# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 00:18:56 2020
#   Inital geometry file: a 157 line input string
#   Ligand name: methyl (2~{R})-3-dimethoxyphosphoryloxy-2-[(2~{Z},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](CO[P](=O)(OC)OC)OC\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
 7B5  7B5  'methyl (2~{R})-3-dimethoxyphosphoryloxy-2-[(2~{Z},6~{E})-3,7,11-trimethyldodeca-2,6,10-trienoxy]propanoate'  ligand  66  29  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7B5
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
 7B5  CAC  C  CH3   0  -0.719   -7.8082   1.5157  -1.4876
 7B5  CAW  C  C     0   0.079   -8.2103   1.6784  -0.0512
 7B5  CAD  C  CH3   0  -0.705   -9.3108   2.6752   0.1727
 7B5  CAJ  C  C1    0  -0.256   -7.6635   1.0140   0.9704
 7B5  CAM  C  CH2   0  -0.488   -6.5602   0.0033   0.9226
 7B5  CAP  C  CH2   0  -0.495   -5.2537   0.5504   1.5182
 7B5  CAX  C  C     0   0.121   -4.1626  -0.4823   1.5531
 7B5  CAE  C  CH3   0  -0.748   -4.3647  -1.6443   2.4934
 7B5  CAK  C  C1    0  -0.274   -3.0917  -0.3801   0.7633
 7B5  CAN  C  CH2   0  -0.488   -1.9835  -1.3804   0.6581
 7B5  CAQ  C  CH2   0  -0.520   -2.1555  -2.2811  -0.5774
 7B5  CAY  C  C     0   0.131   -1.0539  -3.3040  -0.6866
 7B5  CAF  C  CH3   0  -0.719   -1.3502  -4.6272  -0.0465
 7B5  CAL  C  C1    0  -0.322    0.1253  -3.0691  -1.2668
 7B5  CAO  C  CH2   0  -0.201    0.5493  -1.7992  -1.9243
 7B5  OAV  O  O2    0  -0.483    1.6998  -1.3146  -1.2423
 7B5  CBB  C  CH1   0  -0.087    2.2459  -0.1628  -1.7954
 7B5  CBA  C  C     0   0.568    1.5366   1.0824  -1.2632
 7B5  OAH  O  O     0  -0.421    0.6636   1.0710  -0.4385
 7B5  OAS  O  O2    0  -0.456    2.0167   2.1776  -1.8303
 7B5  CAA  C  CH3   0  -0.433    1.4733   3.4324  -1.4111
 7B5  CAR  C  CH2   0  -0.196    3.7269  -0.1083  -1.4746
 7B5  OAW  O  O2    0  -0.592    3.8624   0.0863  -0.0634
 7B5  PBC  P  P     0   1.508    5.3175   0.1901   0.5854
 7B5  OAU  O  O2    0  -0.580    4.8508   0.2145   2.1054
 7B5  CAI  C  CH3   0  -0.420    5.8364   0.2089   3.1465
 7B5  OAI  O  O     0  -0.698    6.3028  -0.8315   0.1896
 7B5  OAT  O  O2    0  -0.584    5.8758   1.6435   0.2394
 7B5  CAB  C  CH3   0  -0.426    5.0913   2.8269   0.4165
 7B5  H1   H  HCH3  0   0.234   -8.6602   1.1955  -2.0932
 7B5  H2   H  HCH3  0   0.234   -7.4794   2.4726  -1.9009
 7B5  H3   H  HCH3  0   0.239   -7.0047   0.7972  -1.6370
 7B5  H4   H  HCH3  0   0.230   -9.0281   3.6625  -0.2019
 7B5  H5   H  HCH3  0   0.230  -10.2148   2.3860  -0.3702
 7B5  H6   H  HCH3  0   0.235   -9.5701   2.7740   1.2266
