# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 16:01:16 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCC(=O)OC[C@@H](CO[P](O)(=O)OCCN)OC(C)=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
 6O9  6O9  '(2S)-2-(acetyloxy)-3-{[(R)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}propyl pentanoate'  ligand  45  22  .  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_6O9
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
 6O9  N01   N  NH2    0  -0.800  -6.0237  -0.9489   2.1280
 6O9  C02   C  CH2    0  -0.316  -6.2910  -1.1768   0.7168
 6O9  C03   C  CH2    0  -0.152  -5.6890  -0.0855  -0.1384
 6O9  O04   O  O2     0  -0.617  -4.2756  -0.1243  -0.0040
 6O9  P05   P  P      0   1.341  -3.4179   1.1074  -0.6580
 6O9  O06   O  OP    -1  -0.800  -3.6787   2.3862   0.0773
 6O9  O07   O  O      0  -0.797  -3.5222   1.0769  -2.1520
 6O9  O08   O  O2     0  -0.613  -1.9764   0.4737  -0.1764
 6O9  C09   C  CH2    0  -0.134  -0.8288   1.2617  -0.3809
 6O9  C10   C  CH1    0  -0.082   0.3854   0.4173  -0.0528
 6O9  C11   C  CH2    0  -0.168   1.6625   1.2083  -0.2282
 6O9  O12   O  O2     0  -0.461   2.7344   0.3561   0.1652
 6O9  C13   C  C      0   0.610   3.9762   0.8215   0.0521
 6O9  C14   C  CH2    0  -0.582   4.9840  -0.1811   0.5418
 6O9  C15   C  CH2    0  -0.412   6.4216   0.1798   0.2034
 6O9  C16   C  CH2    0  -0.422   7.4075  -0.8489   0.7436
 6O9  C17   C  CH3    0  -0.662   8.8504  -0.5087   0.3980
 6O9  O18   O  O      0  -0.450   4.2306   1.9179  -0.3785
 6O9  O19   O  O2     0  -0.456   0.4223  -0.6867  -0.9602
 6O9  C20   C  C      0   0.573   0.3464  -1.9336  -0.5039
 6O9  C21   C  CH3    0  -0.779   0.3715  -2.9394  -1.6171
 6O9  O22   O  O      0  -0.455   0.2652  -2.2271   0.6620
 6O9  H012  H  HNH2   0   0.348  -6.4713  -1.6732   2.6744
 6O9  H011  H  HNH2   0   0.340  -5.0319  -1.0541   2.2995
 6O9  H022  H  HCH2   0   0.199  -5.9432  -2.1520   0.3475
 6O9  H021  H  HCH2   0   0.224  -7.3715  -1.1540   0.5564
 6O9  H032  H  HCH2   0   0.210  -5.9824  -0.2384  -1.1826
 6O9  H031  H  HCH2   0   0.203  -6.0837   0.8857   0.1808
 6O9  H092  H  HCH2   0   0.217  -0.7634   1.6207  -1.4155
 6O9  H091  H  HCH2   0   0.225  -0.8245   2.1402   0.2734
 6O9  H101  H  HCH1   0   0.267   0.3121   0.0623   0.9773
 6O9  H111  H  HCH2   0   0.248   1.7853   1.5294  -1.2656
 6O9  H112  H  HCH2   0   0.251   1.6302   2.0993   0.4037
 6O9  H141  H  HCH2   0   0.277   4.8601  -0.2676   1.6272
 6O9  H142  H  HCH2   0   0.269   4.7255  -1.1643   0.1396
 6O9  H152  H  HCH2   0   0.224   6.5373   0.2580  -0.8816
 6O9  H151  H  HCH2   0   0.225   6.6654   1.1637   0.6122
 6O9  H161  H  HCH2   0   0.216   7.2967  -0.9227   1.8299
 6O9  H162  H  HCH2   0   0.216   7.1577  -1.8370   0.3455
 6O9  H173  H  HCH3   0   0.218   9.1395   0.4561   0.8185
 6O9  H172  H  HCH3   0   0.228   9.5416  -1.2579   0.7852
 6O9  H3    H  HCH3   0   0.217   8.9931  -0.4533  -0.6827
 6O9  H213  H  HCH3   0   0.259   0.5087  -2.4892  -2.5961
 6O9  H212  H  HCH3   0   0.273   1.1718  -3.6568  -1.4373
