# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 18:43:29 2020
#   Inital geometry file: a 164 line input string
#   Ligand name: N-[(1S,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]hexanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(=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
 6CM  6CM  N-[(1S,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]hexanamide  ligand  75  28  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6CM
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
 6CM  O19   O  O     0  -0.495  -3.9530  -0.4760  -1.3408
 6CM  C19   C  C     0   0.559  -4.8143  -0.4804  -0.4723
 6CM  N2    N  NH1   0  -0.639  -5.5858   0.5883  -0.1948
 6CM  C2    C  CH1   0  -0.167  -5.4392   1.8890  -0.8083
 6CM  C1    C  CH2   0  -0.144  -6.7429   2.3078  -1.4689
 6CM  O1    O  OH1   0  -0.676  -7.7421   2.4005  -0.4789
 6CM  C3    C  CH1   0   0.013  -4.9282   2.9193   0.2290
 6CM  C4    C  C1    0  -0.253  -3.6331   2.4665   0.8407
 6CM  C5    C  C1    0  -0.208  -2.4985   3.1577   0.8816
 6CM  C6    C  CH2   0  -0.479  -1.2360   2.6360   1.4925
 6CM  C7    C  CH2   0  -0.413  -0.0953   2.5020   0.4830
 6CM  C8    C  CH2   0  -0.413   1.1489   1.8769   1.1008
 6CM  C9    C  CH2   0  -0.413   2.3183   1.7435   0.1335
 6CM  C10   C  CH2   0  -0.411   3.5172   1.0429   0.7614
 6CM  C11   C  CH2   0  -0.413   4.7093   0.8987  -0.1760
 6CM  C12   C  CH2   0  -0.412   5.8776   0.1623   0.4683
 6CM  C13   C  CH2   0  -0.412   7.0835   0.0025  -0.4486
 6CM  C14   C  CH2   0  -0.411   8.2327  -0.7510   0.2098
 6CM  C15   C  CH2   0  -0.412   9.4478  -0.9198  -0.6932
 6CM  C16   C  CH2   0  -0.406  10.5866  -1.6801  -0.0250
 6CM  C17   C  CH2   0  -0.420  11.8083  -1.8529  -0.9190
 6CM  C18   C  CH3   0  -0.662  12.9346  -2.6159  -0.2355
 6CM  O3    O  OH1   0  -0.657  -4.8614   4.2047  -0.3317
 6CM  C20   C  CH2   0  -0.581  -5.0637  -1.6890   0.4042
 6CM  C21   C  CH2   0  -0.414  -4.9074  -3.0137  -0.3304
 6CM  C22   C  CH2   0  -0.409  -5.0147  -4.2079   0.6092
 6CM  C23   C  CH2   0  -0.420  -4.8825  -5.5454  -0.1084
 6CM  C24   C  CH3   0  -0.662  -4.9455  -6.7311   0.8446
 6CM  HN2   H  HNH1  0   0.395  -6.2863   0.4955   0.5238
 6CM  H2    H  HCH1  0   0.268  -4.6869   1.7966  -1.5954
 6CM  H11   H  HCH2  0   0.204  -6.5988   3.2571  -1.9959
 6CM  H12   H  HCH2  0   0.215  -6.9931   1.5549  -2.2261
 6CM  HO1   H  HOH1  0   0.460  -8.5903   2.5242  -0.9134
 6CM  H3    H  HCH1  0   0.242  -5.6740   2.9851   1.0302
 6CM  H4    H  H     0   0.239  -3.6538   1.4828   1.3003
 6CM  H5    H  H     0   0.229  -2.4460   4.1548   0.4513
 6CM  H61   H  HCH2  0   0.224  -1.4289   1.6635   1.9555
 6CM  H62   H  HCH2  0   0.226  -0.9126   3.3043   2.2985
 6CM  H71   H  HCH2  0   0.213   0.1484   3.4871   0.0716
 6CM  H72   H  HCH2  0   0.215  -0.4300   1.8904  -0.3610
 6CM  H81   H  HCH2  0   0.208   0.8909   0.8859   1.4902
 6CM  H82   H  HCH2  0   0.209   1.4629   2.4689   1.9678
 6CM  H91   H  HCH2  0   0.208   2.6172   2.7362  -0.2203
