# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 03:23:48 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 2-aminoethyl (2R)-2,3-bis(hexanoyloxy)propyl phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCC(=O)OC[C@H](CO[P]([O-])(=O)OCCN)OC(=O)CCCCC
#
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
 6PE  6PE  '2-aminoethyl (2R)-2,3-bis(hexanoyloxy)propyl phosphate'  ligand  60  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6PE
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
 6PE  O1   O  OP    -1  -0.802   1.0028   3.7195  -2.0469
 6PE  O2   O  O      0  -0.782   2.0452   1.3708  -2.2976
 6PE  P1   P  P      0   1.360   1.1988   2.3301  -1.5147
 6PE  O3   O  O2     0  -0.609  -0.2568   1.6610  -1.1531
 6PE  C1   C  CH2    0  -0.189  -1.0985   1.3040  -2.2250
 6PE  C2   C  CH1    0  -0.037  -1.4156  -0.1808  -2.2573
 6PE  C3   C  CH2    0  -0.188  -0.2224  -1.0910  -2.4439
 6PE  O4   O  O2     0  -0.448   0.5683  -1.0825  -1.2643
 6PE  C4   C  C      0   0.629   1.8277  -1.4860  -1.3514
 6PE  O5   O  O      0  -0.471   2.2989  -1.9870  -2.3436
 6PE  C5   C  CH2    0  -0.593   2.5715  -1.2534  -0.0678
 6PE  C6   C  CH2    0  -0.415   3.7706  -2.1698   0.1251
 6PE  C7   C  CH2    0  -0.413   4.4793  -1.8988   1.4461
 6PE  C8   C  CH2    0  -0.418   5.6832  -2.8036   1.6738
 6PE  C9   C  CH3    0  -0.661   6.3924  -2.5177   2.9902
 6PE  O6   O  O2     0  -0.468  -2.0840  -0.5957  -1.0596
 6PE  C10  C  C      0   0.611  -3.4088  -0.4858  -0.9846
 6PE  O7   O  O      0  -0.450  -4.0936  -0.0445  -1.8729
 6PE  C11  C  CH2    0  -0.585  -3.9230  -0.9811   0.3396
 6PE  C12  C  CH2    0  -0.417  -5.4361  -0.9180   0.4672
 6PE  C13  C  CH2    0  -0.409  -5.9176  -1.4227   1.8216
 6PE  C14  C  CH2    0  -0.419  -7.4329  -1.3683   1.9677
 6PE  C15  C  CH3    0  -0.662  -7.9143  -1.8744   3.3202
 6PE  O8   O  O2     0  -0.618   1.6734   2.3930   0.0520
 6PE  C16  C  CH2    0  -0.148   2.8262   3.1660   0.3511
 6PE  C17  C  CH2    0  -0.318   3.1744   2.9905   1.8110
 6PE  N1   N  NH2    0  -0.791   3.5771   1.6247   2.1015
 6PE  H1   H  HCH2   0   0.224  -0.6762   1.5578  -3.2039
 6PE  H2   H  HCH2   0   0.240  -2.0322   1.8679  -2.1429
 6PE  H3   H  HCH1   0   0.264  -2.0631  -0.3408  -3.1251
 6PE  H4   H  HCH2   0   0.243   0.3472  -0.7439  -3.3069
 6PE  H5   H  HCH2   0   0.249  -0.5624  -2.1090  -2.6525
 6PE  H6   H  HCH2   0   0.249   1.8813  -1.3414   0.7746
 6PE  H7   H  HCH2   0   0.281   2.8928  -0.2072  -0.0820
 6PE  H8   H  HCH2   0   0.220   4.4742  -2.0397  -0.7010
 6PE  H9   H  HCH2   0   0.218   3.4475  -3.2148   0.0939
 6PE  H10  H  HCH2   0   0.205   3.7711  -2.0281   2.2724
 6PE  H11  H  HCH2   0   0.216   4.7905  -0.8496   1.4839
 6PE  H12  H  HCH2   0   0.211   6.3871  -2.6869   0.8442
 6PE  H13  H  HCH2   0   0.210   5.3586  -3.8487   1.6505
 6PE  H14  H  HCH3   0   0.216   6.7666  -1.4926   3.0210
 6PE  H15  H  HCH3   0   0.215   5.7158  -2.6446   3.8378
