# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Nov 23 12:32:54 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (2Z)-3-methylhept-2-en-1-yl trihydrogen diphosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(/C)=C\CO[P](O)(=O)O[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
 Y7D  Y7D  "(2Z)-3-methylhept-2-en-1-yl trihydrogen diphosphate"  ligand  35  17  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Y7D
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
 Y7D  C02  C  C     0   0.172  -4.0972  -0.1636  31.5917
 Y7D  C09  C  CH2   0  -0.215  -4.8899  -0.9671  33.8521
 Y7D  O14  O  OH1   0  -0.731  -4.5810  -2.4888  36.4384
 Y7D  C01  C  CH3   0  -0.706  -4.4453   0.2403  30.1890
 Y7D  C03  C  CH2   0  -0.499  -2.6461  -0.0036  31.9524
 Y7D  C04  C  CH2   0  -0.382  -2.2041   1.4610  32.0626
 Y7D  C05  C  CH2   0  -0.392  -2.9607   2.2533  33.1205
 Y7D  C06  C  CH3   0  -0.674  -2.4314   3.6727  33.2734
 Y7D  C08  C  C1    0  -0.359  -5.0515  -0.5962  32.4207
 Y7D  O10  O  O2    0  -0.521  -5.4763  -2.2807  34.0442
 Y7D  O12  O  O     0  -0.758  -5.8844  -4.4565  35.2881
 Y7D  O13  O  O2    0  -0.675  -3.4913  -3.6768  34.6000
 Y7D  O36  O  OH1   0  -0.649  -3.2466  -6.0930  34.2322
 Y7D  O39  O  OH1   0  -0.713  -2.8787  -5.2300  36.5284
 Y7D  O40  O  O     0  -0.686  -1.1231  -4.6165  34.6956
 Y7D  P11  P  P     0   1.462  -4.9779  -3.3110  35.1323
 Y7D  P32  P  P     0   1.433  -2.5278  -4.9115  35.0087
 Y7D  H1   H  HCH2  0   0.277  -3.8462  -0.9555  34.1662
 Y7D  H2   H  HCH2  0   0.302  -5.4365  -0.2747  34.4961
 Y7D  H3   H  HOH1  0   0.482  -5.3242  -2.2524  37.0120
 Y7D  H4   H  HCH3  0   0.205  -5.4943   0.0604  29.9578
 Y7D  H5   H  HCH3  0   0.266  -4.2442   1.3014  30.0259
 Y7D  H6   H  HCH3  0   0.281  -3.8347  -0.3065  29.4668
 Y7D  H7   H  HCH2  0   0.216  -2.4063  -0.5121  32.8880
 Y7D  H8   H  HCH2  0   0.174  -2.0445  -0.4904  31.1784
 Y7D  H9   H  HCH2  0   0.217  -1.1355   1.4750  32.2961
 Y7D  H10  H  HCH2  0   0.207  -2.3047   1.9582  31.0931
 Y7D  H11  H  HCH2  0   0.166  -4.0238   2.2866  32.8664
 Y7D  H12  H  HCH2  0   0.243  -2.8961   1.7301  34.0801
 Y7D  H13  H  HCH3  0   0.238  -2.9871   4.2271  34.0305
 Y7D  H14  H  HCH3  0   0.208  -1.3804   3.6738  33.5678
 Y7D  H15  H  HCH3  0   0.224  -2.5100   4.2269  32.3361
 Y7D  H16  H  H     0   0.234  -6.0707  -0.6527  32.0482
 Y7D  H17  H  HOH1  0   0.439  -2.7137  -6.8954  34.1364
 Y7D  H18  H  HOH1  0   0.519  -2.3422  -4.7525  37.1775

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
 Y7D  C01  C02  single  1.501  0.020  1.501
 Y7D  C02  C03  single  1.504  0.020  1.504
 Y7D  C02  C08  double  1.336  0.020  1.336
 Y7D  C03  C04  single  1.534  0.020  1.534
 Y7D  C04  C05  single  1.523  0.020  1.523
 Y7D  C08  C09  single  1.487  0.020  1.487
 Y7D  C05  C06  single  1.523  0.020  1.523
 Y7D  C09  O10  single  1.451  0.020  1.451
 Y7D  O10  P11  single  1.579  0.020  1.579
