# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:15:31 2021
#   Inital geometry file: a 157 line input string
#   Ligand name: [(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC\C=C\C(=O)NCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[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
 DYF  DYF  '[(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate'  ligand  67  31  .  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
;

data_comp_DYF
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
 DYF  C29  C  CH2   0  -0.408  -17.5317  -22.2507  27.6551
 DYF  C26  C  C1    0  -0.158  -16.2158  -22.1753  24.0306
 DYF  C25  C  C1    0  -0.413  -16.2424  -21.0745  23.2817
 DYF  C21  C  CH2   0  -0.315  -15.4352  -18.3827  22.9098
 DYF  C17  C  C     0   0.561  -18.2402  -17.5972  24.4002
 DYF  O11  O  OH1   0  -0.691  -19.1120  -15.3128  30.1296
 DYF  N22  N  NH1   0  -0.626  -14.9665  -19.4553  22.0605
 DYF  C10  C  CH1   0  -0.032  -20.2826  -16.0429  29.8494
 DYF  N19  N  NH1   0  -0.630  -17.3898  -17.0285  23.5263
 DYF  C30  C  CH2   0  -0.419  -16.8881  -22.0211  29.0173
 DYF  C31  C  CH3   0  -0.664  -17.8981  -22.0251  30.1565
 DYF  N14  N  NH1   0  -0.620  -18.8461  -16.8448  28.0644
 DYF  C28  C  CH2   0  -0.414  -16.5323  -22.1860  26.5071
 DYF  C27  C  CH2   0  -0.491  -17.1863  -22.4136  25.1397
 DYF  C23  C  C     0   0.494  -15.2157  -20.7702  22.2567
 DYF  C20  C  CH2   0  -0.312  -16.7661  -17.7675  22.4534
 DYF  C16  C  CH2   0  -0.576  -18.6328  -16.7540  25.5925
 DYF  C15  C  CH2   0  -0.278  -18.4854  -17.5758  26.8751
 DYF  C12  C  C     0   0.509  -20.1025  -16.7715  28.5193
 DYF  C02  C  CT    0  -0.156  -20.6182  -17.0390  30.9971
 DYF  C03  C  CH3   0  -0.645  -21.9939  -17.6811  30.8047
 DYF  C04  C  CH2   0  -0.170  -20.5996  -16.2919  32.3302
 DYF  O05  O  O2    0  -0.588  -21.6046  -15.2660  32.3412
 DYF  P06  P  P     0   1.474  -21.3801  -13.7924  32.8832
 DYF  O07  O  OH1   0  -0.742  -20.5315  -13.8929  34.2329
 DYF  O08  O  O     0  -0.693  -22.6477  -13.0459  32.9653
 DYF  O09  O  OH1   0  -0.761  -20.2759  -13.2494  31.8565
 DYF  O18  O  O     0  -0.494  -18.6774  -18.7328  24.2614
 DYF  O24  O  O     0  -0.498  -14.6259  -21.6430  21.6295
 DYF  H1   H  HCH2  0   0.208  -18.3115  -21.4983  27.4926
 DYF  H2   H  HCH2  0   0.212  -18.0391  -23.2217  27.6503
 DYF  H3   H  H     0   0.255  -15.4215  -22.9049  23.8972
 DYF  H4   H  H     0   0.294  -17.0312  -20.3506  23.4552
 DYF  H5   H  HCH2  0   0.277  -14.6650  -17.6129  22.9395
 DYF  H6   H  HCH2  0   0.253  -15.5386  -18.7465  23.9331
 DYF  H7   H  HOH1  0   0.469  -19.3499  -14.4889  30.5707
 DYF  H8   H  HNH1  0   0.394  -14.2772  -19.2308  21.3592
 DYF  H9   H  HCH1  0   0.257  -21.1379  -15.3693  29.7133
