# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 30 07:00:04 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (3Z)-3-{(2E,4E,6R)-1-hydroxy-4-methyl-6-[(1S,3R,4R,5S)-1,4,8-trimethyl-6-oxo-2,9-dioxabicyclo[3.3.1]non-7-en-3-yl]hepta-2,4-dien-1-ylidene}pyrrolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](\C=C(C)\C=C\C(O)=C\1C(=O)CNC\1=O)[C@H]2O[C@@]3(C)O[C@@H]([C@@H]2C)C(=O)C=C3C
#
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
 TRK  TRK  (3Z)-3-{(2E,4E,6R)-1-hydroxy-4-methyl-6-[(1S,3R,4R,5S)-1,4,8-trimethyl-6-oxo-2,9-dioxabicyclo[3.3.1]non-7-en-3-yl]hepta-2,4-dien-1-ylidene}pyrrolidine-2,4-dione  ligand  56  29  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TRK
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
 TRK  N     N  NH1   0  -0.151   7.5456  -0.4758   0.8590
 TRK  C1    C  CH1   0   0.352  -2.9211   0.4325  -0.7387
 TRK  O1    O  O2    0  -0.489  -3.1917  -0.9560  -0.6073
 TRK  C2    C  CH1   0   0.007  -1.7960   0.5824  -1.7682
 TRK  O2    O  O     0  -0.690   6.1849  -2.3132   1.1279
 TRK  C3    C  CH3   0  -0.092  -2.1905  -0.0279  -3.1173
 TRK  O3    O  O     0  -0.184   5.5432   2.0450  -0.5267
 TRK  C4    C  C1    0  -0.974  -0.5227  -0.0259  -1.2763
 TRK  O4    O  OH1   0  -0.745   3.7548  -1.9008   0.3637
 TRK  C5    C  C     0   2.626   0.6927   0.5494  -1.2046
 TRK  O5    O  O2    0  -0.575  -3.7316  -0.8164   1.6338
 TRK  C6    C  C1    0   1.331   1.7736  -0.2618  -0.6774
 TRK  C7    C  C1    0   3.023   3.0440   0.1609  -0.5163
 TRK  C8    C  C     0  -0.982   4.0819  -0.6743   0.0306
 TRK  C9    C  C     0  -0.249   5.3831  -0.2456   0.2185
 TRK  C10   C  C     0   0.160   6.3859  -1.1399   0.7826
 TRK  C11   C  CH2   0  -0.433   7.4669   0.8778   0.3671
 TRK  C12   C  C     0  -0.076   6.0080   1.0235  -0.0567
 TRK  C13   C  CH3   0   4.002   0.9996   1.9577  -1.6177
 TRK  C14   C  CH1   0  -0.139  -2.5895   1.0441   0.6244
 TRK  C15   C  CH3   0  -0.257  -2.4234   2.5553   0.5603
 TRK  C16   C  CH1   0   0.267  -3.6420   0.5935   1.6512
 TRK  C17   C  CT    0   0.376  -4.1214  -1.3104   0.3842
 TRK  C18   C  CH3   0  -0.097  -4.1165  -2.8214   0.4882
 TRK  C19   C  C     0  -0.101  -5.4866  -0.7470   0.0033
 TRK  C20   C  CH3   0  -0.449  -6.2951  -1.4865  -1.0047
 TRK  C21   C  C1    0  -0.568  -5.8936   0.4137   0.5347
 TRK  C22   C  C     0   0.049  -5.0138   1.1935   1.4014
 TRK  H     H  HNH1  0  -1.685   8.3960  -0.8904   1.2052
 TRK  H111  H  HCH2  0   0.002   7.7146   1.6117   1.1378
 TRK  H112  H  HCH2  0   0.013   8.1290   1.0445  -0.4861
 TRK  H2    H  HCH1  0  -0.207  -1.6697   1.6562  -1.9222
 TRK  H14   H  HCH1  0  -0.155  -1.6469   0.6080   0.9759
 TRK  H31C  H  HCH3  0  -0.270  -2.2865  -1.1115  -3.0627
 TRK  H32C  H  HCH3  0  -0.921  -3.1441   0.3810  -3.4561
 TRK  H33C  H  HCH3  0  -0.303  -1.4389   0.2044  -3.8717
 TRK  H4    H  H     0  -0.171  -0.6025  -1.0627  -0.9596
 TRK  H6    H  H     0  -0.957   1.5085  -1.2733  -0.3883
 TRK  H131  H  HCH3  0   0.997   1.3780   2.5413  -0.7763
 TRK  H132  H  HCH3  0   1.005   1.7674   1.9786  -2.3934
 TRK  H133  H  HCH3  0   0.950   0.1305   2.4778  -2.0120
