# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 08:25:25 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (14E,17R,18R,19S)-19-amino-17,18,20-trihydroxyicos-14-en-7-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCC(=O)CCCCCC\C=C\C[C@@H](O)[C@H](O)[C@@H](N)CO
#
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
 MYB  MYB  (14E,17R,18R,19S)-19-amino-17,18,20-trihydroxyicos-14-en-7-one  ligand  64  25  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MYB
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
 MYB  N2    N  NH2   0  -0.779  -8.9788   2.1449   0.6306
 MYB  C7    C  CH2   0  -0.147  -6.6196   2.7051   0.4592
 MYB  C6    C  CH1   0  -0.154  -7.7146   1.7373   0.0348
 MYB  C13   C  CH2   0  -0.480  -1.9343  -2.7422   0.0468
 MYB  C8    C  CH1   0   0.019  -7.3403   0.2784   0.3729
 MYB  C14   C  CH2   0  -0.413  -0.8794  -1.6967   0.4119
 MYB  C12   C  C1    0  -0.207  -3.3010  -2.3510   0.5121
 MYB  C11   C  C1    0  -0.207  -4.3274  -2.0687  -0.2851
 MYB  O5    O  OH1   0  -0.670  -5.9565  -0.0219  -1.6205
 MYB  O4    O  OH1   0  -0.667  -7.0025   4.0203   0.1323
 MYB  OAJ   O  OH1   0  -0.667  -8.3996  -0.5910   0.0142
 MYB  CBN   C  CH1   0   0.006  -6.0063  -0.1970  -0.2172
 MYB  C15   C  CH2   0  -0.414   0.5291  -2.0960  -0.0084
 MYB  C16   C  CH2   0  -0.414   1.5713  -1.0371   0.3281
 MYB  C17   C  CH2   0  -0.415   2.9819  -1.4344  -0.0899
 MYB  C18   C  CH2   0  -0.553   3.9986  -0.3541   0.2399
 MYB  C19   C  C     0   0.406   5.4228  -0.6708  -0.1460
 MYB  C20   C  CH2   0  -0.554   6.4387   0.3956   0.1802
 MYB  C21   C  CH2   0  -0.415   7.8742   0.0624  -0.1902
 MYB  C22   C  CH2   0  -0.414   8.8332   1.1888   0.1769
 MYB  C23   C  CH2   0  -0.407  10.2804   0.8819  -0.1848
 MYB  C24   C  CH2   0  -0.418  11.2420   2.0086   0.1737
 MYB  C25   C  CH3   0  -0.663  12.6860   1.6911  -0.1884
 MYB  O19   O  O     0  -0.413   5.7290  -1.7116  -0.6840
 MYB  HN1   H  HNH2  0   0.341  -9.6931   1.4668   0.3964
 MYB  HN2   H  HNH2  0   0.332  -8.8995   2.1154   1.6420
 MYB  H6    H  HCH1  0   0.222  -7.8260   1.8111  -1.0546
 MYB  H71C  H  HCH2  0   0.186  -6.4462   2.5928   1.5410
 MYB  H72C  H  HCH2  0   0.207  -5.6811   2.4390  -0.0382
 MYB  H4    H  HOH1  0   0.452  -6.2647   4.5990   0.3439
 MYB  H8    H  HCH1  0   0.220  -7.2547   0.1993   1.4635
 MYB  H131  H  HCH2  0   0.225  -1.9386  -2.8965  -1.0361
 MYB  H132  H  HCH2  0   0.224  -1.6508  -3.7000   0.4975
 MYB  H141  H  HCH2  0   0.215  -1.1467  -0.7440  -0.0563
 MYB  H142  H  HCH2  0   0.213  -0.9018  -1.5213   1.4928
 MYB  H12   H  H     0   0.227  -3.4348  -2.2724   1.5901
 MYB  HAJ   H  HOH1  0   0.440  -8.5976  -0.4687  -0.9209
 MYB  HBN   H  HCH1  0   0.235  -5.2129   0.4383   0.1884
 MYB  H11   H  H     0   0.230  -4.1881  -2.1464  -1.3607
 MYB  H101  H  HCH2  0   0.237  -6.4488  -2.3090  -0.2056
 MYB  H102  H  HCH2  0   0.242  -5.7325  -1.7130   1.2792
 MYB  H5    H  HOH1  0   0.443  -6.4523  -0.7313  -2.0425
 MYB  H151  H  HCH2  0   0.210   0.8013  -3.0412   0.4741
 MYB  H152  H  HCH2  0   0.210   0.5460  -2.2899  -1.0864
 MYB  H161  H  HCH2  0   0.211   1.2967  -0.0945  -0.1582
 MYB  H162  H  HCH2  0   0.211   1.5514  -0.8385   1.4052
