# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 01:49:43 2021
#   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  57  28  .  2021-08-14  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.262  -74.2103  32.3946  -45.1098
 MFJ  CAF  C  CR16  0  -0.247  -74.5861  32.5981  -43.7674
 MFJ  CAG  C  CR16  0  -0.238  -69.5694  33.0257  -43.9228
 MFJ  CAH  C  CR16  0  -0.283  -69.9299  33.2292  -42.5789
 MFJ  CAI  C  CR16  0  -0.308  -72.8908  32.4540  -45.4600
 MFJ  CAJ  C  CR16  0  -0.326  -70.5300  32.7741  -44.8602
 MFJ  CAK  C  CR16  0  -0.349  -73.6431  32.8499  -42.8084
 MFJ  CAQ  C  CH3   0  -0.665  -68.6607  34.3846  -47.7878
 MFJ  CAR  C  CH2   0  -0.424  -67.3573  34.8239  -48.4370
 MFJ  CAS  C  CH2   0  -0.494  -66.4597  35.6243  -47.4880
 MFJ  CAT  C  C1    0  -0.216  -67.0225  36.9756  -47.1733
 MFJ  CAU  C  C1    0  -0.215  -67.5457  37.4025  -46.0243
 MFJ  CAV  C  CH2   0  -0.489  -67.7096  36.6267  -44.7536
 MFJ  CAW  C  CH2   0  -0.504  -69.1415  36.6670  -44.1901
 MFJ  CAX  C  C1    0  -0.193  -69.5501  38.0347  -43.7486
 MFJ  CAY  C  C1    0  -0.268  -69.9896  38.4073  -42.5426
 MFJ  CAZ  C  C1    0  -0.262  -70.2374  37.5654  -41.3709
 MFJ  CBA  C  C1    0  -0.227  -70.8975  36.4064  -41.3473
 MFJ  CBD  C  CR6   0   0.013  -71.2422  33.1894  -42.1781
 MFJ  CBE  C  CR66  0   0.121  -71.8923  32.7159  -44.4922
 MFJ  CBF  C  CR66  0   0.115  -72.2649  32.9211  -43.1340
 MFJ  CBG  C  CH1   0  -0.289  -71.5583  33.4049  -40.7152
 MFJ  OBC  O  O2    0  -0.482  -70.7092  34.3221  -40.0800
 MFJ  PBH  P  P     0   1.375  -71.3229  31.8305  -39.8074
 MFJ  H1   H  HCR6  0   0.260  -74.9667  32.1937  -45.8570
 MFJ  H2   H  HCR6  0   0.261  -75.6316  32.5533  -43.4917
 MFJ  H3   H  HCR6  0   0.255  -68.5254  33.0692  -44.2053
 MFJ  H4   H  HCR6  0   0.262  -69.1517  33.4310  -41.8554
 MFJ  H5   H  HCR6  0   0.256  -72.5895  32.2985  -46.4890
 MFJ  H6   H  HCR6  0   0.254  -70.2608  32.6089  -45.8962
 MFJ  H7   H  HCR6  0   0.246  -73.9775  32.9961  -41.7912
 MFJ  H8   H  HCH3  0   0.227  -69.3082  33.8711  -48.4999
 MFJ  H9   H  HCH3  0   0.214  -68.4723  33.6972  -46.9606
 MFJ  H10  H  HCH3  0   0.224  -69.2156  35.2339  -47.3852
 MFJ  H11  H  HCH2  0   0.225  -66.8101  33.9447  -48.7862
 MFJ  H12  H  HCH2  0   0.216  -67.5698  35.4233  -49.3272
 MFJ  H13  H  HCH2  0   0.227  -66.2843  35.0442  -46.5796
 MFJ  H14  H  HCH2  0   0.239  -65.4812  35.7580  -47.9589
 MFJ  H15  H  H     0   0.229  -67.0036  37.6799  -48.0013
 MFJ  H16  H  H     0   0.232  -67.8924  38.4319  -45.9986
 MFJ  H17  H  HCH2  0   0.238  -67.4309  35.5820  -44.9019
 MFJ  H18  H  HCH2  0   0.236  -67.0301  37.0226  -43.9909
 MFJ  H19  H  HCH2  0   0.238  -69.8300  36.3008  -44.9591
 MFJ  H20  H  HCH2  0   0.255  -69.2123  35.9634  -43.3606
 MFJ  H21  H  H     0   0.241  -69.4374  38.8267  -44.4825
 MFJ  H22  H  H     0   0.246  -70.1516  39.4689  -42.3793
 MFJ  H23  H  H     0   0.249  -69.8910  37.9765  -40.4245
 MFJ  H24  H  H     0   0.256  -71.3162  35.9989  -42.2623
 MFJ  H25  H  HCH2  0   0.251  -70.6676  36.1595  -39.2419