 6O9  H4    H  HCH3   0   0.276  -0.5654  -3.4973  -1.6147

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
 6O9  C17  C16   single  1.522  0.020  1.522
 6O9  C16  C15   single  1.524  0.020  1.524
 6O9  C15  C14   single  1.520  0.020  1.520
 6O9  C14  C13   single  1.504  0.020  1.504
 6O9  O18  C13   double  1.205  0.020  1.205
 6O9  C13  O12   single  1.331  0.020  1.331
 6O9  O12  C11   single  1.425  0.020  1.425
 6O9  C11  C10   single  1.512  0.020  1.512
 6O9  O19  C10   single  1.430  0.020  1.430
 6O9  O19  C20   single  1.330  0.020  1.330
 6O9  C21  C20   single  1.500  0.020  1.500
 6O9  C10  C09   single  1.515  0.020  1.515
 6O9  C20  O22   double  1.205  0.020  1.205
 6O9  C09  O08   single  1.407  0.020  1.407
 6O9  O08  P05   single  1.647  0.020  1.647
 6O9  P05  O07   deloc   1.498  0.020  1.498
 6O9  P05  O04   single  1.637  0.020  1.637
 6O9  P05  O06   deloc   1.498  0.020  1.498
 6O9  O04  C03   single  1.420  0.020  1.420
 6O9  C03  C02   single  1.512  0.020  1.512
 6O9  C02  N01   single  1.454  0.020  1.454
 6O9  N01  H012  single  0.890  0.020  1.040
 6O9  N01  H011  single  0.890  0.020  1.040
 6O9  C02  H022  single  0.970  0.020  1.090
 6O9  C02  H021  single  0.970  0.020  1.090
 6O9  C03  H032  single  0.970  0.020  1.090
 6O9  C03  H031  single  0.970  0.020  1.090
 6O9  C09  H092  single  0.970  0.020  1.090
 6O9  C09  H091  single  0.970  0.020  1.090
 6O9  C10  H101  single  0.970  0.020  1.090
 6O9  C11  H111  single  0.970  0.020  1.090
 6O9  C11  H112  single  0.970  0.020  1.090
 6O9  C14  H141  single  0.970  0.020  1.090
 6O9  C14  H142  single  0.970  0.020  1.090
 6O9  C15  H152  single  0.970  0.020  1.090
 6O9  C15  H151  single  0.970  0.020  1.090
 6O9  C16  H161  single  0.970  0.020  1.090
 6O9  C16  H162  single  0.970  0.020  1.090
 6O9  C17  H173  single  0.970  0.020  1.090
 6O9  C17  H172  single  0.970  0.020  1.090
 6O9  C17  H3    single  0.970  0.020  1.090
 6O9  C21  H213  single  0.970  0.020  1.090
 6O9  C21  H212  single  0.970  0.020  1.090
 6O9  C21  H4    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
 6O9  H011  N01  H012  105.52  3.000
 6O9  H011  N01  C02   109.17  3.000
 6O9  H012  N01  C02   109.31  3.000
 6O9  H021  C02  H022  106.38  3.000
 6O9  H021  C02  C03   107.20  3.000
 6O9  H022  C02  C03   108.93  3.000
 6O9  H021  C02  N01   108.72  3.000
 6O9  H022  C02  N01   114.01  3.000
 6O9  C03   C02  N01   111.27  3.000
 6O9  H031  C03  H032  107.76  3.000
 6O9  H031  C03  O04   110.80  3.000
 6O9  H032  C03  O04   110.67  3.000
 6O9  H031  C03  C02   109.36  3.000
 6O9  H032  C03  C02   109.39  3.000
 6O9  O04   C03  C02   108.85  3.000
 6O9  P05   O04  C03   117.58  3.000
 6O9  O08   P05  O07   110.17  3.000
 6O9  O07   P05  O06   119.66  3.000
 6O9  O08   P05  O06   109.72  3.000
 6O9  O06   P05  O04   110.79  3.000
 6O9  O07   P05  O04   110.28  3.000
 6O9  O08   P05  O04    93.00  3.000
 6O9  C09   O08  P05   117.13  3.000
 6O9  H091  C09  H092  107.49  3.000
