# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 18:31:40 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: (2R)-2-(dodecanoylamino)hexyl 2-hydroxyethyl hydrogen (R)-phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCC(=O)N[C@H](CCCC)CO[P@](O)(=O)OCCO
#
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
 DHG  DHG  '(2R)-2-(dodecanoylamino)hexyl 2-hydroxyethyl hydrogen (R)-phosphate'  ligand  70  28  .  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_DHG
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
 DHG  C1    C  C     0   0.571   0.2306  -0.1862  -0.0684
 DHG  C2    C  CH2   0  -0.582   0.3562  -0.8737   1.2734
 DHG  C3    C  CH2   0  -0.415   0.3554   0.0979   2.4474
 DHG  C4    C  CH2   0  -0.415   0.4977  -0.6231   3.7816
 DHG  C5    C  CH2   0  -0.413   0.4985   0.3238   4.9751
 DHG  C6    C  CH2   0  -0.412   0.6299  -0.4002   6.3092
 DHG  C7    C  CH2   0  -0.412   0.6304   0.5387   7.5094
 DHG  C8    C  CH2   0  -0.411   0.7585  -0.1921   8.8401
 DHG  C9    C  CH2   0  -0.412   0.7586   0.7407  10.0451
 DHG  C10   C  CH2   0  -0.406   0.8895   0.0044  11.3724
 DHG  C11   C  CH2   0  -0.419   0.8862   0.9311  12.5824
 DHG  C12   C  CH3   0  -0.662   1.0289   0.1805  13.8993
 DHG  O1    O  O     0  -0.501   0.7785   0.8802  -0.3111
 DHG  N     N  NH1   0  -0.646  -0.5146  -0.8435  -0.9775
 DHG  CH1   C  CH2   0  -0.151   0.4111  -0.9099  -3.2063
 DHG  CH2   C  CH1   0  -0.124  -0.7282  -0.3899  -2.3355
 DHG  CH3   C  CH2   0  -0.444  -2.1016  -0.8376  -2.8234
 DHG  CH4   C  CH2   0  -0.408  -3.2502  -0.1762  -2.0724
 DHG  CH5   C  CH2   0  -0.420  -4.6173  -0.6405  -2.5589
 DHG  CH6   C  CH3   0  -0.663  -5.7639   0.0417  -1.8265
 DHG  O1P   O  O     0  -0.712   2.7580  -0.6117  -5.3035
 DHG  O2P   O  OH1   0  -0.741   0.9758  -2.1550  -6.1662
 DHG  O3P   O  O2    0  -0.584   0.2817  -0.3203  -4.5065
 DHG  P     P  P     0   1.476   1.3272  -0.6822  -5.6534
 DHG  OG1   O  O2    0  -0.580   0.7890   0.3439  -6.7430
 DHG  CG1   C  CH2   0  -0.198   1.5290   0.5539  -7.9568
 DHG  CG2   C  CH2   0  -0.179   0.7109   1.4184  -8.8767
 DHG  OG2   O  OH1   0  -0.668   0.5344   2.6833  -8.2885
 DHG  H21   H  HCH2  0   0.267   1.2967  -1.4359   1.2652
 DHG  H22   H  HCH2  0   0.248  -0.4375  -1.6138   1.4009
 DHG  H31   H  HCH2  0   0.222  -0.5736   0.6769   2.4442
 DHG  H32   H  HCH2  0   0.224   1.1693   0.8173   2.3307
 DHG  H41   H  HCH2  0   0.211   1.4240  -1.2088   3.7822
 DHG  H42   H  HCH2  0   0.211  -0.3177  -1.3458   3.8948
 DHG  H51   H  HCH2  0   0.208  -0.4246   0.9143   4.9711
 DHG  H52   H  HCH2  0   0.208   1.3187   1.0421   4.8675
 DHG  H61   H  HCH2  0   0.207   1.5523  -0.9921   6.3120
 DHG  H62   H  HCH2  0   0.207  -0.1905  -1.1190   6.4135
 DHG  H71   H  HCH2  0   0.206  -0.2914   1.1314   7.5070