 MFJ  H26  H  HCH2  0   0.228  -72.2469  35.6810  -39.8603
 MFJ  H27  H  HCH1  0   0.276  -72.6064  33.7040  -40.5862
 MFJ  H28  H  HOH1  0   0.499  -71.8085  31.5651  -37.6951
 MFJ  H29  H  HOH1  0   0.495  -71.9891  30.2757  -41.2000
 MFJ  OAB  O  O     0  -0.700  -69.9214  31.3543  -39.7425
 MFJ  CBB  C  CH2   0  -0.245  -71.1705  35.6667  -40.0759
 MFJ  OAC  O  OH1   0  -0.738  -72.0431  32.1622  -38.4192
 MFJ  OAD  O  OH1   0  -0.741  -72.3621  30.8092  -40.4864

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    1.521  0.020  1.521
 MFJ  CAR  CAS  single    1.532  0.020  1.532
 MFJ  CAT  CAS  single    1.497  0.020  1.497
 MFJ  CAT  CAU  double    1.333  0.020  1.333
 MFJ  CAU  CAV  single    1.498  0.020  1.498
 MFJ  CAI  CAE  aromatic  1.366  0.020  1.366
 MFJ  CAI  CBE  aromatic  1.415  0.020  1.415
 MFJ  CAE  CAF  aromatic  1.409  0.020  1.409
 MFJ  CAJ  CBE  aromatic  1.412  0.020  1.412
 MFJ  CAJ  CAG  aromatic  1.365  0.020  1.365
 MFJ  CBE  CBF  aromatic  1.423  0.020  1.423
 MFJ  CAV  CAW  single    1.539  0.020  1.539
 MFJ  CAF  CAK  aromatic  1.368  0.020  1.368
 MFJ  CAG  CAH  aromatic  1.406  0.020  1.406
 MFJ  CBF  CAK  aromatic  1.418  0.020  1.418
 MFJ  CBF  CBD  aromatic  1.425  0.020  1.425
 MFJ  CAW  CAX  single    1.494  0.020  1.494
 MFJ  CAH  CBD  aromatic  1.373  0.020  1.373
 MFJ  CAX  CAY  double    1.337  0.020  1.337
 MFJ  CBD  CBG  single    1.512  0.020  1.512
 MFJ  CAY  CAZ  single    1.464  0.020  1.464
 MFJ  CBA  CAZ  double    1.334  0.020  1.334
 MFJ  CBA  CBB  single    1.496  0.020  1.496
 MFJ  CBG  OBC  single    1.402  0.020  1.402
 MFJ  CBG  PBH  single    1.833  0.020  1.833
 MFJ  OAB  PBH  double    1.482  0.020  1.482
 MFJ  CBB  OBC  single    1.422  0.020  1.422
 MFJ  PBH  OAD  single    1.608  0.020  1.608
 MFJ  PBH  OAC  single    1.599  0.020  1.599
 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
 MFJ  OAC  H28  single    0.850  0.020  0.980
 MFJ  OAD  H29  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
 MFJ  H1   CAE  CAI  120.41  3.000
 MFJ  H1   CAE  CAF  119.89  3.000
 MFJ  CAI  CAE  CAF  119.70  3.000
 MFJ  H2   CAF  CAK  119.66  3.000
 MFJ  H2   CAF  CAE  119.64  3.000
 MFJ  CAK  CAF  CAE  120.70  3.000
 MFJ  H3   CAG  CAJ  120.45  3.000
 MFJ  H3   CAG  CAH  119.40  3.000
 MFJ  CAJ  CAG  CAH  120.16  3.000
 MFJ  H4   CAH  CBD  119.87  3.000
 MFJ  H4   CAH  CAG  118.80  3.000
 MFJ  CBD  CAH  CAG  121.33  3.000
 MFJ  H5   CAI  CBE  118.68  3.000
 MFJ  H5   CAI  CAE  120.38  3.000
 MFJ  CBE  CAI  CAE  120.94  3.000
 MFJ  H6   CAJ  CBE  118.85  3.000
 MFJ  H6   CAJ  CAG  120.66  3.000
 MFJ  CBE  CAJ  CAG  120.48  3.000
 MFJ  H7   CAK  CBF  120.67  3.000
 MFJ  H7   CAK  CAF  118.12  3.000
 MFJ  CBF  CAK  CAF  121.21  3.000
 MFJ  H10  CAQ  H9   107.34  3.000
 MFJ  H10  CAQ  H8   107.77  3.000
 MFJ  H9   CAQ  H8   107.49  3.000
 MFJ  H10  CAQ  CAR  111.61  3.000
 MFJ  H9   CAQ  CAR  110.94  3.000
 MFJ  H8   CAQ  CAR  111.47  3.000
 MFJ  H12  CAR  H11  106.14  3.000
 MFJ  H12  CAR  CAS  109.37  3.000
 MFJ  H11  CAR  CAS  108.96  3.000
