# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:37:37 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: methyl (2~{R})-2-azanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]sulfanyl-propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)CSC/C=C(C)/CC\C=C(C)\CCC=C(C)C
#
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
 5U0  5U0  'methyl (2~{R})-2-azanyl-3-[(2~{E},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienyl]sulfanyl-propanoate'  ligand  56  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5U0
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
 5U0  CAB  C  CH3   0  -0.719   -8.1210  -1.3667   1.3404
 5U0  CAA  C  C     0   0.077   -8.4850   0.0114   0.8727
 5U0  CAD  C  CH3   0  -0.706   -9.9626   0.2518   0.7567
 5U0  CAC  C  C1    0  -0.252   -7.6066   0.9715   0.5718
 5U0  CAE  C  CH2   0  -0.490   -6.1124   0.9029   0.6079
 5U0  CAF  C  CH2   0  -0.483   -5.5028   1.0103  -0.7997
 5U0  CAG  C  C     0   0.113   -3.9971   1.0191  -0.7857
 5U0  CAI  C  CH3   0  -0.734   -3.3721   2.2399  -0.1751
 5U0  CAH  C  C1    0  -0.271   -3.3109  -0.0196  -1.2697
 5U0  CAJ  C  CH2   0  -0.488   -1.8284  -0.2246  -1.2722
 5U0  CAK  C  CH2   0  -0.486   -1.4164  -1.2910  -0.2424
 5U0  CAL  C  C     0   0.142    0.0557  -1.5975  -0.2759
 5U0  CAN  C  CH3   0  -0.728    0.5159  -2.4800  -1.3965
 5U0  CAM  C  C1    0  -0.291    0.8720  -1.0841   0.6479
 5U0  CAO  C  CH2   0  -0.612    2.3528  -1.2812   0.7182
 5U0  SAP  S  S2    0  -0.006    3.1604  -0.0595  -0.3723
 5U0  CB   C  CH2   0  -0.554    4.8956  -0.3977   0.0407
 5U0  CA   C  CH1   0  -0.211    5.7670   0.7625  -0.4421
 5U0  N    N  NH2   0  -0.770    5.5074   1.0381  -1.8314
 5U0  C    C  C     0   0.574    7.2259   0.4296  -0.1368
 5U0  O    O  O     0  -0.442    8.0492   0.1476  -0.9699
 5U0  OAV  O  O2    0  -0.450    7.4746   0.4715   1.1629
 5U0  CAW  C  CH3   0  -0.424    8.7927   0.1313   1.5972
 5U0  H1   H  HCH3  0   0.239   -7.0486  -1.5395   1.4010
 5U0  H2   H  HCH3  0   0.234   -8.5456  -1.5611   2.3286
 5U0  H3   H  HCH3  0   0.234   -8.5434  -2.1209   0.6716
 5U0  H4   H  HCH3  0   0.230  -10.4655   0.0776   1.7115
 5U0  H5   H  HCH3  0   0.236  -10.1913   1.2670   0.4339
 5U0  H6   H  HCH3  0   0.230  -10.4146  -0.4397   0.0405
 5U0  H7   H  H     0   0.220   -8.0061   1.9258   0.2333
 5U0  H8   H  HCH2  0   0.234   -5.7360   1.7240   1.2260
 5U0  H9   H  HCH2  0   0.235   -5.7593  -0.0183   1.0743
 5U0  H10  H  HCH2  0   0.234   -5.8685   0.1758  -1.4031
 5U0  H11  H  HCH2  0   0.224   -5.8711   1.9283  -1.2726
 5U0  H12  H  HCH3  0   0.234   -3.8197   3.1460  -0.5901
 5U0  H13  H  HCH3  0   0.240   -3.5445   2.2769   0.9031
 5U0  H14  H  HCH3  0   0.243   -2.2972   2.2978  -0.3318
 5U0  H15  H  H     0   0.221   -3.8841  -0.8495  -1.6785
 5U0  H16  H  HCH2  0   0.233   -1.5106  -0.5401  -2.2707
