# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 06:58:14 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: [(R)-{[(2E,4Z,8Z)-dodeca-2,4,8-trien-1-yl]oxy}(naphthalen-1-yl)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC\C=C/CC\C=C/C=C/CO[C@@H](c1cccc2ccccc12)[P](O)(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
 MFJ  MFJ  '[(R)-{[(2E,4Z,8Z)-dodeca-2,4,8-trien-1-yl]oxy}(naphthalen-1-yl)methyl]phosphonic acid'  ligand  55  28  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MFJ
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
 MFJ  CAE  C  CR16   0  -0.267   3.1819   3.2705  -2.0243
 MFJ  CAF  C  CR16   0  -0.254   2.0678   2.4124  -1.9322
 MFJ  CAG  C  CR16   0  -0.243   5.7767   0.1909   0.6418
 MFJ  CAH  C  CR16   0  -0.347   4.6753  -0.6853   0.7211
 MFJ  CAI  C  CR16   0  -0.312   4.3565   2.9199  -1.4191
 MFJ  CAJ  C  CR16   0  -0.336   5.6845   1.3582  -0.0606
 MFJ  CAK  C  CR16   0  -0.323   2.1521   1.2315  -1.2449
 MFJ  CAQ  C  CH3    0  -0.662  -8.1828  -2.1879  -1.3302
 MFJ  CAR  C  CH2    0  -0.418  -8.1861  -0.6668  -1.2771
 MFJ  CAS  C  CH2    0  -0.482  -6.7744  -0.0757  -1.2817
 MFJ  CAT  C  C1     0  -0.210  -6.7908   1.4204  -1.3050
 MFJ  CAU  C  C1     0  -0.216  -6.3487   2.2590  -0.3688
 MFJ  CAV  C  CH2    0  -0.490  -5.6875   1.9126   0.9281
 MFJ  CAW  C  CH2    0  -0.488  -4.2258   2.3849   0.9644
 MFJ  CAX  C  C1     0  -0.217  -3.5986   2.1365   2.2979
 MFJ  CAY  C  C1     0  -0.252  -2.5417   1.3612   2.5707
 MFJ  CAZ  C  C1     0  -0.259  -1.7492   0.6105   1.6115
 MFJ  CBA  C  C1     0  -0.260  -0.7243  -0.1755   1.9549
 MFJ  CBD  C  CR6    0   0.103   3.4808  -0.4052   0.1040
 MFJ  CBE  C  CR66   0   0.107   4.4722   1.7058  -0.7003
 MFJ  CBF  C  CR66   0   0.087   3.3553   0.8281  -0.6111
 MFJ  CBG  C  CH1    0  -0.329   2.2983  -1.3398   0.2179
 MFJ  OBC  O  O2     0  -0.513   1.4303  -0.7267   1.1784
 MFJ  PBH  P  P      0   1.181   2.6618  -3.1538   0.5706
 MFJ  H1   H  HCR6   0   0.253   3.1037   4.2013  -2.5712
 MFJ  H2   H  HCR6   0   0.253   1.1363   2.6916  -2.4080
 MFJ  H3   H  HCR6   0   0.247   6.7009  -0.0713   1.1418
 MFJ  H4   H  HCR6   0   0.252   4.7602  -1.5982   1.2959
 MFJ  H5   H  HCR6   0   0.250   5.2199   3.5720  -1.4790
 MFJ  H6   H  HCR6   0   0.248   6.5298   2.0326  -0.1309
 MFJ  H7   H  HCR6   0   0.244   1.2762   0.6002  -1.1952
 MFJ  H8   H  HCH3   0   0.218  -7.6910  -2.5494  -2.2350
 MFJ  H9   H  HCH3   0   0.218  -7.6525  -2.6119  -0.4755
 MFJ  H10  H  HCH3   0   0.227  -9.1971  -2.5886  -1.3220
 MFJ  H11  H  HCH2   0   0.216  -8.7466  -0.2701  -2.1290
