# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 16:43:01 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  56  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 PERFECT
;

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   1.471   1.6681   0.0745    0.0023
 DOP  O1    O  O2    0  -0.587   0.6264  -0.0194    1.2041
 DOP  O1'   O  O2    0  -0.587   0.6305  -0.0128   -1.2035
 DOP  O2    O  OH1   0  -0.744   2.2674   1.5581    0.0075
 DOP  O3    O  O     0  -0.715   2.7767  -0.8990    0.0017
 DOP  C1    C  CH2   0  -0.159   1.1475  -0.1028    2.5458
 DOP  C2    C  CH2   0  -0.462   0.0130   0.0088    3.5384
 DOP  C3    C  CH2   0  -0.428   0.5574  -0.0532    4.9617
 DOP  C4    C  CH2   0  -0.412  -0.5222   0.0028    6.0340
 DOP  C5    C  CH2   0  -0.411   0.0593  -0.0291    7.4420
 DOP  C6    C  CH2   0  -0.407  -0.9938   0.0052    8.5416
 DOP  C7    C  CH2   0  -0.419  -0.3930  -0.0161    9.9423
 DOP  C8    C  CH3   0  -0.662  -1.4457   0.0111   11.0413
 DOP  C1'   C  CH2   0  -0.159   1.1563  -0.0807   -2.5443
 DOP  C2'   C  CH2   0  -0.462   0.0231   0.0185   -3.5395
 DOP  C3'   C  CH2   0  -0.428   0.5724  -0.0273   -4.9617
 DOP  C4'   C  CH2   0  -0.412  -0.5051   0.0238   -6.0362
 DOP  C5'   C  CH2   0  -0.411   0.0796   0.0083   -7.4434
 DOP  C6'   C  CH2   0  -0.407  -0.9718   0.0413   -8.5444
 DOP  C7'   C  CH2   0  -0.419  -0.3689   0.0301   -9.9444
 DOP  C8'   C  CH3   0  -0.663  -1.4200   0.0604  -11.0447
 DOP  HO2   H  HOH1  0   0.495   1.6199   2.2757    0.0130
 DOP  H11   H  HCH2  0   0.230   1.8704   0.7006    2.7149
 DOP  H12   H  HCH2  0   0.237   1.6688  -1.0547    2.6705
 DOP  H21   H  HCH2  0   0.232  -0.7033  -0.8019    3.3763
 DOP  H22   H  HCH2  0   0.232  -0.5223   0.9502    3.3869
 DOP  H31   H  HCH2  0   0.218   1.2602   0.7727    5.1143
 DOP  H32   H  HCH2  0   0.217   1.1402  -0.9721    5.0872
 DOP  H41   H  HCH2  0   0.211  -1.2121  -0.8377    5.9028
 DOP  H42   H  HCH2  0   0.211  -1.1217   0.9108    5.9072
 DOP  H51   H  HCH2  0   0.208   0.7418   0.8187    7.5684
 DOP  H52   H  HCH2  0   0.208   0.6742  -0.9287    7.5576
 DOP  H61   H  HCH2  0   0.206  -1.6720  -0.8475    8.4245
 DOP  H62   H  HCH2  0   0.206  -1.6141   0.9013    8.4272
 DOP  H71   H  HCH2  0   0.210   0.2815   0.8383   10.0578
 DOP  H72   H  HCH2  0   0.210   0.2313  -0.9085   10.0526
 DOP  H81   H  HCH3  0   0.225  -0.9921  -0.0005   12.0330
 DOP  H82   H  HCH3  0   0.216  -2.0643   0.9080   10.9722
 DOP  H83   H  HCH3  0   0.216  -2.1097  -0.8523   10.9714
 DOP  H1'1  H  HCH2  0   0.231   1.8668   0.7351   -2.7067
 DOP  H1'2  H  HCH2  0   0.236   1.6932  -1.0234   -2.6732
 DOP  H2'1  H  HCH2  0   0.232  -0.6812  -0.8037   -3.3843
 DOP  H2'2  H  HCH2  0   0.231  -0.5273   0.9508   -3.3851
 DOP  H3'1  H  HCH2  0   0.218   1.2657   0.8079   -5.1068
 DOP  H3'2  H  HCH2  0   0.218   1.1666  -0.9381   -5.0918
 DOP  H4'1  H  HCH2  0   0.211  -1.1863  -0.8249   -5.9130
 DOP  H4'2  H  HCH2  0   0.211  -1.1148   0.9243   -5.9048