 DYF  H10  H  HNH1  0   0.403  -17.0325  -16.1100  23.7328
 DYF  H11  H  HCH2  0   0.213  -16.1313  -22.7916  29.1933
 DYF  H12  H  HCH2  0   0.211  -16.3521  -21.0666  29.0079
 DYF  H13  H  HCH3  0   0.227  -17.4125  -21.8888  31.1234
 DYF  H14  H  HCH3  0   0.217  -18.6282  -21.2221  30.0381
 DYF  H15  H  HCH3  0   0.217  -18.4481  -22.9674  30.1935
 DYF  H16  H  HNH1  0   0.406  -18.1259  -16.3507  28.5646
 DYF  H17  H  HCH2  0   0.220  -15.7377  -22.9222  26.6623
 DYF  H18  H  HCH2  0   0.218  -16.0487  -21.2042  26.5072
 DYF  H19  H  HCH2  0   0.236  -18.0365  -21.7345  25.0338
 DYF  H20  H  HCH2  0   0.239  -17.5760  -23.4348  25.0908
 DYF  H21  H  HCH2  0   0.266  -16.6075  -17.0980  21.6081
 DYF  H22  H  HCH2  0   0.254  -17.4463  -18.5504  22.1203
 DYF  H23  H  HCH2  0   0.256  -18.0323  -15.8449  25.6564
 DYF  H24  H  HCH2  0   0.276  -19.6751  -16.4481  25.4730
 DYF  H25  H  HCH2  0   0.248  -19.0987  -18.4731  26.8097
 DYF  H26  H  HCH2  0   0.258  -17.4505  -17.8984  26.9928
 DYF  H27  H  HCH3  0   0.240  -19.7094  -18.7513  31.9780
 DYF  H28  H  HCH3  0   0.242  -19.5764  -18.7893  30.2300
 DYF  H29  H  HCH3  0   0.240  -18.5422  -17.7105  31.1679
 DYF  H30  H  HCH3  0   0.224  -22.2524  -18.2735  31.6847
 DYF  H31  H  HCH3  0   0.233  -22.7788  -16.9373  30.6633
 DYF  H32  H  HCH3  0   0.243  -22.0101  -18.3466  29.9453
 DYF  H33  H  HCH2  0   0.256  -20.8322  -16.9919  33.1359
 DYF  H34  H  HCH2  0   0.250  -19.6074  -15.8828  32.5340
 DYF  H35  H  HOH1  0   0.502  -21.0695  -13.9819  35.0314
 DYF  H36  H  HOH1  0   0.510  -19.9738  -12.3422  32.0038
 DYF  C01  C  CH3   0  -0.670  -19.5472  -18.1280  31.0968
 DYF  O13  O  O     0  -0.498  -21.0561  -17.2703  27.9346

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
 DYF  O24  C23  double  1.226  0.020  1.226
 DYF  C20  C21  single  1.536  0.020  1.536
 DYF  C20  N19  single  1.444  0.020  1.444
 DYF  N22  C23  single  1.353  0.020  1.353
 DYF  N22  C21  single  1.446  0.020  1.446
 DYF  C23  C25  single  1.482  0.020  1.482
 DYF  O18  C17  double  1.225  0.020  1.225
 DYF  N19  C17  single  1.345  0.020  1.345
 DYF  C17  C16  single  1.512  0.020  1.512
 DYF  C26  C25  double  1.332  0.020  1.332
 DYF  C26  C27  single  1.493  0.020  1.493
 DYF  C27  C28  single  1.533  0.020  1.533
 DYF  C16  C15  single  1.530  0.020  1.530
 DYF  C28  C29  single  1.523  0.020  1.523
 DYF  C15  N14  single  1.442  0.020  1.442
 DYF  O13  C12  double  1.225  0.020  1.225
 DYF  C29  C30  single  1.524  0.020  1.524
 DYF  N14  C12  single  1.338  0.020  1.338
 DYF  C30  C31  single  1.522  0.020  1.522
 DYF  C12  C10  single  1.527  0.020  1.527
 DYF  C10  O11  single  1.408  0.020  1.408
 DYF  C10  C02  single  1.556  0.020  1.556
