# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 06:24:38 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC(/C)=C/C=C(C)/C(=O)[C@H]1C(=O)OC(=CC1=O)[C@H](C)CCCC=NC(=O)OC
#
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
 NE6  NE6  'methyl [(1E,5R)-5-{(3S)-3-[(2E,4E)-2,5-dimethylocta-2,4-dienoyl]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hexylidene]carbamate'  ligand  61  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NE6
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
 NE6  O1    O  O2    0  -0.444   -0.3190  -0.1773  -0.8751
 NE6  C2    C  C     0   0.597    0.8041   0.2091  -1.5172
 NE6  C3    C  CH1   0  -0.714    1.6512   1.2656  -0.8674
 NE6  O2    O  O     0  -0.368    1.0940  -0.3523  -2.5303
 NE6  C4    C  C     0   0.496    0.9428   2.1523   0.1400
 NE6  C5    C  C1    0  -0.510   -0.3041   1.6409   0.6533
 NE6  C6    C  C     0   0.487   -0.8497   0.5179   0.1649
 NE6  C7    C  CH1   0  -0.347   -2.1116  -0.1052   0.6629
 NE6  C8    C  CH3   0  -0.665   -1.8398  -1.5212   1.1797
 NE6  C9    C  CH2   0  -0.411   -3.1969  -0.0651  -0.4248
 NE6  C10   C  CH2   0  -0.447   -4.5694  -0.4713   0.0959
 NE6  C11   C  CH2   0  -0.519   -5.6373  -0.3444  -0.9949
 NE6  C12   C  C1    0   0.046   -6.9659  -0.7819  -0.4988
 NE6  C13   C  C     0   0.668   -9.1695  -0.5049   0.0129
 NE6  C14   C  CH3   0  -0.423  -11.0438   0.0301   1.3185
 NE6  C15   C  C     0   0.360    2.7536   0.4814  -0.1065
 NE6  C16   C  C     0  -0.040    4.1049   0.4489  -0.6849
 NE6  C17   C  CH3   0  -0.771    4.3864   1.2017  -1.9517
 NE6  C18   C  C1    0  -0.211    5.0202  -0.2957  -0.0172
 NE6  C19   C  C1    0  -0.308    6.3914  -0.5052  -0.3876
 NE6  C20   C  C     0   0.132    7.2719  -1.2710   0.2923
 NE6  C21   C  CH3   0  -0.730    6.9639  -2.0359   1.5388
 NE6  C22   C  CH2   0  -0.487    8.6860  -1.3869  -0.1969
 NE6  C23   C  CH2   0  -0.423    9.6619  -0.5141   0.6015
 NE6  C24   C  CH3   0  -0.662   11.0989  -0.6956   0.1355
 NE6  N12   N  N     0  -0.417   -7.9526   0.0135  -0.4255
 NE6  O14   O  O2    0  -0.443   -9.7675   0.3837   0.7869
 NE6  O13   O  O     0  -0.466   -9.6412  -1.5705  -0.2997
 NE6  O4    O  O     0  -0.402    1.4545   3.1942   0.4933
 NE6  O15   O  O     0  -0.383    2.4219  -0.0866   0.9124
 NE6  H3    H  HCH1  0   0.362    2.0748   1.8849  -1.6570
 NE6  H5    H  H     0   0.291   -0.8061   2.1644   1.4551
 NE6  H7    H  HCH1  0   0.275   -2.4463   0.5124   1.5009
 NE6  H8    H  HCH3  0   0.235   -1.5691  -2.1999   0.3704
 NE6  H8A   H  HCH3  0   0.247   -1.0365  -1.5261   1.9164
 NE6  H8B   H  HCH3  0   0.252   -2.7284  -1.9216   1.6648
 NE6  H9    H  HCH2  0   0.245   -3.2589   0.9504  -0.8270
 NE6  H9A   H  HCH2  0   0.238   -2.9152  -0.7170  -1.2564
 NE6  H10   H  HCH2  0   0.243   -4.5486  -1.5006   0.4621
 NE6  H10A  H  HCH2  0   0.242   -4.8429   0.1587   0.9471
 NE6  H11   H  HCH2  0   0.255   -5.6982   0.6808  -1.3625
 NE6  H11A  H  HCH2  0   0.264   -5.3627  -0.9894  -1.8365
 NE6  H12   H  H     0   0.256   -7.0398  -1.8249  -0.1764
 NE6  H14   H  HCH3  0   0.254  -11.3531   0.8702   1.9333
 NE6  H14A  H  HCH3  0   0.242  -11.7746  -0.1254   0.5252
 NE6  H14B  H  HCH3  0   0.241  -10.9858  -0.8660   1.9358