 6CM  H92   H  HCH2  0   0.207   1.9977   1.1873  -0.7545
 6CM  H101  H  HCH2  0   0.206   3.2093   0.0495   1.1063
 6CM  H102  H  HCH2  0   0.206   3.8271   1.5903   1.6587
 6CM  H111  H  HCH2  0   0.207   5.0391   1.8904  -0.5045
 6CM  H112  H  HCH2  0   0.206   4.3998   0.3659  -1.0821
 6CM  H121  H  HCH2  0   0.206   5.5407  -0.8275   0.7963
 6CM  H122  H  HCH2  0   0.206   6.1817   0.6933   1.3774
 6CM  H131  H  HCH2  0   0.206   7.4322   0.9906  -0.7692
 6CM  H132  H  HCH2  0   0.206   6.7810  -0.5228  -1.3614
 6CM  H141  H  HCH2  0   0.206   7.8800  -1.7381   0.5293
 6CM  H142  H  HCH2  0   0.206   8.5307  -0.2270   1.1249
 6CM  H151  H  HCH2  0   0.206   9.8059   0.0662  -1.0099
 6CM  H152  H  HCH2  0   0.206   9.1512  -1.4424  -1.6095
 6CM  H161  H  HCH2  0   0.205  10.2275  -2.6661   0.2910
 6CM  H162  H  HCH2  0   0.205  10.8805  -1.1583   0.8929
 6CM  H171  H  HCH2  0   0.210  12.1694  -0.8684  -1.2324
 6CM  H172  H  HCH2  0   0.210  11.5145  -2.3733  -1.8361
 6CM  H181  H  HCH3  0   0.215  13.2573  -2.1054   0.6738
 6CM  H182  H  HCH3  0   0.216  12.6138  -3.6199   0.0487
 6CM  H183  H  HCH3  0   0.225  13.8051  -2.7183  -0.8845
 6CM  HO3   H  HOH1  0   0.447  -4.2133   4.1953  -1.0453
 6CM  H201  H  HCH2  0   0.264  -4.3364  -1.6396   1.2232
 6CM  H202  H  HCH2  0   0.248  -6.0488  -1.6313   0.8745
 6CM  H211  H  HCH2  0   0.222  -5.6703  -3.0917  -1.1110
 6CM  H212  H  HCH2  0   0.223  -3.9408  -3.0376  -0.8385
 6CM  H221  H  HCH2  0   0.210  -4.2385  -4.1315   1.3790
 6CM  H222  H  HCH2  0   0.210  -5.9723  -4.1762   1.1409
 6CM  H231  H  HCH2  0   0.212  -5.6744  -5.6339  -0.8585
 6CM  H232  H  HCH2  0   0.211  -3.9379  -5.5678  -0.6610
 6CM  H241  H  HCH3  0   0.216  -4.1352  -6.6911   1.5746
 6CM  H242  H  HCH3  0   0.216  -5.8866  -6.7415   1.3979
 6CM  H243  H  HCH3  0   0.226  -4.8658  -7.6800   0.3131

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
 6CM  O19  C19   double  1.223  0.020  1.223
 6CM  C19  N2    single  1.347  0.020  1.347
 6CM  C19  C20   single  1.514  0.020  1.514
 6CM  N2   C2    single  1.446  0.020  1.446
 6CM  N2   HN2   single  0.860  0.020  1.020
 6CM  C2   C1    single  1.520  0.020  1.520
 6CM  C2   C3    single  1.549  0.020  1.549
 6CM  C2   H2    single  0.970  0.020  1.090
 6CM  C1   O1    single  1.410  0.020  1.410
 6CM  C1   H11   single  0.970  0.020  1.090
 6CM  C1   H12   single  0.970  0.020  1.090
 6CM  O1   HO1   single  0.850  0.020  0.980
 6CM  C3   C4    single  1.502  0.020  1.502
 6CM  C3   O3    single  1.404  0.020  1.404
 6CM  C3   H3    single  0.970  0.020  1.090
 6CM  C4   C5    double  1.329  0.020  1.329
 6CM  C4   H4    single  0.930  0.020  1.080
 6CM  C5   C6    single  1.496  0.020  1.496
 6CM  C5   H5    single  0.930  0.020  1.080
 6CM  C6   C7    single  1.529  0.020  1.529
 6CM  C6   H61   single  0.970  0.020  1.090
 6CM  C6   H62   single  0.970  0.020  1.090
 6CM  C7   C8    single  1.523  0.020  1.523
 6CM  C7   H71   single  0.970  0.020  1.090
 6CM  C7   H72   single  0.970  0.020  1.090
