# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 23:45:00 2022
#   Inital geometry file: a 99 line input string
#   Ligand name: 4-[(2~{S},3~{R})-3-[3,5-bis(oxidanylidene)piperazin-1-ium-1-yl]butan-2-yl]piperazin-4-ium-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([C@@H](C)[NH+]1CC(=O)NC(=O)C1)[NH+]2CC(=O)NC(=O)C2
#
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
 ITH  ITH  "4-[(2S,3R)-3-[3,5-bis(oxidanylidene)piperazin-1-ium-1-yl]butan-2-yl]piperazin-4-ium-2,6-dione"
  ligand  40  20  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ITH
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
 ITH  C1   C  CH3   0  -0.767  -13.3284  -23.7955  -0.7762
 ITH  C2   C  CH1   0  -0.125  -13.8100  -25.1437  -0.2716
 ITH  C3   C  CH1   0  -0.131  -14.9820  -25.0802   0.7443
 ITH  C4   C  CH3   0  -0.724  -15.2982  -26.4149   1.3885
 ITH  N1   N  NT1   1  -0.580  -14.6888  -24.0021   1.7735
 ITH  C5   C  CH2   0  -0.475  -13.4910  -24.2053   2.6388
 ITH  C6   C  C     0   0.555  -13.7233  -25.0677   3.8571
 ITH  O1   O  O     0  -0.374  -12.8026  -25.6223   4.3943
 ITH  N2   N  NH1   0  -0.664  -15.0043  -25.1282   4.3404
 ITH  C7   C  C     0   0.542  -16.0985  -24.4796   3.8283
 ITH  O2   O  O     0  -0.375  -17.1818  -24.5311   4.3458
 ITH  C8   C  CH2   0  -0.456  -15.8756  -23.6293   2.6023
 ITH  N3   N  NT1   1  -0.580  -14.2199  -26.0646  -1.4131
 ITH  C9   C  CH2   0  -0.453  -13.0742  -26.5183  -2.2659
 ITH  C10  C  C     0   0.541  -12.7207  -25.6104  -3.4191
 ITH  O3   O  O     0  -0.375  -11.6451  -25.6947  -3.9480
 ITH  N4   N  NH1   0  -0.664  -13.6862  -24.7361  -3.8482
 ITH  C11  C  C     0   0.552  -14.9630  -24.6330  -3.3596
 ITH  O4   O  O     0  -0.372  -15.7665  -23.8586  -3.8048
 ITH  C12  C  CH2   0  -0.466  -15.3508  -25.6089  -2.2754
 ITH  H1   H  HCH3  0   0.308  -12.8377  -23.2448   0.0264
 ITH  H2   H  HCH3  0   0.312  -12.5454  -23.8966  -1.5226
 ITH  H3   H  HCH3  0   0.291  -14.1303  -23.1708  -1.1710
 ITH  H4   H  HCH1  0   0.357  -12.9757  -25.6807   0.1847
 ITH  H5   H  HCH1  0   0.352  -15.8722  -24.6892   0.2493
 ITH  H7   H  HCH3  0   0.302  -16.1422  -26.3543   2.0712
 ITH  H8   H  HCH3  0   0.300  -15.6293  -27.1272   0.6336
 ITH  H6   H  HCH3  0   0.285  -14.4399  -26.8550   1.8944
 ITH  H19  H  HNT1  0   0.514  -14.5031  -23.1562   1.2297
 ITH  H10  H  HCH2  0   0.360  -12.6729  -24.6284   2.0623
 ITH  H9   H  HCH2  0   0.385  -13.1779  -23.2154   2.9805
 ITH  H11  H  HNH1  0   0.444  -15.1518  -25.6845   5.1780
 ITH  H12  H  HCH2  0   0.381  -15.7151  -22.5995   2.9315
 ITH  H13  H  HCH2  0   0.365  -16.7650  -23.6462   1.9760
