# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 04:27:55 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: dioctyl hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCOP(O)(=O)OCCCCCCCC
#
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
 DOP  DOP  'dioctyl hydrogen phosphate'  ligand  55  21  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DOP
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
 DOP  P     P  P      0   1.324   1.4182  -0.6148   -0.0009
 DOP  O1    O  O2     0  -0.623   0.4927   0.0061    1.2036
 DOP  O1'   O  O2     0  -0.623   0.5022   0.0254   -1.2016
 DOP  O2    O  OP    -1  -0.807   2.7795   0.0150    0.0096
 DOP  O3    O  O      0  -0.794   1.3010  -2.1098   -0.0139
 DOP  C1    C  CH2    0  -0.131   1.0580  -0.0206    2.5064
 DOP  C2    C  CH2    0  -0.457  -0.0345   0.0290    3.5544
 DOP  C3    C  CH2    0  -0.425   0.5581   0.0447    4.9588
 DOP  C4    C  CH2    0  -0.411  -0.4892   0.0565    6.0643
 DOP  C5    C  CH2    0  -0.411   0.1286   0.0698    7.4572
 DOP  C6    C  CH2    0  -0.406  -0.8999   0.0718    8.5803
 DOP  C7    C  CH2    0  -0.419  -0.2706   0.0857    9.9685
 DOP  C8    C  CH3    0  -0.662  -1.3025   0.0840   11.0876
 DOP  C1'   C  CH2    0  -0.131   1.0652  -0.0053   -2.5056
 DOP  C2'   C  CH2    0  -0.457  -0.0294   0.0382   -3.5517
 DOP  C3'   C  CH2    0  -0.425   0.5604   0.0516   -4.9572
 DOP  C4'   C  CH2    0  -0.410  -0.4889   0.0618   -6.0608
 DOP  C5'   C  CH2    0  -0.411   0.1265   0.0758   -7.4548
 DOP  C6'   C  CH2    0  -0.406  -0.9040   0.0781   -8.5762
 DOP  C7'   C  CH2    0  -0.419  -0.2767   0.0916   -9.9654
 DOP  C8'   C  CH3    0  -0.663  -1.3100   0.0921  -11.0831
 DOP  H11   H  HCH2   0   0.203   1.7376   0.8289    2.6364
 DOP  H12   H  HCH2   0   0.198   1.6541  -0.9283    2.6625
 DOP  H21   H  HCH2   0   0.219  -0.6922  -0.8382    3.4392
 DOP  H22   H  HCH2   0   0.220  -0.6546   0.9189    3.4062
 DOP  H31   H  HCH2   0   0.213   1.2083   0.9196    5.0684
 DOP  H32   H  HCH2   0   0.212   1.2066  -0.8289    5.0882
 DOP  H41   H  HCH2   0   0.209  -1.1389  -0.8195    5.9610
 DOP  H42   H  HCH2   0   0.209  -1.1388   0.9306    5.9450
 DOP  H51   H  HCH2   0   0.207   0.7755   0.9487    7.5567
 DOP  H52   H  HCH2   0   0.207   0.7854  -0.8002    7.5691
 DOP  H61   H  HCH2   0   0.206  -1.5468  -0.8076    8.4842
 DOP  H62   H  HCH2   0   0.206  -1.5573   0.9419    8.4716
 DOP  H71   H  HCH2   0   0.210   0.3738   0.9655   10.0634
 DOP  H72   H  HCH2   0   0.210   0.3883  -0.7821   10.0742
 DOP  H81   H  HCH3   0   0.225  -0.8300   0.0947   12.0705
 DOP  H82   H  HCH3   0   0.216  -1.9528   0.9582   11.0240
 DOP  H83   H  HCH3   0   0.216  -1.9370  -0.8026   11.0359
 DOP  H1'1  H  HCH2   0   0.203   1.7418   0.8459   -2.6395
