# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 05:26:04 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  66  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  -0.492    4.4263   1.2149   1.5105
 D6M  C02   C  C     0   0.573    4.3741   0.5492   0.4884
 D6M  N03   N  NH1   0  -0.641    5.4866   0.1988  -0.1919
 D6M  C04   C  CH1   0  -0.191    6.7934   0.6444   0.1972
 D6M  C05   C  CH2   0  -0.465    7.8751  -0.2259  -0.4507
 D6M  C06   C  CH2   0  -0.577    7.7717  -1.6713   0.0097
 D6M  C07   C  C     0   0.554    8.8439  -2.5486  -0.5746
 D6M  O08   O  O     0  -0.443    9.6767  -2.1917  -1.3700
 D6M  C09   C  C     0   0.550    6.9939   2.1076  -0.1768
 D6M  O10   O  O     0  -0.430    6.2839   2.7251  -0.9255
 D6M  O11   O  OH1   0  -0.591    8.0663   2.6131   0.4159
 D6M  C12   C  CH2   0  -0.588    3.0859   0.0119  -0.0931
 D6M  C13   C  CH2   0  -0.413    1.8286   0.6405   0.4855
 D6M  C14   C  CH2   0  -0.416    0.5701   0.0305  -0.1185
 D6M  C15   C  CH2   0  -0.413   -0.7177   0.6081   0.4535
 D6M  C16   C  CH2   0  -0.412   -1.9658  -0.0273  -0.1454
 D6M  C17   C  CH2   0  -0.413   -3.2676   0.5207   0.4254
 D6M  C18   C  CH2   0  -0.412   -4.5015  -0.1412  -0.1747
 D6M  C19   C  CH2   0  -0.413   -5.8156   0.3856   0.3874
 D6M  C20   C  CH2   0  -0.412   -7.0358  -0.2897  -0.2252
 D6M  C21   C  CH2   0  -0.412   -8.3600   0.2231   0.3259
 D6M  C22   C  CH2   0  -0.411   -9.5696  -0.4675  -0.2915
 D6M  C23   C  CH2   0  -0.412  -10.9010   0.0380   0.2485
 D6M  C24   C  CH2   0  -0.406  -12.1039  -0.6554  -0.3789
 D6M  C25   C  CH2   0  -0.419  -13.4397  -0.1534   0.1543
 D6M  C26   C  CH3   0  -0.663  -14.6328  -0.8570  -0.4777
 D6M  OXT   O  OH1   0  -0.595    8.7684  -3.7907  -0.1086
 D6M  H03   H  HNH1  0   0.403    5.3840  -0.2332  -1.0971
 D6M  H121  H  HCH2  0   0.258    3.1042   0.1349  -1.1803
 D6M  H122  H  HCH2  0   0.271    3.0711  -1.0702   0.0783
 D6M  H04   H  HCH1  0   0.291    6.8894   0.5656   1.2838
 D6M  H051  H  HCH2  0   0.259    7.7910  -0.1618  -1.5387
 D6M  H052  H  HCH2  0   0.273    8.8534   0.1739  -0.1843
 D6M  H061  H  HCH2  0   0.287    7.8348  -1.7313   1.1005
 D6M  H062  H  HCH2  0   0.287    6.8031  -2.1061  -0.2531
 D6M  HX0   H  HOH1  0   0.480    9.4652  -4.3352  -0.5039
 D6M  H11   H  HOH1  0   0.485    8.1991   3.5339   0.1442
 D6M  H131  H  HCH2  0   0.222    1.8120   0.5068   1.5699
 D6M  H132  H  HCH2  0   0.222    1.8349   1.7196   0.3075
 D6M  H141  H  HCH2  0   0.211    0.5807   0.1715  -1.2050
 D6M  H142  H  HCH2  0   0.210    0.5814  -1.0533   0.0428
 D6M  H151  H  HCH2  0   0.208   -0.7254   0.4710   1.5404
 D6M  H152  H  HCH2  0   0.209   -0.7410   1.6903   0.2844