 7B5  H7   H  H     0   0.220   -8.0336   1.2373   1.9691
 7B5  H8   H  HCH2  0   0.235   -6.8675  -0.8836   1.4861
 7B5  H9   H  HCH2  0   0.236   -6.3681  -0.3363  -0.0964
 7B5  H10  H  HCH2  0   0.233   -4.9344   1.4166   0.9329
 7B5  H11  H  HCH2  0   0.228   -5.4522   0.9116   2.5340
 7B5  H12  H  HCH3  0   0.242   -5.2599  -1.5169   3.1020
 7B5  H13  H  HCH3  0   0.241   -4.4710  -2.5891   1.9565
 7B5  H14  H  HCH3  0   0.246   -3.5233  -1.7631   3.1789
 7B5  H15  H  H     0   0.220   -3.0230   0.4751   0.0947
 7B5  H16  H  HCH2  0   0.250   -1.0244  -0.8627   0.5797
 7B5  H17  H  HCH2  0   0.233   -1.9308  -2.0023   1.5547
 7B5  H18  H  HCH2  0   0.244   -3.1190  -2.7936  -0.5059
 7B5  H19  H  HCH2  0   0.243   -2.2149  -1.6567  -1.4708
 7B5  H20  H  HCH3  0   0.240   -2.1928  -5.1160  -0.5416
 7B5  H21  H  HCH3  0   0.240   -0.4974  -5.3041  -0.0787
 7B5  H22  H  HCH3  0   0.237   -1.6406  -4.4978   0.9994
 7B5  H23  H  H     0   0.234    0.8683  -3.8624  -1.2756
 7B5  H24  H  HCH2  0   0.221    0.8075  -1.9877  -2.9761
 7B5  H25  H  HCH2  0   0.222   -0.2484  -1.0520  -1.9185
 7B5  H26  H  HCH1  0   0.274    2.1677  -0.1570  -2.8936
 7B5  H27  H  HCH3  0   0.257    2.0071   4.1914  -1.9742
 7B5  H28  H  HCH3  0   0.251    0.4087   3.4959  -1.6330
 7B5  H29  H  HCH3  0   0.242    1.6295   3.5940  -0.3449
 7B5  H30  H  HCH2  0   0.276    4.1958  -1.0456  -1.7796
 7B5  H31  H  HCH2  0   0.258    4.1975   0.7069  -2.0275
 7B5  H32  H  HCH3  0   0.260    5.2956   0.2314   4.0880
 7B5  H33  H  HCH3  0   0.246    6.4464  -0.6929   3.1047
 7B5  H34  H  HCH3  0   0.241    6.4816   1.0858   3.0880
 7B5  H35  H  HCH3  0   0.258    5.7764   3.6695   0.3861
 7B5  H36  H  HCH3  0   0.237    4.3664   2.9321  -0.3905
 7B5  H37  H  HCH3  0   0.239    4.5687   2.8335   1.3733

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
 7B5  CAF  CAY  single  1.499  0.020  1.499
 7B5  CAA  OAS  single  1.430  0.020  1.430
 7B5  CAL  CAY  double  1.335  0.020  1.335
 7B5  CAL  CAO  single  1.492  0.020  1.492
 7B5  OAH  CBA  double  1.201  0.020  1.201
 7B5  OAV  CAO  single  1.423  0.020  1.423
 7B5  OAV  CBB  single  1.390  0.020  1.390
 7B5  CAY  CAQ  single  1.507  0.020  1.507
 7B5  CBA  OAS  single  1.323  0.020  1.323
 7B5  CBA  CBB  single  1.529  0.020  1.529
 7B5  CBB  CAR  single  1.516  0.020  1.516
 7B5  CAQ  CAN  single  1.539  0.020  1.539
 7B5  CAK  CAN  single  1.497  0.020  1.497
 7B5  CAK  CAX  double  1.335  0.020  1.335
 7B5  CAR  OAW  single  1.431  0.020  1.431
 7B5  CAP  CAX  single  1.503  0.020  1.503
 7B5  CAP  CAM  single  1.537  0.020  1.537
 7B5  CAX  CAE  single  1.508  0.020  1.508