 MFJ  H12  H  HCH2   0   0.218  -8.7112  -0.3267  -0.3805
 MFJ  H13  H  HCH2   0   0.228  -6.2209  -0.4563  -0.4202
 MFJ  H14  H  HCH2   0   0.227  -6.2484  -0.4396  -2.1716
 MFJ  H15  H  H      0   0.228  -7.2416   1.8574  -2.1927
 MFJ  H16  H  H      0   0.230  -6.4527   3.3243  -0.5602
 MFJ  H17  H  HCH2   0   0.236  -6.2307   2.3943   1.7480
 MFJ  H18  H  HCH2   0   0.239  -5.7240   0.8395   1.1228
 MFJ  H19  H  HCH2   0   0.241  -3.6730   1.8996   0.1588
 MFJ  H20  H  HCH2   0   0.239  -4.2003   3.4594   0.7520
 MFJ  H21  H  H      0   0.239  -4.0820   2.6337   3.1342
 MFJ  H22  H  H      0   0.239  -2.2301   1.2767   3.6080
 MFJ  H23  H  H      0   0.242  -2.0068   0.6949   0.5597
 MFJ  H24  H  H      0   0.241  -0.4522  -0.2696   3.0040
 MFJ  H25  H  HCH2   0   0.219  -0.1474  -2.0580   1.1292
 MFJ  H26  H  HCH2   0   0.188  -0.2499  -0.7464  -0.0412
 MFJ  H27  H  HCH1   0   0.173   1.7860  -1.3478  -0.7584
 MFJ  OAB  O  O      0  -0.889   3.2942  -3.2256   1.9666
 MFJ  CBB  C  CH2    0  -0.188   0.0615  -0.9922   0.9870
 MFJ  OAC  O  OP    -1  -0.879   1.2800  -3.8199   0.4973
 MFJ  OAD  O  OP    -1  -0.895   3.5976  -3.5542  -0.5735

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
 MFJ  CAR  CAQ  single    1.522  0.020  1.522
 MFJ  CAR  CAS  single    1.530  0.020  1.530
 MFJ  CAT  CAS  single    1.496  0.020  1.496
 MFJ  CAT  CAU  double    1.332  0.020  1.332
 MFJ  CAU  CAV  single    1.496  0.020  1.496
 MFJ  CAI  CAE  aromatic  1.367  0.020  1.367
 MFJ  CAI  CBE  aromatic  1.416  0.020  1.416
 MFJ  CAE  CAF  aromatic  1.409  0.020  1.409
 MFJ  CAJ  CBE  aromatic  1.414  0.020  1.414
 MFJ  CAJ  CAG  aromatic  1.365  0.020  1.365
 MFJ  CBE  CBF  aromatic  1.423  0.020  1.423
 MFJ  CAV  CAW  single    1.537  0.020  1.537
 MFJ  CAF  CAK  aromatic  1.369  0.020  1.369
 MFJ  CAG  CAH  aromatic  1.410  0.020  1.410
 MFJ  CBF  CAK  aromatic  1.419  0.020  1.419
 MFJ  CBF  CBD  aromatic  1.431  0.020  1.431
 MFJ  CAW  CAX  single    1.494  0.020  1.494
 MFJ  CAH  CBD  aromatic  1.373  0.020  1.373
 MFJ  CAX  CAY  double    1.339  0.020  1.339
 MFJ  CBD  CBG  single    1.512  0.020  1.512
 MFJ  CAY  CAZ  single    1.453  0.020  1.453
 MFJ  CBA  CAZ  double    1.336  0.020  1.336
 MFJ  CBA  CBB  single    1.490  0.020  1.490
 MFJ  CBG  OBC  single    1.432  0.020  1.432
 MFJ  CBG  PBH  single    1.883  0.020  1.883
 MFJ  OAB  PBH  deloc     1.534  0.020  1.534
 MFJ  CBB  OBC  single    1.407  0.020  1.407
 MFJ  PBH  OAD  deloc     1.531  0.020  1.531
 MFJ  PBH  OAC  deloc     1.536  0.020  1.536
 MFJ  CAE  H1   single    0.930  0.020  1.080
