# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 06:04:13 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)c1[nH]cnc1/C=C/2NC(=O)C(/NC/2=O)=C/c3ccccc3
#
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
 PN6  PN6  (3Z,6Z)-3-benzylidene-6-[(5-tert-butyl-1H-imidazol-4-yl)methylidene]piperazine-2,5-dione  ligand  45  25  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PN6
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
 PN6  C6   C  C1    0  -0.439  -1.8327   0.4359  -0.0015
 PN6  C2   C  CR5   0   0.161  -2.9674  -0.4316   0.1645
 PN6  C4   C  CR15  0   0.115  -4.0211  -2.2715   0.4713
 PN6  C23  C  CH3   0  -0.683  -6.5698   0.9764   0.0585
 PN6  C24  C  CH3   0  -0.631  -4.7329   1.7744  -1.4162
 PN6  C25  C  CH3   0  -0.632  -4.6479   2.1857   1.0656
 PN6  C1   C  CR5   0   0.422  -4.3161  -0.1072   0.1513
 PN6  N5   N  NR15  0  -0.630  -4.9457  -1.2975   0.3477
 PN6  N3   N  N     0  -0.505  -2.8185  -1.7864   0.3663
 PN6  C7   C  CR6   0   0.221  -0.5361   0.0670   0.0310
 PN6  C8   C  CR6   0   0.535   0.5144   1.0822  -0.1701
 PN6  O20  O  O     0  -0.461   0.2753   2.2541  -0.4077
 PN6  N9   N  NR16  0  -0.750   1.7899   0.6249  -0.0794
 PN6  N12  N  NR16  0  -0.755  -0.1341  -1.2476   0.2305
 PN6  C11  C  CR6   0   0.532   1.1307  -1.7058   0.3082
 PN6  O21  O  O     0  -0.465   1.3817  -2.8863   0.4884
 PN6  C10  C  CR6   0   0.216   2.1975  -0.6771   0.1766
 PN6  C13  C  C1    0  -0.358   3.4812  -1.0556   0.2812
 PN6  C14  C  CR6   0   0.121   4.6728  -0.2105   0.2155
 PN6  C15  C  CR16  0  -0.335   4.7496   1.0483   0.8210
 PN6  C16  C  CR16  0  -0.236   5.9104   1.8037   0.7378
 PN6  C17  C  CR16  0  -0.262   7.0157   1.3180   0.0529
 PN6  C18  C  CR16  0  -0.239   6.9593   0.0603  -0.5361
 PN6  C19  C  CR16  0  -0.292   5.8038  -0.6984  -0.4477
 PN6  H1   H  H     0   0.261  -2.0159   1.4862  -0.1764
 PN6  H2   H  HCR5  0   0.290  -4.2831  -3.3045   0.6348
 PN6  H3   H  HCH3  0   0.240  -6.9404   0.3061  -0.7199
 PN6  H4   H  HCH3  0   0.240  -6.8696   0.5822   1.0317
 PN6  H5   H  HCH3  0   0.254  -7.0814   1.9300  -0.0747
 PN6  H6   H  HCH3  0   0.235  -5.2858   2.7021  -1.5738
 PN6  H7   H  HCH3  0   0.233  -3.6729   1.9984  -1.5326
 PN6  H8   H  HCH3  0   0.235  -5.0151   1.0775  -2.2064
 PN6  H9   H  HCH3  0   0.236  -4.8993   1.7997   2.0541
 PN6  H10  H  HCH3  0   0.233  -3.5807   2.4046   1.0535
 PN6  H11  H  HCH3  0   0.235  -5.1781   3.1304   0.9304
 PN6  H12  H  HNR5  0   0.432  -5.9427  -1.4412   0.3928
 PN6  H14  H  HNR6  0   0.426  -0.8982  -1.9190   0.3377
 PN6  H15  H  H     0   0.279   3.6499  -2.1195   0.3902
 PN6  H17  H  HCR6  0   0.271   3.9180   1.4302   1.4004
 PN6  H18  H  HCR6  0   0.263   5.9532   2.7709   1.2213
