# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 22 23:21:47 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 17-hydroxy-3,6,9,12,15-pentaoxaheptadec-1-yl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOCCOCCOCCOCCOCCO[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
 PE6  PE6  '17-hydroxy-3,6,9,12,15-pentaoxaheptadec-1-yl dihydrogen phosphate'  ligand  50  23  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PE6
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
 PE6  C3    C  CH2   0  -0.206   0.2376   1.1744  -5.0874
 PE6  O2    O  O2    0  -0.586  -0.3758   0.0736  -5.7711
 PE6  P1    P  P     0   1.457   0.4113  -0.6643  -6.9448
 PE6  OP1   O  O     0  -0.713   1.8094  -1.0431  -6.6679
 PE6  OP2   O  OH1   0  -0.733  -0.6483  -1.8325  -7.1764
 PE6  C4    C  CH2   0  -0.163  -0.7413   1.7251  -4.0869
 PE6  O5    O  O2    0  -0.484  -1.0196   0.7511  -3.1179
 PE6  C6    C  CH2   0  -0.171  -1.9270   1.1961  -2.1402
 PE6  C7    C  CH2   0  -0.168  -2.2243   0.0730  -1.1806
 PE6  O8    O  O2    0  -0.486  -1.0601  -0.2656  -0.4719
 PE6  C9    C  CH2   0  -0.169  -1.2417  -1.3659   0.3823
 PE6  C10   C  CH2   0  -0.169   0.0551  -1.6858   1.0800
 PE6  O11   O  O2    0  -0.485   0.3998  -0.6346   1.9455
 PE6  O20   O  OH1   0  -0.672   0.3869  -0.8411   9.8218
 PE6  C19   C  CH2   0  -0.185  -0.8108  -0.8778   9.0799
 PE6  C18   C  CH2   0  -0.160  -0.9213   0.3674   8.2381
 PE6  O17   O  O2    0  -0.485   0.0939   0.3848   7.2663
 PE6  C16   C  CH2   0  -0.169   0.0264   1.5170   6.4382
 PE6  C15   C  CH2   0  -0.170   1.1298   1.4697   5.4135
 PE6  O14   O  O2    0  -0.485   0.9257   0.3832   4.5470
 PE6  C13   C  CH2   0  -0.169   1.9012   0.3003   3.5395
 PE6  C12   C  CH2   0  -0.169   1.6007  -0.8674   2.6360
 PE6  OP3   O  OH1   0  -0.742   0.3613   0.2973  -8.2213
 PE6  H31   H  HCH2  0   0.245   0.4984   1.9694  -5.7906
 PE6  H32   H  HCH2  0   0.245   1.1516   0.8433  -4.5888
 PE6  HOP2  H  HOH1  0   0.504  -0.3495  -2.5213  -7.7851
 PE6  H41   H  HCH2  0   0.214  -1.6578   2.0530  -4.5974
 PE6  H42   H  HCH2  0   0.216  -0.2867   2.6207  -3.6408
 PE6  H61   H  HCH2  0   0.210  -2.8742   1.5152  -2.5962
 PE6  H62   H  HCH2  0   0.208  -1.5263   2.0634  -1.5963
 PE6  H71   H  HCH2  0   0.205  -2.6165  -0.7929  -1.7331
 PE6  H72   H  HCH2  0   0.208  -3.0219   0.4045  -0.5010
 PE6  H91   H  HCH2  0   0.207  -1.5553  -2.2557  -0.1813
 PE6  H92   H  HCH2  0   0.204  -2.0282  -1.1669   1.1248
 PE6  H101  H  HCH2  0   0.204   0.8450  -1.8599   0.3348
 PE6  H102  H  HCH2  0   0.207  -0.0744  -2.6272   1.6321
 PE6  H20   H  HOH1  0   0.455   0.4326  -1.6408  10.3530
 PE6  H191  H  HCH2  0   0.200  -0.8611  -1.7615   8.4305
 PE6  H192  H  HCH2  0   0.202  -1.6946  -0.9108   9.7295
 PE6  H181  H  HCH2  0   0.204  -1.9153   0.3764   7.7686
 PE6  H182  H  HCH2  0   0.202  -0.8663   1.2594   8.8794
 PE6  H161  H  HCH2  0   0.203  -0.9494   1.5788   5.9342
 PE6  H162  H  HCH2  0   0.207   0.1384   2.4420   7.0215
 PE6  H151  H  HCH2  0   0.207   1.1258   2.4209   4.8626
 PE6  H152  H  HCH2  0   0.204   2.1065   1.3992   5.9142
 PE6  H131  H  HCH2  0   0.204   1.9395   1.2286   2.9511
 PE6  H132  H  HCH2  0   0.207   2.9026   0.1542   3.9677