 ITH  H20  H  HNT1  0   0.505  -14.5381  -26.9283  -0.9668
 ITH  H14  H  HCH2  0   0.381  -13.3635  -27.4882  -2.6775
 ITH  H15  H  HCH2  0   0.365  -12.2002  -26.6642  -1.6340
 ITH  H16  H  HNH1  0   0.444  -13.4383  -24.1217  -4.6190
 ITH  H18  H  HCH2  0   0.358  -16.1426  -25.1772  -1.6712
 ITH  H17  H  HCH2  0   0.384  -15.7569  -26.5029  -2.7550

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
 ITH  O4   C11  double  1.201  0.020  1.201
 ITH  N4   C11  single  1.371  0.020  1.371
 ITH  N4   C10  single  1.371  0.020  1.371
 ITH  C11  C12  single  1.509  0.020  1.509
 ITH  O3   C10  double  1.202  0.020  1.202
 ITH  C10  C9   single  1.510  0.020  1.510
 ITH  C12  N3   single  1.493  0.020  1.493
 ITH  C9   N3   single  1.499  0.020  1.499
 ITH  N3   C2   single  1.523  0.020  1.523
 ITH  C1   C2   single  1.518  0.020  1.518
 ITH  C2   C3   single  1.552  0.020  1.552
 ITH  C3   C4   single  1.515  0.020  1.515
 ITH  C3   N1   single  1.519  0.020  1.519
 ITH  N1   C5   single  1.492  0.020  1.492
 ITH  N1   C8   single  1.495  0.020  1.495
 ITH  C5   C6   single  1.511  0.020  1.511
 ITH  C8   C7   single  1.509  0.020  1.509
 ITH  C7   O2   double  1.202  0.020  1.202
 ITH  C7   N2   single  1.371  0.020  1.371
 ITH  C6   N2   single  1.370  0.020  1.370
 ITH  C6   O1   double  1.202  0.020  1.202
 ITH  C1   H1   single  0.970  0.020  1.090
 ITH  C1   H2   single  0.970  0.020  1.090
 ITH  C1   H3   single  0.970  0.020  1.090
 ITH  C2   H4   single  0.970  0.020  1.090
 ITH  C3   H5   single  0.970  0.020  1.090
 ITH  C4   H7   single  0.970  0.020  1.090
 ITH  C4   H8   single  0.970  0.020  1.090
 ITH  C4   H6   single  0.970  0.020  1.090
 ITH  N1   H19  single  0.890  0.020  1.040
 ITH  C5   H10  single  0.970  0.020  1.090
 ITH  C5   H9   single  0.970  0.020  1.090
 ITH  N2   H11  single  0.860  0.020  1.020
 ITH  C8   H12  single  0.970  0.020  1.090
 ITH  C8   H13  single  0.970  0.020  1.090
 ITH  N3   H20  single  0.890  0.020  1.040
 ITH  C9   H14  single  0.970  0.020  1.090
 ITH  C9   H15  single  0.970  0.020  1.090
 ITH  N4   H16  single  0.860  0.020  1.020
 ITH  C12  H18  single  0.970  0.020  1.090
 ITH  C12  H17  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
 ITH  H3   C1   H2   109.55  3.000
 ITH  H3   C1   H1   107.95  3.000
 ITH  H2   C1   H1   103.20  3.000
 ITH  H3   C1   C2   113.32  3.000
 ITH  H2   C1   C2   111.98  3.000
 ITH  H1   C1   C2   110.29  3.000
 ITH  H4   C2   N3   102.79  3.000
 ITH  H4   C2   C3   108.87  3.000
 ITH  N3   C2   C3   108.19  3.000
 ITH  H4   C2   C1   109.47  3.000
 ITH  C3   C2   C1   114.88  3.000