 PN6  H19  H  HCR6  0   0.261   7.9195   1.9099  -0.0097
 PN6  H20  H  HCR6  0   0.261   7.8196  -0.3319  -1.0625
 PN6  H21  H  HCR6  0   0.258   5.7691  -1.6799  -0.9048
 PN6  H13  H  HNR6  0   0.419   2.5067   1.3141  -0.2657
 PN6  C22  C  CT    0  -0.212  -5.0565   1.1950  -0.0329

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
 PN6  C17  C18  aromatic  1.390  0.020  1.390
 PN6  C17  C16  aromatic  1.388  0.020  1.388
 PN6  C18  C19  aromatic  1.385  0.020  1.385
 PN6  C16  C15  aromatic  1.387  0.020  1.387
 PN6  C19  C14  aromatic  1.399  0.020  1.399
 PN6  C15  C14  aromatic  1.399  0.020  1.399
 PN6  C14  C13  single    1.462  0.020  1.462
 PN6  C13  C10  double    1.342  0.020  1.342
 PN6  N9   C10  single    1.388  0.020  1.388
 PN6  N9   C8   single    1.358  0.020  1.358
 PN6  C10  C11  single    1.488  0.020  1.488
 PN6  O20  C8   double    1.220  0.020  1.220
 PN6  C8   C7   single    1.475  0.020  1.475
 PN6  C11  O21  double    1.220  0.020  1.220
 PN6  C11  N12  single    1.347  0.020  1.347
 PN6  C7   N12  single    1.389  0.020  1.389
 PN6  C7   C6   double    1.348  0.020  1.348
 PN6  C6   C2   single    1.438  0.020  1.438
 PN6  C2   N3   aromatic  1.378  0.020  1.378
 PN6  C2   C1   aromatic  1.387  0.020  1.387
 PN6  N3   C4   aromatic  1.301  0.020  1.301
 PN6  C25  C22  single    1.535  0.020  1.535
 PN6  C1   C22  single    1.509  0.020  1.509
 PN6  C1   N5   aromatic  1.361  0.020  1.361
 PN6  C24  C22  single    1.534  0.020  1.534
 PN6  C22  C23  single    1.532  0.020  1.532
 PN6  C4   N5   aromatic  1.349  0.020  1.349
 PN6  C6   H1   single    0.930  0.020  1.080
 PN6  C4   H2   single    0.930  0.020  1.080
 PN6  C23  H3   single    0.970  0.020  1.090
 PN6  C23  H4   single    0.970  0.020  1.090
 PN6  C23  H5   single    0.970  0.020  1.090
 PN6  C24  H6   single    0.970  0.020  1.090
 PN6  C24  H7   single    0.970  0.020  1.090
 PN6  C24  H8   single    0.970  0.020  1.090
 PN6  C25  H9   single    0.970  0.020  1.090
 PN6  C25  H10  single    0.970  0.020  1.090
 PN6  C25  H11  single    0.970  0.020  1.090
 PN6  N5   H12  single    0.860  0.020  1.020
 PN6  N12  H14  single    0.860  0.020  1.020
 PN6  C13  H15  single    0.930  0.020  1.080
 PN6  C15  H17  single    0.930  0.020  1.080
 PN6  C16  H18  single    0.930  0.020  1.080
 PN6  C17  H19  single    0.930  0.020  1.080
 PN6  C18  H20  single    0.930  0.020  1.080
 PN6  C19  H21  single    0.930  0.020  1.080
 PN6  N9   H13  single    0.860  0.020  1.020

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
 PN6  H1   C6   C7   115.65  3.000
 PN6  H1   C6   C2   118.12  3.000
 PN6  C7   C6   C2   126.22  3.000
 PN6  N3   C2   C1   109.66  3.000
 PN6  C1   C2   C6   128.68  3.000
 PN6  N3   C2   C6   121.66  3.000