 MYB  H171  H  HCH2  0   0.220   3.2598  -2.3678   0.4076
 MYB  H172  H  HCH2  0   0.220   2.9978  -1.6425  -1.1632
 MYB  H181  H  HCH2  0   0.262   3.7238   0.5910  -0.2428
 MYB  H182  H  HCH2  0   0.261   3.9875  -0.1302   1.3128
 MYB  H201  H  HCH2  0   0.262   6.1165   1.3183  -0.3165
 MYB  H202  H  HCH2  0   0.261   6.3579   0.6159   1.2510
 MYB  H211  H  HCH2  0   0.220   8.1850  -0.8567   0.3147
 MYB  H212  H  HCH2  0   0.220   7.9448  -0.1382  -1.2630
 MYB  H221  H  HCH2  0   0.210   8.5201   2.1108  -0.3255
 MYB  H222  H  HCH2  0   0.210   8.7628   1.3915   1.2513
 MYB  H231  H  HCH2  0   0.207  10.5962  -0.0371   0.3219
 MYB  H232  H  HCH2  0   0.207  10.3512   0.6740  -1.2583
 MYB  H241  H  HCH2  0   0.210  10.9274   2.9259  -0.3338
 MYB  H242  H  HCH2  0   0.210  11.1704   2.2170   1.2457
 MYB  H251  H  HCH3  0   0.216  13.0359   0.7999   0.3361
 MYB  H252  H  HCH3  0   0.216  12.7934   1.5051  -1.2587
 MYB  H253  H  HCH3  0   0.226  13.3558   2.5110   0.0736
 MYB  C10   C  CH2   0  -0.528  -5.6795  -1.6369   0.1896

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
 MYB  N2   C6    single  1.456  0.020  1.456
 MYB  C7   C6    single  1.522  0.020  1.522
 MYB  C7   O4    single  1.408  0.020  1.408
 MYB  C6   C8    single  1.544  0.020  1.544
 MYB  C13  C14   single  1.529  0.020  1.529
 MYB  C13  C12   single  1.496  0.020  1.496
 MYB  C8   OAJ   single  1.417  0.020  1.417
 MYB  C8   CBN   single  1.534  0.020  1.534
 MYB  C12  C11   double  1.330  0.020  1.330
 MYB  C11  C10   single  1.497  0.020  1.497
 MYB  C10  CBN   single  1.532  0.020  1.532
 MYB  O5   CBN   single  1.415  0.020  1.415
 MYB  C14  C15   single  1.523  0.020  1.523
 MYB  C15  C16   single  1.523  0.020  1.523
 MYB  C16  C17   single  1.524  0.020  1.524
 MYB  C17  C18   single  1.520  0.020  1.520
 MYB  C18  C19   single  1.509  0.020  1.509
 MYB  C19  C20   single  1.509  0.020  1.509
 MYB  C19  O19   double  1.211  0.020  1.211
 MYB  C20  C21   single  1.519  0.020  1.519
 MYB  C21  C22   single  1.524  0.020  1.524
 MYB  C22  C23   single  1.523  0.020  1.523
 MYB  C23  C24   single  1.524  0.020  1.524
 MYB  C24  C25   single  1.522  0.020  1.522
 MYB  N2   HN1   single  0.890  0.020  1.040
 MYB  N2   HN2   single  0.890  0.020  1.040
 MYB  C6   H6    single  0.970  0.020  1.090
 MYB  C7   H71C  single  0.970  0.020  1.090
 MYB  C7   H72C  single  0.970  0.020  1.090
 MYB  O4   H4    single  0.850  0.020  0.980
 MYB  C8   H8    single  0.970  0.020  1.090
 MYB  C13  H131  single  0.970  0.020  1.090
 MYB  C13  H132  single  0.970  0.020  1.090
 MYB  C14  H141  single  0.970  0.020  1.090
 MYB  C14  H142  single  0.970  0.020  1.090
 MYB  C12  H12   single  0.930  0.020  1.080
 MYB  OAJ  HAJ   single  0.850  0.020  0.980
 MYB  CBN  HBN   single  0.970  0.020  1.090
 MYB  C11  H11   single  0.930  0.020  1.080
 MYB  C10  H101  single  0.970  0.020  1.090
 MYB  C10  H102  single  0.970  0.020  1.090
 MYB  O5   H5    single  0.850  0.020  0.980
 MYB  C15  H151  single  0.970  0.020  1.090
 MYB  C15  H152  single  0.970  0.020  1.090
 MYB  C16  H161  single  0.970  0.020  1.090
 MYB  C16  H162  single  0.970  0.020  1.090
 MYB  C17  H171  single  0.970  0.020  1.090