 5U0  H17  H  HCH2  0   0.238   -1.2891   0.6983  -1.0525
 5U0  H18  H  HCH2  0   0.239   -1.7052  -0.9418   0.7515
 5U0  H19  H  HCH2  0   0.232   -1.9865  -2.2066  -0.4330
 5U0  H20  H  HCH3  0   0.240    0.1214  -2.1327  -2.3534
 5U0  H21  H  HCH3  0   0.242    1.5989  -2.5260  -1.4901
 5U0  H22  H  HCH3  0   0.242    0.1428  -3.4982  -1.2592
 5U0  H23  H  H     0   0.239    0.4440  -0.4447   1.4140
 5U0  H24  H  HCH2  0   0.277    2.7055  -1.1249   1.7388
 5U0  H25  H  HCH2  0   0.270    2.6543  -2.2846   0.4145
 5U0  H26  H  HCH2  0   0.280    4.9853  -0.5166   1.1211
 5U0  H27  H  HCH2  0   0.269    5.2111  -1.3345  -0.4270
 5U0  H28  H  HCH1  0   0.279    5.4987   1.6497   0.1392
 5U0  H29  H  HNH2  0   0.360    6.0340   1.8459  -2.1374
 5U0  H30  H  HNH2  0   0.348    5.8056   0.2626  -2.4105
 5U0  H32  H  HCH3  0   0.241    9.0389  -0.8995   1.3439
 5U0  H33  H  HCH3  0   0.240    9.5386   0.7970   1.1642
 5U0  H34  H  HCH3  0   0.253    8.7907   0.2458   2.6769

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
 5U0  CAD  CAA  single  1.502  0.020  1.502
 5U0  CAB  CAA  single  1.500  0.020  1.500
 5U0  CAA  CAC  double  1.336  0.020  1.336
 5U0  CAC  CAE  single  1.496  0.020  1.496
 5U0  CAE  CAF  single  1.538  0.020  1.538
 5U0  CAF  CAG  single  1.506  0.020  1.506
 5U0  CAH  CAG  double  1.336  0.020  1.336
 5U0  CAH  CAJ  single  1.497  0.020  1.497
 5U0  CAG  CAI  single  1.501  0.020  1.501
 5U0  CAJ  CAK  single  1.539  0.020  1.539
 5U0  CAK  CAL  single  1.504  0.020  1.504
 5U0  CAL  CAM  double  1.335  0.020  1.335
 5U0  CAL  CAN  single  1.499  0.020  1.499
 5U0  CAM  CAO  single  1.496  0.020  1.496
 5U0  CB   SAP  single  1.815  0.020  1.815
 5U0  CB   CA   single  1.529  0.020  1.529
 5U0  SAP  CAO  single  1.826  0.020  1.826
 5U0  N    CA   single  1.440  0.020  1.440
 5U0  CA   C    single  1.527  0.020  1.527
 5U0  O    C    double  1.205  0.020  1.205
 5U0  C    OAV  single  1.324  0.020  1.324
 5U0  OAV  CAW  single  1.429  0.020  1.429
 5U0  CAB  H1   single  0.970  0.020  1.090
 5U0  CAB  H2   single  0.970  0.020  1.090
 5U0  CAB  H3   single  0.970  0.020  1.090
 5U0  CAD  H4   single  0.970  0.020  1.090
 5U0  CAD  H5   single  0.970  0.020  1.090
 5U0  CAD  H6   single  0.970  0.020  1.090
 5U0  CAC  H7   single  0.930  0.020  1.080
 5U0  CAE  H8   single  0.970  0.020  1.090
 5U0  CAE  H9   single  0.970  0.020  1.090
 5U0  CAF  H10  single  0.970  0.020  1.090
 5U0  CAF  H11  single  0.970  0.020  1.090
 5U0  CAI  H12  single  0.970  0.020  1.090
 5U0  CAI  H13  single  0.970  0.020  1.090
 5U0  CAI  H14  single  0.970  0.020  1.090
 5U0  CAH  H15  single  0.930  0.020  1.080
 5U0  CAJ  H16  single  0.970  0.020  1.090
 5U0  CAJ  H17  single  0.970  0.020  1.090
 5U0  CAK  H18  single  0.970  0.020  1.090