 6CM  C8   C9    single  1.523  0.020  1.523
 6CM  C8   H81   single  0.970  0.020  1.090
 6CM  C8   H82   single  0.970  0.020  1.090
 6CM  C9   C10   single  1.524  0.020  1.524
 6CM  C9   H91   single  0.970  0.020  1.090
 6CM  C9   H92   single  0.970  0.020  1.090
 6CM  C10  C11   single  1.523  0.020  1.523
 6CM  C10  H101  single  0.970  0.020  1.090
 6CM  C10  H102  single  0.970  0.020  1.090
 6CM  C11  C12   single  1.524  0.020  1.524
 6CM  C11  H111  single  0.970  0.020  1.090
 6CM  C11  H112  single  0.970  0.020  1.090
 6CM  C12  C13   single  1.523  0.020  1.523
 6CM  C12  H121  single  0.970  0.020  1.090
 6CM  C12  H122  single  0.970  0.020  1.090
 6CM  C13  C14   single  1.524  0.020  1.524
 6CM  C13  H131  single  0.970  0.020  1.090
 6CM  C13  H132  single  0.970  0.020  1.090
 6CM  C14  C15   single  1.523  0.020  1.523
 6CM  C14  H141  single  0.970  0.020  1.090
 6CM  C14  H142  single  0.970  0.020  1.090
 6CM  C15  C16   single  1.524  0.020  1.524
 6CM  C15  H151  single  0.970  0.020  1.090
 6CM  C15  H152  single  0.970  0.020  1.090
 6CM  C16  C17   single  1.524  0.020  1.524
 6CM  C16  H161  single  0.970  0.020  1.090
 6CM  C16  H162  single  0.970  0.020  1.090
 6CM  C17  C18   single  1.523  0.020  1.523
 6CM  C17  H171  single  0.970  0.020  1.090
 6CM  C17  H172  single  0.970  0.020  1.090
 6CM  C18  H181  single  0.970  0.020  1.090
 6CM  C18  H182  single  0.970  0.020  1.090
 6CM  C18  H183  single  0.970  0.020  1.090
 6CM  O3   HO3   single  0.850  0.020  0.980
 6CM  C20  C21   single  1.523  0.020  1.523
 6CM  C20  H201  single  0.970  0.020  1.090
 6CM  C20  H202  single  0.970  0.020  1.090
 6CM  C21  C22   single  1.523  0.020  1.523
 6CM  C21  H211  single  0.970  0.020  1.090
 6CM  C21  H212  single  0.970  0.020  1.090
 6CM  C22  C23   single  1.524  0.020  1.524
 6CM  C22  H221  single  0.970  0.020  1.090
 6CM  C22  H222  single  0.970  0.020  1.090
 6CM  C23  C24   single  1.523  0.020  1.523
 6CM  C23  H231  single  0.970  0.020  1.090
 6CM  C23  H232  single  0.970  0.020  1.090
 6CM  C24  H241  single  0.970  0.020  1.090
 6CM  C24  H242  single  0.970  0.020  1.090
 6CM  C24  H243  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
 6CM  C20   C19  N2    114.83  3.000
 6CM  C20   C19  O19   122.00  3.000
 6CM  N2    C19  O19   123.15  3.000
 6CM  HN2   N2   C2    117.12  3.000
 6CM  HN2   N2   C19   118.16  3.000
 6CM  C2    N2   C19   124.64  3.000
 6CM  H2    C2   C3    108.15  3.000
 6CM  H2    C2   C1    107.50  3.000
 6CM  C3    C2   C1    113.00  3.000
 6CM  H2    C2   N2    107.42  3.000
 6CM  C3    C2   N2    110.35  3.000
 6CM  C1    C2   N2    110.20  3.000
 6CM  H12   C1   H11   107.03  3.000
 6CM  H12   C1   O1    111.61  3.000
 6CM  H11   C1   O1    111.97  3.000
 6CM  H12   C1   C2    107.85  3.000
 6CM  H11   C1   C2    109.57  3.000
 6CM  O1    C1   C2    108.71  3.000
 6CM  HO1   O1   C1    108.46  3.000
 6CM  H3    C3   O3    105.62  3.000
 6CM  H3    C3   C4    107.87  3.000
 6CM  O3    C3   C4    113.43  3.000