 DYF  C03  C02  single  1.530  0.020  1.530
 DYF  O08  P06  double  1.473  0.020  1.473
 DYF  C02  C01  single  1.531  0.020  1.531
 DYF  C02  C04  single  1.528  0.020  1.528
 DYF  O09  P06  single  1.603  0.020  1.603
 DYF  P06  O05  single  1.586  0.020  1.586
 DYF  P06  O07  single  1.598  0.020  1.598
 DYF  O05  C04  single  1.436  0.020  1.436
 DYF  C29  H1   single  0.970  0.020  1.090
 DYF  C29  H2   single  0.970  0.020  1.090
 DYF  C26  H3   single  0.930  0.020  1.080
 DYF  C25  H4   single  0.930  0.020  1.080
 DYF  C21  H5   single  0.970  0.020  1.090
 DYF  C21  H6   single  0.970  0.020  1.090
 DYF  O11  H7   single  0.850  0.020  0.980
 DYF  N22  H8   single  0.860  0.020  1.020
 DYF  C10  H9   single  0.970  0.020  1.090
 DYF  N19  H10  single  0.860  0.020  1.020
 DYF  C30  H11  single  0.970  0.020  1.090
 DYF  C30  H12  single  0.970  0.020  1.090
 DYF  C31  H13  single  0.970  0.020  1.090
 DYF  C31  H14  single  0.970  0.020  1.090
 DYF  C31  H15  single  0.970  0.020  1.090
 DYF  N14  H16  single  0.860  0.020  1.020
 DYF  C28  H17  single  0.970  0.020  1.090
 DYF  C28  H18  single  0.970  0.020  1.090
 DYF  C27  H19  single  0.970  0.020  1.090
 DYF  C27  H20  single  0.970  0.020  1.090
 DYF  C20  H21  single  0.970  0.020  1.090
 DYF  C20  H22  single  0.970  0.020  1.090
 DYF  C16  H23  single  0.970  0.020  1.090
 DYF  C16  H24  single  0.970  0.020  1.090
 DYF  C15  H25  single  0.970  0.020  1.090
 DYF  C15  H26  single  0.970  0.020  1.090
 DYF  C01  H27  single  0.970  0.020  1.090
 DYF  C01  H28  single  0.970  0.020  1.090
 DYF  C01  H29  single  0.970  0.020  1.090
 DYF  C03  H30  single  0.970  0.020  1.090
 DYF  C03  H31  single  0.970  0.020  1.090
 DYF  C03  H32  single  0.970  0.020  1.090
 DYF  C04  H33  single  0.970  0.020  1.090
 DYF  C04  H34  single  0.970  0.020  1.090
 DYF  O07  H35  single  0.850  0.020  0.980
 DYF  O09  H36  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
 DYF  H2   C29  H1   106.16  3.000
 DYF  H2   C29  C28  109.76  3.000
 DYF  H1   C29  C28  109.02  3.000
 DYF  H2   C29  C30  109.45  3.000
 DYF  H1   C29  C30  109.25  3.000
 DYF  C28  C29  C30  112.96  3.000
 DYF  H3   C26  C27  117.34  3.000
 DYF  H3   C26  C25  120.04  3.000
 DYF  C27  C26  C25  122.46  3.000
 DYF  H4   C25  C23  118.51  3.000
 DYF  H4   C25  C26  118.45  3.000
 DYF  C23  C25  C26  123.00  3.000
 DYF  H6   C21  H5   106.08  3.000
 DYF  H6   C21  C20  109.28  3.000
 DYF  H5   C21  C20  109.74  3.000
 DYF  H6   C21  N22  109.52  3.000
 DYF  H5   C21  N22  108.12  3.000
 DYF  C20  C21  N22  113.80  3.000
 DYF  O18  C17  C16  120.91  3.000
 DYF  C16  C17  N19  116.14  3.000
 DYF  O18  C17  N19  122.95  3.000
 DYF  H7   O11  C10  109.20  3.000
 DYF  H8   N22  C23  116.30  3.000
