# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 09:03:27 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: (2~{R})-3-dimethoxyphosphoryloxy-2-[(2~{Z},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P](=O)(OC)OC[C@@H](OC\C=C(C)/CC/C=C(C)/CCC=C(C)C)C(O)=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
 78S  78S  '(2~{R})-3-dimethoxyphosphoryloxy-2-[(2~{Z},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoic acid'  ligand  63  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_78S
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
 78S  CAC  C  CH3   0  -0.719  -7.6339  -1.6014   1.4563
 78S  CAW  C  C     0   0.079  -7.9799  -1.8521   0.0180
 78S  CAD  C  CH3   0  -0.705  -9.0143  -2.9203  -0.1916
 78S  CAJ  C  C1    0  -0.255  -7.4413  -1.2008  -1.0163
 78S  CAM  C  CH2   0  -0.493  -6.4018  -0.1242  -0.9814
 78S  CAP  C  CH2   0  -0.481  -5.0396  -0.6286  -1.4830
 78S  CAX  C  C     0   0.113  -3.9867   0.4479  -1.5164
 78S  CAE  C  CH3   0  -0.732  -4.1843   1.5047  -2.5630
 78S  CAK  C  C1    0  -0.271  -2.9744   0.4264  -0.6452
 78S  CAN  C  CH2   0  -0.495  -1.8694   1.4227  -0.4884
 78S  CAQ  C  CH2   0  -0.518  -2.0774   2.3014   0.7567
 78S  CAY  C  C     0   0.132  -0.9691   3.3092   0.9228
 78S  CAF  C  CH3   0  -0.719  -1.2350   4.6506   0.3078
 78S  CAL  C  C1    0  -0.321   0.1927   3.0470   1.5258
 78S  CAO  C  CH2   0  -0.204   0.5878   1.7549   2.1570
 78S  OAU  O  O2    0  -0.482   1.6961   1.2330   1.4322
 78S  CBA  C  CH1   0  -0.086   2.2519   0.0874   1.9876
 78S  CAZ  C  C     0   0.522   1.4967  -1.1610   1.5375
 78S  OAI  O  O     0  -0.412   0.5798  -1.1637   0.7622
 78S  OAG  O  OH1   0  -0.594   1.9876  -2.2485   2.1179
 78S  CAR  C  CH2   0  -0.195   3.7135   0.0008   1.5931
 78S  OAV  O  O2    0  -0.592   3.7752  -0.2110   0.1794
 78S  PBB  P  P     0   1.510   5.1973  -0.3425  -0.5348
 78S  OAT  O  O2    0  -0.581   4.6688  -0.3296  -2.0348
 78S  CAB  C  CH3   0  -0.420   5.6143  -0.3253  -3.1128
 78S  OAH  O  O     0  -0.699   6.2238   0.6473  -0.1633
 78S  OAS  O  O2    0  -0.584   5.7295  -1.8158  -0.2363
 78S  CAA  C  CH3   0  -0.425   4.9146  -2.9771  -0.4259
 78S  H1   H  HCH3  0   0.234  -8.5189  -1.2906   2.0178
 78S  H2   H  HCH3  0   0.234  -7.2772  -2.5203   1.9284
 78S  H3   H  HCH3  0   0.239  -6.8680  -0.8408   1.5943
 78S  H4   H  HCH3  0   0.230  -9.9518  -2.6574   0.3060
 78S  H5   H  HCH3  0   0.236  -9.2295  -3.0856  -1.2470
 78S  H6   H  HCH3  0   0.230  -8.6909  -3.8705   0.2413