 MFJ  H12  CAR  CAQ  109.83  3.000
 MFJ  H11  CAR  CAQ  109.46  3.000
 MFJ  CAS  CAR  CAQ  112.87  3.000
 MFJ  H14  CAS  H13  106.22  3.000
 MFJ  H14  CAS  CAT  108.44  3.000
 MFJ  H13  CAS  CAT  111.41  3.000
 MFJ  H14  CAS  CAR  108.74  3.000
 MFJ  H13  CAS  CAR  109.38  3.000
 MFJ  CAT  CAS  CAR  112.43  3.000
 MFJ  H15  CAT  CAU  117.12  3.000
 MFJ  H15  CAT  CAS  114.71  3.000
 MFJ  CAU  CAT  CAS  128.16  3.000
 MFJ  H16  CAU  CAV  115.83  3.000
 MFJ  H16  CAU  CAT  116.69  3.000
 MFJ  CAV  CAU  CAT  127.48  3.000
 MFJ  H18  CAV  H17  106.39  3.000
 MFJ  H18  CAV  CAW  108.22  3.000
 MFJ  H17  CAV  CAW  108.20  3.000
 MFJ  H18  CAV  CAU  109.61  3.000
 MFJ  H17  CAV  CAU  110.65  3.000
 MFJ  CAW  CAV  CAU  113.50  3.000
 MFJ  H20  CAW  H19  106.12  3.000
 MFJ  H20  CAW  CAX  110.38  3.000
 MFJ  H19  CAW  CAX  109.97  3.000
 MFJ  H20  CAW  CAV  108.79  3.000
 MFJ  H19  CAW  CAV  108.60  3.000
 MFJ  CAX  CAW  CAV  112.74  3.000
 MFJ  H21  CAX  CAY  116.15  3.000
 MFJ  H21  CAX  CAW  116.08  3.000
 MFJ  CAY  CAX  CAW  127.71  3.000
 MFJ  H22  CAY  CAZ  114.61  3.000
 MFJ  H22  CAY  CAX  117.20  3.000
 MFJ  CAZ  CAY  CAX  128.14  3.000
 MFJ  H23  CAZ  CBA  118.05  3.000
 MFJ  H23  CAZ  CAY  115.14  3.000
 MFJ  CBA  CAZ  CAY  126.70  3.000
 MFJ  H24  CBA  CBB  117.41  3.000
 MFJ  H24  CBA  CAZ  120.13  3.000
 MFJ  CBB  CBA  CAZ  122.34  3.000
 MFJ  CBG  CBD  CBF  121.71  3.000
 MFJ  CBG  CBD  CAH  118.57  3.000
 MFJ  CBF  CBD  CAH  119.71  3.000
 MFJ  CBF  CBE  CAJ  119.68  3.000
 MFJ  CBF  CBE  CAI  119.65  3.000
 MFJ  CAJ  CBE  CAI  120.67  3.000
 MFJ  CBE  CBF  CBD  118.64  3.000
 MFJ  CBD  CBF  CAK  123.56  3.000
 MFJ  CBE  CBF  CAK  117.80  3.000
 MFJ  H27  CBG  PBH  107.37  3.000
 MFJ  H27  CBG  OBC  110.29  3.000
 MFJ  PBH  CBG  OBC  105.06  3.000
 MFJ  H27  CBG  CBD  110.62  3.000
 MFJ  PBH  CBG  CBD  109.27  3.000
 MFJ  OBC  CBG  CBD  113.89  3.000
 MFJ  CBG  OBC  CBB  115.06  3.000
 MFJ  OAD  PBH  OAC  101.97  3.000
 MFJ  OAC  PBH  OAB  117.05  3.000
 MFJ  OAD  PBH  OAB  115.20  3.000
 MFJ  OAC  PBH  CBG  101.19  3.000
 MFJ  OAD  PBH  CBG  104.69  3.000
 MFJ  OAB  PBH  CBG  114.79  3.000
 MFJ  H26  CBB  H25  107.21  3.000
 MFJ  H26  CBB  OBC  109.33  3.000
 MFJ  H25  CBB  OBC  106.25  3.000
 MFJ  H26  CBB  CBA  109.84  3.000
 MFJ  H25  CBB  CBA  110.00  3.000
 MFJ  OBC  CBB  CBA  113.95  3.000
 MFJ  H28  OAC  PBH  114.37  3.000
 MFJ  H29  OAD  PBH  114.41  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    -0.41   0.0  2
 MFJ  Var_02    CAZ  CAY  CAX  CAW    -2.95   0.0  2
 MFJ  Var_03    CBB  CBA  CAZ  CAY  -175.97   0.0  2
 MFJ  Var_04    CAT  CAS  CAR  CAQ   -69.42  30.0  3
 MFJ  Var_05    CAU  CAT  CAS  CAR   108.92  30.0  1
 MFJ  Var_06    CAW  CAV  CAU  CAT  -127.85  30.0  3
 MFJ  Var_07    CAX  CAW  CAV  CAU   -65.73  30.0  3
 MFJ  Var_08    CAY  CAX  CAW  CAV  -123.91  30.0  3
 MFJ  Var_09    CBA  CAZ  CAY  CAX   -46.70  30.0  2
 MFJ  Var_10    OBC  CBB  CBA  CAZ  -125.10  30.0  3
 MFJ  Var_11    H8   CAQ  CAR  CAS   176.47  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