 6CM  H3    C3   C2    107.75  3.000
 6CM  O3    C3   C2    110.93  3.000
 6CM  C4    C3   C2    110.89  3.000
 6CM  H4    C4   C5    118.31  3.000
 6CM  H4    C4   C3    115.40  3.000
 6CM  C5    C4   C3    126.28  3.000
 6CM  H5    C5   C6    116.14  3.000
 6CM  H5    C5   C4    120.40  3.000
 6CM  C6    C5   C4    123.46  3.000
 6CM  H62   C6   H61   106.42  3.000
 6CM  H62   C6   C7    108.59  3.000
 6CM  H61   C6   C7    109.45  3.000
 6CM  H62   C6   C5    109.67  3.000
 6CM  H61   C6   C5    109.51  3.000
 6CM  C7    C6   C5    112.98  3.000
 6CM  H72   C7   H71   106.32  3.000
 6CM  H72   C7   C8    109.46  3.000
 6CM  H71   C7   C8    109.86  3.000
 6CM  H72   C7   C6    109.26  3.000
 6CM  H71   C7   C6    109.59  3.000
 6CM  C8    C7   C6    112.18  3.000
 6CM  H82   C8   H81   105.96  3.000
 6CM  H82   C8   C9    109.25  3.000
 6CM  H81   C8   C9    109.10  3.000
 6CM  H82   C8   C7    109.47  3.000
 6CM  H81   C8   C7    108.84  3.000
 6CM  C9    C8   C7    113.91  3.000
 6CM  H92   C9   H91   106.14  3.000
 6CM  H92   C9   C10   109.31  3.000
 6CM  H91   C9   C10   109.58  3.000
 6CM  H92   C9   C8    109.54  3.000
 6CM  H91   C9   C8    109.58  3.000
 6CM  C10   C9   C8    112.49  3.000
 6CM  H102  C10  H101  105.94  3.000
 6CM  H102  C10  C11   109.26  3.000
 6CM  H101  C10  C11   109.13  3.000
 6CM  H102  C10  C9    109.28  3.000
 6CM  H101  C10  C9    108.99  3.000
 6CM  C11   C10  C9    113.93  3.000
 6CM  H112  C11  H111  106.10  3.000
 6CM  H112  C11  C12   109.34  3.000
 6CM  H111  C11  C12   109.47  3.000
 6CM  H112  C11  C10   109.50  3.000
 6CM  H111  C11  C10   109.54  3.000
 6CM  C12   C11  C10   112.68  3.000
 6CM  H122  C12  H121  105.94  3.000
 6CM  H122  C12  C13   109.30  3.000
 6CM  H121  C12  C13   109.20  3.000
 6CM  H122  C12  C11   109.23  3.000
 6CM  H121  C12  C11   109.11  3.000
 6CM  C13   C12  C11   113.77  3.000
 6CM  H132  C13  H131  106.05  3.000
 6CM  H132  C13  C14   109.33  3.000
 6CM  H131  C13  C14   109.41  3.000
 6CM  H132  C13  C12   109.46  3.000
 6CM  H131  C13  C12   109.48  3.000
 6CM  C14   C13  C12   112.88  3.000
 6CM  H142  C14  H141  105.95  3.000
 6CM  H142  C14  C15   109.33  3.000
 6CM  H141  C14  C15   109.26  3.000
 6CM  H142  C14  C13   109.24  3.000
 6CM  H141  C14  C13   109.19  3.000
 6CM  C15   C14  C13   113.59  3.000
 6CM  H152  C15  H151  106.02  3.000
 6CM  H152  C15  C16   109.33  3.000
 6CM  H151  C15  C16   109.36  3.000
 6CM  H152  C15  C14   109.43  3.000
 6CM  H151  C15  C14   109.41  3.000
 6CM  C16   C15  C14   113.05  3.000
 6CM  H162  C16  H161  105.94  3.000
 6CM  H162  C16  C17   109.29  3.000
 6CM  H161  C16  C17   109.26  3.000
 6CM  H162  C16  C15   109.28  3.000
 6CM  H161  C16  C15   109.30  3.000
 6CM  C17   C16  C15   113.49  3.000
 6CM  H172  C17  H171  106.04  3.000
 6CM  H172  C17  C18   109.66  3.000
 6CM  H171  C17  C18   109.59  3.000
 6CM  H172  C17  C16   109.29  3.000
 6CM  H171  C17  C16   109.30  3.000
 6CM  C18   C17  C16   112.74  3.000
 6CM  H183  C18  H182  107.65  3.000
