# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 12:00:35 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: N-hexadecanoyl-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCCCCC(=O)N[C@@H](CCC(O)=O)C(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
 D6M  D6M  'N-hexadecanoyl-L-glutamic acid'  ligand  64  27  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_D6M
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
 D6M  O01   O  O      0  -0.519    4.2960   0.9486   1.6746
 D6M  C02   C  C      0   0.561    4.3362   0.4503   0.5546
 D6M  N03   N  NH1    0  -0.616    5.4756   0.2741  -0.1256
 D6M  C04   C  CH1    0  -0.194    6.7616   0.7518   0.3239
 D6M  C05   C  CH2    0  -0.440    7.8740  -0.1122  -0.2730
 D6M  C06   C  CH2    0  -0.575    7.7989  -1.5691   0.1541
 D6M  C07   C  C      0   0.410    8.9207  -2.4801  -0.3734
 D6M  O08   O  O      0  -0.610    9.7418  -1.9941  -1.1762
 D6M  C09   C  C      0   0.410    6.9872   2.2524   0.0063
 D6M  O10   O  O      0  -0.599    6.1552   2.8273  -0.7157
 D6M  O11   O  OC    -1  -0.621    8.0156   2.7487   0.5110
 D6M  C12   C  CH2    0  -0.585    3.0947  -0.0837  -0.1347
 D6M  C13   C  CH2    0  -0.411    1.7999   0.5436   0.3575
 D6M  C14   C  CH2    0  -0.415    0.5729  -0.0755  -0.2999
 D6M  C15   C  CH2    0  -0.412   -0.7349   0.5032   0.2234
 D6M  C16   C  CH2    0  -0.412   -1.9720  -0.1364  -0.3940
 D6M  C17   C  CH2    0  -0.412   -3.2737   0.4215   0.1665
 D6M  C18   C  CH2    0  -0.413   -4.5202  -0.2317  -0.4169
 D6M  C19   C  CH2    0  -0.412   -5.8119   0.3178   0.1747
 D6M  C20   C  CH2    0  -0.412   -7.0678  -0.3409  -0.3814
 D6M  C21   C  CH2    0  -0.412   -8.3499   0.2076   0.2321
 D6M  C22   C  CH2    0  -0.412   -9.6135  -0.4507  -0.3069
 D6M  C23   C  CH2    0  -0.411  -10.8888   0.1011   0.3178
 D6M  C24   C  CH2    0  -0.407  -12.1574  -0.5525  -0.2147
 D6M  C25   C  CH2    0  -0.419  -13.4298   0.0046   0.4118
 D6M  C26   C  CH3    0  -0.663  -14.6943  -0.6503  -0.1261
 D6M  OXT   O  OC    -1  -0.635    8.9110  -3.6565   0.0490
 D6M  H03   H  HNH1   0   0.381    5.4063  -0.0303  -1.0835
 D6M  H121  H  HCH2   0   0.245    3.1861   0.0377  -1.2178
 D6M  H122  H  HCH2   0   0.261    3.0624  -1.1655   0.0388
 D6M  H04   H  HCH1   0   0.225    6.7936   0.6385   1.4116
 D6M  H051  H  HCH2   0   0.208    7.8456  -0.0366  -1.3654
 D6M  H052  H  HCH2   0   0.224    8.8286   0.3146   0.0351
 D6M  H061  H  HCH2   0   0.215    7.7952  -1.6292   1.2489
 D6M  H062  H  HCH2   0   0.222    6.8419  -2.0051  -0.1531
 D6M  H131  H  HCH2   0   0.218    1.7246   0.4256   1.4412
 D6M  H132  H  HCH2   0   0.218    1.8120   1.6210   0.1666
 D6M  H141  H  HCH2   0   0.210    0.6265   0.0609  -1.3855
 D6M  H142  H  HCH2   0   0.208    0.5815  -1.1584  -0.1320
 D6M  H151  H  HCH2   0   0.207   -0.7723   0.3795   1.3116
 D6M  H152  H  HCH2   0   0.208   -0.7549   1.5837   0.0433
 D6M  H161  H  HCH2   0   0.207   -1.9516   0.0011  -1.4808
 D6M  H162  H  HCH2   0   0.206   -1.9401  -1.2189  -0.2269
 D6M  H171  H  HCH2   0   0.206   -3.2789   0.2962   1.2552
 D6M  H172  H  HCH2   0   0.207   -3.3132   1.5021  -0.0108
 D6M  H181  H  HCH2   0   0.207   -4.5292  -0.0970  -1.5043
 D6M  H182  H  HCH2   0   0.206   -4.4748  -1.3134  -0.2478
 D6M  H191  H  HCH2   0   0.206   -5.7911   0.1918   1.2631