 78S  H7   H  H     0   0.221  -7.7665  -1.4878  -2.0142
 78S  H8   H  HCH2  0   0.235  -6.7346   0.7071  -1.6103
 78S  H9   H  HCH2  0   0.235  -6.2784   0.2844   0.0232
 78S  H10  H  HCH2  0   0.234  -4.7137  -1.4497  -0.8390
 78S  H11  H  HCH2  0   0.225  -5.1662  -1.0484  -2.4878
 78S  H12  H  HCH3  0   0.234  -4.2697   1.0505  -3.5535
 78S  H13  H  HCH3  0   0.240  -5.1140   2.0546  -2.3980
 78S  H14  H  HCH3  0   0.240  -3.3793   2.2356  -2.5993
 78S  H15  H  H     0   0.220  -2.9528  -0.3907   0.0733
 78S  H16  H  HCH2  0   0.249  -0.9196   0.8927  -0.3805
 78S  H17  H  HCH2  0   0.235  -1.7706   2.0583  -1.3705
 78S  H18  H  HCH2  0   0.244  -3.0324   2.8251   0.6619
 78S  H19  H  HCH2  0   0.243  -2.1732   1.6597   1.6351
 78S  H20  H  HCH3  0   0.240  -2.0805   5.1396   0.7978
 78S  H21  H  HCH3  0   0.240  -0.3740   5.3148   0.3709
 78S  H22  H  HCH3  0   0.237  -1.5076   4.5475  -0.7457
 78S  H23  H  H     0   0.233   0.9443   3.8308   1.5700
 78S  H24  H  HCH2  0   0.222   0.8875   1.9242   3.2007
 78S  H25  H  HCH2  0   0.222  -0.2376   1.0384   2.1713
 78S  H26  H  HCH1  0   0.275   2.2317   0.1131   3.0880
 78S  H27  H  HOH1  0   0.487   1.5065  -3.0360   1.8208
 78S  H28  H  HCH2  0   0.276   4.2117   0.9333   1.8643
 78S  H29  H  HCH2  0   0.258   4.1977  -0.8160   2.1319
 78S  H30  H  HCH3  0   0.246   6.2326   0.5713  -3.0880
 78S  H31  H  HCH3  0   0.240   6.2539  -1.2078  -3.0851
 78S  H32  H  HCH3  0   0.260   5.0380  -0.3371  -4.0333
 78S  H33  H  HCH3  0   0.257   5.5760  -3.8377  -0.3803
 78S  H34  H  HCH3  0   0.236   4.1680  -3.0621   0.3634
 78S  H35  H  HCH3  0   0.239   4.4137  -2.9698  -1.3941

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
 78S  OAS  CAA  single  1.431  0.020  1.431
 78S  OAS  PBB  single  1.595  0.020  1.595
 78S  OAH  PBB  double  1.474  0.020  1.474
 78S  PBB  OAT  single  1.590  0.020  1.590
 78S  PBB  OAV  single  1.597  0.020  1.597
 78S  OAT  CAB  single  1.434  0.020  1.434
 78S  OAV  CAR  single  1.431  0.020  1.431
 78S  CAR  CBA  single  1.516  0.020  1.516
 78S  CBA  OAU  single  1.389  0.020  1.389
 78S  CBA  CAZ  single  1.527  0.020  1.527
 78S  OAU  CAO  single  1.423  0.020  1.423
 78S  CAZ  OAI  double  1.201  0.020  1.201
 78S  CAZ  OAG  single  1.327  0.020  1.327
 78S  CAO  CAL  single  1.491  0.020  1.491
 78S  CAE  CAX  single  1.500  0.020  1.500
 78S  CAQ  CAY  single  1.507  0.020  1.507
 78S  CAQ  CAN  single  1.538  0.020  1.538
 78S  CAL  CAY  double  1.335  0.020  1.335
 78S  CAY  CAF  single  1.499  0.020  1.499
