# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:26:04 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: N~2~-{[(4-bromobenzyl)oxy]carbonyl}-N-[(1S)-1-formylpentyl]-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCC[C@H](NC(=O)[C@H](CC(C)C)NC(=O)OCc1ccc(Br)cc1)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
 MYE  MYE  N~2~-{[(4-bromobenzyl)oxy]carbonyl}-N-[(1S)-1-formylpentyl]-L-leucinamide  ligand  56  27  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_MYE
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
 MYE  C2    C   CH2   0  -0.419  -1.0694  -6.3687   5.9120
 MYE  C3    C   CH2   0  -0.421  -1.5066  -4.9396   5.6123
 MYE  C4    C   CH2   0  -0.418  -1.7489  -4.1220   6.8744
 MYE  C5    C   CH1   0  -0.214  -2.1783  -2.6905   6.5771
 MYE  N6    N   NH1   0  -0.642  -1.1936  -1.9484   5.8229
 MYE  C7    C   C     0   0.573  -1.3601  -1.5613   4.5437
 MYE  O8    O   O     0  -0.478  -2.3760  -1.7519   3.8993
 MYE  C9    C   CH1   0  -0.215  -0.1746  -0.7888   3.9603
 MYE  C10   C   CH2   0  -0.457  -0.4081   0.7089   4.1838
 MYE  C11   C   CH1   0  -0.226   0.7967   1.6358   3.9657
 MYE  C12   C   CH3   0  -0.665   1.2261   1.7898   2.5092
 MYE  C13   C   CH3   0  -0.668   1.9835   1.2565   4.8485
 MYE  N14   N   NH1   0  -0.653  -0.0187  -1.0846   2.5608
 MYE  C15   C   C     0   0.771   0.3226  -2.3280   2.1716
 MYE  O16   O   O     0  -0.507   0.6507  -3.2187   2.9280
 MYE  O17   O   O2    0  -0.478   0.2854  -2.4495   0.8420
 MYE  C18   C   CH2   0  -0.238   0.6370  -3.7300   0.3043
 MYE  C19   C   CR6   0   0.079   0.5183  -3.6284  -1.1849
 MYE  C20   C   CR16  0  -0.292  -0.5925  -4.1305  -1.8504
 MYE  C21   C   CR16  0  -0.213  -0.7080  -4.0306  -3.2303
 MYE  C22   C   CR6   0  -0.118   0.3062  -3.4128  -3.9451
 MYE  BR2   BR  BR    0  -0.043   0.1722  -3.2820  -5.8240
 MYE  C24   C   CR16  0  -0.215   1.4280  -2.9032  -3.3062
 MYE  C25   C   CR16  0  -0.278   1.5222  -3.0130  -1.9275
 MYE  C26   C   C1    0   0.193  -2.5407  -1.8830   7.8041
 MYE  O27   O   O     0  -0.367  -2.7330  -2.3455   8.8976
 MYE  C1    C   CH3   0  -0.660  -0.8391  -7.1820   4.6458
 MYE  H21A  H   HCH2  0   0.212  -0.1497  -6.3498   6.5060
 MYE  H22   H   HCH2  0   0.212  -1.8224  -6.8617   6.5342
 MYE  H31   H   HCH2  0   0.230  -0.7472  -4.4566   4.9911
 MYE  H32   H   HCH2  0   0.211  -2.4229  -4.9587   5.0125
 MYE  H41   H   HCH2  0   0.228  -0.8442  -4.1105   7.4911
 MYE  H42   H   HCH2  0   0.237  -2.5258  -4.6007   7.4755
 MYE  H5    H   HCH1  0   0.294  -3.0903  -2.7072   5.9668
 MYE  HN6   H   HNH1  0   0.404  -0.2819  -1.8328   6.2391
 MYE  H9    H   HCH1  0   0.273   0.7365  -1.0923   4.4828
 MYE  H101  H   HCH2  0   0.255  -0.7342   0.8375   5.2192
 MYE  H102  H   HCH2  0   0.250  -1.2459   1.0298   3.5561
 MYE  H11   H   HCH1  0   0.233   0.4535   2.6225   4.2945
 MYE  H121  H   HCH3  0   0.230   1.9519   2.5995   2.4139
 MYE  H122  H   HCH3  0   0.224   0.3790   2.0365   1.8656
 MYE  H123  H   HCH3  0   0.222   1.6943   0.8858   2.1193
 MYE  H131  H   HCH3  0   0.219   2.4450   0.3190   4.5309
 MYE  H132  H   HCH3  0   0.235   2.7564   2.0246   4.8034
 MYE  H133  H   HCH3  0   0.228   1.6872   1.1441   5.8933
 MYE  H14   H   HNH1  0   0.402  -0.4375  -0.4608   1.8882
 MYE  H181  H   HCH2  0   0.253  -0.0304  -4.5013   0.6928
 MYE  H182  H   HCH2  0   0.252   1.6587  -3.9911   0.5879
 MYE  H20   H   HCR6  0   0.269  -1.3860  -4.6110  -1.2913