 PN6  H2   C4   N3   126.45  3.000
 PN6  H2   C4   N5   122.63  3.000
 PN6  N3   C4   N5   110.92  3.000
 PN6  H5   C23  H4   107.20  3.000
 PN6  H5   C23  H3   106.89  3.000
 PN6  H4   C23  H3   108.69  3.000
 PN6  H5   C23  C22  109.36  3.000
 PN6  H4   C23  C22  112.09  3.000
 PN6  H3   C23  C22  112.35  3.000
 PN6  H8   C24  H7   107.80  3.000
 PN6  H8   C24  H6   107.90  3.000
 PN6  H7   C24  H6   107.62  3.000
 PN6  H8   C24  C22  110.94  3.000
 PN6  H7   C24  C22  112.28  3.000
 PN6  H6   C24  C22  110.14  3.000
 PN6  H11  C25  H10  107.48  3.000
 PN6  H11  C25  H9   107.85  3.000
 PN6  H10  C25  H9   107.88  3.000
 PN6  H11  C25  C22  109.92  3.000
 PN6  H10  C25  C22  112.50  3.000
 PN6  H9   C25  C22  111.04  3.000
 PN6  N5   C1   C22  123.05  3.000
 PN6  N5   C1   C2   104.11  3.000
 PN6  C22  C1   C2   132.84  3.000
 PN6  H12  N5   C1   126.06  3.000
 PN6  H12  N5   C4   124.81  3.000
 PN6  C1   N5   C4   109.13  3.000
 PN6  C4   N3   C2   106.18  3.000
 PN6  N12  C7   C8   117.70  3.000
 PN6  N12  C7   C6   122.73  3.000
 PN6  C8   C7   C6   119.56  3.000
 PN6  N9   C8   O20  121.39  3.000
 PN6  O20  C8   C7   123.26  3.000
 PN6  N9   C8   C7   115.35  3.000
 PN6  H13  N9   C10  117.70  3.000
 PN6  H13  N9   C8   115.07  3.000
 PN6  C10  N9   C8   127.16  3.000
 PN6  H14  N12  C11  118.16  3.000
 PN6  H14  N12  C7   114.84  3.000
 PN6  C11  N12  C7   127.00  3.000
 PN6  C10  C11  O21  122.30  3.000
 PN6  O21  C11  N12  122.05  3.000
 PN6  C10  C11  N12  115.65  3.000
 PN6  C13  C10  C11  118.94  3.000
 PN6  C11  C10  N9   117.01  3.000
 PN6  C13  C10  N9   124.03  3.000
 PN6  H15  C13  C14  116.45  3.000
 PN6  H15  C13  C10  115.72  3.000
 PN6  C14  C13  C10  127.79  3.000
 PN6  C19  C14  C15  118.33  3.000
 PN6  C15  C14  C13  123.05  3.000
 PN6  C19  C14  C13  118.59  3.000
 PN6  H17  C15  C16  118.84  3.000
 PN6  H17  C15  C14  120.44  3.000
 PN6  C16  C15  C14  120.66  3.000
 PN6  H18  C16  C17  120.11  3.000
 PN6  H18  C16  C15  119.54  3.000
 PN6  C17  C16  C15  120.35  3.000
 PN6  H19  C17  C18  120.28  3.000
 PN6  H19  C17  C16  120.15  3.000
 PN6  C18  C17  C16  119.57  3.000
 PN6  H20  C18  C19  119.72  3.000
 PN6  H20  C18  C17  120.12  3.000
 PN6  C19  C18  C17  120.16  3.000
 PN6  H21  C19  C18  119.74  3.000
 PN6  H21  C19  C14  119.35  3.000
 PN6  C18  C19  C14  120.91  3.000
 PN6  C1   C22  C25  109.82  3.000
 PN6  C1   C22  C24  109.42  3.000
 PN6  C25  C22  C24  110.21  3.000
 PN6  C24  C22  C23  108.43  3.000
 PN6  C1   C22  C23  110.75  3.000
 PN6  C25  C22  C23  108.21  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
 PN6  CONST_01  N5   C4   N3   C2      0.00   0.0  0
 PN6  CONST_02  C4   N5   C1   C2      0.00   0.0  0
 PN6  CONST_03  C1   C2   N3   C4      0.00   0.0  0