 NE6  H17   H  HCH3  0   0.255    4.2160   2.2735  -1.8329
 NE6  H17A  H  HCH3  0   0.270    5.4171   1.0806  -2.2734
 NE6  H17B  H  HCH3  0   0.253    3.7540   0.8600  -2.7731
 NE6  H18   H  H     0   0.268    4.6779  -0.7889   0.8846
 NE6  H19   H  H     0   0.250    6.7533  -0.0211  -1.2874
 NE6  H21   H  HCH3  0   0.256    7.0967  -3.1047   1.3541
 NE6  H21A  H  HCH3  0   0.253    7.6650  -1.7742   2.3339
 NE6  H21B  H  HCH3  0   0.254    5.9583  -1.8848   1.9218
 NE6  H22   H  HCH2  0   0.238    9.0072  -2.4316  -0.1272
 NE6  H22A  H  HCH2  0   0.243    8.7433  -1.1062  -1.2516
 NE6  H23   H  HCH2  0   0.227    9.3673   0.5334   0.4991
 NE6  H23A  H  HCH2  0   0.225    9.5918  -0.7527   1.6656
 NE6  H24   H  HCH3  0   0.232   11.7801  -0.0564   0.6978
 NE6  H24A  H  HCH3  0   0.221   11.4291  -1.7278   0.2656
 NE6  H24B  H  HCH3  0   0.221   11.2079  -0.4451  -0.9211

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
 NE6  C6   O1    single  1.359  0.020  1.359
 NE6  C2   O1    single  1.350  0.020  1.350
 NE6  C3   C2    single  1.502  0.020  1.502
 NE6  C2   O2    double  1.194  0.020  1.194
 NE6  C4   C3    single  1.518  0.020  1.518
 NE6  C15  C3    single  1.552  0.020  1.552
 NE6  C3   H3    single  0.970  0.020  1.090
 NE6  O4   C4    double  1.213  0.020  1.213
 NE6  C4   C5    single  1.442  0.020  1.442
 NE6  C5   C6    double  1.341  0.020  1.341
 NE6  C5   H5    single  0.930  0.020  1.080
 NE6  C6   C7    single  1.493  0.020  1.493
 NE6  C8   C7    single  1.532  0.020  1.532
 NE6  C7   C9    single  1.537  0.020  1.537
 NE6  C7   H7    single  0.970  0.020  1.090
 NE6  C8   H8    single  0.970  0.020  1.090
 NE6  C8   H8A   single  0.970  0.020  1.090
 NE6  C8   H8B   single  0.970  0.020  1.090
 NE6  C9   C10   single  1.523  0.020  1.523
 NE6  C9   H9    single  0.970  0.020  1.090
 NE6  C9   H9A   single  0.970  0.020  1.090
 NE6  C10  C11   single  1.532  0.020  1.532
 NE6  C10  H10   single  0.970  0.020  1.090
 NE6  C10  H10A  single  0.970  0.020  1.090
 NE6  C11  C12   single  1.484  0.020  1.484
 NE6  C11  H11   single  0.970  0.020  1.090
 NE6  C11  H11A  single  0.970  0.020  1.090
 NE6  C12  N12   double  1.270  0.020  1.270
 NE6  C12  H12   single  0.930  0.020  1.080
 NE6  N12  C13   single  1.393  0.020  1.393
 NE6  O13  C13   double  1.207  0.020  1.207
 NE6  C13  O14   single  1.321  0.020  1.321
 NE6  O14  C14   single  1.427  0.020  1.427
 NE6  C14  H14   single  0.970  0.020  1.090
 NE6  C14  H14A  single  0.970  0.020  1.090
 NE6  C14  H14B  single  0.970  0.020  1.090
 NE6  O15  C15   double  1.213  0.020  1.213
 NE6  C15  C16   single  1.470  0.020  1.470
 NE6  C17  C16   single  1.500  0.020  1.500
 NE6  C16  C18   double  1.356  0.020  1.356
 NE6  C17  H17   single  0.970  0.020  1.090
 NE6  C17  H17A  single  0.970  0.020  1.090
 NE6  C17  H17B  single  0.970  0.020  1.090
 NE6  C18  C19   single  1.436  0.020  1.436
 NE6  C18  H18   single  0.930  0.020  1.080
 NE6  C19  C20   double  1.351  0.020  1.351
 NE6  C19  H19   single  0.930  0.020  1.080
 NE6  C20  C21   single  1.495  0.020  1.495
 NE6  C20  C22   single  1.501  0.020  1.501
 NE6  C21  H21   single  0.970  0.020  1.090
 NE6  C21  H21A  single  0.970  0.020  1.090