 MFJ  CAF  H2   single    0.930  0.020  1.080
 MFJ  CAG  H3   single    0.930  0.020  1.080
 MFJ  CAH  H4   single    0.930  0.020  1.080
 MFJ  CAI  H5   single    0.930  0.020  1.080
 MFJ  CAJ  H6   single    0.930  0.020  1.080
 MFJ  CAK  H7   single    0.930  0.020  1.080
 MFJ  CAQ  H8   single    0.970  0.020  1.090
 MFJ  CAQ  H9   single    0.970  0.020  1.090
 MFJ  CAQ  H10  single    0.970  0.020  1.090
 MFJ  CAR  H11  single    0.970  0.020  1.090
 MFJ  CAR  H12  single    0.970  0.020  1.090
 MFJ  CAS  H13  single    0.970  0.020  1.090
 MFJ  CAS  H14  single    0.970  0.020  1.090
 MFJ  CAT  H15  single    0.930  0.020  1.080
 MFJ  CAU  H16  single    0.930  0.020  1.080
 MFJ  CAV  H17  single    0.970  0.020  1.090
 MFJ  CAV  H18  single    0.970  0.020  1.090
 MFJ  CAW  H19  single    0.970  0.020  1.090
 MFJ  CAW  H20  single    0.970  0.020  1.090
 MFJ  CAX  H21  single    0.930  0.020  1.080
 MFJ  CAY  H22  single    0.930  0.020  1.080
 MFJ  CAZ  H23  single    0.930  0.020  1.080
 MFJ  CBA  H24  single    0.930  0.020  1.080
 MFJ  CBB  H25  single    0.970  0.020  1.090
 MFJ  CBB  H26  single    0.970  0.020  1.090
 MFJ  CBG  H27  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
 MFJ  H1   CAE  CAI  120.42  3.000
 MFJ  H1   CAE  CAF  119.97  3.000
 MFJ  CAI  CAE  CAF  119.62  3.000
 MFJ  H2   CAF  CAK  119.74  3.000
 MFJ  H2   CAF  CAE  119.63  3.000
 MFJ  CAK  CAF  CAE  120.62  3.000
 MFJ  H3   CAG  CAJ  120.14  3.000
 MFJ  H3   CAG  CAH  119.36  3.000
 MFJ  CAJ  CAG  CAH  120.50  3.000
 MFJ  H4   CAH  CBD  118.62  3.000
 MFJ  H4   CAH  CAG  119.54  3.000
 MFJ  CBD  CAH  CAG  121.84  3.000
 MFJ  H5   CAI  CBE  118.62  3.000
 MFJ  H5   CAI  CAE  120.39  3.000
 MFJ  CBE  CAI  CAE  120.99  3.000
 MFJ  H6   CAJ  CBE  119.10  3.000
 MFJ  H6   CAJ  CAG  120.85  3.000
 MFJ  CBE  CAJ  CAG  120.05  3.000
 MFJ  H7   CAK  CBF  120.05  3.000
 MFJ  H7   CAK  CAF  118.49  3.000
 MFJ  CBF  CAK  CAF  121.46  3.000
 MFJ  H10  CAQ  H9   107.66  3.000
 MFJ  H10  CAQ  H8   107.68  3.000
 MFJ  H9   CAQ  H8   107.55  3.000
 MFJ  H10  CAQ  CAR  111.40  3.000
 MFJ  H9   CAQ  CAR  111.22  3.000
 MFJ  H8   CAQ  CAR  111.15  3.000
 MFJ  H12  CAR  H11  106.24  3.000
 MFJ  H12  CAR  CAS  108.98  3.000
 MFJ  H11  CAR  CAS  109.27  3.000
 MFJ  H12  CAR  CAQ  109.91  3.000
 MFJ  H11  CAR  CAQ  109.66  3.000
 MFJ  CAS  CAR  CAQ  112.57  3.000
 MFJ  H14  CAS  H13  106.35  3.000
 MFJ  H14  CAS  CAT  108.94  3.000
 MFJ  H13  CAS  CAT  111.48  3.000
 MFJ  H14  CAS  CAR  108.48  3.000
 MFJ  H13  CAS  CAR  109.29  3.000
 MFJ  CAT  CAS  CAR  112.09  3.000