 PE6  H121  H  HCH2  0   0.207   2.4427  -0.9870   1.9396
 PE6  H122  H  HCH2  0   0.204   1.5441  -1.7936   3.2263
 PE6  HOP3  H  HOH1  0   0.495  -0.5226   0.5494  -8.5210

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
 PE6  C3   O2    single  1.434  0.020  1.434
 PE6  C3   C4    single  1.504  0.020  1.504
 PE6  C3   H31   single  0.970  0.020  1.090
 PE6  C3   H32   single  0.970  0.020  1.090
 PE6  O2   P1    single  1.594  0.020  1.594
 PE6  P1   OP1   double  1.475  0.020  1.475
 PE6  P1   OP2   single  1.594  0.020  1.594
 PE6  P1   OP3   single  1.599  0.020  1.599
 PE6  OP2  HOP2  single  0.850  0.020  0.980
 PE6  C4   O5    single  1.402  0.020  1.402
 PE6  C4   H41   single  0.970  0.020  1.090
 PE6  C4   H42   single  0.970  0.020  1.090
 PE6  O5   C6    single  1.406  0.020  1.406
 PE6  C6   C7    single  1.507  0.020  1.507
 PE6  C6   H61   single  0.970  0.020  1.090
 PE6  C6   H62   single  0.970  0.020  1.090
 PE6  C7   O8    single  1.404  0.020  1.404
 PE6  C7   H71   single  0.970  0.020  1.090
 PE6  C7   H72   single  0.970  0.020  1.090
 PE6  O8   C9    single  1.405  0.020  1.405
 PE6  C9   C10   single  1.507  0.020  1.507
 PE6  C9   H91   single  0.970  0.020  1.090
 PE6  C9   H92   single  0.970  0.020  1.090
 PE6  C10  O11   single  1.405  0.020  1.405
 PE6  C10  H101  single  0.970  0.020  1.090
 PE6  C10  H102  single  0.970  0.020  1.090
 PE6  O11  C12   single  1.405  0.020  1.405
 PE6  O20  C19   single  1.409  0.020  1.409
 PE6  O20  H20   single  0.850  0.020  0.980
 PE6  C19  C18   single  1.507  0.020  1.507
 PE6  C19  H191  single  0.970  0.020  1.090
 PE6  C19  H192  single  0.970  0.020  1.090
 PE6  C18  O17   single  1.405  0.020  1.405
 PE6  C18  H181  single  0.970  0.020  1.090
 PE6  C18  H182  single  0.970  0.020  1.090
 PE6  O17  C16   single  1.404  0.020  1.404
 PE6  C16  C15   single  1.507  0.020  1.507
 PE6  C16  H161  single  0.970  0.020  1.090
 PE6  C16  H162  single  0.970  0.020  1.090
 PE6  C15  O14   single  1.405  0.020  1.405
 PE6  C15  H151  single  0.970  0.020  1.090
 PE6  C15  H152  single  0.970  0.020  1.090
 PE6  O14  C13   single  1.405  0.020  1.405
 PE6  C13  C12   single  1.507  0.020  1.507
 PE6  C13  H131  single  0.970  0.020  1.090
 PE6  C13  H132  single  0.970  0.020  1.090
 PE6  C12  H121  single  0.970  0.020  1.090
 PE6  C12  H122  single  0.970  0.020  1.090
 PE6  OP3  HOP3  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
 PE6  H32   C3   H31   108.32  3.000
 PE6  H32   C3   C4    110.60  3.000
 PE6  H31   C3   C4    108.48  3.000
 PE6  H32   C3   O2    110.04  3.000
 PE6  H31   C3   O2    110.71  3.000
 PE6  C4    C3   O2    108.66  3.000
 PE6  P1    O2   C3    119.69  3.000
 PE6  OP3   P1   OP2   107.69  3.000
 PE6  OP3   P1   OP1   109.52  3.000
 PE6  OP2   P1   OP1   117.98  3.000
 PE6  OP3   P1   O2    107.09  3.000
 PE6  OP2   P1   O2     96.77  3.000
 PE6  OP1   P1   O2    116.66  3.000
 PE6  HOP2  OP2  P1    114.10  3.000
 PE6  H42   C4   H41   106.88  3.000
 PE6  H42   C4   O5    111.58  3.000
 PE6  H41   C4   O5    111.28  3.000
 PE6  H42   C4   C3    107.40  3.000
 PE6  H41   C4   C3    110.05  3.000
 PE6  O5    C4   C3    109.55  3.000