 6PE  H16  H  HCH3   0   0.225   7.2416  -3.1845   3.1435
 6PE  H17  H  HCH2   0   0.272  -3.5659  -2.0057   0.4848
 6PE  H18  H  HCH2   0   0.274  -3.4460  -0.3926   1.1301
 6PE  H19  H  HCH2   0   0.224  -5.7763   0.1107   0.3215
 6PE  H20  H  HCH2   0   0.224  -5.8996  -1.5110  -0.3256
 6PE  H21  H  HCH2   0   0.211  -5.5762  -2.4530   1.9720
 6PE  H22  H  HCH2   0   0.211  -5.4547  -0.8315   2.6194
 6PE  H23  H  HCH2   0   0.212  -7.7736  -0.3390   1.8179
 6PE  H24  H  HCH2   0   0.212  -7.8938  -1.9584   1.1696
 6PE  H25  H  HCH3   0   0.216  -7.6350  -2.9185   3.4727
 6PE  H26  H  HCH3   0   0.216  -7.4780  -1.2953   4.1363
 6PE  H27  H  HCH3   0   0.227  -8.9990  -1.8076   3.4109
 6PE  H28  H  HCH2   0   0.200   3.6785   2.8485  -0.2611
 6PE  H29  H  HCH2   0   0.211   2.6436   4.2258   0.1459
 6PE  H30  H  HCH2   0   0.225   4.0164   3.6537   2.0233
 6PE  H31  H  HCH2   0   0.198   2.3360   3.3501   2.4248
 6PE  H32  H  HNH2   0   0.348   3.8772   1.5547   3.0648
 6PE  H33  H  HNH2   0   0.345   2.7798   1.0089   2.0157

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
 6PE  O1   P1   deloc   1.501  0.020  1.501
 6PE  O2   P1   deloc   1.500  0.020  1.500
 6PE  P1   O3   single  1.642  0.020  1.642
 6PE  P1   O8   single  1.638  0.020  1.638
 6PE  O3   C1   single  1.409  0.020  1.409
 6PE  C1   C2   single  1.519  0.020  1.519
 6PE  C1   H1   single  0.970  0.020  1.090
 6PE  C1   H2   single  0.970  0.020  1.090
 6PE  C2   C3   single  1.512  0.020  1.512
 6PE  C2   O6   single  1.433  0.020  1.433
 6PE  C2   H3   single  0.970  0.020  1.090
 6PE  C3   O4   single  1.420  0.020  1.420
 6PE  C3   H4   single  0.970  0.020  1.090
 6PE  C3   H5   single  0.970  0.020  1.090
 6PE  O4   C4   single  1.325  0.020  1.325
 6PE  C4   O5   double  1.207  0.020  1.207
 6PE  C4   C5   single  1.502  0.020  1.502
 6PE  C5   C6   single  1.521  0.020  1.521
 6PE  C5   H6   single  0.970  0.020  1.090
 6PE  C5   H7   single  0.970  0.020  1.090
 6PE  C6   C7   single  1.523  0.020  1.523
 6PE  C6   H8   single  0.970  0.020  1.090
 6PE  C6   H9   single  0.970  0.020  1.090
 6PE  C7   C8   single  1.523  0.020  1.523
 6PE  C7   H10  single  0.970  0.020  1.090
 6PE  C7   H11  single  0.970  0.020  1.090
 6PE  C8   C9   single  1.522  0.020  1.522
 6PE  C8   H12  single  0.970  0.020  1.090
 6PE  C8   H13  single  0.970  0.020  1.090
 6PE  C9   H14  single  0.970  0.020  1.090
 6PE  C9   H15  single  0.970  0.020  1.090
 6PE  C9   H16  single  0.970  0.020  1.090
 6PE  O6   C10  single  1.331  0.020  1.331
 6PE  C10  O7   double  1.205  0.020  1.205
 6PE  C10  C11  single  1.504  0.020  1.504
 6PE  C11  C12  single  1.520  0.020  1.520
 6PE  C11  H17  single  0.970  0.020  1.090
 6PE  C11  H18  single  0.970  0.020  1.090
 6PE  C12  C13  single  1.523  0.020  1.523
 6PE  C12  H19  single  0.970  0.020  1.090
 6PE  C12  H20  single  0.970  0.020  1.090
 6PE  C13  C14  single  1.523  0.020  1.523
