  ligand  50  20  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SCK
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
 SCK  O13   O  O     0  -0.439  -1.4910  -2.0137  -0.0074
 SCK  C12   C  C     0   0.627  -1.7289  -0.8454   0.1531
 SCK  O14   O  O2    0  -0.460  -2.9635  -0.3684   0.3096
 SCK  C15   C  CH2   0  -0.215  -4.0439  -1.2941   0.2416
 SCK  C16   C  CH2   0  -0.356  -5.3354  -0.5921   0.5772
 SCK  N17   N  NT    1  -0.385  -5.8824   0.3897  -0.4260
 SCK  C20   C  CH3   0  -0.555  -6.0536  -0.2413  -1.7630
 SCK  C19   C  CH3   0  -0.539  -5.0248   1.6035  -0.5605
 SCK  C18   C  CH3   0  -0.547  -7.2215   0.8156   0.0780
 SCK  C11   C  CH2   0  -0.588  -0.7124   0.2606   0.1881
 SCK  C6    C  CH2   0  -0.588   0.7089  -0.2694   0.1985
 SCK  C5    C  C     0   0.628   1.7258   0.8359   0.1567
 SCK  O7    O  O     0  -0.439   1.4885   2.0038  -0.0081
 SCK  O4    O  O2    0  -0.460   2.9602   0.3586   0.3142
 SCK  C3    C  CH2   0  -0.216   4.0413   1.2834   0.2440
 SCK  C2    C  CH2   0  -0.356   5.3316   0.5809   0.5826
 SCK  N1    N  NT    1  -0.386   5.8844  -0.3958  -0.4220
 SCK  C8    C  CH3   0  -0.555   6.0802   0.2461  -1.7506
 SCK  C9    C  CH3   0  -0.547   7.2122  -0.8381   0.0967
 SCK  C10   C  CH3   0  -0.539   5.0186  -1.6010  -0.5804
 SCK  H151  H  HCH2  0   0.288  -3.9254  -2.0763   0.9941
 SCK  H152  H  HCH2  0   0.270  -4.0754  -1.7856  -0.7326
 SCK  H161  H  HCH2  0   0.319  -5.2523  -0.0602   1.5246
 SCK  H162  H  HCH2  0   0.319  -6.0996  -1.3607   0.6921
 SCK  H201  H  HCH3  0   0.297  -5.0845  -0.4795  -2.1905
 SCK  H202  H  HCH3  0   0.299  -6.6481  -1.1457  -1.6629
 SCK  H203  H  HCH3  0   0.302  -6.5649   0.4615  -2.4155
 SCK  H191  H  HCH3  0   0.293  -5.5539   2.3272  -1.1743
 SCK  H192  H  HCH3  0   0.296  -4.8401   2.0242   0.4239
 SCK  H193  H  HCH3  0   0.294  -4.0874   1.3456  -1.0384
 SCK  H181  H  HCH3  0   0.298  -7.8772  -0.0490   0.1273
 SCK  H182  H  HCH3  0   0.298  -7.1078   1.2493   1.0679
 SCK  H183  H  HCH3  0   0.297  -7.6372   1.5540  -0.6015
 SCK  H111  H  HCH2  0   0.295  -0.8836   0.8985  -0.6836
 SCK  H112  H  HCH2  0   0.293  -0.9034   0.8908   1.0594
 SCK  H61   H  HCH2  0   0.293   0.8919  -0.8854   1.0818
 SCK  H62   H  HCH2  0   0.295   0.8881  -0.9215  -0.6610
 SCK  H31   H  HCH2  0   0.270   4.0736   1.7725  -0.7313
 SCK  H32   H  HCH2  0   0.288   3.9232   2.0676   0.9946
 SCK  H21   H  HCH2  0   0.319   6.0952   1.3488   0.7057
 SCK  H22   H  HCH2  0   0.319   5.2426   0.0443   1.5270
 SCK  H81   H  HCH3  0   0.299   6.6890   1.1390  -1.6349
 SCK  H82   H  HCH3  0   0.302   6.5857  -0.4591  -2.4050
 SCK  H83   H  HCH3  0   0.297   5.1200   0.5060  -2.1855
 SCK  H91   H  HCH3  0   0.298   7.0791  -1.2909   1.0757
 SCK  H92   H  HCH3  0   0.297   7.6372  -1.5643  -0.5900
 SCK  H93   H  HCH3  0   0.298   7.8714   0.0217   0.1761
 SCK  H101  H  HCH3  0   0.294   4.0915  -1.3312  -1.0720
 SCK  H102  H  HCH3  0   0.293   5.5515  -2.3244  -1.1911
 SCK  H103  H  HCH3  0   0.296   4.8140  -2.0276   0.3974

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
 SCK  O13  C12   double  1.203  0.020  1.203
 SCK  C12  O14   single  1.333  0.020  1.333
 SCK  C12  C11   single  1.503  0.020  1.503
 SCK  O14  C15   single  1.424  0.020  1.424