 D6M  H161  H  HCH2  0   0.207   -1.9587   0.1145  -1.2320
 D6M  H162  H  HCH2  0   0.206   -1.9303  -1.1107   0.0156
 D6M  H171  H  HCH2  0   0.206   -3.2738   0.3840   1.5126
 D6M  H172  H  HCH2  0   0.207   -3.3150   1.6023   0.2572
 D6M  H181  H  HCH2  0   0.206   -4.4922  -0.0046  -1.2620
 D6M  H182  H  HCH2  0   0.206   -4.4459  -1.2229  -0.0084
 D6M  H191  H  HCH2  0   0.206   -5.8296   0.2449   1.4739
 D6M  H192  H  HCH2  0   0.206   -5.8761   1.4672   0.2227
 D6M  H201  H  HCH2  0   0.206   -7.0182  -0.1508  -1.3120
 D6M  H202  H  HCH2  0   0.206   -6.9705  -1.3710  -0.0598
 D6M  H211  H  HCH2  0   0.206   -8.3795   0.0870   1.4130
 D6M  H212  H  HCH2  0   0.206   -8.4315   1.3032   0.1560
 D6M  H221  H  HCH2  0   0.206   -9.5456  -0.3344  -1.3789
 D6M  H222  H  HCH2  0   0.206   -9.4950  -1.5471  -0.1195
 D6M  H231  H  HCH2  0   0.206  -10.9290  -0.0996   1.3353
 D6M  H232  H  HCH2  0   0.206  -10.9758   1.1182   0.0801
 D6M  H241  H  HCH2  0   0.205  -12.0733  -0.5191  -1.4658
 D6M  H242  H  HCH2  0   0.205  -12.0289  -1.7354  -0.2094
 D6M  H251  H  HCH2  0   0.210  -13.4692  -0.2866   1.2403
 D6M  H252  H  HCH2  0   0.210  -13.5158   0.9246  -0.0192
 D6M  H261  H  HCH3  0   0.215  -14.5932  -1.9339  -0.3028
 D6M  H262  H  HCH3  0   0.226  -15.5764  -0.4912  -0.0714
 D6M  H263  H  HCH3  0   0.216  -14.6556  -0.7021  -1.5582

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  1.221  0.020  1.221
 D6M  C02  N03   single  1.350  0.020  1.350
 D6M  C02  C12   single  1.512  0.020  1.512
 D6M  N03  C04   single  1.434  0.020  1.434
 D6M  C04  C05   single  1.532  0.020  1.532
 D6M  C04  C09   single  1.523  0.020  1.523
 D6M  C05  C06   single  1.520  0.020  1.520
 D6M  C06  C07   single  1.504  0.020  1.504
 D6M  C07  O08   double  1.206  0.020  1.206
 D6M  C07  OXT   single  1.329  0.020  1.329
 D6M  C09  O10   double  1.202  0.020  1.202
 D6M  C09  O11   single  1.325  0.020  1.325
 D6M  C12  C13   single  1.520  0.020  1.520
 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  1.524  0.020  1.524
 D6M  C22  C23   single  1.523  0.020  1.523
 D6M  C23  C24   single  1.524  0.020  1.524
 D6M  C24  C25   single  1.523  0.020  1.523
 D6M  C25  C26   single  1.523  0.020  1.523
 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  OXT  HX0   single  0.850  0.020  0.980
 D6M  O11  H11   single  0.850  0.020  0.980
 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   114.58  3.000
 D6M  C12   C02  O01   123.51  3.000
 D6M  N03   C02  O01   121.87  3.000
 D6M  H03   N03  C04   118.00  3.000
 D6M  H03   N03  C02   118.66  3.000
 D6M  C04   N03  C02   122.23  3.000
 D6M  H04   C04  C09   107.55  3.000
 D6M  H04   C04  C05   108.50  3.000