 D6M  H192  H  HCH2   0   0.206   -5.8611   1.3982  -0.0010
 D6M  H201  H  HCH2   0   0.206   -7.0986  -0.2093  -1.4688
 D6M  H202  H  HCH2   0   0.206   -7.0167  -1.4220  -0.2102
 D6M  H211  H  HCH2   0   0.206   -8.3122   0.0806   1.3199
 D6M  H212  H  HCH2   0   0.206   -8.4019   1.2882   0.0579
 D6M  H221  H  HCH2   0   0.206   -9.6561  -0.3216  -1.3942
 D6M  H222  H  HCH2   0   0.206   -9.5620  -1.5314  -0.1338
 D6M  H231  H  HCH2   0   0.206  -10.8439  -0.0275   1.4052
 D6M  H232  H  HCH2   0   0.206  -10.9385   1.1821   0.1452
 D6M  H241  H  HCH2   0   0.205  -12.2035  -0.4248  -1.3021
 D6M  H242  H  HCH2   0   0.206  -12.1105  -1.6334  -0.0407
 D6M  H251  H  HCH2   0   0.210  -13.3841  -0.1240   1.4978
 D6M  H252  H  HCH2   0   0.210  -13.4741   1.0844   0.2382
 D6M  H261  H  HCH3   0   0.216  -14.6948  -1.7249   0.0661
 D6M  H262  H  HCH3   0   0.225  -15.5900  -0.2321   0.3345
 D6M  H263  H  HCH3   0   0.215  -14.7819  -0.5114  -1.2055

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
 D6M  O01  C02   double  1.226  0.020  1.226
 D6M  C02  N03   single  1.339  0.020  1.339
 D6M  C02  C12   single  1.517  0.020  1.517
 D6M  N03  C04   single  1.444  0.020  1.444
 D6M  C04  C05   single  1.530  0.020  1.530
 D6M  C04  C09   single  1.550  0.020  1.550
 D6M  C05  C06   single  1.520  0.020  1.520
 D6M  C06  C07   single  1.538  0.020  1.538
 D6M  C07  O08   deloc   1.247  0.020  1.247
 D6M  C07  OXT   deloc   1.250  0.020  1.250
 D6M  C09  O10   deloc   1.243  0.020  1.243
 D6M  C09  O11   deloc   1.249  0.020  1.249
 D6M  C12  C13   single  1.521  0.020  1.521
 D6M  C13  C14   single  1.523  0.020  1.523
 D6M  C14  C15   single  1.523  0.020  1.523
 D6M  C15  C16   single  1.523  0.020  1.523
 D6M  C16  C17   single  1.523  0.020  1.523
 D6M  C17  C18   single  1.523  0.020  1.523
 D6M  C18  C19   single  1.523  0.020  1.523
 D6M  C19  C20   single  1.523  0.020  1.523
 D6M  C20  C21   single  1.523  0.020  1.523
 D6M  C21  C22   single  1.523  0.020  1.523
 D6M  C22  C23   single  1.523  0.020  1.523
 D6M  C23  C24   single  1.523  0.020  1.523
 D6M  C24  C25   single  1.524  0.020  1.524
 D6M  C25  C26   single  1.522  0.020  1.522
 D6M  N03  H03   single  0.860  0.020  1.020
 D6M  C12  H121  single  0.970  0.020  1.090
 D6M  C12  H122  single  0.970  0.020  1.090
 D6M  C04  H04   single  0.970  0.020  1.090
 D6M  C05  H051  single  0.970  0.020  1.090
 D6M  C05  H052  single  0.970  0.020  1.090
 D6M  C06  H061  single  0.970  0.020  1.090
 D6M  C06  H062  single  0.970  0.020  1.090
 D6M  C13  H131  single  0.970  0.020  1.090
 D6M  C13  H132  single  0.970  0.020  1.090
 D6M  C14  H141  single  0.970  0.020  1.090
 D6M  C14  H142  single  0.970  0.020  1.090
 D6M  C15  H151  single  0.970  0.020  1.090
 D6M  C15  H152  single  0.970  0.020  1.090
 D6M  C16  H161  single  0.970  0.020  1.090
 D6M  C16  H162  single  0.970  0.020  1.090
 D6M  C17  H171  single  0.970  0.020  1.090
 D6M  C17  H172  single  0.970  0.020  1.090
 D6M  C18  H181  single  0.970  0.020  1.090
 D6M  C18  H182  single  0.970  0.020  1.090
 D6M  C19  H191  single  0.970  0.020  1.090
 D6M  C19  H192  single  0.970  0.020  1.090
 D6M  C20  H201  single  0.970  0.020  1.090
 D6M  C20  H202  single  0.970  0.020  1.090
 D6M  C21  H211  single  0.970  0.020  1.090