 SCK  C15  C16   single  1.508  0.020  1.508
 SCK  C15  H151  single  0.970  0.020  1.090
 SCK  C15  H152  single  0.970  0.020  1.090
 SCK  C16  N17   single  1.506  0.020  1.506
 SCK  C16  H161  single  0.970  0.020  1.090
 SCK  C16  H162  single  0.970  0.020  1.090
 SCK  N17  C20   single  1.488  0.020  1.488
 SCK  N17  C19   single  1.492  0.020  1.492
 SCK  N17  C18   single  1.493  0.020  1.493
 SCK  C20  H201  single  0.970  0.020  1.090
 SCK  C20  H202  single  0.970  0.020  1.090
 SCK  C20  H203  single  0.970  0.020  1.090
 SCK  C19  H191  single  0.970  0.020  1.090
 SCK  C19  H192  single  0.970  0.020  1.090
 SCK  C19  H193  single  0.970  0.020  1.090
 SCK  C18  H181  single  0.970  0.020  1.090
 SCK  C18  H182  single  0.970  0.020  1.090
 SCK  C18  H183  single  0.970  0.020  1.090
 SCK  C11  C6    single  1.517  0.020  1.517
 SCK  C11  H111  single  0.970  0.020  1.090
 SCK  C11  H112  single  0.970  0.020  1.090
 SCK  C6   C5    single  1.503  0.020  1.503
 SCK  C6   H61   single  0.970  0.020  1.090
 SCK  C6   H62   single  0.970  0.020  1.090
 SCK  C5   O7    double  1.203  0.020  1.203
 SCK  C5   O4    single  1.333  0.020  1.333
 SCK  O4   C3    single  1.424  0.020  1.424
 SCK  C3   C2    single  1.508  0.020  1.508
 SCK  C3   H31   single  0.970  0.020  1.090
 SCK  C3   H32   single  0.970  0.020  1.090
 SCK  C2   N1    single  1.506  0.020  1.506
 SCK  C2   H21   single  0.970  0.020  1.090
 SCK  C2   H22   single  0.970  0.020  1.090
 SCK  N1   C8    single  1.489  0.020  1.489
 SCK  N1   C9    single  1.493  0.020  1.493
 SCK  N1   C10   single  1.492  0.020  1.492
 SCK  C8   H81   single  0.970  0.020  1.090
 SCK  C8   H82   single  0.970  0.020  1.090
 SCK  C8   H83   single  0.970  0.020  1.090
 SCK  C9   H91   single  0.970  0.020  1.090
 SCK  C9   H92   single  0.970  0.020  1.090
 SCK  C9   H93   single  0.970  0.020  1.090
 SCK  C10  H101  single  0.970  0.020  1.090
 SCK  C10  H102  single  0.970  0.020  1.090
 SCK  C10  H103  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
 SCK  C11   C12  O14   111.13  3.000
 SCK  C11   C12  O13   125.75  3.000
 SCK  O14   C12  O13   123.12  3.000
 SCK  C15   O14  C12   117.67  3.000
 SCK  H152  C15  H151  107.19  3.000
 SCK  H152  C15  C16   112.55  3.000
 SCK  H151  C15  C16   105.84  3.000
 SCK  H152  C15  O14   110.93  3.000
 SCK  H151  C15  O14   110.51  3.000
 SCK  C16   C15  O14   109.67  3.000
 SCK  H162  C16  H161  107.82  3.000
 SCK  H162  C16  N17   105.97  3.000
 SCK  H161  C16  N17   106.77  3.000
 SCK  H162  C16  C15   107.20  3.000
 SCK  H161  C16  C15   110.82  3.000
 SCK  N17   C16  C15   117.79  3.000
 SCK  C18   N17  C19   108.29  3.000
 SCK  C18   N17  C20   108.73  3.000
 SCK  C19   N17  C20   109.26  3.000
 SCK  C18   N17  C16   106.67  3.000
 SCK  C19   N17  C16   112.43  3.000
 SCK  C20   N17  C16   111.33  3.000
 SCK  H203  C20  H202  109.64  3.000
 SCK  H203  C20  H201  109.00  3.000
 SCK  H202  C20  H201  109.99  3.000
 SCK  H203  C20  N17   108.62  3.000
 SCK  H202  C20  N17   109.44  3.000
 SCK  H201  C20  N17   110.13  3.000
 SCK  H193  C19  H192  110.17  3.000
 SCK  H193  C19  H191  109.32  3.000
 SCK  H192  C19  H191  109.68  3.000
 SCK  H193  C19  N17   110.09  3.000
 SCK  H192  C19  N17   109.32  3.000
 SCK  H191  C19  N17   108.23  3.000