 Y7D  O13  P11  single  1.621  0.020  1.621
 Y7D  O13  P32  single  1.619  0.020  1.619
 Y7D  P11  O12  double  1.469  0.020  1.469
 Y7D  P11  O14  single  1.593  0.020  1.593
 Y7D  O40  P32  double  1.469  0.020  1.469
 Y7D  O36  P32  single  1.586  0.020  1.586
 Y7D  P32  O39  single  1.592  0.020  1.592
 Y7D  C09  H1   single  0.970  0.020  1.090
 Y7D  C09  H2   single  0.970  0.020  1.090
 Y7D  O14  H3   single  0.850  0.020  0.980
 Y7D  C01  H4   single  0.970  0.020  1.090
 Y7D  C01  H5   single  0.970  0.020  1.090
 Y7D  C01  H6   single  0.970  0.020  1.090
 Y7D  C03  H7   single  0.970  0.020  1.090
 Y7D  C03  H8   single  0.970  0.020  1.090
 Y7D  C04  H9   single  0.970  0.020  1.090
 Y7D  C04  H10  single  0.970  0.020  1.090
 Y7D  C05  H11  single  0.970  0.020  1.090
 Y7D  C05  H12  single  0.970  0.020  1.090
 Y7D  C06  H13  single  0.970  0.020  1.090
 Y7D  C06  H14  single  0.970  0.020  1.090
 Y7D  C06  H15  single  0.970  0.020  1.090
 Y7D  C08  H16  single  0.930  0.020  1.080
 Y7D  O36  H17  single  0.850  0.020  0.980
 Y7D  O39  H18  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
 Y7D  C08  C02  C03  125.08  3.000
 Y7D  C08  C02  C01  120.10  3.000
 Y7D  C03  C02  C01  114.80  3.000
 Y7D  H2   C09  H1   107.61  3.000
 Y7D  H2   C09  O10  107.07  3.000
 Y7D  H1   C09  O10  111.00  3.000
 Y7D  H2   C09  C08  110.79  3.000
 Y7D  H1   C09  C08  112.25  3.000
 Y7D  O10  C09  C08  108.01  3.000
 Y7D  H3   O14  P11  114.86  3.000
 Y7D  H6   C01  H5   106.54  3.000
 Y7D  H6   C01  H4   108.38  3.000
 Y7D  H5   C01  H4   107.82  3.000
 Y7D  H6   C01  C02  110.71  3.000
 Y7D  H5   C01  C02  111.00  3.000
 Y7D  H4   C01  C02  112.17  3.000
 Y7D  H8   C03  H7   106.15  3.000
 Y7D  H8   C03  C04  108.48  3.000
 Y7D  H7   C03  C04  108.66  3.000
 Y7D  H8   C03  C02  108.27  3.000
 Y7D  H7   C03  C02  111.60  3.000
 Y7D  C04  C03  C02  113.39  3.000
 Y7D  H10  C04  H9   105.85  3.000
 Y7D  H10  C04  C05  109.47  3.000
 Y7D  H9   C04  C05  109.29  3.000
 Y7D  H10  C04  C03  110.10  3.000
 Y7D  H9   C04  C03  108.01  3.000
 Y7D  C05  C04  C03  113.80  3.000
 Y7D  H12  C05  H11  105.99  3.000
 Y7D  H12  C05  C06  109.69  3.000
 Y7D  H11  C05  C06  109.45  3.000
 Y7D  H12  C05  C04  109.32  3.000
 Y7D  H11  C05  C04  109.72  3.000
 Y7D  C06  C05  C04  112.46  3.000
 Y7D  H15  C06  H14  107.48  3.000
 Y7D  H15  C06  H13  107.53  3.000
 Y7D  H14  C06  H13  107.63  3.000
 Y7D  H15  C06  C05  111.22  3.000
 Y7D  H14  C06  C05  111.27  3.000
 Y7D  H13  C06  C05  111.50  3.000
 Y7D  H16  C08  C09  114.76  3.000
 Y7D  H16  C08  C02  118.30  3.000
 Y7D  C09  C08  C02  126.89  3.000
 Y7D  P11  O10  C09  123.66  3.000
 Y7D  P32  O13  P11  129.43  3.000
 Y7D  H17  O36  P32  114.61  3.000
 Y7D  H18  O39  P32  114.79  3.000
 Y7D  O13  P11  O12  115.13  3.000
 Y7D  O12  P11  O10  112.77  3.000
 Y7D  O13  P11  O10  102.15  3.000
 Y7D  O12  P11  O14  117.98  3.000