 D6M  C21  H212  single  0.970  0.020  1.090
 D6M  C22  H221  single  0.970  0.020  1.090
 D6M  C22  H222  single  0.970  0.020  1.090
 D6M  C23  H231  single  0.970  0.020  1.090
 D6M  C23  H232  single  0.970  0.020  1.090
 D6M  C24  H241  single  0.970  0.020  1.090
 D6M  C24  H242  single  0.970  0.020  1.090
 D6M  C25  H251  single  0.970  0.020  1.090
 D6M  C25  H252  single  0.970  0.020  1.090
 D6M  C26  H261  single  0.970  0.020  1.090
 D6M  C26  H262  single  0.970  0.020  1.090
 D6M  C26  H263  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
 D6M  C12   C02  N03   114.79  3.000
 D6M  C12   C02  O01   122.08  3.000
 D6M  N03   C02  O01   123.05  3.000
 D6M  H03   N03  C04   117.21  3.000
 D6M  H03   N03  C02   117.67  3.000
 D6M  C04   N03  C02   123.81  3.000
 D6M  H04   C04  C09   107.44  3.000
 D6M  H04   C04  C05   107.95  3.000
 D6M  C09   C04  C05   111.16  3.000
 D6M  H04   C04  N03   107.53  3.000
 D6M  C09   C04  N03   112.71  3.000
 D6M  C05   C04  N03   109.84  3.000
 D6M  H052  C05  H051  106.11  3.000
 D6M  H052  C05  C06   109.82  3.000
 D6M  H051  C05  C06   110.18  3.000
 D6M  H052  C05  C04   107.78  3.000
 D6M  H051  C05  C04   109.35  3.000
 D6M  C06   C05  C04   113.32  3.000
 D6M  H062  C06  H061  104.78  3.000
 D6M  H062  C06  C07   107.77  3.000
 D6M  H061  C06  C07   108.20  3.000
 D6M  H062  C06  C05   110.23  3.000
 D6M  H061  C06  C05   109.46  3.000
 D6M  C07   C06  C05   115.80  3.000
 D6M  OXT   C07  O08   126.12  3.000
 D6M  OXT   C07  C06   115.84  3.000
 D6M  O08   C07  C06   118.04  3.000
 D6M  O11   C09  O10   127.05  3.000
 D6M  O11   C09  C04   114.95  3.000
 D6M  O10   C09  C04   118.00  3.000
 D6M  H122  C12  H121  105.59  3.000
 D6M  H122  C12  C13   109.32  3.000
 D6M  H121  C12  C13   110.24  3.000
 D6M  H122  C12  C02   107.44  3.000
 D6M  H121  C12  C02   110.02  3.000
 D6M  C13   C12  C02   113.86  3.000
 D6M  H132  C13  H131  106.27  3.000
 D6M  H132  C13  C14   109.50  3.000
 D6M  H131  C13  C14   109.18  3.000
 D6M  H132  C13  C12   109.90  3.000
 D6M  H131  C13  C12   109.58  3.000
 D6M  C14   C13  C12   112.24  3.000
 D6M  H142  C14  H141  105.93  3.000
 D6M  H142  C14  C15   109.24  3.000
 D6M  H141  C14  C15   109.59  3.000
 D6M  H142  C14  C13   109.22  3.000
 D6M  H141  C14  C13   109.73  3.000
 D6M  C15   C14  C13   112.89  3.000
 D6M  H152  C15  H151  105.90  3.000
 D6M  H152  C15  C16   109.43  3.000
 D6M  H151  C15  C16   109.11  3.000
 D6M  H152  C15  C14   109.50  3.000
 D6M  H151  C15  C14   109.13  3.000
 D6M  C16   C15  C14   113.49  3.000
 D6M  H162  C16  H161  105.95  3.000
 D6M  H162  C16  C17   109.30  3.000
 D6M  H161  C16  C17   109.57  3.000
 D6M  H162  C16  C15   109.23  3.000
 D6M  H161  C16  C15   109.53  3.000
 D6M  C17   C16  C15   113.02  3.000
 D6M  H172  C17  H171  105.86  3.000
 D6M  H172  C17  C18   109.35  3.000
 D6M  H171  C17  C18   109.12  3.000
 D6M  H172  C17  C16   109.42  3.000
 D6M  H171  C17  C16   109.14  3.000
 D6M  C18   C17  C16   113.66  3.000
 D6M  H182  C18  H181  105.95  3.000
 D6M  H182  C18  C19   109.34  3.000
 D6M  H181  C18  C19   109.52  3.000
 D6M  H182  C18  C17   109.29  3.000
 D6M  H181  C18  C17   109.52  3.000
 D6M  C19   C18  C17   112.98  3.000
 D6M  H192  C19  H191  105.87  3.000
 D6M  H192  C19  C20   109.32  3.000
