# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:10:45 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: ethyl (R)-{10-[(hept-6-yn-1-ylcarbamoyl)oxy]decyl}phosphonofluoridate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCO[P@](F)(=O)CCCCCCCCCCOC(=O)NCCCCCC#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
 SEF  SEF  'ethyl (R)-{10-[(hept-6-yn-1-ylcarbamoyl)oxy]decyl}phosphonofluoridate'  ligand  64  27  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SEF
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
 SEF  F     F  F     0  -0.432   -9.4110   1.1115   1.1799
 SEF  C1    C  CH2   0  -0.753   -7.8462  -0.6783  -0.0074
 SEF  O1    O  O     0  -0.701   -9.6179   1.0404  -1.3398
 SEF  P1    P  P     0   1.469   -9.3958   0.2080  -0.1398
 SEF  C2    C  CH2   0  -0.440   -6.6288   0.2440  -0.0894
 SEF  O2    O  O2    0  -0.588  -10.4980  -0.8900   0.1866
 SEF  C3    C  CH2   0  -0.409   -5.3256  -0.5447  -0.0479
 SEF  C4    C  CH2   0  -0.415   -4.0980   0.3552  -0.1037
 SEF  C5    C  CH2   0  -0.414   -2.7835  -0.4149  -0.0774
 SEF  C6    C  CH2   0  -0.413   -1.5649   0.4988  -0.1145
 SEF  C7    C  CH2   0  -0.413   -0.2381  -0.2495  -0.0860
 SEF  C8    C  CH2   0  -0.426    0.9608   0.6902  -0.1109
 SEF  C9    C  CH2   0  -0.466    2.3006  -0.0365  -0.0727
 SEF  C01   C  CH2   0  -0.171  -11.9008  -0.6640  -0.0756
 SEF  N01   N  NH1   0  -0.674    6.8919   0.1798  -0.0190
 SEF  O01   O  O2    0  -0.491    4.6759   0.2348  -0.0519
 SEF  C02   C  CH3   0  -0.685  -12.6589  -1.9036   0.3271
 SEF  O02   O  O     0  -0.528    5.8243   2.1741  -0.1105
 SEF  C10   C  CH2   0  -0.148    3.4431   0.9565  -0.0983
 SEF  C12   C  C     0   0.755    5.8009   0.9588  -0.0634
 SEF  C14   C  CH2   0  -0.230    8.2243   0.7456   0.0000
 SEF  C15   C  CH2   0  -0.475    9.2799  -0.3469   0.0112
 SEF  C16   C  CH2   0  -0.424   10.6839   0.2430   0.0378
 SEF  C17   C  CH2   0  -0.421   11.7730  -0.8197   0.0519
 SEF  C18   C  CH2   0  -0.577   13.1698  -0.1927   0.0831
 SEF  C19   C  CSP   0   0.287   14.2377  -1.1837   0.1106
 SEF  C20   C  CSP1  0  -0.570   15.1091  -2.0128   0.1353
 SEF  H1    H  HCH2  0   0.294   -7.8415  -1.2475   0.9251
 SEF  H1A   H  HCH2  0   0.295   -7.8278  -1.4036  -0.8252
 SEF  H2    H  HCH2  0   0.238   -6.6687   0.8307  -1.0111
 SEF  H41   H  HCH2  0   0.238   -6.6461   0.9586   0.7376
 SEF  H3    H  HCH2  0   0.218   -5.2948  -1.1496   0.8647
 SEF  H61   H  HCH2  0   0.218   -5.3019  -1.2506  -0.8848
 SEF  H4    H  HCH2  0   0.211   -4.1399   0.9703  -1.0096
 SEF  H4A   H  HCH2  0   0.211   -4.1249   1.0547   0.7392
 SEF  H5    H  HCH2  0   0.209   -2.7438  -1.0386   0.8228
 SEF  H5A   H  HCH2  0   0.209   -2.7478  -1.1056  -0.9271
 SEF  H6    H  HCH2  0   0.209   -1.6085   1.1229  -1.0143
 SEF  H6A   H  HCH2  0   0.209   -1.6075   1.1901   0.7344
 SEF  H7    H  HCH2  0   0.210   -0.1911  -0.8767   0.8112
 SEF  H7A   H  HCH2  0   0.211   -0.1837  -0.9340  -0.9394
 SEF  H8    H  HCH2  0   0.216    0.9095   1.3152  -1.0092
 SEF  H8A   H  HCH2  0   0.216    0.8946   1.3772   0.7397
 SEF  H9    H  HCH2  0   0.228    2.3609  -0.6500   0.8313
 SEF  H9A   H  HCH2  0   0.228    2.3781  -0.7152  -0.9273