 DHG  H72   H  HCH2  0   0.207   1.4521   1.2564   7.4076
 DHG  H81   H  HCH2  0   0.206   1.6804  -0.7849   8.8414
 DHG  H82   H  HCH2  0   0.206  -0.0627  -0.9107   8.9397
 DHG  H91   H  HCH2  0   0.206  -0.1639   1.3325  10.0463
 DHG  H92   H  HCH2  0   0.206   1.5792   1.4601   9.9459
 DHG  H101  H  HCH2  0   0.205   1.8136  -0.5851  11.3713
 DHG  H102  H  HCH2  0   0.206   0.0713  -0.7181  11.4697
 DHG  H111  H  HCH2  0   0.210  -0.0404   1.5139  12.5889
 DHG  H112  H  HCH2  0   0.210   1.6995   1.6565  12.4833
 DHG  H121  H  HCH3  0   0.225   1.0185   0.8581  14.7538
 DHG  H122  H  HCH3  0   0.215   0.2152  -0.5350  14.0353
 DHG  H123  H  HCH3  0   0.215   1.9658  -0.3792  13.9327
 DHG  HN    H  HNH1  0   0.399  -0.9188  -1.7291  -0.7154
 DHG  HH11  H  HCH2  0   0.254   1.3711  -0.6287  -2.7682
 DHG  HH12  H  HCH2  0   0.235   0.3655  -2.0012  -3.2727
 DHG  HH2   H  HCH1  0   0.255  -0.6854   0.7026  -2.3344
 DHG  HH31  H  HCH2  0   0.244  -2.1897  -0.6084  -3.8878
 DHG  HH32  H  HCH2  0   0.224  -2.1762  -1.9288  -2.7407
 DHG  HH41  H  HCH2  0   0.217  -3.1628  -0.3769  -1.0004
 DHG  HH42  H  HCH2  0   0.215  -3.1722   0.9107  -2.1848
 DHG  HH51  H  HCH2  0   0.213  -4.7036  -0.4523  -3.6335
 DHG  HH52  H  HCH2  0   0.213  -4.6950  -1.7250  -2.4345
 DHG  HH61  H  HCH3  0   0.227  -6.7326  -0.3109  -2.1815
 DHG  HH62  H  HCH3  0   0.217  -5.7152  -0.1495  -0.7529
 DHG  HH63  H  HCH3  0   0.217  -5.7330   1.1237  -1.9680
 DHG  HOP2  H  HOH1  0   0.496   0.0585  -2.3046  -6.4321
 DHG  HG11  H  HCH2  0   0.246   2.4847   1.0304  -7.7273
 DHG  HG12  H  HCH2  0   0.243   1.7309  -0.3967  -8.4562
 DHG  HG21  H  HCH2  0   0.211   1.2576   1.4749  -9.8267
 DHG  HG22  H  HCH2  0   0.211  -0.2447   0.9230  -9.0887
 DHG  HOG2  H  HOH1  0   0.459  -0.0273   3.2076  -8.8660

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
 DHG  C1   C2    single  1.513  0.020  1.513
 DHG  C1   O1    double  1.223  0.020  1.223
 DHG  C1   N     single  1.347  0.020  1.347
 DHG  C2   C3    single  1.524  0.020  1.524
 DHG  C2   H21   single  0.970  0.020  1.090
 DHG  C2   H22   single  0.970  0.020  1.090
 DHG  C3   C4    single  1.523  0.020  1.523
 DHG  C3   H31   single  0.970  0.020  1.090
 DHG  C3   H32   single  0.970  0.020  1.090
 DHG  C4   C5    single  1.524  0.020  1.524
 DHG  C4   H41   single  0.970  0.020  1.090
 DHG  C4   H42   single  0.970  0.020  1.090
 DHG  C5   C6    single  1.523  0.020  1.523
 DHG  C5   H51   single  0.970  0.020  1.090
 DHG  C5   H52   single  0.970  0.020  1.090
 DHG  C6   C7    single  1.524  0.020  1.524
 DHG  C6   H61   single  0.970  0.020  1.090
 DHG  C6   H62   single  0.970  0.020  1.090
 DHG  C7   C8    single  1.524  0.020  1.524
 DHG  C7   H71   single  0.970  0.020  1.090
 DHG  C7   H72   single  0.970  0.020  1.090
 DHG  C8   C9    single  1.524  0.020  1.524
