# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 00:51:34 2022
#   Inital geometry file: a 133 line input string
#   Ligand name: (2~{S})-3-methyl-2-[[(2~{S},4~{R})-1-methyl-4-[(2~{E},4~{E})-octa-2,4-dienoyl]-3,5-bis(oxidanylidene)pyrrolidin-2-yl]methyl]-2-oxidanyl-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC/C=C/C=C/C(=O)[C@@H]1C(=O)[C@H](C[C@](O)(C(C)C)C(O)=O)N(C)C1=O
#
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
 J3L  J3L  '(2~{S})-3-methyl-2-[[(2~{S},4~{R})-1-methyl-4-[(2~{E},4~{E})-octa-2,4-dienoyl]-3,5-bis(oxidanylidene)pyrrolidin-2-yl]methyl]-2-oxidanyl-butanoic acid'  ligand  52  26  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_J3L
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
 J3L  C13  C  CH3    0  -0.554  35.7854  -22.2134  35.2691
 J3L  C14  C  CR15   0  -0.142  33.2532  -22.2292  35.0037
 J3L  C15  C  CH2    0  -0.473  32.9434  -21.1585  36.0666
 J3L  C16  C  CT     0   0.128  32.2108  -21.7119  37.2932
 J3L  C24  C  CR5    0   0.391  32.3850  -22.1156  33.7588
 J3L  C01  C  CH3    0  -0.657  35.4954  -15.3636  34.0107
 J3L  C02  C  CH2    0  -0.433  34.1707  -15.1701  34.7340
 J3L  C03  C  CH2    0  -0.491  32.9512  -15.3881  33.8308
 J3L  C04  C  C1     0  -0.172  32.8722  -16.7835  33.3176
 J3L  C05  C  C1     0  -0.264  32.8834  -17.1236  32.0227
 J3L  C06  C  C1     0  -0.178  32.8219  -18.4810  31.5127
 J3L  C07  C  C1     0  -0.377  33.1006  -19.6012  32.2002
 J3L  C08  C  C      0   0.419  32.9748  -20.9322  31.6002
 J3L  C09  C  CR15   0  -0.653  33.2801  -22.0924  32.5355
 J3L  C10  C  CR5    0   0.558  34.6781  -22.0319  33.1149
 J3L  C18  C  CH1    0  -0.230  31.7652  -20.5610  38.2315
 J3L  C19  C  CH3    0  -0.666  31.1104  -21.0923  39.5052
 J3L  C20  C  CH3    0  -0.663  32.8468  -19.5467  38.5961
 J3L  C21  C  C      0   0.424  33.1084  -22.7391  38.0444
 J3L  N12  N  NR5    0  -0.473  34.5959  -22.1279  34.4503
 J3L  O11  O  O      0  -0.466  35.7045  -21.9265  32.4690
 J3L  O17  O  OH1    0  -0.699  31.0588  -22.4017  36.8670
 J3L  O23  O  O      0  -0.569  34.2416  -22.3859  38.4075
 J3L  O25  O  O      0  -0.338  31.1892  -22.0331  33.7324
 J3L  O26  O  O      0  -0.386  32.6500  -21.1309  30.4495
 J3L  H1   H  HCH3   0   0.268  35.4987  -22.3688  36.3049
 J3L  H2   H  HCH3   0   0.252  36.4117  -23.0479  34.9536
 J3L  H3   H  HCH3   0   0.249  36.3744  -21.2980  35.2095
 J3L  H4   H  HCR5   0   0.297  33.1020  -23.2343  35.4196
 J3L  H5   H  HCH2   0   0.269  33.8812  -20.6996  36.3783
 J3L  H6   H  HCH2   0   0.248  32.3496  -20.3512  35.6253
 J3L  H8   H  HCH3   0   0.230  36.3369  -15.1413  34.6673
 J3L  H9   H  HCH3   0   0.221  35.6165  -16.3883  33.6569
 J3L  H10  H  HCH3   0   0.217  35.5686  -14.7055  33.1428
 J3L  H11  H  HCH2   0   0.232  34.1177  -14.1583  35.1419
 J3L  H12  H  HCH2   0   0.222  34.1127  -15.8477  35.5906