 SEF  H01   H  HCH2  0   0.239  -12.2451   0.2005   0.4961
 SEF  H201  H  HCH2  0   0.241  -12.0394  -0.4493  -1.1360
 SEF  HN01  H  HNH1  0   0.399    6.7840  -0.8201   0.0391
 SEF  H02   H  HCH3  0   0.241  -13.7185  -1.7562   0.1197
 SEF  H02A  H  HCH3  0   0.238  -12.3254  -2.7745  -0.2374
 SEF  H24   H  HCH3  0   0.238  -12.5501  -2.1112   1.3914
 SEF  H10   H  HCH2  0   0.223    3.3967   1.5624  -1.0071
 SEF  H10A  H  HCH2  0   0.223    3.3723   1.6341   0.7566
 SEF  H14   H  HCH2  0   0.230    8.3689   1.3837  -0.8761
 SEF  H14A  H  HCH2  0   0.228    8.3506   1.3840   0.8797
 SEF  H15   H  HCH2  0   0.232    9.1363  -0.9913   0.8844
 SEF  H15A  H  HCH2  0   0.233    9.1632  -0.9829  -0.8722
 SEF  H16   H  HCH2  0   0.223   10.8210   0.8937  -0.8320
 SEF  H16A  H  HCH2  0   0.223   10.7914   0.8850   0.9184
 SEF  H17   H  HCH2  0   0.231   11.6490  -1.4687   0.9227
 SEF  H17A  H  HCH2  0   0.232   11.6827  -1.4590  -0.8301
 SEF  H18   H  HCH2  0   0.267   13.3034   0.4532  -0.7893
 SEF  H18A  H  HCH2  0   0.266   13.2629   0.4556   0.9593
 SEF  H20   H  H     0   0.277   15.8834  -2.7451   0.1581

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
 SEF  C1   P1    single  1.790  0.020  1.790
 SEF  P1   F     single  1.599  0.020  1.599
 SEF  P1   O1    double  1.477  0.020  1.477
 SEF  C2   C1    single  1.530  0.020  1.530
 SEF  O2   P1    single  1.590  0.020  1.590
 SEF  C3   C2    single  1.524  0.020  1.524
 SEF  C4   C3    single  1.523  0.020  1.523
 SEF  C5   C4    single  1.524  0.020  1.524
 SEF  C6   C5    single  1.524  0.020  1.524
 SEF  C7   C6    single  1.523  0.020  1.523
 SEF  C7   C8    single  1.523  0.020  1.523
 SEF  C9   C8    single  1.525  0.020  1.525
 SEF  C9   C10   single  1.514  0.020  1.514
 SEF  C01  O2    single  1.445  0.020  1.445
 SEF  N01  C14   single  1.448  0.020  1.448
 SEF  O01  C12   single  1.338  0.020  1.338
 SEF  C02  C01   single  1.508  0.020  1.508
 SEF  O02  C12   double  1.216  0.020  1.216
 SEF  C10  O01   single  1.429  0.020  1.429
 SEF  C12  N01   single  1.341  0.020  1.341
 SEF  C14  C15   single  1.519  0.020  1.519
 SEF  C15  C16   single  1.523  0.020  1.523
 SEF  C16  C17   single  1.522  0.020  1.522
 SEF  C17  C18   single  1.531  0.020  1.531
 SEF  C18  C19   single  1.457  0.020  1.457
 SEF  C19  C20   triple  1.203  0.020  1.203
 SEF  C1   H1    single  0.939  0.020  1.096
 SEF  C1   H1A   single  0.939  0.020  1.096
 SEF  C2   H2    single  0.939  0.020  1.096
 SEF  C2   H41   single  0.939  0.020  1.096
 SEF  C3   H3    single  0.939  0.020  1.096
 SEF  C3   H61   single  0.939  0.020  1.096
 SEF  C4   H4    single  0.939  0.020  1.096
 SEF  C4   H4A   single  0.939  0.020  1.096
 SEF  C5   H5    single  0.939  0.020  1.096
 SEF  C5   H5A   single  0.939  0.020  1.096
 SEF  C6   H6    single  0.939  0.020  1.096
 SEF  C6   H6A   single  0.939  0.020  1.096
 SEF  C7   H7    single  0.939  0.020  1.096
 SEF  C7   H7A   single  0.939  0.020  1.096
 SEF  C8   H8    single  0.939  0.020  1.096
 SEF  C8   H8A   single  0.939  0.020  1.096
 SEF  C9   H9    single  0.939  0.020  1.096
 SEF  C9   H9A   single  0.939  0.020  1.096
 SEF  C01  H01   single  0.939  0.020  1.096