 6PE  C13  H21  single  0.970  0.020  1.090
 6PE  C13  H22  single  0.970  0.020  1.090
 6PE  C14  C15  single  1.522  0.020  1.522
 6PE  C14  H23  single  0.970  0.020  1.090
 6PE  C14  H24  single  0.970  0.020  1.090
 6PE  C15  H25  single  0.970  0.020  1.090
 6PE  C15  H26  single  0.970  0.020  1.090
 6PE  C15  H27  single  0.970  0.020  1.090
 6PE  O8   C16  single  1.420  0.020  1.420
 6PE  C16  C17  single  1.511  0.020  1.511
 6PE  C16  H28  single  0.970  0.020  1.090
 6PE  C16  H29  single  0.970  0.020  1.090
 6PE  C17  N1   single  1.453  0.020  1.453
 6PE  C17  H30  single  0.970  0.020  1.090
 6PE  C17  H31  single  0.970  0.020  1.090
 6PE  N1   H32  single  0.890  0.020  1.040
 6PE  N1   H33  single  0.890  0.020  1.040

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
 6PE  O8   P1   O3    93.54  3.000
 6PE  O8   P1   O2   111.12  3.000
 6PE  O3   P1   O2   110.76  3.000
 6PE  O8   P1   O1   109.96  3.000
 6PE  O3   P1   O1   109.85  3.000
 6PE  O2   P1   O1   118.74  3.000
 6PE  C1   O3   P1   117.73  3.000
 6PE  H2   C1   H1   106.06  3.000
 6PE  H2   C1   C2   109.11  3.000
 6PE  H1   C1   C2   106.73  3.000
 6PE  H2   C1   O3   108.80  3.000
 6PE  H1   C1   O3   112.99  3.000
 6PE  C2   C1   O3   112.87  3.000
 6PE  H3   C2   O6   110.15  3.000
 6PE  H3   C2   C3   106.32  3.000
 6PE  O6   C2   C3   107.27  3.000
 6PE  H3   C2   C1   106.46  3.000
 6PE  O6   C2   C1   111.27  3.000
 6PE  C3   C2   C1   115.23  3.000
 6PE  H5   C3   H4   107.93  3.000
 6PE  H5   C3   O4   109.70  3.000
 6PE  H4   C3   O4   111.38  3.000
 6PE  H5   C3   C2   109.79  3.000
 6PE  H4   C3   C2   108.55  3.000
 6PE  O4   C3   C2   109.47  3.000
 6PE  C4   O4   C3   118.21  3.000
 6PE  C5   C4   O5   124.99  3.000
 6PE  C5   C4   O4   111.55  3.000
 6PE  O5   C4   O4   123.45  3.000
 6PE  H7   C5   H6   105.81  3.000
 6PE  H7   C5   C6   110.25  3.000
 6PE  H6   C5   C6   110.59  3.000
 6PE  H7   C5   C4   106.40  3.000
 6PE  H6   C5   C4   109.49  3.000
 6PE  C6   C5   C4   113.92  3.000
 6PE  H9   C6   H8   106.39  3.000
 6PE  H9   C6   C7   109.39  3.000
 6PE  H8   C6   C7   109.56  3.000
 6PE  H9   C6   C5   109.81  3.000
 6PE  H8   C6   C5   109.87  3.000
 6PE  C7   C6   C5   111.68  3.000
 6PE  H11  C7   H10  105.70  3.000
 6PE  H11  C7   C8   109.84  3.000
 6PE  H10  C7   C8   109.15  3.000
 6PE  H11  C7   C6   109.43  3.000
 6PE  H10  C7   C6   109.40  3.000
 6PE  C8   C7   C6   113.06  3.000
 6PE  H13  C8   H12  106.05  3.000
 6PE  H13  C8   C9   109.62  3.000
 6PE  H12  C8   C9   109.63  3.000
 6PE  H13  C8   C7   109.25  3.000
 6PE  H12  C8   C7   109.38  3.000
 6PE  C9   C8   C7   112.70  3.000
 6PE  H16  C9   H15  107.60  3.000
 6PE  H16  C9   H14  107.65  3.000
 6PE  H15  C9   H14  107.44  3.000
 6PE  H16  C9   C8   111.68  3.000
 6PE  H15  C9   C8   111.14  3.000
 6PE  H14  C9   C8   111.13  3.000
 6PE  C10  O6   C2   119.16  3.000
 6PE  C11  C10  O7   125.10  3.000
 6PE  C11  C10  O6   111.25  3.000