 D6M  H191  C19  C20   109.18  3.000
 D6M  H192  C19  C18   109.36  3.000
 D6M  H191  C19  C18   109.16  3.000
 D6M  C20   C19  C18   113.67  3.000
 D6M  H202  C20  H201  105.96  3.000
 D6M  H202  C20  C21   109.36  3.000
 D6M  H201  C20  C21   109.44  3.000
 D6M  H202  C20  C19   109.33  3.000
 D6M  H201  C20  C19   109.48  3.000
 D6M  C21   C20  C19   113.03  3.000
 D6M  H212  C21  H211  105.88  3.000
 D6M  H212  C21  C22   109.30  3.000
 D6M  H211  C21  C22   109.25  3.000
 D6M  H212  C21  C20   109.33  3.000
 D6M  H211  C21  C20   109.21  3.000
 D6M  C22   C21  C20   113.58  3.000
 D6M  H222  C22  H221  105.95  3.000
 D6M  H222  C22  C23   109.38  3.000
 D6M  H221  C22  C23   109.37  3.000
 D6M  H222  C22  C21   109.35  3.000
 D6M  H221  C22  C21   109.41  3.000
 D6M  C23   C22  C21   113.13  3.000
 D6M  H232  C23  H231  105.90  3.000
 D6M  H232  C23  C24   109.30  3.000
 D6M  H231  C23  C24   109.31  3.000
 D6M  H232  C23  C22   109.31  3.000
 D6M  H231  C23  C22   109.27  3.000
 D6M  C24   C23  C22   113.48  3.000
 D6M  H242  C24  H241  105.92  3.000
 D6M  H242  C24  C25   109.34  3.000
 D6M  H241  C24  C25   109.29  3.000
 D6M  H242  C24  C23   109.39  3.000
 D6M  H241  C24  C23   109.38  3.000
 D6M  C25   C24  C23   113.26  3.000
 D6M  H252  C25  H251  105.96  3.000
 D6M  H252  C25  C26   109.56  3.000
 D6M  H251  C25  C26   109.56  3.000
 D6M  H252  C25  C24   109.23  3.000
 D6M  H251  C25  C24   109.27  3.000
 D6M  C26   C25  C24   113.02  3.000
 D6M  H263  C26  H262  107.63  3.000
 D6M  H263  C26  H261  107.41  3.000
 D6M  H262  C26  H261  107.61  3.000
 D6M  H263  C26  C25   111.18  3.000
 D6M  H262  C26  C25   111.59  3.000
 D6M  H261  C26  C25   111.21  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
 D6M  CONST_01  C04   N03  C02  O01     0.00   0.0  0
 D6M  CONST_02  C12   C02  N03  C04   180.00   0.0  0
 D6M  CONST_03  H03   N03  C02  O01   180.00   0.0  0
 D6M  Var_01    C13   C12  C02  O01    24.36  30.0  3
 D6M  Var_02    C14   C13  C12  C02  -176.68  30.0  3
 D6M  Var_03    C07   C06  C05  C04  -177.90  30.0  3
 D6M  Var_04    O08   C07  C06  C05    -5.02  30.0  3
 D6M  Var_05    C15   C14  C13  C12   177.69  30.0  3
 D6M  Var_06    C16   C15  C14  C13  -178.24  30.0  3
 D6M  Var_07    C17   C16  C15  C14   178.31  30.0  3
 D6M  Var_08    C18   C17  C16  C15  -178.61  30.0  3
 D6M  Var_09    C19   C18  C17  C16   178.83  30.0  3
 D6M  Var_10    C20   C19  C18  C17  -179.05  30.0  3
 D6M  Var_11    C21   C20  C19  C18   179.31  30.0  3
 D6M  Var_12    C22   C21  C20  C19  -179.52  30.0  3
 D6M  Var_13    C23   C22  C21  C20   179.75  30.0  3
 D6M  Var_14    C24   C23  C22  C21  -179.95  30.0  3
 D6M  Var_15    C25   C24  C23  C22  -179.91  30.0  3
 D6M  Var_16    C26   C25  C24  C23   179.89  30.0  3
 D6M  Var_17    H261  C26  C25  C24    60.04  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
 D6M  chir_01  C04  N03  C05  C09  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
 D6M  plan-1  O01  0.020
 D6M  plan-1  C02  0.020
 D6M  plan-1  N03  0.020
 D6M  plan-1  C04  0.020
 D6M  plan-1  C12  0.020
 D6M  plan-1  H03  0.020
 D6M  plan-2  C06  0.020
 D6M  plan-2  C07  0.020
 D6M  plan-2  O08  0.020
 D6M  plan-2  OXT  0.020
 D6M  plan-3  C04  0.020
 D6M  plan-3  C09  0.020
 D6M  plan-3  O10  0.020
 D6M  plan-3  O11  0.020