 7B5  OAW  PBC  single  1.597  0.020  1.597
 7B5  CAJ  CAM  single  1.497  0.020  1.497
 7B5  CAJ  CAW  double  1.336  0.020  1.336
 7B5  CAD  CAW  single  1.502  0.020  1.502
 7B5  OAT  PBC  single  1.595  0.020  1.595
 7B5  OAT  CAB  single  1.431  0.020  1.431
 7B5  PBC  OAU  single  1.590  0.020  1.590
 7B5  PBC  OAI  double  1.473  0.020  1.473
 7B5  CAW  CAC  single  1.500  0.020  1.500
 7B5  OAU  CAI  single  1.434  0.020  1.434
 7B5  CAC  H1   single  0.970  0.020  1.090
 7B5  CAC  H2   single  0.970  0.020  1.090
 7B5  CAC  H3   single  0.970  0.020  1.090
 7B5  CAD  H4   single  0.970  0.020  1.090
 7B5  CAD  H5   single  0.970  0.020  1.090
 7B5  CAD  H6   single  0.970  0.020  1.090
 7B5  CAJ  H7   single  0.930  0.020  1.080
 7B5  CAM  H8   single  0.970  0.020  1.090
 7B5  CAM  H9   single  0.970  0.020  1.090
 7B5  CAP  H10  single  0.970  0.020  1.090
 7B5  CAP  H11  single  0.970  0.020  1.090
 7B5  CAE  H12  single  0.970  0.020  1.090
 7B5  CAE  H13  single  0.970  0.020  1.090
 7B5  CAE  H14  single  0.970  0.020  1.090
 7B5  CAK  H15  single  0.930  0.020  1.080
 7B5  CAN  H16  single  0.970  0.020  1.090
 7B5  CAN  H17  single  0.970  0.020  1.090
 7B5  CAQ  H18  single  0.970  0.020  1.090
 7B5  CAQ  H19  single  0.970  0.020  1.090
 7B5  CAF  H20  single  0.970  0.020  1.090
 7B5  CAF  H21  single  0.970  0.020  1.090
 7B5  CAF  H22  single  0.970  0.020  1.090
 7B5  CAL  H23  single  0.930  0.020  1.080
 7B5  CAO  H24  single  0.970  0.020  1.090
 7B5  CAO  H25  single  0.970  0.020  1.090
 7B5  CBB  H26  single  0.970  0.020  1.090
 7B5  CAA  H27  single  0.970  0.020  1.090
 7B5  CAA  H28  single  0.970  0.020  1.090
 7B5  CAA  H29  single  0.970  0.020  1.090
 7B5  CAR  H30  single  0.970  0.020  1.090
 7B5  CAR  H31  single  0.970  0.020  1.090
 7B5  CAI  H32  single  0.970  0.020  1.090
 7B5  CAI  H33  single  0.970  0.020  1.090
 7B5  CAI  H34  single  0.970  0.020  1.090
 7B5  CAB  H35  single  0.970  0.020  1.090
 7B5  CAB  H36  single  0.970  0.020  1.090
 7B5  CAB  H37  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
 7B5  H3   CAC  H2   107.70  3.000
 7B5  H3   CAC  H1   107.82  3.000
 7B5  H2   CAC  H1   106.34  3.000
 7B5  H3   CAC  CAW  113.64  3.000
 7B5  H2   CAC  CAW  110.35  3.000
 7B5  H1   CAC  CAW  110.68  3.000
 7B5  CAJ  CAW  CAD  121.07  3.000
 7B5  CAD  CAW  CAC  114.27  3.000
 7B5  CAJ  CAW  CAC  124.65  3.000
 7B5  H6   CAD  H5   107.90  3.000
 7B5  H6   CAD  H4   108.12  3.000
 7B5  H5   CAD  H4   106.42  3.000
 7B5  H6   CAD  CAW  112.25  3.000
 7B5  H5   CAD  CAW  110.88  3.000
 7B5  H4   CAD  CAW  111.03  3.000