 NE6  C21  H21B  single  0.970  0.020  1.090
 NE6  C22  C23   single  1.533  0.020  1.533
 NE6  C22  H22   single  0.970  0.020  1.090
 NE6  C22  H22A  single  0.970  0.020  1.090
 NE6  C23  C24   single  1.522  0.020  1.522
 NE6  C23  H23   single  0.970  0.020  1.090
 NE6  C23  H23A  single  0.970  0.020  1.090
 NE6  C24  H24   single  0.970  0.020  1.090
 NE6  C24  H24A  single  0.970  0.020  1.090
 NE6  C24  H24B  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
 NE6  C6    O1   C2    122.85  3.000
 NE6  O2    C2   C3    124.12  3.000
 NE6  O2    C2   O1    118.09  3.000
 NE6  C3    C2   O1    117.69  3.000
 NE6  H3    C3   C15   111.49  3.000
 NE6  H3    C3   C4    109.30  3.000
 NE6  C15   C3   C4    107.54  3.000
 NE6  H3    C3   C2    107.80  3.000
 NE6  C15   C3   C2    104.91  3.000
 NE6  C4    C3   C2    115.79  3.000
 NE6  O4    C4   C5    124.44  3.000
 NE6  C5    C4   C3    115.64  3.000
 NE6  O4    C4   C3    119.88  3.000
 NE6  H5    C5   C6    119.14  3.000
 NE6  H5    C5   C4    119.58  3.000
 NE6  C6    C5   C4    121.28  3.000
 NE6  C7    C6   C5    124.89  3.000
 NE6  C7    C6   O1    111.83  3.000
 NE6  C5    C6   O1    123.26  3.000
 NE6  H7    C7   C9    108.15  3.000
 NE6  H7    C7   C8    108.53  3.000
 NE6  C9    C7   C8    112.84  3.000
 NE6  H7    C7   C6    106.18  3.000
 NE6  C9    C7   C6    110.48  3.000
 NE6  C8    C7   C6    110.39  3.000
 NE6  H8B   C8   H8A   107.37  3.000
 NE6  H8B   C8   H8    107.73  3.000
 NE6  H8A   C8   H8    108.42  3.000
 NE6  H8B   C8   C7    110.22  3.000
 NE6  H8A   C8   C7    111.28  3.000
 NE6  H8    C8   C7    111.66  3.000
 NE6  H9A   C9   H9    106.76  3.000
 NE6  H9A   C9   C10   109.46  3.000
 NE6  H9    C9   C10   108.80  3.000
 NE6  H9A   C9   C7    109.92  3.000
 NE6  H9    C9   C7    108.93  3.000
 NE6  C10   C9   C7    112.79  3.000
 NE6  H10A  C10  H10   106.65  3.000
 NE6  H10A  C10  C11   109.40  3.000
 NE6  H10   C10  C11   109.27  3.000
 NE6  H10A  C10  C9    109.74  3.000
 NE6  H10   C10  C9    110.40  3.000
 NE6  C11   C10  C9    111.26  3.000
 NE6  H11A  C11  H11   107.97  3.000
 NE6  H11A  C11  C12   107.92  3.000
 NE6  H11   C11  C12   109.86  3.000
 NE6  H11A  C11  C10   108.88  3.000
 NE6  H11   C11  C10   110.91  3.000
 NE6  C12   C11  C10   111.20  3.000
 NE6  H12   C12  N12   121.85  3.000
 NE6  H12   C12  C11   116.10  3.000
 NE6  N12   C12  C11   122.03  3.000
 NE6  O13   C13  O14   124.66  3.000
 NE6  O14   C13  N12   109.23  3.000
 NE6  O13   C13  N12   126.05  3.000
 NE6  H14B  C14  H14A  109.31  3.000
 NE6  H14B  C14  H14   109.31  3.000
 NE6  H14A  C14  H14   109.36  3.000
 NE6  H14B  C14  O14   111.54  3.000
 NE6  H14A  C14  O14   111.34  3.000
 NE6  H14   C14  O14   105.90  3.000
 NE6  O15   C15  C16   124.85  3.000
 NE6  C16   C15  C3    118.10  3.000
 NE6  O15   C15  C3    117.02  3.000
 NE6  C18   C16  C17   124.38  3.000
 NE6  C18   C16  C15   116.03  3.000
 NE6  C17   C16  C15   119.58  3.000
 NE6  H17B  C17  H17A  106.97  3.000
 NE6  H17B  C17  H17   107.38  3.000
 NE6  H17A  C17  H17   106.84  3.000
 NE6  H17B  C17  C16   111.69  3.000
 NE6  H17A  C17  C16   111.85  3.000
 NE6  H17   C17  C16   111.81  3.000
 NE6  H18   C18  C19   116.75  3.000
 NE6  H18   C18  C16   116.53  3.000