 DHG  C8   H81   single  0.970  0.020  1.090
 DHG  C8   H82   single  0.970  0.020  1.090
 DHG  C9   C10   single  1.523  0.020  1.523
 DHG  C9   H91   single  0.970  0.020  1.090
 DHG  C9   H92   single  0.970  0.020  1.090
 DHG  C10  C11   single  1.524  0.020  1.524
 DHG  C10  H101  single  0.970  0.020  1.090
 DHG  C10  H102  single  0.970  0.020  1.090
 DHG  C11  C12   single  1.523  0.020  1.523
 DHG  C11  H111  single  0.970  0.020  1.090
 DHG  C11  H112  single  0.970  0.020  1.090
 DHG  C12  H121  single  0.970  0.020  1.090
 DHG  C12  H122  single  0.970  0.020  1.090
 DHG  C12  H123  single  0.970  0.020  1.090
 DHG  N    CH2   single  1.448  0.020  1.448
 DHG  N    HN    single  0.860  0.020  1.020
 DHG  CH1  CH2   single  1.525  0.020  1.525
 DHG  CH1  O3P   single  1.434  0.020  1.434
 DHG  CH1  HH11  single  0.970  0.020  1.090
 DHG  CH1  HH12  single  0.970  0.020  1.090
 DHG  CH2  CH3   single  1.525  0.020  1.525
 DHG  CH2  HH2   single  0.970  0.020  1.090
 DHG  CH3  CH4   single  1.523  0.020  1.523
 DHG  CH3  HH31  single  0.970  0.020  1.090
 DHG  CH3  HH32  single  0.970  0.020  1.090
 DHG  CH4  CH5   single  1.524  0.020  1.524
 DHG  CH4  HH41  single  0.970  0.020  1.090
 DHG  CH4  HH42  single  0.970  0.020  1.090
 DHG  CH5  CH6   single  1.522  0.020  1.522
 DHG  CH5  HH51  single  0.970  0.020  1.090
 DHG  CH5  HH52  single  0.970  0.020  1.090
 DHG  CH6  HH61  single  0.970  0.020  1.090
 DHG  CH6  HH62  single  0.970  0.020  1.090
 DHG  CH6  HH63  single  0.970  0.020  1.090
 DHG  O1P  P     double  1.475  0.020  1.475
 DHG  O2P  P     single  1.599  0.020  1.599
 DHG  O2P  HOP2  single  0.850  0.020  0.980
 DHG  O3P  P     single  1.594  0.020  1.594
 DHG  P    OG1   single  1.591  0.020  1.591
 DHG  OG1  CG1   single  1.437  0.020  1.437
 DHG  CG1  CG2   single  1.504  0.020  1.504
 DHG  CG1  HG11  single  0.970  0.020  1.090
 DHG  CG1  HG12  single  0.970  0.020  1.090
 DHG  CG2  OG2   single  1.406  0.020  1.406
 DHG  CG2  HG21  single  0.970  0.020  1.090
 DHG  CG2  HG22  single  0.970  0.020  1.090
 DHG  OG2  HOG2  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
 DHG  N     C1   O1    122.64  3.000
 DHG  N     C1   C2    115.01  3.000
 DHG  O1    C1   C2    122.34  3.000
 DHG  H22   C2   H21   106.07  3.000
 DHG  H22   C2   C3    109.97  3.000
 DHG  H21   C2   C3    109.47  3.000
 DHG  H22   C2   C1    110.55  3.000
 DHG  H21   C2   C1    107.32  3.000
 DHG  C3    C2   C1    113.17  3.000
 DHG  H32   C3   H31   106.48  3.000
 DHG  H32   C3   C4    109.61  3.000
 DHG  H31   C3   C4    109.41  3.000
 DHG  H32   C3   C2    109.70  3.000
 DHG  H31   C3   C2    109.59  3.000
 DHG  C4    C3   C2    111.90  3.000
 DHG  H42   C4   H41   106.05  3.000
 DHG  H42   C4   C5    109.24  3.000
 DHG  H41   C4   C5    109.35  3.000
 DHG  H42   C4   C3    109.47  3.000