 7B5  H7   CAJ  CAM  114.74  3.000
 7B5  H7   CAJ  CAW  117.43  3.000
 7B5  CAM  CAJ  CAW  127.81  3.000
 7B5  H9   CAM  H8   106.14  3.000
 7B5  H9   CAM  CAP  108.85  3.000
 7B5  H8   CAM  CAP  109.12  3.000
 7B5  H9   CAM  CAJ  111.70  3.000
 7B5  H8   CAM  CAJ  108.88  3.000
 7B5  CAP  CAM  CAJ  111.96  3.000
 7B5  H11  CAP  H10  106.74  3.000
 7B5  H11  CAP  CAX  109.65  3.000
 7B5  H10  CAP  CAX  110.18  3.000
 7B5  H11  CAP  CAM  108.81  3.000
 7B5  H10  CAP  CAM  108.84  3.000
 7B5  CAX  CAP  CAM  112.44  3.000
 7B5  CAK  CAX  CAE  122.37  3.000
 7B5  CAE  CAX  CAP  116.53  3.000
 7B5  CAK  CAX  CAP  121.08  3.000
 7B5  H14  CAE  H13  106.84  3.000
 7B5  H14  CAE  H12  107.16  3.000
 7B5  H13  CAE  H12  107.20  3.000
 7B5  H14  CAE  CAX  111.83  3.000
 7B5  H13  CAE  CAX  111.91  3.000
 7B5  H12  CAE  CAX  111.60  3.000
 7B5  H15  CAK  CAN  115.82  3.000
 7B5  H15  CAK  CAX  118.34  3.000
 7B5  CAN  CAK  CAX  125.77  3.000
 7B5  H17  CAN  H16  106.63  3.000
 7B5  H17  CAN  CAQ  109.34  3.000
 7B5  H16  CAN  CAQ  108.53  3.000
 7B5  H17  CAN  CAK  111.01  3.000
 7B5  H16  CAN  CAK  109.77  3.000
 7B5  CAQ  CAN  CAK  111.40  3.000
 7B5  H19  CAQ  H18  105.89  3.000
 7B5  H19  CAQ  CAY  111.63  3.000
 7B5  H18  CAQ  CAY  109.31  3.000
 7B5  H19  CAQ  CAN  109.17  3.000
 7B5  H18  CAQ  CAN  108.68  3.000
 7B5  CAY  CAQ  CAN  111.94  3.000
 7B5  CAL  CAY  CAF  121.02  3.000
 7B5  CAL  CAY  CAQ  123.90  3.000
 7B5  CAF  CAY  CAQ  115.06  3.000
 7B5  H22  CAF  H21  108.05  3.000
 7B5  H22  CAF  H20  106.36  3.000
 7B5  H21  CAF  H20  108.20  3.000
 7B5  H22  CAF  CAY  110.88  3.000
 7B5  H21  CAF  CAY  112.40  3.000
 7B5  H20  CAF  CAY  110.71  3.000
 7B5  H23  CAL  CAO  115.05  3.000
 7B5  H23  CAL  CAY  118.62  3.000
 7B5  CAO  CAL  CAY  126.33  3.000
 7B5  H25  CAO  H24  107.08  3.000
 7B5  H25  CAO  OAV  110.78  3.000
 7B5  H24  CAO  OAV  109.10  3.000
 7B5  H25  CAO  CAL  111.85  3.000
 7B5  H24  CAO  CAL  110.03  3.000
 7B5  OAV  CAO  CAL  107.98  3.000
 7B5  CBB  OAV  CAO  114.17  3.000
 7B5  H26  CBB  CAR  106.28  3.000
 7B5  H26  CBB  CBA  108.06  3.000
 7B5  CAR  CBB  CBA  110.50  3.000
 7B5  H26  CBB  OAV  111.93  3.000
 7B5  CAR  CBB  OAV  109.24  3.000
 7B5  CBA  CBB  OAV  110.75  3.000
 7B5  OAS  CBA  OAH  124.46  3.000
 7B5  OAS  CBA  CBB  110.89  3.000
 7B5  OAH  CBA  CBB  124.65  3.000
 7B5  CAA  OAS  CBA  117.55  3.000
 7B5  H29  CAA  H28  109.32  3.000
 7B5  H29  CAA  H27  109.48  3.000
 7B5  H28  CAA  H27  109.52  3.000
 7B5  H29  CAA  OAS  111.25  3.000
 7B5  H28  CAA  OAS  111.27  3.000
 7B5  H27  CAA  OAS  105.94  3.000
 7B5  H31  CAR  H30  108.33  3.000