 5U0  CAK  H19  single  0.970  0.020  1.090
 5U0  CAN  H20  single  0.970  0.020  1.090
 5U0  CAN  H21  single  0.970  0.020  1.090
 5U0  CAN  H22  single  0.970  0.020  1.090
 5U0  CAM  H23  single  0.930  0.020  1.080
 5U0  CAO  H24  single  0.970  0.020  1.090
 5U0  CAO  H25  single  0.970  0.020  1.090
 5U0  CB   H26  single  0.970  0.020  1.090
 5U0  CB   H27  single  0.970  0.020  1.090
 5U0  CA   H28  single  0.970  0.020  1.090
 5U0  N    H29  single  0.890  0.020  1.040
 5U0  N    H30  single  0.890  0.020  1.040
 5U0  CAW  H32  single  0.970  0.020  1.090
 5U0  CAW  H33  single  0.970  0.020  1.090
 5U0  CAW  H34  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
 5U0  H3   CAB  H2   106.28  3.000
 5U0  H3   CAB  H1   107.79  3.000
 5U0  H2   CAB  H1   107.72  3.000
 5U0  H3   CAB  CAA  110.44  3.000
 5U0  H2   CAB  CAA  110.55  3.000
 5U0  H1   CAB  CAA  113.73  3.000
 5U0  CAC  CAA  CAD  120.98  3.000
 5U0  CAC  CAA  CAB  124.82  3.000
 5U0  CAD  CAA  CAB  114.20  3.000
 5U0  H6   CAD  H5   107.97  3.000
 5U0  H6   CAD  H4   106.34  3.000
 5U0  H5   CAD  H4   108.10  3.000
 5U0  H6   CAD  CAA  110.86  3.000
 5U0  H5   CAD  CAA  112.25  3.000
 5U0  H4   CAD  CAA  111.08  3.000
 5U0  H7   CAC  CAE  114.47  3.000
 5U0  H7   CAC  CAA  117.32  3.000
 5U0  CAE  CAC  CAA  128.20  3.000
 5U0  H9   CAE  H8   106.30  3.000
 5U0  H9   CAE  CAF  108.78  3.000
 5U0  H8   CAE  CAF  109.16  3.000
 5U0  H9   CAE  CAC  111.85  3.000
 5U0  H8   CAE  CAC  108.83  3.000
 5U0  CAF  CAE  CAC  111.75  3.000
 5U0  H11  CAF  H10  106.79  3.000
 5U0  H11  CAF  CAG  109.57  3.000
 5U0  H10  CAF  CAG  110.13  3.000
 5U0  H11  CAF  CAE  108.68  3.000
 5U0  H10  CAF  CAE  108.63  3.000
 5U0  CAG  CAF  CAE  112.85  3.000
 5U0  CAH  CAG  CAI  124.47  3.000
 5U0  CAI  CAG  CAF  115.14  3.000
 5U0  CAH  CAG  CAF  120.38  3.000
 5U0  H14  CAI  H13  107.23  3.000
 5U0  H14  CAI  H12  107.81  3.000
 5U0  H13  CAI  H12  106.39  3.000
 5U0  H14  CAI  CAG  113.33  3.000
 5U0  H13  CAI  CAG  111.30  3.000
 5U0  H12  CAI  CAG  110.45  3.000
 5U0  H15  CAH  CAJ  114.62  3.000
 5U0  H15  CAH  CAG  117.30  3.000
 5U0  CAJ  CAH  CAG  128.03  3.000
 5U0  H17  CAJ  H16  106.50  3.000
 5U0  H17  CAJ  CAK  108.61  3.000
 5U0  H16  CAJ  CAK  109.46  3.000
 5U0  H17  CAJ  CAH  111.92  3.000
 5U0  H16  CAJ  CAH  109.19  3.000
 5U0  CAK  CAJ  CAH  111.05  3.000
 5U0  H19  CAK  H18  106.74  3.000
 5U0  H19  CAK  CAL  109.58  3.000
 5U0  H18  CAK  CAL  110.13  3.000
 5U0  H19  CAK  CAJ  108.88  3.000
 5U0  H18  CAK  CAJ  108.46  3.000
 5U0  CAL  CAK  CAJ  112.85  3.000
 5U0  CAM  CAL  CAN  123.77  3.000
 5U0  CAN  CAL  CAK  115.92  3.000
 5U0  CAM  CAL  CAK  120.30  3.000
 5U0  H22  CAN  H21  108.13  3.000
 5U0  H22  CAN  H20  106.45  3.000
 5U0  H21  CAN  H20  107.33  3.000
 5U0  H22  CAN  CAL  110.47  3.000