 DHG  H41   C4   C3    109.42  3.000
 DHG  C5    C4   C3    113.08  3.000
 DHG  H52   C5   H51   106.07  3.000
 DHG  H52   C5   C6    109.46  3.000
 DHG  H51   C5   C6    109.39  3.000
 DHG  H52   C5   C4    109.33  3.000
 DHG  H51   C5   C4    109.37  3.000
 DHG  C6    C5   C4    113.00  3.000
 DHG  H62   C6   H61   106.00  3.000
 DHG  H62   C6   C7    109.23  3.000
 DHG  H61   C6   C7    109.29  3.000
 DHG  H62   C6   C5    109.30  3.000
 DHG  H61   C6   C5    109.36  3.000
 DHG  C7    C6   C5    113.39  3.000
 DHG  H72   C7   H71   106.04  3.000
 DHG  H72   C7   C8    109.41  3.000
 DHG  H71   C7   C8    109.39  3.000
 DHG  H72   C7   C6    109.31  3.000
 DHG  H71   C7   C6    109.34  3.000
 DHG  C8    C7   C6    113.11  3.000
 DHG  H82   C8   H81   105.99  3.000
 DHG  H82   C8   C9    109.25  3.000
 DHG  H81   C8   C9    109.27  3.000
 DHG  H82   C8   C7    109.33  3.000
 DHG  H81   C8   C7    109.34  3.000
 DHG  C9    C8   C7    113.40  3.000
 DHG  H92   C9   H91   106.02  3.000
 DHG  H92   C9   C10   109.38  3.000
 DHG  H91   C9   C10   109.40  3.000
 DHG  H92   C9   C8    109.29  3.000
 DHG  H91   C9   C8    109.35  3.000
 DHG  C10   C9   C8    113.15  3.000
 DHG  H102  C10  H101  105.96  3.000
 DHG  H102  C10  C11   109.19  3.000
 DHG  H101  C10  C11   109.24  3.000
 DHG  H102  C10  C9    109.38  3.000
 DHG  H101  C10  C9    109.36  3.000
 DHG  C11   C10  C9    113.43  3.000
 DHG  H112  C11  H111  106.06  3.000
 DHG  H112  C11  C12   109.60  3.000
 DHG  H111  C11  C12   109.68  3.000
 DHG  H112  C11  C10   109.24  3.000
 DHG  H111  C11  C10   109.29  3.000
 DHG  C12   C11  C10   112.75  3.000
 DHG  H123  C12  H122  107.44  3.000
 DHG  H123  C12  H121  107.62  3.000
 DHG  H122  C12  H121  107.60  3.000
 DHG  H123  C12  C11   111.08  3.000
 DHG  H122  C12  C11   111.16  3.000
 DHG  H121  C12  C11   111.75  3.000
 DHG  HN    N    CH2   117.38  3.000
 DHG  HN    N    C1    118.37  3.000
 DHG  CH2   N    C1    124.19  3.000
 DHG  HH12  CH1  HH11  108.53  3.000
 DHG  HH12  CH1  O3P   110.57  3.000
 DHG  HH11  CH1  O3P   109.71  3.000
 DHG  HH12  CH1  CH2   110.09  3.000
 DHG  HH11  CH1  CH2   109.87  3.000
 DHG  O3P   CH1  CH2   108.07  3.000
 DHG  HH2   CH2  CH3   109.21  3.000
 DHG  HH2   CH2  CH1   108.18  3.000
 DHG  CH3   CH2  CH1   112.96  3.000
 DHG  HH2   CH2  N     107.84  3.000
 DHG  CH3   CH2  N     109.94  3.000
 DHG  CH1   CH2  N     108.57  3.000
 DHG  HH32  CH3  HH31  106.07  3.000
 DHG  HH32  CH3  CH4   110.09  3.000
 DHG  HH31  CH3  CH4   109.17  3.000
 DHG  HH32  CH3  CH2   109.23  3.000
 DHG  HH31  CH3  CH2   108.84  3.000
 DHG  CH4   CH3  CH2   113.20  3.000
 DHG  HH42  CH4  HH41  106.07  3.000
 DHG  HH42  CH4  CH5   109.48  3.000
 DHG  HH41  CH4  CH5   109.19  3.000
 DHG  HH42  CH4  CH3   109.06  3.000
 DHG  HH41  CH4  CH3   110.06  3.000