 PE6  C6    O5   C4    112.88  3.000
 PE6  H62   C6   H61   106.88  3.000
 PE6  H62   C6   C7    110.17  3.000
 PE6  H61   C6   C7    108.10  3.000
 PE6  H62   C6   O5    111.01  3.000
 PE6  H61   C6   O5    111.08  3.000
 PE6  C7    C6   O5    109.53  3.000
 PE6  H72   C7   H71   106.82  3.000
 PE6  H72   C7   O8    111.24  3.000
 PE6  H71   C7   O8    111.06  3.000
 PE6  H72   C7   C6    108.19  3.000
 PE6  H71   C7   C6    109.72  3.000
 PE6  O8    C7   C6    109.72  3.000
 PE6  C9    O8   C7    112.86  3.000
 PE6  H92   C9   H91   106.78  3.000
 PE6  H92   C9   C10   109.96  3.000
 PE6  H91   C9   C10   108.13  3.000
 PE6  H92   C9   O8    111.18  3.000
 PE6  H91   C9   O8    111.05  3.000
 PE6  C10   C9   O8    109.67  3.000
 PE6  H102  C10  H101  106.82  3.000
 PE6  H102  C10  O11   111.12  3.000
 PE6  H101  C10  O11   111.08  3.000
 PE6  H102  C10  C9    108.24  3.000
 PE6  H101  C10  C9    109.76  3.000
 PE6  O11   C10  C9    109.73  3.000
 PE6  C12   O11  C10   112.87  3.000
 PE6  H20   O20  C19   108.04  3.000
 PE6  H192  C19  H191  106.80  3.000
 PE6  H192  C19  C18   107.24  3.000
 PE6  H191  C19  C18   109.34  3.000
 PE6  H192  C19  O20   111.94  3.000
 PE6  H191  C19  O20   111.80  3.000
 PE6  C18   C19  O20   109.56  3.000
 PE6  H182  C18  H181  106.71  3.000
 PE6  H182  C18  O17   110.91  3.000
 PE6  H181  C18  O17   110.96  3.000
 PE6  H182  C18  C19   109.92  3.000
 PE6  H181  C18  C19   108.16  3.000
 PE6  O17   C18  C19   110.09  3.000
 PE6  C16   O17  C18   112.52  3.000
 PE6  H162  C16  H161  106.64  3.000
 PE6  H162  C16  C15   108.22  3.000
 PE6  H161  C16  C15   109.86  3.000
 PE6  H162  C16  O17   111.14  3.000
 PE6  H161  C16  O17   110.98  3.000
 PE6  C15   C16  O17   109.91  3.000
 PE6  H152  C15  H151  106.67  3.000
 PE6  H152  C15  O14   111.11  3.000
 PE6  H151  C15  O14   111.08  3.000
 PE6  H152  C15  C16   110.05  3.000
 PE6  H151  C15  C16   108.13  3.000
 PE6  O14   C15  C16   109.72  3.000
 PE6  C13   O14  C15   112.78  3.000
 PE6  H132  C13  H131  106.80  3.000
 PE6  H132  C13  C12   108.20  3.000
 PE6  H131  C13  C12   109.89  3.000
 PE6  H132  C13  O14   111.17  3.000
 PE6  H131  C13  O14   110.99  3.000
 PE6  C12   C13  O14   109.71  3.000
 PE6  H122  C12  H121  106.73  3.000
 PE6  H122  C12  C13   109.94  3.000
 PE6  H121  C12  C13   108.15  3.000
 PE6  H122  C12  O11   111.06  3.000
 PE6  H121  C12  O11   111.20  3.000
 PE6  C13   C12  O11   109.68  3.000
 PE6  HOP3  OP3  P1    115.66  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
 PE6  Var_01  OP1  P1   O2   C3     47.94  30.0  3
 PE6  Var_02  O5   C4   C3   O2     63.68  30.0  3
 PE6  Var_03  C4   C3   O2   P1    177.08  30.0  1
 PE6  Var_04  C7   C6   O5   C4    177.19  30.0  3
 PE6  Var_05  O8   C7   C6   O5     65.13  30.0  3
 PE6  Var_06  C10  C9   O8   C7    178.69  30.0  3
 PE6  Var_07  O11  C10  C9   O8     66.26  30.0  3
 PE6  Var_08  C13  C12  O11  C10   179.97  30.0  3
 PE6  Var_09  O14  C13  C12  O11    65.71  30.0  2
 PE6  Var_10  O17  C18  C19  O20    65.62  30.0  3
 PE6  Var_11  C15  C16  O17  C18  -179.47  30.0  3
 PE6  Var_12  O14  C15  C16  O17    65.44  30.0  3
 PE6  Var_13  C12  C13  O14  C15  -178.82  30.0  3