 6O9  H091  C09  C10   108.33  3.000
 6O9  H092  C09  C10   109.81  3.000
 6O9  H091  C09  O08   111.44  3.000
 6O9  H092  C09  O08   111.65  3.000
 6O9  C10   C09  O08   108.06  3.000
 6O9  H101  C10  O19   110.45  3.000
 6O9  H101  C10  C11   109.64  3.000
 6O9  O19   C10  C11   107.97  3.000
 6O9  H101  C10  C09   109.37  3.000
 6O9  O19   C10  C09   108.28  3.000
 6O9  C11   C10  C09   111.11  3.000
 6O9  H112  C11  H111  108.23  3.000
 6O9  H112  C11  O12   110.50  3.000
 6O9  H111  C11  O12   110.69  3.000
 6O9  H112  C11  C10   109.54  3.000
 6O9  H111  C11  C10   111.01  3.000
 6O9  O12   C11  C10   106.88  3.000
 6O9  C13   O12  C11   117.98  3.000
 6O9  O18   C13  C14   125.56  3.000
 6O9  O18   C13  O12   123.06  3.000
 6O9  C14   C13  O12   111.38  3.000
 6O9  H142  C14  H141  105.46  3.000
 6O9  H142  C14  C15   110.80  3.000
 6O9  H141  C14  C15   110.25  3.000
 6O9  H142  C14  C13   108.75  3.000
 6O9  H141  C14  C13   107.42  3.000
 6O9  C15   C14  C13   113.77  3.000
 6O9  H151  C15  H152  106.44  3.000
 6O9  H151  C15  C16   109.31  3.000
 6O9  H152  C15  C16   109.36  3.000
 6O9  H151  C15  C14   109.96  3.000
 6O9  H152  C15  C14   109.74  3.000
 6O9  C16   C15  C14   111.88  3.000
 6O9  H162  C16  H161  106.09  3.000
 6O9  H162  C16  C17   109.61  3.000
 6O9  H161  C16  C17   109.66  3.000
 6O9  H162  C16  C15   109.44  3.000
 6O9  H161  C16  C15   109.38  3.000
 6O9  C17   C16  C15   112.45  3.000
 6O9  H3    C17  H172  107.67  3.000
 6O9  H3    C17  H173  107.57  3.000
 6O9  H172  C17  H173  107.61  3.000
 6O9  H3    C17  C16   111.11  3.000
 6O9  H172  C17  C16   111.51  3.000
 6O9  H173  C17  C16   111.18  3.000
 6O9  C20   O19  C10   120.32  3.000
 6O9  O22   C20  C21   123.76  3.000
 6O9  O22   C20  O19   124.34  3.000
 6O9  C21   C20  O19   111.90  3.000
 6O9  H4    C21  H212  107.09  3.000
 6O9  H4    C21  H213  108.81  3.000
 6O9  H212  C21  H213  109.19  3.000
 6O9  H4    C21  C20   109.09  3.000
 6O9  H212  C21  C20   109.34  3.000
 6O9  H213  C21  C20   113.14  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
 6O9  Var_01  O04   C03  C02  N01    63.92  30.0  1
 6O9  Var_02  O08   P05  O04  C03  -179.89  30.0  1
 6O9  Var_03  C10   C09  O08  P05  -172.11  30.0  1
 6O9  Var_04  C21   C20  O19  C10   178.72  30.0  3
 6O9  Var_05  C14   C13  O12  C11   178.44  30.0  2
 6O9  Var_06  C15   C14  C13  O12   169.24  30.0  1
 6O9  Var_07  C16   C15  C14  C13   178.83  30.0  1
 6O9  Var_08  C17   C16  C15  C14   179.33  30.0  1
 6O9  Var_09  H012  N01  C02  C03   177.65  30.0  3
 6O9  Var_10  H111  C11  O12  C13    56.66  30.0  3
 6O9  Var_11  H173  C17  C16  C15    60.33  30.0  3
 6O9  Var_12  H213  C21  C20  O19     3.57  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
 6O9  chir_02  C10  C11  O19  C09  positiv

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
 6O9  plan-1  O12  0.020
 6O9  plan-1  C13  0.020
 6O9  plan-1  C14  0.020
 6O9  plan-1  O18  0.020
 6O9  plan-2  O19  0.020
 6O9  plan-2  C20  0.020
 6O9  plan-2  C21  0.020
 6O9  plan-2  O22  0.020