 D6M  C09   C04  C05   110.42  3.000
 D6M  H04   C04  N03   109.09  3.000
 D6M  C09   C04  N03   110.59  3.000
 D6M  C05   C04  N03   110.61  3.000
 D6M  H052  C05  H051  106.90  3.000
 D6M  H052  C05  C06   109.62  3.000
 D6M  H051  C05  C06   110.60  3.000
 D6M  H052  C05  C04   108.79  3.000
 D6M  H051  C05  C04   109.47  3.000
 D6M  C06   C05  C04   111.35  3.000
 D6M  H062  C06  H061  105.59  3.000
 D6M  H062  C06  C07   107.82  3.000
 D6M  H061  C06  C07   108.31  3.000
 D6M  H062  C06  C05   111.43  3.000
 D6M  H061  C06  C05   110.49  3.000
 D6M  C07   C06  C05   112.86  3.000
 D6M  OXT   C07  O08   123.18  3.000
 D6M  OXT   C07  C06   111.63  3.000
 D6M  O08   C07  C06   125.19  3.000
 D6M  O11   C09  O10   124.07  3.000
 D6M  O11   C09  C04   111.29  3.000
 D6M  O10   C09  C04   124.64  3.000
 D6M  H11   O11  C09   110.36  3.000
 D6M  H122  C12  H121  105.47  3.000
 D6M  H122  C12  C13   109.74  3.000
 D6M  H121  C12  C13   110.22  3.000
 D6M  H122  C12  C02   107.59  3.000
 D6M  H121  C12  C02   109.14  3.000
 D6M  C13   C12  C02   114.29  3.000
 D6M  H132  C13  H131  106.40  3.000
 D6M  H132  C13  C14   109.59  3.000
 D6M  H131  C13  C14   109.38  3.000
 D6M  H132  C13  C12   109.96  3.000
 D6M  H131  C13  C12   109.86  3.000
 D6M  C14   C13  C12   111.52  3.000
 D6M  H142  C14  H141  105.85  3.000
 D6M  H142  C14  C15   109.18  3.000
 D6M  H141  C14  C15   109.38  3.000
 D6M  H142  C14  C13   109.22  3.000
 D6M  H141  C14  C13   109.49  3.000
 D6M  C15   C14  C13   113.44  3.000
 D6M  H152  C15  H151  106.06  3.000
 D6M  H152  C15  C16   109.51  3.000
 D6M  H151  C15  C16   109.39  3.000
 D6M  H152  C15  C14   109.56  3.000
 D6M  H151  C15  C14   109.34  3.000
 D6M  C16   C15  C14   112.77  3.000
 D6M  H162  C16  H161  105.87  3.000
 D6M  H162  C16  C17   109.16  3.000
 D6M  H161  C16  C17   109.30  3.000
 D6M  H162  C16  C15   109.15  3.000
 D6M  H161  C16  C15   109.30  3.000
 D6M  C17   C16  C15   113.75  3.000
 D6M  H172  C17  H171  105.98  3.000
 D6M  H172  C17  C18   109.47  3.000
 D6M  H171  C17  C18   109.39  3.000
 D6M  H172  C17  C16   109.55  3.000
 D6M  H171  C17  C16   109.38  3.000
 D6M  C18   C17  C16   112.85  3.000
 D6M  H182  C18  H181  105.85  3.000
 D6M  H182  C18  C19   109.21  3.000
 D6M  H181  C18  C19   109.29  3.000
 D6M  H182  C18  C17   109.15  3.000
 D6M  H181  C18  C17   109.26  3.000
 D6M  C19   C18  C17   113.78  3.000
 D6M  H192  C19  H191  105.97  3.000
 D6M  H192  C19  C20   109.45  3.000
 D6M  H191  C19  C20   109.37  3.000
 D6M  H192  C19  C18   109.48  3.000
 D6M  H191  C19  C18   109.42  3.000
 D6M  C20   C19  C18   112.92  3.000
 D6M  H202  C20  H201  105.89  3.000
 D6M  H202  C20  C21   109.23  3.000