 6PE  O7   C10  O6   123.65  3.000
 6PE  H18  C11  H17  105.37  3.000
 6PE  H18  C11  C12  110.54  3.000
 6PE  H17  C11  C12  110.64  3.000
 6PE  H18  C11  C10  108.04  3.000
 6PE  H17  C11  C10  108.27  3.000
 6PE  C12  C11  C10  113.62  3.000
 6PE  H20  C12  H19  106.37  3.000
 6PE  H20  C12  C13  109.33  3.000
 6PE  H19  C12  C13  109.38  3.000
 6PE  H20  C12  C11  109.80  3.000
 6PE  H19  C12  C11  109.73  3.000
 6PE  C13  C12  C11  112.06  3.000
 6PE  H22  C13  H21  106.02  3.000
 6PE  H22  C13  C14  109.34  3.000
 6PE  H21  C13  C14  109.29  3.000
 6PE  H22  C13  C12  109.58  3.000
 6PE  H21  C13  C12  109.58  3.000
 6PE  C14  C13  C12  112.82  3.000
 6PE  H24  C14  H23  106.04  3.000
 6PE  H24  C14  C15  109.60  3.000
 6PE  H23  C14  C15  109.62  3.000
 6PE  H24  C14  C13  109.25  3.000
 6PE  H23  C14  C13  109.28  3.000
 6PE  C15  C14  C13  112.82  3.000
 6PE  H27  C15  H26  107.63  3.000
 6PE  H27  C15  H25  107.55  3.000
 6PE  H26  C15  H25  107.50  3.000
 6PE  H27  C15  C14  111.59  3.000
 6PE  H26  C15  C14  111.19  3.000
 6PE  H25  C15  C14  111.18  3.000
 6PE  C16  O8   P1   117.23  3.000
 6PE  H29  C16  H28  107.78  3.000
 6PE  H29  C16  C17  109.39  3.000
 6PE  H28  C16  C17  109.07  3.000
 6PE  H29  C16  O8   110.62  3.000
 6PE  H28  C16  O8   110.85  3.000
 6PE  C17  C16  O8   109.11  3.000
 6PE  H31  C17  H30  106.29  3.000
 6PE  H31  C17  N1   114.03  3.000
 6PE  H30  C17  N1   108.54  3.000
 6PE  H31  C17  C16  109.01  3.000
 6PE  H30  C17  C16  107.14  3.000
 6PE  N1   C17  C16  111.48  3.000
 6PE  H33  N1   H32  105.82  3.000
 6PE  H33  N1   C17  109.69  3.000
 6PE  H32  N1   C17  109.74  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
 6PE  Var_01  C2   C1   O3   P1    119.20  30.0  3
 6PE  Var_02  C17  C16  O8   P1   -174.61  30.0  3
 6PE  Var_03  O8   P1   O3   C1   -176.30  30.0  1
 6PE  Var_04  O7   C10  O6   C2     -0.44  30.0  3
 6PE  Var_05  O5   C4   O4   C3     -7.83  30.0  3
 6PE  Var_06  C6   C5   C4   O4    155.72  30.0  3
 6PE  Var_07  C7   C6   C5   C4   -179.51  30.0  3
 6PE  Var_08  C8   C7   C6   C5    179.79  30.0  3
 6PE  Var_09  C9   C8   C7   C6    179.50  30.0  3
 6PE  Var_10  C12  C11  C10  O6   -178.30  30.0  3
 6PE  Var_11  C13  C12  C11  C10  -179.80  30.0  3
 6PE  Var_12  C14  C13  C12  C11  -179.95  30.0  3
 6PE  Var_13  C15  C14  C13  C12   179.92  30.0  3
 6PE  Var_14  N1   C17  C16  O8     65.52  30.0  3
 6PE  Var_15  H4   C3   O4   C4    -40.54  30.0  1
 6PE  Var_16  H14  C9   C8   C7    -60.66  30.0  3
 6PE  Var_17  H25  C15  C14  C13   -61.09  30.0  3
 6PE  Var_18  H32  N1   C17  C16   175.32  30.0  3

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
 6PE  chir_01  C2  C1  C3  O6  negativ

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
 6PE  plan-1  O4   0.020
 6PE  plan-1  C4   0.020
 6PE  plan-1  O5   0.020
 6PE  plan-1  C5   0.020
 6PE  plan-2  O6   0.020
 6PE  plan-2  C10  0.020
 6PE  plan-2  O7   0.020
 6PE  plan-2  C11  0.020