 SCK  H183  C18  H182  109.80  3.000
 SCK  H183  C18  H181  109.79  3.000
 SCK  H182  C18  H181  109.84  3.000
 SCK  H183  C18  N17   109.03  3.000
 SCK  H182  C18  N17   109.12  3.000
 SCK  H181  C18  N17   109.25  3.000
 SCK  H112  C11  H111  105.78  3.000
 SCK  H112  C11  C6    111.10  3.000
 SCK  H111  C11  C6    110.85  3.000
 SCK  H112  C11  C12   108.97  3.000
 SCK  H111  C11  C12   107.75  3.000
 SCK  C6    C11  C12   112.14  3.000
 SCK  H62   C6   H61   105.77  3.000
 SCK  H62   C6   C5    107.81  3.000
 SCK  H61   C6   C5    108.90  3.000
 SCK  H62   C6   C11   110.89  3.000
 SCK  H61   C6   C11   111.07  3.000
 SCK  C5    C6   C11   112.15  3.000
 SCK  O4    C5   O7    123.13  3.000
 SCK  O4    C5   C6    111.11  3.000
 SCK  O7    C5   C6    125.76  3.000
 SCK  C3    O4   C5    117.68  3.000
 SCK  H32   C3   H31   107.19  3.000
 SCK  H32   C3   C2    105.83  3.000
 SCK  H31   C3   C2    112.59  3.000
 SCK  H32   C3   O4    110.51  3.000
 SCK  H31   C3   O4    110.94  3.000
 SCK  C2    C3   O4    109.63  3.000
 SCK  H22   C2   H21   107.83  3.000
 SCK  H22   C2   N1    106.78  3.000
 SCK  H21   C2   N1    105.97  3.000
 SCK  H22   C2   C3    110.75  3.000
 SCK  H21   C2   C3    107.25  3.000
 SCK  N1    C2   C3    117.80  3.000
 SCK  C10   N1   C9    108.28  3.000
 SCK  C10   N1   C8    109.26  3.000
 SCK  C9    N1   C8    108.72  3.000
 SCK  C10   N1   C2    112.43  3.000
 SCK  C9    N1   C2    106.67  3.000
 SCK  C8    N1   C2    111.34  3.000
 SCK  H83   C8   H82   109.00  3.000
 SCK  H83   C8   H81   109.97  3.000
 SCK  H82   C8   H81   109.67  3.000
 SCK  H83   C8   N1    110.15  3.000
 SCK  H82   C8   N1    108.58  3.000
 SCK  H81   C8   N1    109.45  3.000
 SCK  H93   C9   H92   109.76  3.000
 SCK  H93   C9   H91   109.77  3.000
 SCK  H92   C9   H91   109.81  3.000
 SCK  H93   C9   N1    109.31  3.000
 SCK  H92   C9   N1    109.05  3.000
 SCK  H91   C9   N1    109.12  3.000
 SCK  H103  C10  H102  109.68  3.000
 SCK  H103  C10  H101  110.19  3.000
 SCK  H102  C10  H101  109.30  3.000
 SCK  H103  C10  N1    109.32  3.000
 SCK  H102  C10  N1    108.23  3.000
 SCK  H101  C10  N1    110.09  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
 SCK  Var_01  C6    C11  C12  O13    -8.37  30.0  3
 SCK  Var_02  C16   C15  O14  C12   174.38  30.0  3
 SCK  Var_03  C5    C6   C11  C12   176.84  30.0  3
 SCK  Var_04  N17   C16  C15  O14    70.85  30.0  3
 SCK  Var_05  C11   C12  O14  C15   177.39  30.0  1
 SCK  Var_06  C20   N17  C16  C15    55.37  30.0  3
 SCK  Var_07  O7    C5   C6   C11    -7.49  30.0  3
 SCK  Var_08  C2    C3   O4   C5    174.32  30.0  3
 SCK  Var_09  N1    C2   C3   O4     71.36  30.0  3
 SCK  Var_10  C8    N1   C2   C3     56.18  30.0  3
 SCK  Var_11  H201  C20  N17  C16   -67.83  30.0  3
 SCK  Var_12  H191  C19  N17  C16  -171.26  30.0  3
 SCK  Var_13  H181  C18  N17  C16   -62.01  30.0  3
 SCK  Var_14  H81   C8   N1   C2     53.75  30.0  3
 SCK  Var_15  H91   C9   N1   C2     58.75  30.0  3
 SCK  Var_16  H101  C10  N1   C2     69.51  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
 SCK  plan-1  O13  0.020
 SCK  plan-1  C12  0.020
 SCK  plan-1  O14  0.020
 SCK  plan-1  C11  0.020
 SCK  plan-2  C6   0.020
 SCK  plan-2  C5   0.020
 SCK  plan-2  O7   0.020
 SCK  plan-2  O4   0.020