 ITH  N3   C2   C1   111.92  3.000
 ITH  H5   C3   N1   102.15  3.000
 ITH  H5   C3   C4   109.77  3.000
 ITH  N1   C3   C4   112.17  3.000
 ITH  H5   C3   C2   109.50  3.000
 ITH  N1   C3   C2   109.07  3.000
 ITH  C4   C3   C2   113.56  3.000
 ITH  H6   C4   H8   107.29  3.000
 ITH  H6   C4   H7   110.04  3.000
 ITH  H8   C4   H7   103.63  3.000
 ITH  H6   C4   C3   112.88  3.000
 ITH  H8   C4   C3   110.17  3.000
 ITH  H7   C4   C3   112.32  3.000
 ITH  H19  N1   C8   103.46  3.000
 ITH  H19  N1   C5   105.99  3.000
 ITH  C8   N1   C5   110.48  3.000
 ITH  H19  N1   C3   105.18  3.000
 ITH  C8   N1   C3   113.55  3.000
 ITH  C5   N1   C3   116.83  3.000
 ITH  H9   C5   H10  107.62  3.000
 ITH  H9   C5   C6   108.00  3.000
 ITH  H10  C5   C6   108.75  3.000
 ITH  H9   C5   N1   106.74  3.000
 ITH  H10  C5   N1   110.48  3.000
 ITH  C6   C5   N1   114.97  3.000
 ITH  N2   C6   O1   122.56  3.000
 ITH  O1   C6   C5   120.41  3.000
 ITH  N2   C6   C5   116.96  3.000
 ITH  H11  N2   C7   116.80  3.000
 ITH  H11  N2   C6   116.77  3.000
 ITH  C7   N2   C6   126.40  3.000
 ITH  C8   C7   O2   120.49  3.000
 ITH  O2   C7   N2   122.56  3.000
 ITH  C8   C7   N2   116.88  3.000
 ITH  H13  C8   H12  107.95  3.000
 ITH  H13  C8   C7   109.77  3.000
 ITH  H12  C8   C7   107.94  3.000
 ITH  H13  C8   N1   109.03  3.000
 ITH  H12  C8   N1   106.58  3.000
 ITH  C7   C8   N1   115.30  3.000
 ITH  H20  N3   C12  105.90  3.000
 ITH  H20  N3   C9   103.32  3.000
 ITH  C12  N3   C9   110.05  3.000
 ITH  H20  N3   C2   105.50  3.000
 ITH  C9   N3   C2   113.82  3.000
 ITH  C12  N3   C2   116.88  3.000
 ITH  H15  C9   H14  108.20  3.000
 ITH  H15  C9   C10  109.64  3.000
 ITH  H14  C9   C10  107.94  3.000
 ITH  H15  C9   N3   108.92  3.000
 ITH  H14  C9   N3   106.30  3.000
 ITH  C10  C9   N3   115.57  3.000
 ITH  N4   C10  O3   122.50  3.000
 ITH  O3   C10  C9   120.24  3.000
 ITH  N4   C10  C9   117.23  3.000
 ITH  H16  N4   C11  116.87  3.000
 ITH  H16  N4   C10  116.80  3.000
 ITH  C11  N4   C10  126.30  3.000
 ITH  C12  C11  O4   120.73  3.000
 ITH  C12  C11  N4   116.53  3.000
 ITH  O4   C11  N4   122.63  3.000
 ITH  H17  C12  H18  107.37  3.000
 ITH  H17  C12  C11  108.01  3.000
 ITH  H18  C12  C11  109.27  3.000
 ITH  H17  C12  N3   106.57  3.000
 ITH  H18  C12  N3   110.63  3.000
 ITH  C11  C12  N3   114.67  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
 ITH  CONST_01  C7   N2   C6   C5      0.00   0.0  0
 ITH  CONST_02  C11  N4   C10  C9      0.00   0.0  0
 ITH  CONST_03  C7   N2   C6   O1    180.00   0.0  0
 ITH  CONST_04  C11  N4   C10  O3    180.00   0.0  0
 ITH  CONST_05  H11  N2   C6   C5    180.00   0.0  0