 D6M  H201  C20  C21   109.28  3.000
 D6M  H202  C20  C19   109.21  3.000
 D6M  H201  C20  C19   109.26  3.000
 D6M  C21   C20  C19   113.68  3.000
 D6M  H212  C21  H211  105.97  3.000
 D6M  H212  C21  C22   109.40  3.000
 D6M  H211  C21  C22   109.36  3.000
 D6M  H212  C21  C20   109.42  3.000
 D6M  H211  C21  C20   109.43  3.000
 D6M  C22   C21  C20   113.02  3.000
 D6M  H222  C22  H221  105.89  3.000
 D6M  H222  C22  C23   109.32  3.000
 D6M  H221  C22  C23   109.31  3.000
 D6M  H222  C22  C21   109.20  3.000
 D6M  H221  C22  C21   109.25  3.000
 D6M  C23   C22  C21   113.58  3.000
 D6M  H232  C23  H231  105.93  3.000
 D6M  H232  C23  C24   109.36  3.000
 D6M  H231  C23  C24   109.34  3.000
 D6M  H232  C23  C22   109.41  3.000
 D6M  H231  C23  C22   109.41  3.000
 D6M  C24   C23  C22   113.15  3.000
 D6M  H242  C24  H241  105.90  3.000
 D6M  H242  C24  C25   109.31  3.000
 D6M  H241  C24  C25   109.31  3.000
 D6M  H242  C24  C23   109.32  3.000
 D6M  H241  C24  C23   109.26  3.000
 D6M  C25   C24  C23   113.47  3.000
 D6M  H252  C25  H251  105.98  3.000
 D6M  H252  C25  C26   109.56  3.000
 D6M  H251  C25  C26   109.54  3.000
 D6M  H252  C25  C24   109.27  3.000
 D6M  H251  C25  C24   109.32  3.000
 D6M  C26   C25  C24   112.93  3.000
 D6M  H263  C26  H262  107.64  3.000
 D6M  H263  C26  H261  107.42  3.000
 D6M  H262  C26  H261  107.61  3.000
 D6M  H263  C26  C25   111.20  3.000
 D6M  H262  C26  C25   111.61  3.000
 D6M  H261  C26  C25   111.16  3.000
 D6M  HX0   OXT  C07   109.97  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  CONST_04  H11   O11  C09  C04   180.00   0.0  0
 D6M  CONST_05  HX0   OXT  C07  C06   180.00   0.0  0
 D6M  Var_01    C13   C12  C02  O01    14.46  30.0  3
 D6M  Var_02    C14   C13  C12  C02  -178.61  30.0  3
 D6M  Var_03    C07   C06  C05  C04  -178.30  30.0  3
 D6M  Var_04    O08   C07  C06  C05    -3.05  30.0  3
 D6M  Var_05    C15   C14  C13  C12   178.74  30.0  3
 D6M  Var_06    C16   C15  C14  C13  -179.12  30.0  3
 D6M  Var_07    C17   C16  C15  C14   179.19  30.0  3
 D6M  Var_08    C18   C17  C16  C15  -179.27  30.0  3
 D6M  Var_09    C19   C18  C17  C16   179.66  30.0  3
 D6M  Var_10    C20   C19  C18  C17  -179.97  30.0  3
 D6M  Var_11    C21   C20  C19  C18   179.93  30.0  3
 D6M  Var_12    C22   C21  C20  C19  -179.69  30.0  3
 D6M  Var_13    C23   C22  C21  C20  -179.87  30.0  3
 D6M  Var_14    C24   C23  C22  C21   179.79  30.0  3
 D6M  Var_15    C25   C24  C23  C22  -179.89  30.0  3
 D6M  Var_16    C26   C25  C24  C23  -179.83  30.0  3
 D6M  Var_17    H261  C26  C25  C24    59.08  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-2  HX0  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
 D6M  plan-3  H11  0.020