 SEF  C01  H201  single  0.939  0.020  1.096
 SEF  N01  HN01  single  0.868  0.020  1.013
 SEF  C02  H02   single  0.939  0.020  1.096
 SEF  C02  H02A  single  0.939  0.020  1.096
 SEF  C02  H24   single  0.939  0.020  1.096
 SEF  C10  H10   single  0.939  0.020  1.096
 SEF  C10  H10A  single  0.939  0.020  1.096
 SEF  C14  H14   single  0.939  0.020  1.096
 SEF  C14  H14A  single  0.939  0.020  1.096
 SEF  C15  H15   single  0.939  0.020  1.096
 SEF  C15  H15A  single  0.939  0.020  1.096
 SEF  C16  H16   single  0.939  0.020  1.096
 SEF  C16  H16A  single  0.939  0.020  1.096
 SEF  C17  H17   single  0.939  0.020  1.096
 SEF  C17  H17A  single  0.939  0.020  1.096
 SEF  C18  H18   single  0.939  0.020  1.096
 SEF  C18  H18A  single  0.939  0.020  1.096
 SEF  C20  H20   single  0.913  0.020  1.066

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
 SEF  H1A   C1   H1    107.02  3.000
 SEF  H1A   C1   C2    110.28  3.000
 SEF  H1    C1   C2    110.88  3.000
 SEF  H1A   C1   P1    106.73  3.000
 SEF  H1    C1   P1    108.95  3.000
 SEF  C2    C1   P1    112.74  3.000
 SEF  O2    P1   O1    116.86  3.000
 SEF  O2    P1   C1    104.07  3.000
 SEF  O1    P1   C1    117.98  3.000
 SEF  O2    P1   F     102.37  3.000
 SEF  O1    P1   F     110.52  3.000
 SEF  C1    P1   F     103.12  3.000
 SEF  H41   C2   H2    106.65  3.000
 SEF  H41   C2   C3    109.35  3.000
 SEF  H2    C2   C3    109.38  3.000
 SEF  H41   C2   C1    109.94  3.000
 SEF  H2    C2   C1    109.86  3.000
 SEF  C3    C2   C1    111.54  3.000
 SEF  C01   O2   P1    121.86  3.000
 SEF  H61   C3   H3    106.27  3.000
 SEF  H61   C3   C4    109.59  3.000
 SEF  H3    C3   C4    109.52  3.000
 SEF  H61   C3   C2    109.35  3.000
 SEF  H3    C3   C2    109.43  3.000
 SEF  C4    C3   C2    112.48  3.000
 SEF  H4A   C4   H4    106.06  3.000
 SEF  H4A   C4   C5    109.30  3.000
 SEF  H4    C4   C5    109.32  3.000
 SEF  H4A   C4   C3    109.22  3.000
 SEF  H4    C4   C3    109.34  3.000
 SEF  C5    C4   C3    113.33  3.000
 SEF  H5A   C5   H5    106.08  3.000
 SEF  H5A   C5   C6    109.46  3.000
 SEF  H5    C5   C6    109.41  3.000
 SEF  H5A   C5   C4    109.47  3.000
 SEF  H5    C5   C4    109.46  3.000
 SEF  C6    C5   C4    112.74  3.000
 SEF  H6A   C6   H6    105.98  3.000
 SEF  H6A   C6   C7    109.23  3.000
 SEF  H6    C6   C7    109.26  3.000
 SEF  H6A   C6   C5    109.17  3.000
 SEF  H6    C6   C5    109.25  3.000
 SEF  C7    C6   C5    113.68  3.000
 SEF  H7A   C7   H7    106.15  3.000
 SEF  H7A   C7   C8    109.48  3.000
 SEF  H7    C7   C8    109.44  3.000
 SEF  H7A   C7   C6    109.61  3.000
 SEF  H7    C7   C6    109.51  3.000
 SEF  C8    C7   C6    112.46  3.000
 SEF  H8A   C8   H8    106.02  3.000
 SEF  H8A   C8   C9    109.42  3.000
 SEF  H8    C8   C9    109.48  3.000
 SEF  H8A   C8   C7    109.07  3.000
 SEF  H8    C8   C7    109.18  3.000
 SEF  C9    C8   C7    113.40  3.000
 SEF  H9A   C9   H9    107.07  3.000
 SEF  H9A   C9   C10   109.89  3.000
 SEF  H9    C9   C10   109.88  3.000
 SEF  H9A   C9   C8    109.78  3.000
 SEF  H9    C9   C8    109.66  3.000
 SEF  C10   C9   C8    110.50  3.000
 SEF  H201  C01  H01   108.24  3.000
 SEF  H201  C01  C02   110.95  3.000
 SEF  H01   C01  C02   110.64  3.000