 MYB  C17  H172  single  0.970  0.020  1.090
 MYB  C18  H181  single  0.970  0.020  1.090
 MYB  C18  H182  single  0.970  0.020  1.090
 MYB  C20  H201  single  0.970  0.020  1.090
 MYB  C20  H202  single  0.970  0.020  1.090
 MYB  C21  H211  single  0.970  0.020  1.090
 MYB  C21  H212  single  0.970  0.020  1.090
 MYB  C22  H221  single  0.970  0.020  1.090
 MYB  C22  H222  single  0.970  0.020  1.090
 MYB  C23  H231  single  0.970  0.020  1.090
 MYB  C23  H232  single  0.970  0.020  1.090
 MYB  C24  H241  single  0.970  0.020  1.090
 MYB  C24  H242  single  0.970  0.020  1.090
 MYB  C25  H251  single  0.970  0.020  1.090
 MYB  C25  H252  single  0.970  0.020  1.090
 MYB  C25  H253  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
 MYB  HN2   N2   HN1   105.44  3.000
 MYB  HN2   N2   C6    109.38  3.000
 MYB  HN1   N2   C6    109.29  3.000
 MYB  H72C  C7   H71C  106.65  3.000
 MYB  H72C  C7   O4    110.77  3.000
 MYB  H71C  C7   O4    111.47  3.000
 MYB  H72C  C7   C6    109.60  3.000
 MYB  H71C  C7   C6    108.81  3.000
 MYB  O4    C7   C6    109.49  3.000
 MYB  H6    C6   C8    107.79  3.000
 MYB  H6    C6   C7    107.89  3.000
 MYB  C8    C6   C7    111.44  3.000
 MYB  H6    C6   N2    107.41  3.000
 MYB  C8    C6   N2    112.68  3.000
 MYB  C7    C6   N2    109.42  3.000
 MYB  H132  C13  H131  106.55  3.000
 MYB  H132  C13  C12   109.70  3.000
 MYB  H131  C13  C12   109.95  3.000
 MYB  H132  C13  C14   108.72  3.000
 MYB  H131  C13  C14   109.60  3.000
 MYB  C12   C13  C14   112.16  3.000
 MYB  H8    C8   CBN   107.00  3.000
 MYB  H8    C8   OAJ   105.42  3.000
 MYB  CBN   C8   OAJ   111.26  3.000
 MYB  H8    C8   C6    107.75  3.000
 MYB  CBN   C8   C6    114.80  3.000
 MYB  OAJ   C8   C6    110.08  3.000
 MYB  H142  C14  H141  106.13  3.000
 MYB  H142  C14  C15   109.46  3.000
 MYB  H141  C14  C15   109.63  3.000
 MYB  H142  C14  C13   109.32  3.000
 MYB  H141  C14  C13   108.93  3.000
 MYB  C15   C14  C13   113.12  3.000
 MYB  H12   C12  C11   118.89  3.000
 MYB  H12   C12  C13   116.04  3.000
 MYB  C11   C12  C13   125.04  3.000
 MYB  H11   C11  C10   116.75  3.000
 MYB  H11   C11  C12   118.62  3.000
 MYB  C10   C11  C12   124.63  3.000
 MYB  H5    O5   CBN   108.99  3.000
 MYB  H4    O4   C7    107.61  3.000
 MYB  HAJ   OAJ  C8    108.75  3.000
 MYB  HBN   CBN  O5    105.68  3.000
 MYB  HBN   CBN  C10   107.02  3.000
 MYB  O5    CBN  C10   111.85  3.000
 MYB  HBN   CBN  C8    107.94  3.000
 MYB  O5    CBN  C8    111.94  3.000
 MYB  C10   CBN  C8    112.00  3.000
 MYB  H152  C15  H151  106.07  3.000
 MYB  H152  C15  C16   109.25  3.000
 MYB  H151  C15  C16   109.42  3.000
 MYB  H152  C15  C14   109.41  3.000
 MYB  H151  C15  C14   109.54  3.000
 MYB  C16   C15  C14   112.92  3.000
 MYB  H162  C16  H161  106.01  3.000
 MYB  H162  C16  C17   109.50  3.000
 MYB  H161  C16  C17   109.55  3.000
 MYB  H162  C16  C15   109.32  3.000
 MYB  H161  C16  C15   109.18  3.000
 MYB  C17   C16  C15   113.05  3.000
 MYB  H172  C17  H171  106.28  3.000
 MYB  H172  C17  C18   109.79  3.000
 MYB  H171  C17  C18   109.76  3.000
 MYB  H172  C17  C16   109.41  3.000
 MYB  H171  C17  C16   109.45  3.000
 MYB  C18   C17  C16   111.99  3.000