 NE6  C19   C18  C16   126.72  3.000
 NE6  H19   C19  C20   116.97  3.000
 NE6  H19   C19  C18   117.89  3.000
 NE6  C20   C19  C18   125.14  3.000
 NE6  C22   C20  C21   115.25  3.000
 NE6  C22   C20  C19   119.60  3.000
 NE6  C21   C20  C19   125.15  3.000
 NE6  H21B  C21  H21A  107.71  3.000
 NE6  H21B  C21  H21   107.95  3.000
 NE6  H21A  C21  H21   106.23  3.000
 NE6  H21B  C21  C20   114.42  3.000
 NE6  H21A  C21  C20   110.63  3.000
 NE6  H21   C21  C20   109.54  3.000
 NE6  H22A  C22  H22   106.93  3.000
 NE6  H22A  C22  C23   108.84  3.000
 NE6  H22   C22  C23   108.85  3.000
 NE6  H22A  C22  C20   110.13  3.000
 NE6  H22   C22  C20   109.22  3.000
 NE6  C23   C22  C20   112.70  3.000
 NE6  H23A  C23  H23   106.45  3.000
 NE6  H23A  C23  C24   109.44  3.000
 NE6  H23   C23  C24   109.89  3.000
 NE6  H23A  C23  C22   110.00  3.000
 NE6  H23   C23  C22   108.97  3.000
 NE6  C24   C23  C22   111.94  3.000
 NE6  H24B  C24  H24A  107.60  3.000
 NE6  H24B  C24  H24   107.60  3.000
 NE6  H24A  C24  H24   107.69  3.000
 NE6  H24B  C24  C23   111.31  3.000
 NE6  H24A  C24  C23   111.22  3.000
 NE6  H24   C24  C23   111.23  3.000
 NE6  C13   N12  C12   117.63  3.000
 NE6  C14   O14  C13   117.15  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
 NE6  Var_01  C4   C5   C6   O1     -3.35  30.0  1
 NE6  Var_02  C5   C6   O1   C2     -0.51  30.0  1
 NE6  Var_03  C6   C5   C4   C3     -6.19  30.0  1
 NE6  Var_04  C17  C16  C15  C3      2.00  30.0  2
 NE6  Var_05  C19  C18  C16  C15   178.85   0.0  2
 NE6  Var_06  C21  C20  C19  C18     0.44   0.0  2
 NE6  Var_07  C11  C10  C9   C7    176.84  30.0  3
 NE6  Var_08  C12  C11  C10  C9    178.18  30.0  3
 NE6  Var_09  N12  C12  C11  C10   117.17  30.0  3
 NE6  Var_10  O13  C13  N12  C12   -41.39  30.0  3
 NE6  Var_11  N12  C13  O14  C14   179.24  30.0  2
 NE6  Var_12  C20  C19  C18  C16  -178.97  30.0  2
 NE6  Var_13  C23  C22  C20  C19   101.77  30.0  3
 NE6  Var_14  C24  C23  C22  C20   177.24  30.0  3
 NE6  Var_15  H12  C12  N12  C13    -3.55   0.0  2
 NE6  Var_16  H14  C14  O14  C13   178.90  30.0  3
 NE6  Var_17  H17  C17  C16  C15    61.01  30.0  3
 NE6  Var_18  H21  C21  C20  C19   117.53  30.0  3
 NE6  Var_19  H24  C24  C23  C22   178.93  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
 NE6  chir_01  C3  C2  C4  C15  negativ
 NE6  chir_02  C7  C6  C8  C9   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
 NE6  plan-1  C18  0.020
 NE6  plan-1  C19  0.020
 NE6  plan-1  C20  0.020
 NE6  plan-1  C21  0.020
 NE6  plan-1  C22  0.020
 NE6  plan-1  H19  0.020
 NE6  plan-2  C3   0.020
 NE6  plan-2  C4   0.020
 NE6  plan-2  C5   0.020
 NE6  plan-2  O4   0.020
 NE6  plan-3  C3   0.020
 NE6  plan-3  C15  0.020
 NE6  plan-3  C16  0.020
 NE6  plan-3  O15  0.020
 NE6  plan-4  O1   0.020
 NE6  plan-4  C2   0.020
 NE6  plan-4  C3   0.020
 NE6  plan-4  O2   0.020
 NE6  plan-5  C11  0.020
 NE6  plan-5  C12  0.020
 NE6  plan-5  C13  0.020
 NE6  plan-5  N12  0.020
 NE6  plan-5  H12  0.020
 NE6  plan-6  C13  0.020
 NE6  plan-6  N12  0.020
 NE6  plan-6  O14  0.020
 NE6  plan-6  O13  0.020
 NE6  plan-7  C15  0.020
 NE6  plan-7  C16  0.020
 NE6  plan-7  C17  0.020
 NE6  plan-7  C18  0.020
 NE6  plan-7  C19  0.020
 NE6  plan-7  H18  0.020