 DOP  H1'2  H  HCH2   0   0.198   1.6639  -0.9116   -2.6590
 DOP  H2'1  H  HCH2   0   0.219  -0.6847  -0.8305   -3.4331
 DOP  H2'2  H  HCH2   0   0.220  -0.6515   0.9269   -3.4047
 DOP  H3'1  H  HCH2   0   0.213   1.2102   0.9264   -5.0693
 DOP  H3'2  H  HCH2   0   0.212   1.2088  -0.8221   -5.0865
 DOP  H4'1  H  HCH2   0   0.209  -1.1369  -0.8154   -5.9567
 DOP  H4'2  H  HCH2   0   0.209  -1.1396   0.9349   -5.9403
 DOP  H5'1  H  HCH2   0   0.207   0.7732   0.9547   -7.5553
 DOP  H5'2  H  HCH2   0   0.207   0.7829  -0.7942   -7.5682
 DOP  H6'1  H  HCH2   0   0.206  -1.5508  -0.8013   -8.4792
 DOP  H6'2  H  HCH2   0   0.206  -1.5609   0.9484   -8.4667
 DOP  H7'1  H  HCH2   0   0.210   0.3689   0.9705  -10.0606
 DOP  H7'2  H  HCH2   0   0.210   0.3807  -0.7771  -10.0722
 DOP  H8'1  H  HCH3   0   0.225  -0.8389   0.1007  -12.0667
 DOP  H8'2  H  HCH3   0   0.216  -1.9472  -0.7925  -11.0298
 DOP  H8'3  H  HCH3   0   0.216  -1.9578   0.9683  -11.0193

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
 DOP  P    O1    single  1.641  0.020  1.641
 DOP  P    O1'   single  1.640  0.020  1.640
 DOP  P    O2    deloc   1.500  0.020  1.500
 DOP  P    O3    deloc   1.500  0.020  1.500
 DOP  O1   C1    single  1.420  0.020  1.420
 DOP  O1'  C1'   single  1.421  0.020  1.421
 DOP  C1   C2    single  1.515  0.020  1.515
 DOP  C1   H11   single  0.970  0.020  1.090
 DOP  C1   H12   single  0.970  0.020  1.090
 DOP  C2   C3    single  1.524  0.020  1.524
 DOP  C2   H21   single  0.970  0.020  1.090
 DOP  C2   H22   single  0.970  0.020  1.090
 DOP  C3   C4    single  1.523  0.020  1.523
 DOP  C3   H31   single  0.970  0.020  1.090
 DOP  C3   H32   single  0.970  0.020  1.090
 DOP  C4   C5    single  1.524  0.020  1.524
 DOP  C4   H41   single  0.970  0.020  1.090
 DOP  C4   H42   single  0.970  0.020  1.090
 DOP  C5   C6    single  1.523  0.020  1.523
 DOP  C5   H51   single  0.970  0.020  1.090
 DOP  C5   H52   single  0.970  0.020  1.090
 DOP  C6   C7    single  1.524  0.020  1.524
 DOP  C6   H61   single  0.970  0.020  1.090
 DOP  C6   H62   single  0.970  0.020  1.090
 DOP  C7   C8    single  1.522  0.020  1.522
 DOP  C7   H71   single  0.970  0.020  1.090
 DOP  C7   H72   single  0.970  0.020  1.090
 DOP  C8   H81   single  0.970  0.020  1.090
 DOP  C8   H82   single  0.970  0.020  1.090
 DOP  C8   H83   single  0.970  0.020  1.090
 DOP  C1'  C2'   single  1.515  0.020  1.515
 DOP  C1'  H1'1  single  0.970  0.020  1.090
 DOP  C1'  H1'2  single  0.970  0.020  1.090
 DOP  C2'  C3'   single  1.524  0.020  1.524
 DOP  C2'  H2'1  single  0.970  0.020  1.090
 DOP  C2'  H2'2  single  0.970  0.020  1.090
 DOP  C3'  C4'   single  1.523  0.020  1.523
 DOP  C3'  H3'1  single  0.970  0.020  1.090