 MFJ  H15  CAT  CAU  117.28  3.000
 MFJ  H15  CAT  CAS  114.77  3.000
 MFJ  CAU  CAT  CAS  127.93  3.000
 MFJ  H16  CAU  CAV  114.94  3.000
 MFJ  H16  CAU  CAT  117.46  3.000
 MFJ  CAV  CAU  CAT  127.58  3.000
 MFJ  H18  CAV  H17  106.40  3.000
 MFJ  H18  CAV  CAW  109.26  3.000
 MFJ  H17  CAV  CAW  108.60  3.000
 MFJ  H18  CAV  CAU  111.57  3.000
 MFJ  H17  CAV  CAU  109.14  3.000
 MFJ  CAW  CAV  CAU  111.70  3.000
 MFJ  H20  CAW  H19  106.34  3.000
 MFJ  H20  CAW  CAX  109.05  3.000
 MFJ  H19  CAW  CAX  111.86  3.000
 MFJ  H20  CAW  CAV  108.60  3.000
 MFJ  H19  CAW  CAV  109.14  3.000
 MFJ  CAX  CAW  CAV  111.67  3.000
 MFJ  H21  CAX  CAY  117.35  3.000
 MFJ  H21  CAX  CAW  115.09  3.000
 MFJ  CAY  CAX  CAW  127.55  3.000
 MFJ  H22  CAY  CAZ  115.70  3.000
 MFJ  H22  CAY  CAX  117.78  3.000
 MFJ  CAZ  CAY  CAX  126.52  3.000
 MFJ  H23  CAZ  CBA  118.45  3.000
 MFJ  H23  CAZ  CAY  118.02  3.000
 MFJ  CBA  CAZ  CAY  123.53  3.000
 MFJ  H24  CBA  CBB  116.55  3.000
 MFJ  H24  CBA  CAZ  119.38  3.000
 MFJ  CBB  CBA  CAZ  124.03  3.000
 MFJ  CBG  CBD  CBF  120.13  3.000
 MFJ  CBG  CBD  CAH  121.36  3.000
 MFJ  CBF  CBD  CAH  118.46  3.000
 MFJ  CBF  CBE  CAJ  119.52  3.000
 MFJ  CBF  CBE  CAI  119.77  3.000
 MFJ  CAJ  CBE  CAI  120.71  3.000
 MFJ  CBE  CBF  CBD  119.60  3.000
 MFJ  CBD  CBF  CAK  122.86  3.000
 MFJ  CBE  CBF  CAK  117.54  3.000
 MFJ  H27  CBG  PBH  104.39  3.000
 MFJ  H27  CBG  OBC  108.38  3.000
 MFJ  PBH  CBG  OBC  113.80  3.000
 MFJ  H27  CBG  CBD  107.53  3.000
 MFJ  PBH  CBG  CBD  117.30  3.000
 MFJ  OBC  CBG  CBD  105.07  3.000
 MFJ  CBG  OBC  CBB  114.67  3.000
 MFJ  OAD  PBH  OAC  113.62  3.000
 MFJ  OAC  PBH  OAB  113.20  3.000
 MFJ  OAD  PBH  OAB  114.56  3.000
 MFJ  OAC  PBH  CBG  103.60  3.000
 MFJ  OAD  PBH  CBG  103.29  3.000
 MFJ  OAB  PBH  CBG  107.16  3.000
 MFJ  H26  CBB  H25  106.51  3.000
 MFJ  H26  CBB  OBC  111.08  3.000
 MFJ  H25  CBB  OBC  110.57  3.000
 MFJ  H26  CBB  CBA  109.56  3.000
 MFJ  H25  CBB  CBA  110.38  3.000
 MFJ  OBC  CBB  CBA  108.73  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
 MFJ  CONST_01  CAJ  CBE  CAI  CAE   180.00   0.0  0
 MFJ  CONST_02  CBF  CBE  CAI  CAE     0.00   0.0  0
 MFJ  CONST_03  CBF  CAK  CAF  CAE     0.00   0.0  0
 MFJ  CONST_04  CBE  CAI  CAE  CAF     0.00   0.0  0
 MFJ  CONST_05  CBE  CBF  CAK  CAF     0.00   0.0  0
 MFJ  CONST_06  CBD  CBF  CAK  CAF   180.00   0.0  0
 MFJ  CONST_07  CAI  CBE  CAJ  CAG   180.00   0.0  0
 MFJ  CONST_08  CBF  CBE  CAJ  CAG     0.00   0.0  0
 MFJ  CONST_09  CBF  CBD  CAH  CAG     0.00   0.0  0
 MFJ  CONST_10  CBE  CAJ  CAG  CAH     0.00   0.0  0