 J3L  H13  H  HCH2   0   0.238  32.9733  -14.6813  32.9972
 J3L  H14  H  HCH2   0   0.251  32.0470  -15.1733  34.4096
 J3L  H15  H  H      0   0.257  32.7997  -17.5610  34.0753
 J3L  H16  H  H      0   0.256  32.9102  -16.3369  31.2755
 J3L  H17  H  H      0   0.272  32.5342  -18.5815  30.4708
 J3L  H18  H  H      0   0.270  33.4366  -19.5394  33.2303
 J3L  H19  H  HCR5   0   0.358  33.1620  -23.0329  31.9859
 J3L  H20  H  HCH1   0   0.212  30.9954  -20.0187  37.6674
 J3L  H21  H  HCH3   0   0.223  30.6566  -20.2743  40.0670
 J3L  H22  H  HCH3   0   0.223  30.3272  -21.8194  39.2934
 J3L  H23  H  HCH3   0   0.213  31.8430  -21.5659  40.1629
 J3L  H24  H  HCH3   0   0.218  32.4155  -18.7567  39.2137
 J3L  H25  H  HCH3   0   0.221  33.6538  -20.0078  39.1636
 J3L  H26  H  HCH3   0   0.222  33.2824  -19.0649  37.7203
 J3L  H27  H  HOH1   0   0.425  31.1831  -23.2773  37.2858
 J3L  O22  O  OC    -1  -0.598  32.5768  -23.8614  38.2146

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
 J3L  C05  C06  single  1.451  0.020  1.451
 J3L  C05  C04  double  1.339  0.020  1.339
 J3L  C03  C04  single  1.489  0.020  1.489
 J3L  C03  C02  single  1.533  0.020  1.533
 J3L  C06  C07  double  1.344  0.020  1.344
 J3L  C02  C01  single  1.522  0.020  1.522
 J3L  O26  C08  double  1.212  0.020  1.212
 J3L  C07  C08  single  1.465  0.020  1.465
 J3L  C08  C09  single  1.521  0.020  1.521
 J3L  C09  C10  single  1.514  0.020  1.514
 J3L  C09  C24  single  1.516  0.020  1.516
 J3L  O11  C10  double  1.217  0.020  1.217
 J3L  C10  N12  single  1.341  0.020  1.341
 J3L  C24  O25  double  1.199  0.020  1.199
 J3L  C24  C14  single  1.522  0.020  1.522
 J3L  N12  C14  single  1.456  0.020  1.456
 J3L  N12  C13  single  1.447  0.020  1.447
 J3L  C14  C15  single  1.540  0.020  1.540
 J3L  O23  C21  deloc   1.241  0.020  1.241
 J3L  C15  C16  single  1.532  0.020  1.532
 J3L  C21  O22  deloc   1.253  0.020  1.253
 J3L  C21  C16  single  1.557  0.020  1.557
 J3L  C16  O17  single  1.409  0.020  1.409
 J3L  C16  C18  single  1.550  0.020  1.550
 J3L  C20  C18  single  1.527  0.020  1.527
 J3L  C18  C19  single  1.528  0.020  1.528
 J3L  C13  H1   single  0.970  0.020  1.090
 J3L  C13  H2   single  0.970  0.020  1.090
 J3L  C13  H3   single  0.970  0.020  1.090
 J3L  C14  H4   single  0.970  0.020  1.090
 J3L  C15  H5   single  0.970  0.020  1.090
 J3L  C15  H6   single  0.970  0.020  1.090
 J3L  C01  H8   single  0.970  0.020  1.090
 J3L  C01  H9   single  0.970  0.020  1.090
 J3L  C01  H10  single  0.970  0.020  1.090
 J3L  C02  H11  single  0.970  0.020  1.090
 J3L  C02  H12  single  0.970  0.020  1.090
 J3L  C03  H13  single  0.970  0.020  1.090
 J3L  C03  H14  single  0.970  0.020  1.090
 J3L  C04  H15  single  0.930  0.020  1.080
 J3L  C05  H16  single  0.930  0.020  1.080