 DOP  H5'1  H  HCH2  0   0.208   0.7547   0.8631   -7.5619
 DOP  H5'2  H  HCH2  0   0.208   0.7031  -0.8846   -7.5641
 DOP  H6'1  H  HCH2  0   0.206  -1.6456  -0.8156   -8.4325
 DOP  H6'2  H  HCH2  0   0.206  -1.5972   0.9335   -8.4269
 DOP  H7'1  H  HCH2  0   0.210   0.3031   0.8873  -10.0537
 DOP  H7'2  H  HCH2  0   0.210   0.2583  -0.8597  -10.0587
 DOP  H8'1  H  HCH3  0   0.226  -0.9649   0.0529  -12.0358
 DOP  H8'2  H  HCH3  0   0.216  -2.0832  -0.8039  -10.9792
 DOP  H8'3  H  HCH3  0   0.216  -2.0395   0.9563  -10.9732

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  1.593  0.020  1.593
 DOP  P    O1'   single  1.593  0.020  1.593
 DOP  P    O2    single  1.600  0.020  1.600
 DOP  P    O3    double  1.475  0.020  1.475
 DOP  O1   C1    single  1.442  0.020  1.442
 DOP  O1'  C1'   single  1.442  0.020  1.442
 DOP  O2   HO2   single  0.850  0.020  0.980
 DOP  C1   C2    single  1.512  0.020  1.512
 DOP  C1   H11   single  0.970  0.020  1.090
 DOP  C1   H12   single  0.970  0.020  1.090
 DOP  C2   C3    single  1.525  0.020  1.525
 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  1.511  0.020  1.511
 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  1.525  0.020  1.525
 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    109.29  3.000
 DOP  O3    P    O1'   116.93  3.000
 DOP  O2    P    O1'   107.29  3.000
 DOP  O3    P    O1    116.92  3.000
 DOP  O2    P    O1    107.28  3.000
 DOP  O1'   P    O1     98.16  3.000
 DOP  C1    O1   P     117.98  3.000
 DOP  C1'   O1'  P     117.96  3.000
 DOP  HO2   O2   P     115.94  3.000
 DOP  H12   C1   H11   107.87  3.000
 DOP  H12   C1   C2    110.33  3.000
 DOP  H11   C1   C2    109.89  3.000
 DOP  H12   C1   O1    109.22  3.000
 DOP  H11   C1   O1    109.89  3.000
 DOP  C2    C1   O1    109.61  3.000
 DOP  H22   C2   H21   107.27  3.000
 DOP  H22   C2   C3    109.82  3.000
 DOP  H21   C2   C3    109.99  3.000
 DOP  H22   C2   C1    109.88  3.000
 DOP  H21   C2   C1    109.85  3.000
 DOP  C3    C2   C1    109.99  3.000
 DOP  H32   C3   H31   105.98  3.000
 DOP  H32   C3   C4    109.11  3.000
 DOP  H31   C3   C4    109.22  3.000
 DOP  H32   C3   C2    109.32  3.000
 DOP  H31   C3   C2    109.18  3.000
 DOP  C4    C3   C2    113.74  3.000
 DOP  H42   C4   H41   106.12  3.000
 DOP  H42   C4   C5    109.46  3.000
 DOP  H41   C4   C5    109.58  3.000
 DOP  H42   C4   C3    109.69  3.000
 DOP  H41   C4   C3    109.52  3.000
 DOP  C5    C4   C3    112.29  3.000
 DOP  H52   C5   H51   105.87  3.000
 DOP  H52   C5   C6    109.29  3.000
 DOP  H51   C5   C6    109.28  3.000
 DOP  H52   C5   C4    109.19  3.000
 DOP  H51   C5   C4    109.15  3.000
 DOP  C6    C5   C4    113.76  3.000
 DOP  H62   C6   H61   105.95  3.000
 DOP  H62   C6   C7    109.29  3.000
 DOP  H61   C6   C7    109.35  3.000
 DOP  H62   C6   C5    109.54  3.000
 DOP  H61   C6   C5    109.47  3.000
 DOP  C7    C6   C5    113.00  3.000
 DOP  H72   C7   H71   105.92  3.000
 DOP  H72   C7   C8    109.65  3.000