 MYB  H182  C18  H181  104.61  3.000
 MYB  H182  C18  C19   107.62  3.000
 MYB  H181  C18  C19   107.75  3.000
 MYB  H182  C18  C17   110.54  3.000
 MYB  H181  C18  C17   110.46  3.000
 MYB  C19   C18  C17   115.26  3.000
 MYB  O19   C19  C20   122.23  3.000
 MYB  O19   C19  C18   122.18  3.000
 MYB  C20   C19  C18   115.59  3.000
 MYB  H202  C20  H201  104.59  3.000
 MYB  H202  C20  C21   110.60  3.000
 MYB  H201  C20  C21   110.59  3.000
 MYB  H202  C20  C19   107.68  3.000
 MYB  H201  C20  C19   107.40  3.000
 MYB  C21   C20  C19   115.37  3.000
 MYB  H212  C21  H211  106.28  3.000
 MYB  H212  C21  C22   109.34  3.000
 MYB  H211  C21  C22   109.33  3.000
 MYB  H212  C21  C20   109.90  3.000
 MYB  H211  C21  C20   109.89  3.000
 MYB  C22   C21  C20   111.94  3.000
 MYB  H222  C22  H221  106.00  3.000
 MYB  H222  C22  C23   109.35  3.000
 MYB  H221  C22  C23   109.41  3.000
 MYB  H222  C22  C21   109.42  3.000
 MYB  H221  C22  C21   109.36  3.000
 MYB  C23   C22  C21   113.07  3.000
 MYB  H232  C23  H231  105.98  3.000
 MYB  H232  C23  C24   109.26  3.000
 MYB  H231  C23  C24   109.23  3.000
 MYB  H232  C23  C22   109.41  3.000
 MYB  H231  C23  C22   109.45  3.000
 MYB  C24   C23  C22   113.25  3.000
 MYB  H242  C24  H241  106.01  3.000
 MYB  H242  C24  C25   109.56  3.000
 MYB  H241  C24  C25   109.70  3.000
 MYB  H242  C24  C23   109.26  3.000
 MYB  H241  C24  C23   109.23  3.000
 MYB  C25   C24  C23   112.86  3.000
 MYB  H253  C25  H252  107.65  3.000
 MYB  H253  C25  H251  107.54  3.000
 MYB  H252  C25  H251  107.49  3.000
 MYB  H253  C25  C24   111.63  3.000
 MYB  H252  C25  C24   111.23  3.000
 MYB  H251  C25  C24   111.10  3.000
 MYB  H102  C10  H101  106.42  3.000
 MYB  H102  C10  CBN   108.65  3.000
 MYB  H101  C10  CBN   109.34  3.000
 MYB  H102  C10  C11   109.86  3.000
 MYB  H101  C10  C11   110.06  3.000
 MYB  CBN   C10  C11   112.32  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
 MYB  Var_01  C10   C11  C12  C13  -178.00   0.0  2
 MYB  Var_02  C16   C15  C14  C13   178.65  30.0  3
 MYB  Var_03  C11   C12  C13  C14   114.44  30.0  3
 MYB  Var_04  C17   C16  C15  C14   179.94  30.0  3
 MYB  Var_05  C15   C14  C13  C12   177.97  30.0  3
 MYB  Var_06  CBN   C10  C11  C12   113.83  30.0  3
 MYB  Var_07  C18   C17  C16  C15   179.24  30.0  3
 MYB  Var_08  C19   C18  C17  C16  -179.89  30.0  3
 MYB  Var_09  C20   C19  C18  C17  -179.90  30.0  3
 MYB  Var_10  C21   C20  C19  C18   179.06  30.0  3
 MYB  Var_11  C22   C21  C20  C19  -179.81  30.0  3
 MYB  Var_12  C23   C22  C21  C20  -179.95  30.0  3
 MYB  Var_13  C24   C23  C22  C21   179.69  30.0  3
 MYB  Var_14  C25   C24  C23  C22   179.86  30.0  3
 MYB  Var_15  H251  C25  C24  C23   -60.13  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
 MYB  chir_01  C6   N2   C7  C8   negativ
 MYB  chir_02  C8   OAJ  C6  CBN  positiv
 MYB  chir_03  CBN  O5   C8  C10  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
 MYB  plan-1  C18  0.020
 MYB  plan-1  C19  0.020
 MYB  plan-1  C20  0.020
 MYB  plan-1  O19  0.020
 MYB  plan-2  C13  0.020
 MYB  plan-2  C12  0.020
 MYB  plan-2  C11  0.020
 MYB  plan-2  H12  0.020
 MYB  plan-2  H11  0.020
 MYB  plan-2  C10  0.020