 SEF  H201  C01  O2    109.30  3.000
 SEF  H01   C01  O2    109.57  3.000
 SEF  C02   C01  O2    108.12  3.000
 SEF  HN01  N01  C14   119.06  3.000
 SEF  HN01  N01  C12   119.43  3.000
 SEF  C14   N01  C12   121.47  3.000
 SEF  C12   O01  C10   116.85  3.000
 SEF  H24   C02  H02A  108.84  3.000
 SEF  H24   C02  H02   107.98  3.000
 SEF  H02A  C02  H02   107.88  3.000
 SEF  H24   C02  C01   111.54  3.000
 SEF  H02A  C02  C01   111.39  3.000
 SEF  H02   C02  C01   109.08  3.000
 SEF  H10A  C10  H10   107.69  3.000
 SEF  H10A  C10  O01   110.09  3.000
 SEF  H10   C10  O01   110.09  3.000
 SEF  H10A  C10  C9    110.15  3.000
 SEF  H10   C10  C9    110.21  3.000
 SEF  O01   C10  C9    108.61  3.000
 SEF  O02   C12  O01   123.86  3.000
 SEF  O02   C12  N01   124.47  3.000
 SEF  O01   C12  N01   111.67  3.000
 SEF  H14A  C14  H14   106.76  3.000
 SEF  H14A  C14  C15   109.47  3.000
 SEF  H14   C14  C15   109.49  3.000
 SEF  H14A  C14  N01   110.17  3.000
 SEF  H14   C14  N01   109.83  3.000
 SEF  C15   C14  N01   111.01  3.000
 SEF  H15A  C15  H15   106.71  3.000
 SEF  H15A  C15  C16   109.72  3.000
 SEF  H15   C15  C16   109.57  3.000
 SEF  H15A  C15  C14   109.74  3.000
 SEF  H15   C15  C14   109.76  3.000
 SEF  C16   C15  C14   111.23  3.000
 SEF  H16A  C16  H16   106.15  3.000
 SEF  H16A  C16  C17   109.38  3.000
 SEF  H16   C16  C17   109.44  3.000
 SEF  H16A  C16  C15   109.36  3.000
 SEF  H16   C16  C15   109.37  3.000
 SEF  C17   C16  C15   112.92  3.000
 SEF  H17A  C17  H17   106.64  3.000
 SEF  H17A  C17  C18   109.35  3.000
 SEF  H17   C17  C18   109.28  3.000
 SEF  H17A  C17  C16   109.99  3.000
 SEF  H17   C17  C16   109.92  3.000
 SEF  C18   C17  C16   111.53  3.000
 SEF  H18A  C18  H18   106.17  3.000
 SEF  H18A  C18  C19   109.00  3.000
 SEF  H18   C18  C19   109.10  3.000
 SEF  H18A  C18  C17   109.67  3.000
 SEF  H18   C18  C17   109.69  3.000
 SEF  C19   C18  C17   112.98  3.000
 SEF  C20   C19  C18   180.00  3.000
 SEF  H20   C20  C19   180.00  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
 SEF  Var_01  C2   C1   P1   F     -65.22  30.0  1
 SEF  Var_02  C4   C3   C2   C1   -179.00  30.0  1
 SEF  Var_03  C3   C2   C1   P1   -177.00  30.0  1
 SEF  Var_04  C02  C01  O2   P1    179.12  30.0  1
 SEF  Var_05  C5   C4   C3   C2   -179.42  30.0  2
 SEF  Var_06  C6   C5   C4   C3   -179.21  30.0  1
 SEF  Var_07  C7   C6   C5   C4    179.87  30.0  2
 SEF  Var_08  C8   C7   C6   C5   -179.46  30.0  1
 SEF  Var_09  C9   C8   C7   C6    179.58  30.0  3
 SEF  Var_10  C10  C9   C8   C7   -179.93  30.0  2
 SEF  Var_11  O01  C10  C9   C8    179.61  30.0  3
 SEF  Var_12  C16  C15  C14  N01  -179.74  30.0  3
 SEF  Var_13  C14  N01  C12  O01  -178.99  30.0  2
 SEF  Var_14  C15  C14  N01  C12  -178.40  30.0  3
 SEF  Var_15  C17  C16  C15  C14   179.91  30.0  3
 SEF  Var_16  C18  C17  C16  C15  -179.81  30.0  3
 SEF  Var_17  C19  C18  C17  C16   179.43  30.0  3
 SEF  Var_18  H02  C02  C01  O2   -179.04  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
 SEF  chir_01  P1  F  O1  O2  both

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
 SEF  plan-1  N01  0.020
 SEF  plan-1  O01  0.020
 SEF  plan-1  O02  0.020
 SEF  plan-1  C12  0.020