 ITH  CONST_06  H16  N4   C10  C9    180.00   0.0  0
 ITH  CONST_07  H11  N2   C6   O1      0.00   0.0  0
 ITH  CONST_08  H16  N4   C10  O3      0.00   0.0  0
 ITH  Var_01    N2   C6   C5   N1    -25.15  30.0  1
 ITH  Var_02    N2   C7   C8   N1     23.81  30.0  1
 ITH  Var_03    C8   C7   N2   C6      0.83  30.0  1
 ITH  Var_04    N4   C11  C12  N3     29.32  30.0  1
 ITH  Var_05    N4   C10  C9   N3    -20.62  30.0  1
 ITH  Var_06    C12  C11  N4   C10    -2.12  30.0  1
 ITH  Var_07    O1   C6   C5   N1    157.81  30.0  1
 ITH  Var_08    O2   C7   C8   N1   -158.93  30.0  1
 ITH  Var_09    O2   C7   N2   C6   -176.36  30.0  1
 ITH  Var_10    O4   C11  C12  N3   -154.29  30.0  1
 ITH  Var_11    O3   C10  C9   N3    161.43  30.0  1
 ITH  Var_12    O4   C11  N4   C10  -178.43  30.0  1
 ITH  Var_13    H12  C8   C7   N2    -95.19  30.0  1
 ITH  Var_14    H13  C8   C7   N2    147.39  30.0  1
 ITH  Var_15    H10  C5   C6   N2   -149.60  30.0  1
 ITH  Var_16    H9   C5   C6   N2     93.89  30.0  1
 ITH  Var_17    H11  N2   C7   C8    178.71  30.0  1
 ITH  Var_18    H18  C12  C11  N4    154.16  30.0  1
 ITH  Var_19    H17  C12  C11  N4    -89.33  30.0  1
 ITH  Var_20    H14  C9   C10  N4     98.20  30.0  1
 ITH  Var_21    H15  C9   C10  N4   -144.15  30.0  1
 ITH  Var_22    H16  N4   C11  C12   176.19  30.0  1
 ITH  Var_23    H10  C5   C6   O1     33.35  30.0  1
 ITH  Var_24    H9   C5   C6   O1    -83.16  30.0  1
 ITH  Var_25    H12  C8   C7   O2     82.07  30.0  1
 ITH  Var_26    H13  C8   C7   O2    -35.36  30.0  1
 ITH  Var_27    H11  N2   C7   O2      1.52  30.0  1
 ITH  Var_28    H14  C9   C10  O3    -79.75  30.0  1
 ITH  Var_29    H15  C9   C10  O3     37.90  30.0  1
 ITH  Var_30    H16  N4   C11  O4     -0.12  30.0  1
 ITH  Var_31    H18  C12  C11  O4    -29.45  30.0  1
 ITH  Var_32    H17  C12  C11  O4     87.06  30.0  1

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
 ITH  chir_01  C2  N3  C1  C3   negativ
 ITH  chir_02  C3  N1  C2  C4   negativ
 ITH  chir_03  N1  C3  C5  C8   positiv
 ITH  chir_04  N3  C2  C9  C12  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
 ITH  plan-1  N2   0.020
 ITH  plan-1  C7   0.020
 ITH  plan-1  O2   0.020
 ITH  plan-1  C8   0.020
 ITH  plan-2  N4   0.020
 ITH  plan-2  C11  0.020
 ITH  plan-2  O4   0.020
 ITH  plan-2  C12  0.020
 ITH  plan-3  C5   0.020
 ITH  plan-3  C6   0.020
 ITH  plan-3  O1   0.020
 ITH  plan-3  N2   0.020
 ITH  plan-3  C7   0.020
 ITH  plan-3  H11  0.020
 ITH  plan-4  C9   0.020
 ITH  plan-4  C10  0.020
 ITH  plan-4  O3   0.020
 ITH  plan-4  N4   0.020
 ITH  plan-4  C11  0.020
 ITH  plan-4  H16  0.020