 5U0  H21  CAN  CAL  113.25  3.000
 5U0  H20  CAN  CAL  110.92  3.000
 5U0  H23  CAM  CAO  115.77  3.000
 5U0  H23  CAM  CAL  118.26  3.000
 5U0  CAO  CAM  CAL  125.96  3.000
 5U0  H25  CAO  H24  107.63  3.000
 5U0  H25  CAO  SAP  109.08  3.000
 5U0  H24  CAO  SAP  108.66  3.000
 5U0  H25  CAO  CAM  112.44  3.000
 5U0  H24  CAO  CAM  110.19  3.000
 5U0  SAP  CAO  CAM  108.76  3.000
 5U0  CB   SAP  CAO   99.33  3.000
 5U0  H27  CB   H26  107.86  3.000
 5U0  H27  CB   CA   110.52  3.000
 5U0  H26  CB   CA   110.40  3.000
 5U0  H27  CB   SAP  109.76  3.000
 5U0  H26  CB   SAP  108.93  3.000
 5U0  CA   CB   SAP  109.36  3.000
 5U0  H28  CA   C    107.75  3.000
 5U0  H28  CA   N    108.25  3.000
 5U0  C    CA   N    114.00  3.000
 5U0  H28  CA   CB   107.92  3.000
 5U0  C    CA   CB   108.41  3.000
 5U0  N    CA   CB   110.31  3.000
 5U0  H30  N    H29  106.57  3.000
 5U0  H30  N    CA   110.61  3.000
 5U0  H29  N    CA   110.54  3.000
 5U0  OAV  C    O    123.91  3.000
 5U0  OAV  C    CA   111.64  3.000
 5U0  O    C    CA   124.45  3.000
 5U0  CAW  OAV  C    117.65  3.000
 5U0  H34  CAW  H33  109.39  3.000
 5U0  H34  CAW  H32  109.35  3.000
 5U0  H33  CAW  H32  109.33  3.000
 5U0  H34  CAW  OAV  105.99  3.000
 5U0  H33  CAW  OAV  111.42  3.000
 5U0  H32  CAW  OAV  111.29  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
 5U0  Var_01  CAE  CAC  CAA  CAB     0.91   0.0  2
 5U0  Var_02  CAJ  CAH  CAG  CAF  -176.29   0.0  2
 5U0  Var_03  CAO  CAM  CAL  CAK  -178.65   0.0  2
 5U0  Var_04  CAF  CAE  CAC  CAA   113.24  30.0  3
 5U0  Var_05  CAG  CAF  CAE  CAC   176.89  30.0  3
 5U0  Var_06  CAH  CAG  CAF  CAE   110.98  30.0  3
 5U0  Var_07  CAK  CAJ  CAH  CAG   106.82  30.0  3
 5U0  Var_08  CAL  CAK  CAJ  CAH   176.08  30.0  3
 5U0  Var_09  CAM  CAL  CAK  CAJ   101.92  30.0  3
 5U0  Var_10  SAP  CAO  CAM  CAL    84.42  30.0  3
 5U0  Var_11  CA   CB   SAP  CAO  -163.90  30.0  1
 5U0  Var_12  H4   CAD  CAA  CAB    57.72  30.0  3
 5U0  Var_13  H1   CAB  CAA  CAD   178.74  30.0  3
 5U0  Var_14  H12  CAI  CAG  CAF   -48.98  30.0  3
 5U0  Var_15  H20  CAN  CAL  CAK    48.65  30.0  3
 5U0  Var_16  H32  CAW  OAV  C     -62.26  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
 5U0  chir_01  CA  CB  N  C  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
 5U0  plan-1  CAB  0.020
 5U0  plan-1  CAA  0.020
 5U0  plan-1  CAD  0.020
 5U0  plan-1  CAC  0.020
 5U0  plan-1  CAE  0.020
 5U0  plan-1  H7   0.020
 5U0  plan-2  CAF  0.020
 5U0  plan-2  CAG  0.020
 5U0  plan-2  CAI  0.020
 5U0  plan-2  CAH  0.020
 5U0  plan-2  CAJ  0.020
 5U0  plan-2  H15  0.020
 5U0  plan-3  CAK  0.020
 5U0  plan-3  CAL  0.020
 5U0  plan-3  CAN  0.020
 5U0  plan-3  CAM  0.020
 5U0  plan-3  CAO  0.020
 5U0  plan-3  H23  0.020
 5U0  plan-4  CA   0.020
 5U0  plan-4  C    0.020
 5U0  plan-4  O    0.020
 5U0  plan-4  OAV  0.020