 J3L  C06  H17  single  0.930  0.020  1.080
 J3L  C07  H18  single  0.930  0.020  1.080
 J3L  C09  H19  single  0.970  0.020  1.090
 J3L  C18  H20  single  0.970  0.020  1.090
 J3L  C19  H21  single  0.970  0.020  1.090
 J3L  C19  H22  single  0.970  0.020  1.090
 J3L  C19  H23  single  0.970  0.020  1.090
 J3L  C20  H24  single  0.970  0.020  1.090
 J3L  C20  H25  single  0.970  0.020  1.090
 J3L  C20  H26  single  0.970  0.020  1.090
 J3L  O17  H27  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
 J3L  H3   C13  H2   108.45  3.000
 J3L  H3   C13  H1   108.35  3.000
 J3L  H2   C13  H1   108.55  3.000
 J3L  H3   C13  N12  111.33  3.000
 J3L  H2   C13  N12  110.73  3.000
 J3L  H1   C13  N12  109.35  3.000
 J3L  H4   C14  N12  109.55  3.000
 J3L  H4   C14  C24  107.43  3.000
 J3L  N12  C14  C24  102.12  3.000
 J3L  H4   C14  C15  110.31  3.000
 J3L  N12  C14  C15  113.55  3.000
 J3L  C24  C14  C15  113.45  3.000
 J3L  H6   C15  H5   105.75  3.000
 J3L  H6   C15  C16  109.24  3.000
 J3L  H5   C15  C16  109.55  3.000
 J3L  H6   C15  C14  110.08  3.000
 J3L  H5   C15  C14  108.49  3.000
 J3L  C16  C15  C14  113.43  3.000
 J3L  O17  C16  C21  107.11  3.000
 J3L  O17  C16  C18  108.15  3.000
 J3L  C21  C16  C18  111.31  3.000
 J3L  C18  C16  C15  110.72  3.000
 J3L  O17  C16  C15  109.01  3.000
 J3L  C21  C16  C15  110.41  3.000
 J3L  O25  C24  C09  124.76  3.000
 J3L  O25  C24  C14  126.30  3.000
 J3L  C09  C24  C14  108.93  3.000
 J3L  H10  C01  H9   107.51  3.000
 J3L  H10  C01  H8   107.71  3.000
 J3L  H9   C01  H8   107.53  3.000
 J3L  H10  C01  C02  111.08  3.000
 J3L  H9   C01  C02  111.73  3.000
 J3L  H8   C01  C02  111.08  3.000
 J3L  H12  C02  H11  106.19  3.000
 J3L  H12  C02  C03  109.34  3.000
 J3L  H11  C02  C03  108.25  3.000
 J3L  H12  C02  C01  109.86  3.000
 J3L  H11  C02  C01  109.72  3.000
 J3L  C03  C02  C01  113.22  3.000
 J3L  H14  C03  H13  107.04  3.000
 J3L  H14  C03  C04  108.80  3.000
 J3L  H13  C03  C04  110.13  3.000
 J3L  H14  C03  C02  108.51  3.000
 J3L  H13  C03  C02  109.95  3.000
 J3L  C04  C03  C02  112.24  3.000
 J3L  H15  C04  C05  119.51  3.000
 J3L  H15  C04  C03  115.67  3.000
 J3L  C05  C04  C03  124.82  3.000
 J3L  H16  C05  C06  115.92  3.000
 J3L  H16  C05  C04  118.81  3.000
 J3L  C06  C05  C04  125.24  3.000
 J3L  H17  C06  C07  117.96  3.000
 J3L  H17  C06  C05  115.79  3.000
 J3L  C07  C06  C05  126.25  3.000
 J3L  H18  C07  C08  117.84  3.000
 J3L  H18  C07  C06  120.15  3.000
 J3L  C08  C07  C06  122.01  3.000
 J3L  O26  C08  C09  120.83  3.000
 J3L  C09  C08  C07  115.07  3.000
 J3L  O26  C08  C07  124.10  3.000
 J3L  H19  C09  C10  109.01  3.000
 J3L  H19  C09  C08  108.94  3.000
 J3L  C10  C09  C08  112.96  3.000
 J3L  H19  C09  C24  109.14  3.000
 J3L  C10  C09  C24  103.70  3.000
 J3L  C08  C09  C24  112.92  3.000
 J3L  O11  C10  N12  125.88  3.000