 DOP  H71   C7   C8    109.64  3.000
 DOP  H72   C7   C6    109.19  3.000
 DOP  H71   C7   C6    109.20  3.000
 DOP  C8    C7   C6    113.00  3.000
 DOP  H83   C8   H82   107.53  3.000
 DOP  H83   C8   H81   107.63  3.000
 DOP  H82   C8   H81   107.58  3.000
 DOP  H83   C8   C7    111.12  3.000
 DOP  H82   C8   C7    111.15  3.000
 DOP  H81   C8   C7    111.63  3.000
 DOP  H1'2  C1'  H1'1  107.87  3.000
 DOP  H1'2  C1'  C2'   110.33  3.000
 DOP  H1'1  C1'  C2'   109.90  3.000
 DOP  H1'2  C1'  O1'   109.24  3.000
 DOP  H1'1  C1'  O1'   109.86  3.000
 DOP  C2'   C1'  O1'   109.62  3.000
 DOP  H2'2  C2'  H2'1  107.26  3.000
 DOP  H2'2  C2'  C3'   109.79  3.000
 DOP  H2'1  C2'  C3'   109.98  3.000
 DOP  H2'2  C2'  C1'   109.90  3.000
 DOP  H2'1  C2'  C1'   109.88  3.000
 DOP  C3'   C2'  C1'   110.00  3.000
 DOP  H3'2  C3'  H3'1  105.96  3.000
 DOP  H3'2  C3'  C4'   109.15  3.000
 DOP  H3'1  C3'  C4'   109.20  3.000
 DOP  H3'2  C3'  C2'   109.34  3.000
 DOP  H3'1  C3'  C2'   109.18  3.000
 DOP  C4'   C3'  C2'   113.72  3.000
 DOP  H4'2  C4'  H4'1  106.10  3.000
 DOP  H4'2  C4'  C5'   109.44  3.000
 DOP  H4'1  C4'  C5'   109.55  3.000
 DOP  H4'2  C4'  C3'   109.68  3.000
 DOP  H4'1  C4'  C3'   109.56  3.000
 DOP  C5'   C4'  C3'   112.32  3.000
 DOP  H5'2  C5'  H5'1  105.86  3.000
 DOP  H5'2  C5'  C6'   109.32  3.000
 DOP  H5'1  C5'  C6'   109.29  3.000
 DOP  H5'2  C5'  C4'   109.17  3.000
 DOP  H5'1  C5'  C4'   109.17  3.000
 DOP  C6'   C5'  C4'   113.73  3.000
 DOP  H6'2  C6'  H6'1  105.95  3.000
 DOP  H6'2  C6'  C7'   109.28  3.000
 DOP  H6'1  C6'  C7'   109.35  3.000
 DOP  H6'2  C6'  C5'   109.52  3.000
 DOP  H6'1  C6'  C5'   109.50  3.000
 DOP  C7'   C6'  C5'   113.00  3.000
 DOP  H7'2  C7'  H7'1  105.92  3.000
 DOP  H7'2  C7'  C8'   109.66  3.000
 DOP  H7'1  C7'  C8'   109.65  3.000
 DOP  H7'2  C7'  C6'   109.17  3.000
 DOP  H7'1  C7'  C6'   109.20  3.000
 DOP  C8'   C7'  C6'   113.00  3.000
 DOP  H8'3  C8'  H8'2  107.53  3.000
 DOP  H8'3  C8'  H8'1  107.58  3.000
 DOP  H8'2  C8'  H8'1  107.62  3.000
 DOP  H8'3  C8'  C7'   111.15  3.000
 DOP  H8'2  C8'  C7'   111.13  3.000
 DOP  H8'1  C8'  C7'   111.63  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     172.25  30.0  3
 DOP  Var_02  C2'   C1'  O1'  P    -172.91  30.0  3
 DOP  Var_03  C3    C2   C1   O1   -178.98  30.0  3
 DOP  Var_04  C3'   C2'  C1'  O1'   178.99  30.0  3
 DOP  Var_05  C4    C3   C2   C1   -177.97  30.0  3
 DOP  Var_06  C5    C4   C3   C2   -178.69  30.0  3
 DOP  Var_07  C6    C5   C4   C3   -179.17  30.0  3
 DOP  Var_08  C7    C6   C5   C4   -179.54  30.0  3
 DOP  Var_09  C8    C7   C6   C5   -179.71  30.0  3
 DOP  Var_10  C4'   C3'  C2'  C1'   178.22  30.0  3
 DOP  Var_11  C5'   C4'  C3'  C2'   178.70  30.0  3
 DOP  Var_12  C6'   C5'  C4'  C3'   179.29  30.0  3
 DOP  Var_13  C7'   C6'  C5'  C4'   179.80  30.0  3
 DOP  Var_14  C8'   C7'  C6'  C5'   179.89  30.0  3
 DOP  Var_15  H81   C8   C7   C6   -179.76  30.0  3
 DOP  Var_16  H8'1  C8'  C7'  C6'   179.94  30.0  3