 6CM  H183  C18  H181  107.68  3.000
 6CM  H182  C18  H181  107.47  3.000
 6CM  H183  C18  C17   111.74  3.000
 6CM  H182  C18  C17   111.12  3.000
 6CM  H181  C18  C17   110.99  3.000
 6CM  HO3   O3   C3    108.58  3.000
 6CM  H202  C20  H201  105.90  3.000
 6CM  H202  C20  C21   110.24  3.000
 6CM  H201  C20  C21   109.36  3.000
 6CM  H202  C20  C19   110.82  3.000
 6CM  H201  C20  C19   106.69  3.000
 6CM  C21   C20  C19   113.48  3.000
 6CM  H212  C21  H211  106.47  3.000
 6CM  H212  C21  C22   109.39  3.000
 6CM  H211  C21  C22   109.57  3.000
 6CM  H212  C21  C20   109.53  3.000
 6CM  H211  C21  C20   109.55  3.000
 6CM  C22   C21  C20   112.16  3.000
 6CM  H222  C22  H221  106.03  3.000
 6CM  H222  C22  C23   109.25  3.000
 6CM  H221  C22  C23   109.30  3.000
 6CM  H222  C22  C21   109.77  3.000
 6CM  H221  C22  C21   109.20  3.000
 6CM  C23   C22  C21   113.06  3.000
 6CM  H232  C23  H231  106.07  3.000
 6CM  H232  C23  C24   109.62  3.000
 6CM  H231  C23  C24   109.65  3.000
 6CM  H232  C23  C22   109.30  3.000
 6CM  H231  C23  C22   109.33  3.000
 6CM  C24   C23  C22   112.66  3.000
 6CM  H243  C24  H242  107.56  3.000
 6CM  H243  C24  H241  107.68  3.000
 6CM  H242  C24  H241  107.54  3.000
 6CM  H243  C24  C23   111.68  3.000
 6CM  H242  C24  C23   111.12  3.000
 6CM  H241  C24  C23   111.07  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
 6CM  CONST_01  C2    N2   C19  O19     0.00   0.0  0
 6CM  CONST_02  C20   C19  N2   C2    180.00   0.0  0
 6CM  CONST_03  HN2   N2   C19  O19   180.00   0.0  0
 6CM  Var_01    C6    C5   C4   C3   -179.12   0.0  2
 6CM  Var_02    C21   C20  C19  O19   -36.80  30.0  3
 6CM  Var_03    C22   C21  C20  C19   173.78  30.0  3
 6CM  Var_04    C7    C6   C5   C4    117.58  30.0  3
 6CM  Var_05    C8    C7   C6   C5   -175.91  30.0  3
 6CM  Var_06    C9    C8   C7   C6   -179.15  30.0  3
 6CM  Var_07    C10   C9   C8   C7   -176.72  30.0  3
 6CM  Var_08    C11   C10  C9   C8   -179.68  30.0  3
 6CM  Var_09    C12   C11  C10  C9   -178.48  30.0  3
 6CM  Var_10    C13   C12  C11  C10   179.93  30.0  3
 6CM  Var_11    C14   C13  C12  C11  -179.30  30.0  3
 6CM  Var_12    C15   C14  C13  C12  -179.98  30.0  3
 6CM  Var_13    C16   C15  C14  C13  -179.74  30.0  3
 6CM  Var_14    C17   C16  C15  C14  -179.92  30.0  3
 6CM  Var_15    C18   C17  C16  C15  -179.93  30.0  3
 6CM  Var_16    C23   C22  C21  C20   179.12  30.0  3
 6CM  Var_17    C24   C23  C22  C21   178.13  30.0  3
 6CM  Var_18    H181  C18  C17  C16   -59.01  30.0  3
 6CM  Var_19    H241  C24  C23  C22   -60.71  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
 6CM  chir_01  C2  N2  C1  C3  negativ
 6CM  chir_02  C3  O3  C2  C4  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
 6CM  plan-1  O19  0.020
 6CM  plan-1  C19  0.020
 6CM  plan-1  N2   0.020
 6CM  plan-1  C2   0.020
 6CM  plan-1  C20  0.020
 6CM  plan-1  HN2  0.020
 6CM  plan-2  C3   0.020
 6CM  plan-2  C4   0.020
 6CM  plan-2  C5   0.020
 6CM  plan-2  C6   0.020
 6CM  plan-2  H4   0.020
 6CM  plan-2  H5   0.020