 Y7D  O13  P11  O14   99.04  3.000
 Y7D  O10  P11  O14  107.86  3.000
 Y7D  O40  P32  O39  117.03  3.000
 Y7D  O39  P32  O36  102.62  3.000
 Y7D  O40  P32  O36  118.59  3.000
 Y7D  O39  P32  O13  105.22  3.000
 Y7D  O36  P32  O13  100.07  3.000
 Y7D  O40  P32  O13  111.23  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
 Y7D  Var_01  C01  C02  C08  C09  -176.67   0.0  2
 Y7D  Var_02  C03  C02  C08  C09     1.74   0.0  2
 Y7D  Var_03  C05  C04  C03  C02    60.18  30.0  3
 Y7D  Var_04  O10  C09  C08  C02  -128.96  30.0  3
 Y7D  Var_05  O13  P11  O10  C09   -66.35  30.0  3
 Y7D  Var_06  O12  P11  O10  C09   169.49  30.0  3
 Y7D  Var_07  O14  P11  O10  C09    37.43  30.0  3
 Y7D  Var_08  P32  O13  P11  O14    85.38  30.0  1
 Y7D  Var_09  C04  C03  C02  C01    69.67  30.0  3
 Y7D  Var_10  C06  C05  C04  C03   175.90  30.0  3
 Y7D  Var_11  C08  C02  C03  C04  -108.82  30.0  3
 Y7D  Var_12  P11  O10  C09  C08   150.45  30.0  3
 Y7D  Var_13  P32  O13  P11  O10  -164.02  30.0  1
 Y7D  Var_14  P32  O13  P11  O12   -41.45  30.0  1
 Y7D  Var_15  P11  O13  P32  O36    74.92  30.0  2
 Y7D  Var_16  P11  O13  P32  O39   -31.23  30.0  2
 Y7D  Var_17  P11  O13  P32  O40  -158.89  30.0  2
 Y7D  Var_18  H16  C08  C02  C01     0.49   0.0  2
 Y7D  Var_19  H16  C08  C02  C03   178.91   0.0  2
 Y7D  Var_20  H9   C04  C03  C02  -178.28  30.0  3
 Y7D  Var_21  H10  C04  C03  C02   -63.14  30.0  3
 Y7D  Var_22  H1   C09  C08  C02    -6.26  30.0  3
 Y7D  Var_23  H2   C09  C08  C02   114.07  30.0  3
 Y7D  Var_24  H7   C03  C02  C01  -167.23  30.0  3
 Y7D  Var_25  H8   C03  C02  C01   -50.76  30.0  3
 Y7D  Var_26  H4   C01  C02  C03   177.12  30.0  3
 Y7D  Var_27  H5   C01  C02  C03   -62.18  30.0  3
 Y7D  Var_28  H6   C01  C02  C03    55.92  30.0  3
 Y7D  Var_29  H11  C05  C04  C03   -62.03  30.0  3
 Y7D  Var_30  H12  C05  C04  C03    53.81  30.0  3
 Y7D  Var_31  H13  C06  C05  C04   179.71  30.0  3
 Y7D  Var_32  H14  C06  C05  C04   -60.11  30.0  3
 Y7D  Var_33  H15  C06  C05  C04    59.69  30.0  3
 Y7D  Var_34  H7   C03  C04  C05   -64.52  30.0  1
 Y7D  Var_35  H8   C03  C04  C05  -179.51  30.0  1
 Y7D  Var_36  H9   C04  C05  C06    55.09  30.0  2
 Y7D  Var_37  H10  C04  C05  C06   -60.43  30.0  2
 Y7D  Var_38  H4   C01  C02  C08    -4.30  30.0  3
 Y7D  Var_39  H5   C01  C02  C08   116.39  30.0  3
 Y7D  Var_40  H6   C01  C02  C08  -125.51  30.0  3
 Y7D  Var_41  H7   C03  C02  C08    14.28  30.0  3
 Y7D  Var_42  H8   C03  C02  C08   130.75  30.0  3
 Y7D  Var_43  H16  C08  C09  O10    53.79  30.0  1
 Y7D  Var_44  H1   C09  O10  P11    26.99  30.0  2
 Y7D  Var_45  H2   C09  O10  P11   -90.19  30.0  2

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
 Y7D  chir_01  P11  O13  O12  O14  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
 Y7D  plan-1  C02  0.020
 Y7D  plan-1  C09  0.020
 Y7D  plan-1  C01  0.020
 Y7D  plan-1  C03  0.020
 Y7D  plan-1  C08  0.020
 Y7D  plan-1  H16  0.020