 DYF  H8   N22  C21  117.69  3.000
 DYF  C23  N22  C21  125.18  3.000
 DYF  H9   C10  C02  108.44  3.000
 DYF  H9   C10  C12  106.07  3.000
 DYF  C02  C10  C12  111.24  3.000
 DYF  H9   C10  O11  110.77  3.000
 DYF  C02  C10  O11  111.37  3.000
 DYF  C12  C10  O11  108.82  3.000
 DYF  H10  N19  C20  117.76  3.000
 DYF  H10  N19  C17  118.46  3.000
 DYF  C20  N19  C17  122.63  3.000
 DYF  H12  C30  H11  106.06  3.000
 DYF  H12  C30  C31  109.48  3.000
 DYF  H11  C30  C31  109.67  3.000
 DYF  H12  C30  C29  109.30  3.000
 DYF  H11  C30  C29  109.25  3.000
 DYF  C31  C30  C29  112.84  3.000
 DYF  H15  C31  H14  107.56  3.000
 DYF  H15  C31  H13  107.59  3.000
 DYF  H14  C31  H13  107.58  3.000
 DYF  H15  C31  C30  111.22  3.000
 DYF  H14  C31  C30  111.14  3.000
 DYF  H13  C31  C30  111.57  3.000
 DYF  H16  N14  C12  118.42  3.000
 DYF  H16  N14  C15  118.67  3.000
 DYF  C12  N14  C15  122.89  3.000
 DYF  H18  C28  H17  106.42  3.000
 DYF  H18  C28  C27  108.77  3.000
 DYF  H17  C28  C27  109.66  3.000
 DYF  H18  C28  C29  109.14  3.000
 DYF  H17  C28  C29  109.93  3.000
 DYF  C27  C28  C29  112.71  3.000
 DYF  H20  C27  H19  107.36  3.000
 DYF  H20  C27  C28  109.30  3.000
 DYF  H19  C27  C28  109.03  3.000
 DYF  H20  C27  C26  110.32  3.000
 DYF  H19  C27  C26  109.54  3.000
 DYF  C28  C27  C26  111.21  3.000
 DYF  O24  C23  N22  121.96  3.000
 DYF  N22  C23  C25  115.30  3.000
 DYF  O24  C23  C25  122.74  3.000
 DYF  H22  C20  H21  107.17  3.000
 DYF  H22  C20  N19  108.98  3.000
 DYF  H21  C20  N19  108.94  3.000
 DYF  H22  C20  C21  110.13  3.000
 DYF  H21  C20  C21  110.51  3.000
 DYF  N19  C20  C21  111.01  3.000
 DYF  H24  C16  H23  107.34  3.000
 DYF  H24  C16  C15  109.50  3.000
 DYF  H23  C16  C15  110.19  3.000
 DYF  H24  C16  C17  108.51  3.000
 DYF  H23  C16  C17  111.58  3.000
 DYF  C15  C16  C17  109.66  3.000
 DYF  H26  C15  H25  107.29  3.000
 DYF  H26  C15  C16  109.92  3.000
 DYF  H25  C15  C16  109.75  3.000
 DYF  H26  C15  N14  107.37  3.000
 DYF  H25  C15  N14  109.05  3.000
 DYF  C16  C15  N14  113.26  3.000
 DYF  N14  C12  C10  115.66  3.000
 DYF  C10  C12  O13  121.21  3.000
 DYF  N14  C12  O13  123.12  3.000
 DYF  C04  C02  C03  109.01  3.000
 DYF  C04  C02  C01  106.41  3.000
 DYF  C03  C02  C01  109.80  3.000
 DYF  C04  C02  C10  109.13  3.000
 DYF  C01  C02  C10  110.64  3.000
 DYF  C03  C02  C10  111.70  3.000
 DYF  H32  C03  H31  107.72  3.000
 DYF  H32  C03  H30  107.55  3.000
 DYF  H31  C03  H30  107.71  3.000
 DYF  H32  C03  C02  111.69  3.000
 DYF  H31  C03  C02  112.15  3.000
 DYF  H30  C03  C02  109.83  3.000
 DYF  H34  C04  H33  107.21  3.000
 DYF  H34  C04  O05  111.51  3.000
 DYF  H33  C04  O05  107.65  3.000
 DYF  H34  C04  C02  110.90  3.000