 7B5  H31  CAR  OAW  110.92  3.000
 7B5  H30  CAR  OAW  110.59  3.000
 7B5  H31  CAR  CBB  109.92  3.000
 7B5  H30  CAR  CBB  109.24  3.000
 7B5  OAW  CAR  CBB  107.82  3.000
 7B5  PBC  OAW  CAR  119.73  3.000
 7B5  OAT  PBC  OAI  109.85  3.000
 7B5  OAI  PBC  OAU  117.62  3.000
 7B5  OAT  PBC  OAU  107.22  3.000
 7B5  OAI  PBC  OAW  117.08  3.000
 7B5  OAU  PBC  OAW   97.00  3.000
 7B5  OAT  PBC  OAW  106.86  3.000
 7B5  CAI  OAU  PBC  119.49  3.000
 7B5  H34  CAI  H33  109.41  3.000
 7B5  H34  CAI  H32  108.93  3.000
 7B5  H33  CAI  H32  109.22  3.000
 7B5  H34  CAI  OAU  111.39  3.000
 7B5  H33  CAI  OAU  111.12  3.000
 7B5  H32  CAI  OAU  106.69  3.000
 7B5  CAB  OAT  PBC  122.34  3.000
 7B5  H37  CAB  H36  109.30  3.000
 7B5  H37  CAB  H35  108.80  3.000
 7B5  H36  CAB  H35  108.89  3.000
 7B5  H37  CAB  OAT  112.12  3.000
 7B5  H36  CAB  OAT  110.66  3.000
 7B5  H35  CAB  OAT  106.99  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
 7B5  Var_01  CAM  CAJ  CAW  CAC     0.56   0.0  2
 7B5  Var_02  CAN  CAK  CAX  CAP  -176.50   0.0  2
 7B5  Var_03  CAO  CAL  CAY  CAQ    -1.49   0.0  2
 7B5  Var_04  CAP  CAM  CAJ  CAW   108.97  30.0  3
 7B5  Var_05  CAX  CAP  CAM  CAJ   176.47  30.0  1
 7B5  Var_06  CAK  CAX  CAP  CAM   110.96  30.0  3
 7B5  Var_07  CAQ  CAN  CAK  CAX    99.71  30.0  3
 7B5  Var_08  CAY  CAQ  CAN  CAK  -179.35  30.0  1
 7B5  Var_09  CAF  CAY  CAQ  CAN    92.57  30.0  2
 7B5  Var_10  OAV  CAO  CAL  CAY   119.99  30.0  3
 7B5  Var_11  OAT  PBC  OAW  CAR    76.02  30.0  3
 7B5  Var_12  H4   CAD  CAW  CAC   -58.31  30.0  3
 7B5  Var_13  H1   CAC  CAW  CAD   -59.00  30.0  3
 7B5  Var_14  H12  CAE  CAX  CAP    -5.51  30.0  3
 7B5  Var_15  H20  CAF  CAY  CAQ    63.58  30.0  3
 7B5  Var_16  H27  CAA  OAS  CBA   178.96  30.0  3
 7B5  Var_17  H30  CAR  OAW  PBC    60.81  30.0  1
 7B5  Var_18  H35  CAB  OAT  PBC   164.14  30.0  3
 7B5  Var_19  H32  CAI  OAU  PBC   179.83  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
 7B5  chir_01  CBB  OAV  CBA  CAR  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
 7B5  plan-1  CAQ  0.020
 7B5  plan-1  CAY  0.020
 7B5  plan-1  CAF  0.020
 7B5  plan-1  CAL  0.020
 7B5  plan-1  CAO  0.020
 7B5  plan-1  H23  0.020
 7B5  plan-2  CBB  0.020
 7B5  plan-2  CBA  0.020
 7B5  plan-2  OAH  0.020
 7B5  plan-2  OAS  0.020
 7B5  plan-3  CAP  0.020
 7B5  plan-3  CAX  0.020
 7B5  plan-3  CAE  0.020
 7B5  plan-3  CAK  0.020
 7B5  plan-3  CAN  0.020
 7B5  plan-3  H15  0.020
 7B5  plan-4  CAC  0.020
 7B5  plan-4  CAW  0.020
 7B5  plan-4  CAD  0.020
 7B5  plan-4  CAJ  0.020
 7B5  plan-4  CAM  0.020
 7B5  plan-4  H7   0.020