 DHG  CH5   CH4  CH3   112.76  3.000
 DHG  HH52  CH5  HH51  106.05  3.000
 DHG  HH52  CH5  CH6   109.63  3.000
 DHG  HH51  CH5  CH6   109.64  3.000
 DHG  HH52  CH5  CH4   109.23  3.000
 DHG  HH51  CH5  CH4   109.39  3.000
 DHG  CH6   CH5  CH4   112.69  3.000
 DHG  HH63  CH6  HH62  107.45  3.000
 DHG  HH63  CH6  HH61  107.67  3.000
 DHG  HH62  CH6  HH61  107.65  3.000
 DHG  HH63  CH6  CH5   111.14  3.000
 DHG  HH62  CH6  CH5   111.17  3.000
 DHG  HH61  CH6  CH5   111.57  3.000
 DHG  HOP2  O2P  P     116.07  3.000
 DHG  P     O3P  CH1   120.01  3.000
 DHG  OG1   P    O3P    97.15  3.000
 DHG  OG1   P    O2P   107.47  3.000
 DHG  O3P   P    O2P   107.21  3.000
 DHG  OG1   P    O1P   117.39  3.000
 DHG  O3P   P    O1P   117.06  3.000
 DHG  O2P   P    O1P   109.48  3.000
 DHG  CG1   OG1  P     119.91  3.000
 DHG  HG12  CG1  HG11  108.30  3.000
 DHG  HG12  CG1  CG2   108.72  3.000
 DHG  HG11  CG1  CG2   110.71  3.000
 DHG  HG12  CG1  OG1   110.73  3.000
 DHG  HG11  CG1  OG1   109.68  3.000
 DHG  CG2   CG1  OG1   108.69  3.000
 DHG  HG22  CG2  HG21  106.86  3.000
 DHG  HG22  CG2  OG2   112.19  3.000
 DHG  HG21  CG2  OG2   112.22  3.000
 DHG  HG22  CG2  CG1   109.42  3.000
 DHG  HG21  CG2  CG1   106.74  3.000
 DHG  OG2   CG2  CG1   109.23  3.000
 DHG  HOG2  OG2  CG2   108.22  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
 DHG  CONST_01  CH2   N    C1   C2    180.00   0.0  0
 DHG  CONST_02  CH2   N    C1   O1      0.00   0.0  0
 DHG  CONST_03  HN    N    C1   C2      0.00   0.0  0
 DHG  Var_01    C4    C3   C2   C1   -179.41  30.0  3
 DHG  Var_02    C5    C4   C3   C2   -179.93  30.0  3
 DHG  Var_03    O1    C1   C2   C3     37.86  30.0  2
 DHG  Var_04    C6    C5   C4   C3    179.55  30.0  3
 DHG  Var_05    C7    C6   C5   C4   -179.95  30.0  3
 DHG  Var_06    C8    C7   C6   C5    179.85  30.0  3
 DHG  Var_07    C9    C8   C7   C6   -179.95  30.0  3
 DHG  Var_08    C10   C9   C8   C7   -179.89  30.0  3
 DHG  Var_09    C11   C10  C9   C8   -179.83  30.0  3
 DHG  Var_10    C12   C11  C10  C9   -179.54  30.0  3
 DHG  Var_11    O1P   P    O3P  CH1   -48.53  30.0  3
 DHG  Var_12    CH5   CH4  CH3  CH2  -179.46  30.0  3
 DHG  Var_13    CH6   CH5  CH4  CH3  -178.87  30.0  3
 DHG  Var_14    CG2   CG1  OG1  P     172.42  30.0  3
 DHG  Var_15    OG2   CG2  CG1  OG1    64.00  30.0  3
 DHG  Var_16    H121  C12  C11  C10  -179.65  30.0  3
 DHG  Var_17    HH61  CH6  CH5  CH4  -179.42  30.0  3
 DHG  Var_18    HH11  CH1  O3P  P      60.75  30.0  1

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
 DHG  chir_01  CH2  N    CH1  CH3  negativ
 DHG  chir_02  P    O2P  O3P  OG1  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
 DHG  plan-1  C1   0.020
 DHG  plan-1  C2   0.020
 DHG  plan-1  O1   0.020
 DHG  plan-1  N    0.020
 DHG  plan-1  CH2  0.020
 DHG  plan-1  HN   0.020