 DYF  H33  C04  C02  109.12  3.000
 DYF  O05  C04  C02  110.33  3.000
 DYF  P06  O05  C04  124.56  3.000
 DYF  O09  P06  O08  117.18  3.000
 DYF  O09  P06  O07  101.34  3.000
 DYF  O08  P06  O07  116.22  3.000
 DYF  O07  P06  O05  107.78  3.000
 DYF  O09  P06  O05  101.15  3.000
 DYF  O08  P06  O05  111.60  3.000
 DYF  H35  O07  P06  114.08  3.000
 DYF  H36  O09  P06  115.81  3.000
 DYF  H29  C01  H28  107.98  3.000
 DYF  H29  C01  H27  107.63  3.000
 DYF  H28  C01  H27  106.94  3.000
 DYF  H29  C01  C02  112.13  3.000
 DYF  H28  C01  C02  111.15  3.000
 DYF  H27  C01  C02  110.79  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
 DYF  CONST_01  C21  N22  C23  C25     0.00   0.0  0
 DYF  CONST_02  C15  N14  C12  O13     0.00   0.0  0
 DYF  CONST_03  O24  C23  N22  C21   180.00   0.0  0
 DYF  CONST_04  C15  N14  C12  C10   180.00   0.0  0
 DYF  CONST_05  O18  C17  N19  C20     0.00   0.0  0
 DYF  CONST_06  C16  C17  N19  C20   180.00   0.0  0
 DYF  CONST_07  H8   N22  C23  C25   180.00   0.0  0
 DYF  CONST_08  H16  N14  C12  O13   180.00   0.0  0
 DYF  CONST_09  H10  N19  C17  C16     0.00   0.0  0
 DYF  Var_01    C23  C25  C26  C27   174.52   0.0  2
 DYF  Var_02    C26  C27  C28  C29   172.90  30.0  1
 DYF  Var_03    O24  C23  C25  C26    30.94  30.0  1
 DYF  Var_04    C28  C27  C26  C25  -104.23  30.0  3
 DYF  Var_05    C17  N19  C20  C21   -89.43  30.0  3
 DYF  Var_06    N14  C15  C16  C17  -179.78  30.0  3
 DYF  Var_07    N19  C20  C21  N22   161.71  30.0  1
 DYF  Var_08    O05  C04  C02  C10    62.10  30.0  3
 DYF  Var_09    C15  C16  C17  N19  -131.69  30.0  3
 DYF  Var_10    C27  C28  C29  C30  -179.83  30.0  1
 DYF  Var_11    C28  C29  C30  C31   177.46  30.0  1
 DYF  Var_12    C20  C21  N22  C23   -93.10  30.0  3
 DYF  Var_13    C12  N14  C15  C16    86.33  30.0  3
 DYF  Var_14    O08  P06  O05  C04  -170.68  30.0  1
 DYF  Var_15    H13  C31  C30  C29   178.31  30.0  3
 DYF  Var_16    H30  C03  C02  C10  -172.86  30.0  3
 DYF  Var_17    H27  C01  C02  C10   172.72  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
 DYF  chir_01  C10  C12  O11  C02  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
 DYF  plan-1  C17  0.020
 DYF  plan-1  N19  0.020
 DYF  plan-1  C20  0.020
 DYF  plan-1  C16  0.020
 DYF  plan-1  O18  0.020
 DYF  plan-1  H10  0.020
 DYF  plan-2  C25  0.020
 DYF  plan-2  C21  0.020
 DYF  plan-2  N22  0.020
 DYF  plan-2  C23  0.020
 DYF  plan-2  O24  0.020
 DYF  plan-2  H8   0.020
 DYF  plan-3  C10  0.020
 DYF  plan-3  N14  0.020
 DYF  plan-3  C15  0.020
 DYF  plan-3  C12  0.020
 DYF  plan-3  H16  0.020
 DYF  plan-3  O13  0.020
 DYF  plan-4  C26  0.020
 DYF  plan-4  C25  0.020
 DYF  plan-4  C27  0.020
 DYF  plan-4  C23  0.020
 DYF  plan-4  H3   0.020
 DYF  plan-4  H4   0.020