 MFJ  CONST_11  CBE  CBF  CBD  CAH     0.00   0.0  0
 MFJ  CONST_12  CAK  CBF  CBD  CAH   180.00   0.0  0
 MFJ  CONST_13  CAK  CAF  CAE  CAI     0.00   0.0  0
 MFJ  CONST_14  CAK  CBF  CBE  CAI     0.00   0.0  0
 MFJ  CONST_15  CBD  CBF  CBE  CAI   180.00   0.0  0
 MFJ  CONST_16  CAK  CBF  CBE  CAJ   180.00   0.0  0
 MFJ  CONST_17  CBD  CBF  CBE  CAJ     0.00   0.0  0
 MFJ  CONST_18  CBD  CAH  CAG  CAJ     0.00   0.0  0
 MFJ  CONST_19  CBG  CBD  CAH  CAG   180.00   0.0  0
 MFJ  CONST_20  CBG  CBD  CBF  CAK     0.00   0.0  0
 MFJ  CONST_21  CBG  CBD  CBF  CBE   180.00   0.0  0
 MFJ  CONST_22  H7   CAK  CAF  CAE   180.00   0.0  0
 MFJ  CONST_23  H5   CAI  CAE  CAF   180.00   0.0  0
 MFJ  CONST_24  H6   CAJ  CAG  CAH   180.00   0.0  0
 MFJ  CONST_25  H2   CAF  CAE  CAI   180.00   0.0  0
 MFJ  CONST_26  H4   CAH  CAG  CAJ   180.00   0.0  0
 MFJ  CONST_27  H1   CAE  CAF  CAK   180.00   0.0  0
 MFJ  CONST_28  H3   CAG  CAH  CBD   180.00   0.0  0
 MFJ  Var_01    CAV  CAU  CAT  CAS     1.89   0.0  2
 MFJ  Var_02    CAZ  CAY  CAX  CAW     1.57   0.0  2
 MFJ  Var_03    CBB  CBA  CAZ  CAY   177.47   0.0  2
 MFJ  Var_04    CAT  CAS  CAR  CAQ   176.87  30.0  3
 MFJ  Var_05    CAU  CAT  CAS  CAR   115.61  30.0  2
 MFJ  Var_06    CAW  CAV  CAU  CAT   114.07  30.0  3
 MFJ  Var_07    CAX  CAW  CAV  CAU   175.47  30.0  3
 MFJ  Var_08    CAY  CAX  CAW  CAV   118.60  30.0  3
 MFJ  Var_09    CBA  CAZ  CAY  CAX  -178.15  30.0  2
 MFJ  Var_10    OBC  CBB  CBA  CAZ   128.65  30.0  3
 MFJ  Var_11    H8   CAQ  CAR  CAS   -60.14  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
 MFJ  chir_01  CBG  CBD  OBC  PBH  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
 MFJ  plan-1  CAE  0.020
 MFJ  plan-1  CAF  0.020
 MFJ  plan-1  CAG  0.020
 MFJ  plan-1  CAH  0.020
 MFJ  plan-1  CAI  0.020
 MFJ  plan-1  CAJ  0.020
 MFJ  plan-1  CAK  0.020
 MFJ  plan-1  CBD  0.020
 MFJ  plan-1  CBE  0.020
 MFJ  plan-1  CBF  0.020
 MFJ  plan-1  CBG  0.020
 MFJ  plan-1  H1   0.020
 MFJ  plan-1  H2   0.020
 MFJ  plan-1  H3   0.020
 MFJ  plan-1  H4   0.020
 MFJ  plan-1  H5   0.020
 MFJ  plan-1  H6   0.020
 MFJ  plan-1  H7   0.020
 MFJ  plan-2  CAS  0.020
 MFJ  plan-2  CAT  0.020
 MFJ  plan-2  CAU  0.020
 MFJ  plan-2  CAV  0.020
 MFJ  plan-2  H15  0.020
 MFJ  plan-2  H16  0.020
 MFJ  plan-3  CAW  0.020
 MFJ  plan-3  CAX  0.020
 MFJ  plan-3  CAY  0.020
 MFJ  plan-3  CAZ  0.020
 MFJ  plan-3  H21  0.020
 MFJ  plan-3  H22  0.020
 MFJ  plan-4  CAY  0.020
 MFJ  plan-4  CAZ  0.020
 MFJ  plan-4  CBA  0.020
 MFJ  plan-4  H23  0.020
 MFJ  plan-4  H24  0.020
 MFJ  plan-4  CBB  0.020