 TRK  H16   H  HCH1  0  -0.724  -3.3134   0.8812   2.6530
 TRK  H7    H  H     0   1.006   3.3404   1.1620  -0.7932
 TRK  H151  H  HCH3  0  -0.208  -3.2575   3.0452   0.0564
 TRK  H152  H  HCH3  0  -0.779  -2.3397   2.9803   1.5609
 TRK  H153  H  HCH3  0   0.071  -1.5131   2.8216   0.0234
 TRK  H181  H  HCH3  0  -0.282  -3.1332  -3.1653   0.8089
 TRK  H182  H  HCH3  0  -0.522  -4.8558  -3.1575   1.2146
 TRK  H183  H  HCH3  0  -0.428  -4.3441  -3.2837  -0.4701
 TRK  H201  H  HCH3  0  -0.349  -6.6011  -2.4640  -0.6283
 TRK  H202  H  HCH3  0  -0.095  -7.1900  -0.9321  -1.2799
 TRK  H203  H  HCH3  0  -0.151  -5.7121  -1.6674  -1.9099
 TRK  H21   H  H     0  -0.058  -6.8598   0.8377   0.2828
 TRK  HO4   H  HOH1  0   0.341   4.5683  -2.3551   0.7229
 TRK  H1    H  HCH1  0  -0.302  -3.8013   0.9463  -1.1554
 TRK  O6    O  O     0  -0.760  -5.3287   2.2754   1.8571

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
 TRK  N    C10   single  1.339  0.020  1.339
 TRK  N    C11   single  1.442  0.020  1.442
 TRK  C1   O1    single  1.421  0.020  1.421
 TRK  C1   C2    single  1.532  0.020  1.532
 TRK  C1   C14   single  1.530  0.020  1.530
 TRK  O1   C17   single  1.405  0.020  1.405
 TRK  C2   C3    single  1.532  0.020  1.532
 TRK  C2   C4    single  1.494  0.020  1.494
 TRK  O2   C10   double  1.240  0.020  1.240
 TRK  O3   C12   double  1.217  0.020  1.217
 TRK  C4   C5    double  1.347  0.020  1.347
 TRK  O4   C8    single  1.312  0.020  1.312
 TRK  C5   C6    single  1.451  0.020  1.451
 TRK  C5   C13   single  1.499  0.020  1.499
 TRK  O5   C16   single  1.413  0.020  1.413
 TRK  O5   C17   single  1.399  0.020  1.399
 TRK  C6   C7    double  1.349  0.020  1.349
 TRK  O6   C22   double  1.215  0.020  1.215
 TRK  C7   C8    single  1.440  0.020  1.440
 TRK  C8   C9    double  1.383  0.020  1.383
 TRK  C9   C10   single  1.457  0.020  1.457
 TRK  C9   C12   single  1.441  0.020  1.441
 TRK  C11  C12   single  1.526  0.020  1.526
 TRK  C14  C15   single  1.522  0.020  1.522
 TRK  C14  C16   single  1.538  0.020  1.538
 TRK  C16  C22   single  1.518  0.020  1.518
 TRK  C17  C18   single  1.515  0.020  1.515
 TRK  C17  C19   single  1.525  0.020  1.525
 TRK  C19  C20   single  1.489  0.020  1.489
 TRK  C19  C21   double  1.340  0.020  1.340
 TRK  C21  C22   single  1.461  0.020  1.461
 TRK  N    H     single  0.860  0.020  1.020
 TRK  C11  H111  single  0.970  0.020  1.090
 TRK  C11  H112  single  0.970  0.020  1.090
 TRK  C1   H1    single  0.970  0.020  1.090
 TRK  C2   H2    single  0.970  0.020  1.090
 TRK  C14  H14   single  0.970  0.020  1.090
 TRK  C3   H31C  single  0.970  0.020  1.090
 TRK  C3   H32C  single  0.970  0.020  1.090
 TRK  C3   H33C  single  0.970  0.020  1.090
 TRK  C4   H4    single  0.930  0.020  1.080
 TRK  C6   H6    single  0.930  0.020  1.080
 TRK  C13  H131  single  0.970  0.020  1.090
 TRK  C13  H132  single  0.970  0.020  1.090
 TRK  C13  H133  single  0.970  0.020  1.090
 TRK  C16  H16   single  0.970  0.020  1.090
 TRK  C7   H7    single  0.930  0.020  1.080
 TRK  C15  H151  single  0.970  0.020  1.090
 TRK  C15  H152  single  0.970  0.020  1.090