 78S  CAN  CAK  single  1.496  0.020  1.496
 78S  CAX  CAK  double  1.336  0.020  1.336
 78S  CAX  CAP  single  1.506  0.020  1.506
 78S  CAJ  CAM  single  1.497  0.020  1.497
 78S  CAJ  CAW  double  1.336  0.020  1.336
 78S  CAM  CAP  single  1.537  0.020  1.537
 78S  CAD  CAW  single  1.502  0.020  1.502
 78S  CAW  CAC  single  1.500  0.020  1.500
 78S  CAC  H1   single  0.970  0.020  1.090
 78S  CAC  H2   single  0.970  0.020  1.090
 78S  CAC  H3   single  0.970  0.020  1.090
 78S  CAD  H4   single  0.970  0.020  1.090
 78S  CAD  H5   single  0.970  0.020  1.090
 78S  CAD  H6   single  0.970  0.020  1.090
 78S  CAJ  H7   single  0.930  0.020  1.080
 78S  CAM  H8   single  0.970  0.020  1.090
 78S  CAM  H9   single  0.970  0.020  1.090
 78S  CAP  H10  single  0.970  0.020  1.090
 78S  CAP  H11  single  0.970  0.020  1.090
 78S  CAE  H12  single  0.970  0.020  1.090
 78S  CAE  H13  single  0.970  0.020  1.090
 78S  CAE  H14  single  0.970  0.020  1.090
 78S  CAK  H15  single  0.930  0.020  1.080
 78S  CAN  H16  single  0.970  0.020  1.090
 78S  CAN  H17  single  0.970  0.020  1.090
 78S  CAQ  H18  single  0.970  0.020  1.090
 78S  CAQ  H19  single  0.970  0.020  1.090
 78S  CAF  H20  single  0.970  0.020  1.090
 78S  CAF  H21  single  0.970  0.020  1.090
 78S  CAF  H22  single  0.970  0.020  1.090
 78S  CAL  H23  single  0.930  0.020  1.080
 78S  CAO  H24  single  0.970  0.020  1.090
 78S  CAO  H25  single  0.970  0.020  1.090
 78S  CBA  H26  single  0.970  0.020  1.090
 78S  OAG  H27  single  0.850  0.020  0.980
 78S  CAR  H28  single  0.970  0.020  1.090
 78S  CAR  H29  single  0.970  0.020  1.090
 78S  CAB  H30  single  0.970  0.020  1.090
 78S  CAB  H31  single  0.970  0.020  1.090
 78S  CAB  H32  single  0.970  0.020  1.090
 78S  CAA  H33  single  0.970  0.020  1.090
 78S  CAA  H34  single  0.970  0.020  1.090
 78S  CAA  H35  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
 78S  H3   CAC  H2   107.65  3.000
 78S  H3   CAC  H1   107.81  3.000
 78S  H2   CAC  H1   106.35  3.000
 78S  H3   CAC  CAW  113.62  3.000
 78S  H2   CAC  CAW  110.42  3.000
 78S  H1   CAC  CAW  110.68  3.000
 78S  CAJ  CAW  CAD  121.10  3.000
 78S  CAD  CAW  CAC  114.30  3.000
 78S  CAJ  CAW  CAC  124.60  3.000
 78S  H6   CAD  H5   108.07  3.000
 78S  H6   CAD  H4   106.41  3.000
 78S  H5   CAD  H4   107.93  3.000
 78S  H6   CAD  CAW  111.06  3.000
 78S  H5   CAD  CAW  112.28  3.000
 78S  H4   CAD  CAW  110.86  3.000
 78S  H7   CAJ  CAM  114.75  3.000
 78S  H7   CAJ  CAW  117.46  3.000