 J3L  N12  C10  C09  108.75  3.000
 J3L  O11  C10  C09  125.36  3.000
 J3L  H20  C18  C20  106.93  3.000
 J3L  H20  C18  C19  107.44  3.000
 J3L  C20  C18  C19  109.60  3.000
 J3L  H20  C18  C16  104.91  3.000
 J3L  C19  C18  C16  111.70  3.000
 J3L  C20  C18  C16  115.72  3.000
 J3L  H23  C19  H22  108.05  3.000
 J3L  H23  C19  H21  107.10  3.000
 J3L  H22  C19  H21  107.54  3.000
 J3L  H23  C19  C18  111.43  3.000
 J3L  H22  C19  C18  112.22  3.000
 J3L  H21  C19  C18  110.29  3.000
 J3L  H26  C20  H25  108.03  3.000
 J3L  H26  C20  H24  107.01  3.000
 J3L  H25  C20  H24  107.73  3.000
 J3L  H26  C20  C18  112.62  3.000
 J3L  H25  C20  C18  111.60  3.000
 J3L  H24  C20  C18  109.63  3.000
 J3L  O23  C21  O22  127.03  3.000
 J3L  O22  C21  C16  114.31  3.000
 J3L  O23  C21  C16  118.66  3.000
 J3L  C10  N12  C14  116.10  3.000
 J3L  C14  N12  C13  122.62  3.000
 J3L  C10  N12  C13  121.16  3.000
 J3L  H27  O17  C16  101.82  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
 J3L  CONST_01  C09  C10  N12  C14     0.00   0.0  0
 J3L  CONST_02  C09  C10  N12  C13   180.00   0.0  0
 J3L  CONST_03  O11  C10  N12  C14   180.00   0.0  0
 J3L  CONST_04  O11  C10  N12  C13     0.00   0.0  0
 J3L  CONST_05  C06  C05  C04  C03   180.00   0.0  0
 J3L  CONST_06  H16  C05  C04  C03     0.00   0.0  0
 J3L  CONST_07  H15  C04  C05  C06     0.00   0.0  0
 J3L  Var_01    H1   C13  N12  C14     0.61  30.0  3
 J3L  Var_02    C09  C08  C07  C06  -177.81  30.0  2
 J3L  Var_03    C08  C07  C06  C05   178.42   0.0  2
 J3L  Var_04    C04  C03  C02  C01    63.01  30.0  1
 J3L  Var_05    C05  C04  C03  C02  -120.28  30.0  3
 J3L  Var_06    C07  C06  C05  C04   -19.07  30.0  2
 J3L  Var_07    H24  C20  C18  C16   177.08  30.0  3
 J3L  Var_08    H21  C19  C18  C16  -170.45  30.0  3
 J3L  Var_09    H8   C01  C02  C03   176.53  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
 J3L  chir_01  C14  C24  N12  C15  negativ
 J3L  chir_02  C16  C18  C21  C15  positiv
 J3L  chir_03  C09  C08  C10  C24  negativ

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
 J3L  plan-1  C14  0.020
 J3L  plan-1  C24  0.020
 J3L  plan-1  C09  0.020
 J3L  plan-1  O25  0.020
 J3L  plan-2  C07  0.020
 J3L  plan-2  C08  0.020
 J3L  plan-2  C09  0.020
 J3L  plan-2  O26  0.020
 J3L  plan-3  C13  0.020
 J3L  plan-3  C14  0.020
 J3L  plan-3  C09  0.020
 J3L  plan-3  C10  0.020
 J3L  plan-3  N12  0.020
 J3L  plan-3  O11  0.020
 J3L  plan-4  C16  0.020
 J3L  plan-4  C21  0.020
 J3L  plan-4  O23  0.020
 J3L  plan-4  O22  0.020
 J3L  plan-5  C03  0.020
 J3L  plan-5  C04  0.020
 J3L  plan-5  C05  0.020
 J3L  plan-5  C06  0.020
 J3L  plan-5  H15  0.020
 J3L  plan-5  H16  0.020
 J3L  plan-6  C05  0.020
 J3L  plan-6  C06  0.020
 J3L  plan-6  C07  0.020
 J3L  plan-6  C08  0.020
 J3L  plan-6  H17  0.020
 J3L  plan-6  H18  0.020