 TRK  C15  H153  single  0.970  0.020  1.090
 TRK  C18  H181  single  0.970  0.020  1.090
 TRK  C18  H182  single  0.970  0.020  1.090
 TRK  C18  H183  single  0.970  0.020  1.090
 TRK  C20  H201  single  0.970  0.020  1.090
 TRK  C20  H202  single  0.970  0.020  1.090
 TRK  C20  H203  single  0.970  0.020  1.090
 TRK  C21  H21   single  0.930  0.020  1.080
 TRK  O4   HO4   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
 TRK  H     N    C11   123.33  3.000
 TRK  H     N    C10   123.14  3.000
 TRK  C11   N    C10   113.51  3.000
 TRK  H1    C1   C14   108.90  3.000
 TRK  H1    C1   C2    106.68  3.000
 TRK  C14   C1   C2    113.59  3.000
 TRK  H1    C1   O1    109.80  3.000
 TRK  C14   C1   O1    110.45  3.000
 TRK  C2    C1   O1    107.32  3.000
 TRK  C17   O1   C1    115.98  3.000
 TRK  H2    C2   C4    110.37  3.000
 TRK  H2    C2   C3    107.29  3.000
 TRK  C4    C2   C3    110.30  3.000
 TRK  H2    C2   C1    106.01  3.000
 TRK  C4    C2   C1    111.38  3.000
 TRK  C3    C2   C1    111.32  3.000
 TRK  H33C  C3   H32C  107.93  3.000
 TRK  H33C  C3   H31C  107.91  3.000
 TRK  H32C  C3   H31C  108.13  3.000
 TRK  H33C  C3   C2    110.30  3.000
 TRK  H32C  C3   C2    110.42  3.000
 TRK  H31C  C3   C2    112.01  3.000
 TRK  H4    C4   C5    117.28  3.000
 TRK  H4    C4   C2    114.93  3.000
 TRK  C5    C4   C2    127.78  3.000
 TRK  HO4   O4   C8    108.27  3.000
 TRK  C13   C5   C6    118.22  3.000
 TRK  C13   C5   C4    124.84  3.000
 TRK  C6    C5   C4    116.94  3.000
 TRK  C17   O5   C16   112.40  3.000
 TRK  H6    C6   C7    119.38  3.000
 TRK  H6    C6   C5    115.86  3.000
 TRK  C7    C6   C5    124.76  3.000
 TRK  H7    C7   C8    115.92  3.000
 TRK  H7    C7   C6    121.22  3.000
 TRK  C8    C7   C6    122.86  3.000
 TRK  C9    C8   C7    123.37  3.000
 TRK  C9    C8   O4    119.33  3.000
 TRK  C7    C8   O4    117.31  3.000
 TRK  C12   C9   C10   108.41  3.000
 TRK  C12   C9   C8    130.93  3.000
 TRK  C10   C9   C8    120.66  3.000
 TRK  C9    C10  O2    125.24  3.000
 TRK  C9    C10  N     108.29  3.000
 TRK  O2    C10  N     126.46  3.000
 TRK  H112  C11  H111  108.11  3.000
 TRK  H112  C11  C12   110.36  3.000
 TRK  H111  C11  C12   110.39  3.000
 TRK  H112  C11  N     112.11  3.000
 TRK  H111  C11  N     112.17  3.000
 TRK  C12   C11  N     103.68  3.000
 TRK  C11   C12  C9    106.11  3.000
 TRK  C11   C12  O3    123.54  3.000
 TRK  C9    C12  O3    130.35  3.000
 TRK  H133  C13  H132  107.18  3.000
 TRK  H133  C13  H131  107.52  3.000
 TRK  H132  C13  H131  107.07  3.000
 TRK  H133  C13  C5    112.69  3.000
 TRK  H132  C13  C5    110.96  3.000
 TRK  H131  C13  C5    111.15  3.000
 TRK  H14   C14  C16   104.94  3.000
 TRK  H14   C14  C15   108.34  3.000
 TRK  C16   C14  C15   113.19  3.000
 TRK  H14   C14  C1    108.23  3.000
 TRK  C16   C14  C1    109.23  3.000
 TRK  C15   C14  C1    112.52  3.000
 TRK  H153  C15  H152  107.02  3.000
 TRK  H153  C15  H151  107.54  3.000
 TRK  H152  C15  H151  107.91  3.000
 TRK  H153  C15  C14   110.77  3.000
 TRK  H152  C15  C14   110.90  3.000
 TRK  H151  C15  C14   112.46  3.000
 TRK  H16   C16  C22   108.58  3.000