 78S  CAM  CAJ  CAW  127.78  3.000
 78S  H9   CAM  H8   106.20  3.000
 78S  H9   CAM  CAP  108.85  3.000
 78S  H8   CAM  CAP  109.35  3.000
 78S  H9   CAM  CAJ  111.66  3.000
 78S  H8   CAM  CAJ  108.77  3.000
 78S  CAP  CAM  CAJ  111.83  3.000
 78S  H11  CAP  H10  106.66  3.000
 78S  H11  CAP  CAX  109.52  3.000
 78S  H10  CAP  CAX  109.96  3.000
 78S  H11  CAP  CAM  108.82  3.000
 78S  H10  CAP  CAM  108.57  3.000
 78S  CAX  CAP  CAM  113.10  3.000
 78S  CAK  CAX  CAE  124.48  3.000
 78S  CAK  CAX  CAP  120.26  3.000
 78S  CAE  CAX  CAP  115.26  3.000
 78S  H14  CAE  H13  107.25  3.000
 78S  H14  CAE  H12  107.87  3.000
 78S  H13  CAE  H12  106.23  3.000
 78S  H14  CAE  CAX  113.52  3.000
 78S  H13  CAE  CAX  111.18  3.000
 78S  H12  CAE  CAX  110.47  3.000
 78S  H15  CAK  CAN  114.59  3.000
 78S  H15  CAK  CAX  117.24  3.000
 78S  CAN  CAK  CAX  128.13  3.000
 78S  H17  CAN  H16  106.47  3.000
 78S  H17  CAN  CAQ  109.50  3.000
 78S  H16  CAN  CAQ  108.34  3.000
 78S  H17  CAN  CAK  111.71  3.000
 78S  H16  CAN  CAK  109.22  3.000
 78S  CAQ  CAN  CAK  111.43  3.000
 78S  H19  CAQ  H18  105.93  3.000
 78S  H19  CAQ  CAY  111.65  3.000
 78S  H18  CAQ  CAY  109.36  3.000
 78S  H19  CAQ  CAN  109.11  3.000
 78S  H18  CAQ  CAN  108.76  3.000
 78S  CAY  CAQ  CAN  111.82  3.000
 78S  CAL  CAY  CAF  121.02  3.000
 78S  CAF  CAY  CAQ  115.00  3.000
 78S  CAL  CAY  CAQ  123.94  3.000
 78S  H22  CAF  H21  108.09  3.000
 78S  H22  CAF  H20  106.35  3.000
 78S  H21  CAF  H20  108.23  3.000
 78S  H22  CAF  CAY  110.80  3.000
 78S  H21  CAF  CAY  112.43  3.000
 78S  H20  CAF  CAY  110.71  3.000
 78S  H23  CAL  CAO  115.11  3.000
 78S  H23  CAL  CAY  118.59  3.000
 78S  CAO  CAL  CAY  126.30  3.000
 78S  H25  CAO  H24  107.12  3.000
 78S  H25  CAO  OAU  110.75  3.000
 78S  H24  CAO  OAU  109.13  3.000
 78S  H25  CAO  CAL  111.92  3.000
 78S  H24  CAO  CAL  109.92  3.000
 78S  OAU  CAO  CAL  107.97  3.000
 78S  CBA  OAU  CAO  114.23  3.000
 78S  H26  CBA  CAR  106.20  3.000
 78S  H26  CBA  CAZ  107.73  3.000
 78S  CAR  CBA  CAZ  110.69  3.000
 78S  H26  CBA  OAU  111.90  3.000
 78S  CAZ  CBA  OAU  111.01  3.000
 78S  CAR  CBA  OAU  109.20  3.000
 78S  OAG  CAZ  OAI  124.28  3.000
 78S  OAG  CAZ  CBA  110.99  3.000
 78S  OAI  CAZ  CBA  124.73  3.000
 78S  H27  OAG  CAZ  110.37  3.000
 78S  H29  CAR  H28  108.31  3.000
 78S  H29  CAR  OAV  110.96  3.000
 78S  H28  CAR  OAV  110.63  3.000
 78S  H29  CAR  CBA  109.99  3.000
 78S  H28  CAR  CBA  109.05  3.000
 78S  OAV  CAR  CBA  107.88  3.000