 PN6  CONST_04  N3   C4   N5   C1      0.00   0.0  0
 PN6  CONST_05  N3   C2   C1   N5      0.00   0.0  0
 PN6  CONST_06  C17  C18  C19  C14     0.00   0.0  0
 PN6  CONST_07  C17  C16  C15  C14     0.00   0.0  0
 PN6  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 PN6  CONST_09  C18  C19  C14  C15     0.00   0.0  0
 PN6  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 PN6  CONST_11  C19  C14  C15  C16     0.00   0.0  0
 PN6  CONST_12  C10  N9   C8   C7      0.00   0.0  0
 PN6  CONST_13  C10  C11  N12  C7      0.00   0.0  0
 PN6  CONST_14  C4   N3   C2   C6    180.00   0.0  0
 PN6  CONST_15  N5   C1   C2   C6    180.00   0.0  0
 PN6  CONST_16  C22  C1   N5   C4    180.00   0.0  0
 PN6  CONST_17  N3   C2   C1   C22   180.00   0.0  0
 PN6  CONST_18  C18  C19  C14  C13   180.00   0.0  0
 PN6  CONST_19  C16  C15  C14  C13   180.00   0.0  0
 PN6  CONST_20  O21  C11  N12  C7    180.00   0.0  0
 PN6  CONST_21  C10  N9   C8   O20   180.00   0.0  0
 PN6  CONST_22  H2   C4   N3   C2    180.00   0.0  0
 PN6  CONST_23  H12  N5   C1   C2    180.00   0.0  0
 PN6  CONST_24  H20  C18  C19  C14   180.00   0.0  0
 PN6  CONST_25  H18  C16  C15  C14   180.00   0.0  0
 PN6  CONST_26  H19  C17  C16  C15   180.00   0.0  0
 PN6  CONST_27  H21  C19  C14  C15   180.00   0.0  0
 PN6  CONST_28  H17  C15  C16  C17   180.00   0.0  0
 PN6  CONST_29  H13  N9   C8   C7    180.00   0.0  0
 PN6  CONST_30  H14  N12  C11  C10   180.00   0.0  0
 PN6  Var_01    C8   C7   C6   C2    179.44  30.0  2
 PN6  Var_02    C7   C6   C2   C1    179.43  30.0  2
 PN6  Var_03    C14  C13  C10  N9      3.06  30.0  2
 PN6  Var_04    C19  C14  C13  C10  -141.27  30.0  3
 PN6  Var_05    C25  C22  C1   C2    -59.98  30.0  2
 PN6  Var_06    H9   C25  C22  C1    -61.09  30.0  3
 PN6  Var_07    H6   C24  C22  C1    178.32  30.0  3
 PN6  Var_08    H3   C23  C22  C1    -61.64  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
 PN6  plan-1  C6   0.020
 PN6  plan-1  C2   0.020
 PN6  plan-1  C4   0.020
 PN6  plan-1  C1   0.020
 PN6  plan-1  N5   0.020
 PN6  plan-1  N3   0.020
 PN6  plan-1  H2   0.020
 PN6  plan-1  H12  0.020
 PN6  plan-1  C22  0.020
 PN6  plan-2  C6   0.020
 PN6  plan-2  C7   0.020
 PN6  plan-2  C8   0.020
 PN6  plan-2  O20  0.020
 PN6  plan-2  N9   0.020
 PN6  plan-2  N12  0.020
 PN6  plan-2  C11  0.020
 PN6  plan-2  O21  0.020
 PN6  plan-2  C10  0.020
 PN6  plan-2  C13  0.020
 PN6  plan-2  H14  0.020
 PN6  plan-2  H13  0.020
 PN6  plan-3  C13  0.020
 PN6  plan-3  C14  0.020
 PN6  plan-3  C15  0.020
 PN6  plan-3  C16  0.020
 PN6  plan-3  C17  0.020
 PN6  plan-3  C18  0.020
 PN6  plan-3  C19  0.020
 PN6  plan-3  H17  0.020
 PN6  plan-3  H18  0.020
 PN6  plan-3  H19  0.020
 PN6  plan-3  H20  0.020
 PN6  plan-3  H21  0.020