 DOP  C3'  H3'2  single  0.970  0.020  1.090
 DOP  C4'  C5'   single  1.524  0.020  1.524
 DOP  C4'  H4'1  single  0.970  0.020  1.090
 DOP  C4'  H4'2  single  0.970  0.020  1.090
 DOP  C5'  C6'   single  1.523  0.020  1.523
 DOP  C5'  H5'1  single  0.970  0.020  1.090
 DOP  C5'  H5'2  single  0.970  0.020  1.090
 DOP  C6'  C7'   single  1.524  0.020  1.524
 DOP  C6'  H6'1  single  0.970  0.020  1.090
 DOP  C6'  H6'2  single  0.970  0.020  1.090
 DOP  C7'  C8'   single  1.522  0.020  1.522
 DOP  C7'  H7'1  single  0.970  0.020  1.090
 DOP  C7'  H7'2  single  0.970  0.020  1.090
 DOP  C8'  H8'1  single  0.970  0.020  1.090
 DOP  C8'  H8'2  single  0.970  0.020  1.090
 DOP  C8'  H8'3  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
 DOP  O3    P    O2    119.31  3.000
 DOP  O3    P    O1'   109.82  3.000
 DOP  O2    P    O1'   110.37  3.000
 DOP  O3    P    O1    109.85  3.000
 DOP  O2    P    O1    110.35  3.000
 DOP  O1'   P    O1     94.28  3.000
 DOP  C1    O1   P     116.21  3.000
 DOP  C1'   O1'  P     116.24  3.000
 DOP  H12   C1   H11   106.72  3.000
 DOP  H12   C1   C2    108.69  3.000
 DOP  H11   C1   C2    109.87  3.000
 DOP  H12   C1   O1    111.24  3.000
 DOP  H11   C1   O1    109.95  3.000
 DOP  C2    C1   O1    110.30  3.000
 DOP  H22   C2   H21   106.83  3.000
 DOP  H22   C2   C3    109.67  3.000
 DOP  H21   C2   C3    109.80  3.000
 DOP  H22   C2   C1    109.97  3.000
 DOP  H21   C2   C1    109.54  3.000
 DOP  C3    C2   C1    110.94  3.000
 DOP  H32   C3   H31   105.88  3.000
 DOP  H32   C3   C4    109.12  3.000
 DOP  H31   C3   C4    109.23  3.000
 DOP  H32   C3   C2    109.31  3.000
 DOP  H31   C3   C2    109.34  3.000
 DOP  C4    C3   C2    113.67  3.000
 DOP  H42   C4   H41   106.02  3.000
 DOP  H42   C4   C5    109.45  3.000
 DOP  H41   C4   C5    109.49  3.000
 DOP  H42   C4   C3    109.57  3.000
 DOP  H41   C4   C3    109.47  3.000
 DOP  C5    C4   C3    112.63  3.000
 DOP  H52   C5   H51   105.88  3.000
 DOP  H52   C5   C6    109.30  3.000
 DOP  H51   C5   C6    109.30  3.000
 DOP  H52   C5   C4    109.24  3.000
 DOP  H51   C5   C4    109.23  3.000
 DOP  C6    C5   C4    113.60  3.000
 DOP  H62   C6   H61   105.92  3.000
 DOP  H62   C6   C7    109.32  3.000
 DOP  H61   C6   C7    109.32  3.000
 DOP  H62   C6   C5    109.46  3.000
 DOP  H61   C6   C5    109.44  3.000
 DOP  C7    C6   C5    113.13  3.000
 DOP  H72   C7   H71   105.93  3.000
 DOP  H72   C7   C8    109.64  3.000
 DOP  H71   C7   C8    109.65  3.000
 DOP  H72   C7   C6    109.22  3.000
 DOP  H71   C7   C6    109.22  3.000
 DOP  C8    C7   C6    112.93  3.000
 DOP  H83   C8   H82   107.55  3.000
 DOP  H83   C8   H81   107.61  3.000
 DOP  H82   C8   H81   107.62  3.000
 DOP  H83   C8   C7    111.11  3.000