 TRK  H16   C16  C14   109.21  3.000
 TRK  C22   C16  C14   113.13  3.000
 TRK  H16   C16  O5    107.04  3.000
 TRK  C22   C16  O5    109.58  3.000
 TRK  C14   C16  O5    109.12  3.000
 TRK  C19   C17  C18   112.87  3.000
 TRK  C19   C17  O5    109.99  3.000
 TRK  C18   C17  O5    106.86  3.000
 TRK  C19   C17  O1    108.84  3.000
 TRK  C18   C17  O1    107.34  3.000
 TRK  O5    C17  O1    110.92  3.000
 TRK  H183  C18  H182  108.31  3.000
 TRK  H183  C18  H181  108.29  3.000
 TRK  H182  C18  H181  108.58  3.000
 TRK  H183  C18  C17   111.27  3.000
 TRK  H182  C18  C17   110.57  3.000
 TRK  H181  C18  C17   109.75  3.000
 TRK  C21   C19  C20   122.26  3.000
 TRK  C21   C19  C17   119.53  3.000
 TRK  C20   C19  C17   118.14  3.000
 TRK  H203  C20  H202  108.29  3.000
 TRK  H203  C20  H201  106.69  3.000
 TRK  H202  C20  H201  108.24  3.000
 TRK  H203  C20  C19   110.71  3.000
 TRK  H202  C20  C19   111.40  3.000
 TRK  H201  C20  C19   111.33  3.000
 TRK  H21   C21  C22   117.75  3.000
 TRK  H21   C21  C19   121.13  3.000
 TRK  C22   C21  C19   120.99  3.000
 TRK  C21   C22  C16   115.53  3.000
 TRK  C21   C22  O6    122.80  3.000
 TRK  C16   C22  O6    121.62  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
 TRK  CONST_01  C11   N    C10  C9      0.00   0.0  0
 TRK  CONST_02  C11   N    C10  O2    180.00   0.0  0
 TRK  CONST_03  H     N    C10  C9    180.00   0.0  0
 TRK  CONST_04  C6    C5   C4   C2    180.00   0.0  0
 TRK  CONST_05  C13   C5   C4   C2      0.00   0.0  0
 TRK  CONST_06  H4    C4   C5   C6      0.00   0.0  0
 TRK  Var_01    C12   C9   C10  N       0.28  30.0  1
 TRK  Var_02    C9    C12  C11  N      -0.28  30.0  1
 TRK  Var_03    C12   C11  N    C10     0.49  30.0  1
 TRK  Var_04    C11   C12  C9   C10     0.02  30.0  1
 TRK  Var_05    C19   C21  C22  C16    -0.37  30.0  2
 TRK  Var_06    C22   C21  C19  C17     4.23  30.0  2
 TRK  Var_07    H201  C20  C19  C17    65.74  30.0  3
 TRK  Var_08    C9    C8   C7   C6   -179.03  30.0  2
 TRK  Var_09    C8    C7   C6   C5    179.04   0.0  2
 TRK  Var_10    C7    C6   C5   C4   -178.87  30.0  2
 TRK  Var_11    H131  C13  C5   C4    119.44  30.0  3

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
 TRK  chir_01  C1   O1  C2   C14  positiv
 TRK  chir_02  C2   C1  C3   C4   positiv
 TRK  chir_03  C14  C1  C15  C16  negativ
 TRK  chir_04  C16  O5  C22  C14  positiv
 TRK  chir_05  C17  O1  O5   C18  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
 TRK  plan-1  O3   0.020
 TRK  plan-1  C9   0.020
 TRK  plan-1  C11  0.020
 TRK  plan-1  C12  0.020
 TRK  plan-2  C16  0.020
 TRK  plan-2  C21  0.020
 TRK  plan-2  C22  0.020
 TRK  plan-2  O6   0.020
 TRK  plan-3  N    0.020
 TRK  plan-3  O2   0.020
 TRK  plan-3  C9   0.020
 TRK  plan-3  C10  0.020
 TRK  plan-3  C11  0.020
 TRK  plan-3  H    0.020
 TRK  plan-4  C2   0.020
 TRK  plan-4  C4   0.020
 TRK  plan-4  C5   0.020
 TRK  plan-4  C6   0.020
 TRK  plan-4  C13  0.020
 TRK  plan-4  H4   0.020
 TRK  plan-5  C5   0.020
 TRK  plan-5  C6   0.020
 TRK  plan-5  C7   0.020
 TRK  plan-5  C8   0.020
 TRK  plan-5  H6   0.020
 TRK  plan-5  H7   0.020