 78S  PBB  OAV  CAR  119.51  3.000
 78S  OAS  PBB  OAH  109.93  3.000
 78S  OAH  PBB  OAT  117.63  3.000
 78S  OAS  PBB  OAT  107.16  3.000
 78S  OAT  PBB  OAV   97.20  3.000
 78S  OAH  PBB  OAV  116.89  3.000
 78S  OAS  PBB  OAV  106.83  3.000
 78S  CAB  OAT  PBB  119.34  3.000
 78S  H32  CAB  H31  108.91  3.000
 78S  H32  CAB  H30  109.24  3.000
 78S  H31  CAB  H30  109.43  3.000
 78S  H32  CAB  OAT  106.70  3.000
 78S  H31  CAB  OAT  111.42  3.000
 78S  H30  CAB  OAT  111.08  3.000
 78S  CAA  OAS  PBB  122.33  3.000
 78S  H35  CAA  H34  109.21  3.000
 78S  H35  CAA  H33  108.81  3.000
 78S  H34  CAA  H33  108.96  3.000
 78S  H35  CAA  OAS  111.96  3.000
 78S  H34  CAA  OAS  110.94  3.000
 78S  H33  CAA  OAS  106.89  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
 78S  CONST_01  H27  OAG  CAZ  CBA   180.00   0.0  0
 78S  Var_01    CAM  CAJ  CAW  CAC     0.61   0.0  2
 78S  Var_02    CAN  CAK  CAX  CAP  -177.58   0.0  2
 78S  Var_03    CAO  CAL  CAY  CAQ    -1.45   0.0  2
 78S  Var_04    CAP  CAM  CAJ  CAW   107.64  30.0  3
 78S  Var_05    CAX  CAP  CAM  CAJ   177.51  30.0  3
 78S  Var_06    CAE  CAX  CAP  CAM   -69.77  30.0  2
 78S  Var_07    CAQ  CAN  CAK  CAX   105.10  30.0  1
 78S  Var_08    CAY  CAQ  CAN  CAK  -179.97  30.0  1
 78S  Var_09    CAL  CAY  CAQ  CAN   -84.65  30.0  3
 78S  Var_10    OAU  CAO  CAL  CAY   116.08  30.0  1
 78S  Var_11    OAS  PBB  OAV  CAR    77.77  30.0  1
 78S  Var_12    H4   CAD  CAW  CAC    60.05  30.0  3
 78S  Var_13    H1   CAC  CAW  CAD   -59.79  30.0  3
 78S  Var_14    H12  CAE  CAX  CAP   -55.43  30.0  3
 78S  Var_15    H20  CAF  CAY  CAQ    64.14  30.0  3
 78S  Var_16    H33  CAA  OAS  PBB   166.92  30.0  3
 78S  Var_17    H30  CAB  OAT  PBB   -62.17  30.0  3
 78S  Var_18    H28  CAR  OAV  PBB    60.71  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
 78S  chir_01  CBA  CAR  OAU  CAZ  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
 78S  plan-1  CBA  0.020
 78S  plan-1  CAZ  0.020
 78S  plan-1  OAI  0.020
 78S  plan-1  OAG  0.020
 78S  plan-1  H27  0.020
 78S  plan-2  CAQ  0.020
 78S  plan-2  CAY  0.020
 78S  plan-2  CAF  0.020
 78S  plan-2  CAL  0.020
 78S  plan-2  CAO  0.020
 78S  plan-2  H23  0.020
 78S  plan-3  CAP  0.020
 78S  plan-3  CAX  0.020
 78S  plan-3  CAE  0.020
 78S  plan-3  CAK  0.020
 78S  plan-3  CAN  0.020
 78S  plan-3  H15  0.020
 78S  plan-4  CAC  0.020
 78S  plan-4  CAW  0.020
 78S  plan-4  CAD  0.020
 78S  plan-4  CAJ  0.020
 78S  plan-4  CAM  0.020
 78S  plan-4  H7   0.020