 DOP  H82   C8   C7    111.11  3.000
 DOP  H81   C8   C7    111.65  3.000
 DOP  H1'2  C1'  H1'1  106.72  3.000
 DOP  H1'2  C1'  C2'   108.75  3.000
 DOP  H1'1  C1'  C2'   109.85  3.000
 DOP  H1'2  C1'  O1'   111.25  3.000
 DOP  H1'1  C1'  O1'   109.89  3.000
 DOP  C2'   C1'  O1'   110.30  3.000
 DOP  H2'2  C2'  H2'1  106.83  3.000
 DOP  H2'2  C2'  C3'   109.67  3.000
 DOP  H2'1  C2'  C3'   109.79  3.000
 DOP  H2'2  C2'  C1'   109.95  3.000
 DOP  H2'1  C2'  C1'   109.57  3.000
 DOP  C3'   C2'  C1'   110.94  3.000
 DOP  H3'2  C3'  H3'1  105.88  3.000
 DOP  H3'2  C3'  C4'   109.12  3.000
 DOP  H3'1  C3'  C4'   109.22  3.000
 DOP  H3'2  C3'  C2'   109.32  3.000
 DOP  H3'1  C3'  C2'   109.32  3.000
 DOP  C4'   C3'  C2'   113.68  3.000
 DOP  H4'2  C4'  H4'1  106.04  3.000
 DOP  H4'2  C4'  C5'   109.46  3.000
 DOP  H4'1  C4'  C5'   109.46  3.000
 DOP  H4'2  C4'  C3'   109.57  3.000
 DOP  H4'1  C4'  C3'   109.47  3.000
 DOP  C5'   C4'  C3'   112.63  3.000
 DOP  H5'2  C5'  H5'1  105.89  3.000
 DOP  H5'2  C5'  C6'   109.29  3.000
 DOP  H5'1  C5'  C6'   109.30  3.000
 DOP  H5'2  C5'  C4'   109.23  3.000
 DOP  H5'1  C5'  C4'   109.24  3.000
 DOP  C6'   C5'  C4'   113.60  3.000
 DOP  H6'2  C6'  H6'1  105.94  3.000
 DOP  H6'2  C6'  C7'   109.31  3.000
 DOP  H6'1  C6'  C7'   109.31  3.000
 DOP  H6'2  C6'  C5'   109.46  3.000
 DOP  H6'1  C6'  C5'   109.44  3.000
 DOP  C7'   C6'  C5'   113.11  3.000
 DOP  H7'2  C7'  H7'1  105.94  3.000
 DOP  H7'2  C7'  C8'   109.65  3.000
 DOP  H7'1  C7'  C8'   109.64  3.000
 DOP  H7'2  C7'  C6'   109.21  3.000
 DOP  H7'1  C7'  C6'   109.22  3.000
 DOP  C8'   C7'  C6'   112.94  3.000
 DOP  H8'3  C8'  H8'2  107.53  3.000
 DOP  H8'3  C8'  H8'1  107.62  3.000
 DOP  H8'2  C8'  H8'1  107.61  3.000
 DOP  H8'3  C8'  C7'   111.12  3.000
 DOP  H8'2  C8'  C7'   111.11  3.000
 DOP  H8'1  C8'  C7'   111.65  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
 DOP  Var_01  C2    C1   O1   P    -156.86  30.0  3
 DOP  Var_02  C2'   C1'  O1'  P     155.73  30.0  3
 DOP  Var_03  C3    C2   C1   O1   -178.24  30.0  3
 DOP  Var_04  C3'   C2'  C1'  O1'   178.16  30.0  3
 DOP  Var_05  C4    C3   C2   C1   -178.44  30.0  3
 DOP  Var_06  C5    C4   C3   C2    179.90  30.0  3
 DOP  Var_07  C6    C5   C4   C3   -179.60  30.0  3
 DOP  Var_08  C7    C6   C5   C4   -179.98  30.0  3
 DOP  Var_09  C8    C7   C6   C5   -179.85  30.0  3
 DOP  Var_10  C4'   C3'  C2'  C1'   178.63  30.0  3
 DOP  Var_11  C5'   C4'  C3'  C2'   179.97  30.0  3
 DOP  Var_12  C6'   C5'  C4'  C3'   179.67  30.0  3
 DOP  Var_13  C7'   C6'  C5'  C4'  -179.98  30.0  3
 DOP  Var_14  C8'   C7'  C6'  C5'   179.93  30.0  3
 DOP  Var_15  H81   C8   C7   C6   -179.96  30.0  3
 DOP  Var_16  H8'1  C8'  C7'  C6'  -179.94  30.0  3