 MYE  H21   H   HCR6  0   0.283  -1.5804  -4.4314  -3.7276
 MYE  H24   H   HCR6  0   0.282   2.2260  -2.4333  -3.8650
 MYE  H25   H   HCR6  0   0.268   2.4004  -2.6190  -1.4307
 MYE  H26   H   H     0   0.208  -2.6339  -0.7979   7.6108
 MYE  H11A  H   HCH3  0   0.216  -1.7512  -7.2437   4.0480
 MYE  H12   H   HCH3  0   0.215  -0.0676  -6.7287   4.0205
 MYE  H13   H   HCH3  0   0.226  -0.5221  -8.2002   4.8741

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
 MYE  C2   C3    single    1.524  0.020  1.524
 MYE  C2   C1    single    1.522  0.020  1.522
 MYE  C2   H21A  single    0.970  0.020  1.090
 MYE  C2   H22   single    0.970  0.020  1.090
 MYE  C3   C4    single    1.523  0.020  1.523
 MYE  C3   H31   single    0.970  0.020  1.090
 MYE  C3   H32   single    0.970  0.020  1.090
 MYE  C4   C5    single    1.524  0.020  1.524
 MYE  C4   H41   single    0.970  0.020  1.090
 MYE  C4   H42   single    0.970  0.020  1.090
 MYE  C5   N6    single    1.445  0.020  1.445
 MYE  C5   C26   single    1.513  0.020  1.513
 MYE  C5   H5    single    0.970  0.020  1.090
 MYE  N6   C7    single    1.347  0.020  1.347
 MYE  N6   HN6   single    0.860  0.020  1.020
 MYE  C7   O8    double    1.218  0.020  1.218
 MYE  C7   C9    single    1.531  0.020  1.531
 MYE  C9   C10   single    1.532  0.020  1.532
 MYE  C9   N14   single    1.439  0.020  1.439
 MYE  C9   H9    single    0.970  0.020  1.090
 MYE  C10  C11   single    1.536  0.020  1.536
 MYE  C10  H101  single    0.970  0.020  1.090
 MYE  C10  H102  single    0.970  0.020  1.090
 MYE  C11  C12   single    1.526  0.020  1.526
 MYE  C11  C13   single    1.527  0.020  1.527
 MYE  C11  H11   single    0.970  0.020  1.090
 MYE  C12  H121  single    0.970  0.020  1.090
 MYE  C12  H122  single    0.970  0.020  1.090
 MYE  C12  H123  single    0.970  0.020  1.090
 MYE  C13  H131  single    0.970  0.020  1.090
 MYE  C13  H132  single    0.970  0.020  1.090
 MYE  C13  H133  single    0.970  0.020  1.090
 MYE  N14  C15   single    1.347  0.020  1.347
 MYE  N14  H14   single    0.860  0.020  1.020
 MYE  C15  O16   double    1.214  0.020  1.214
 MYE  C15  O17   single    1.336  0.020  1.336
 MYE  O17  C18   single    1.433  0.020  1.433
 MYE  C18  C19   single    1.497  0.020  1.497
 MYE  C18  H181  single    0.970  0.020  1.090
 MYE  C18  H182  single    0.970  0.020  1.090
 MYE  C19  C20   aromatic  1.389  0.020  1.389
 MYE  C19  C25   aromatic  1.392  0.020  1.392
 MYE  C20  C21   aromatic  1.388  0.020  1.388
 MYE  C20  H20   single    0.930  0.020  1.080
 MYE  C21  C22   aromatic  1.386  0.020  1.386
 MYE  C21  H21   single    0.930  0.020  1.080
 MYE  C22  BR2   single    1.888  0.020  1.888
 MYE  C22  C24   aromatic  1.388  0.020  1.388
 MYE  C24  C25   aromatic  1.386  0.020  1.386
 MYE  C24  H24   single    0.930  0.020  1.080
 MYE  C25  H25   single    0.930  0.020  1.080
 MYE  C26  O27   double    1.203  0.020  1.203
 MYE  C26  H26   single    0.930  0.020  1.080
 MYE  C1   H11A  single    0.970  0.020  1.090
 MYE  C1   H12   single    0.970  0.020  1.090
 MYE  C1   H13   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
 MYE  H22   C2   H21A  106.10  3.000
 MYE  H22   C2   C1    109.65  3.000
 MYE  H21A  C2   C1    109.47  3.000
 MYE  H22   C2   C3    109.69  3.000
 MYE  H21A  C2   C3    109.36  3.000
 MYE  C1    C2   C3    112.38  3.000
 MYE  H32   C3   H31   106.12  3.000
 MYE  H32   C3   C4    109.27  3.000
 MYE  H31   C3   C4    110.12  3.000
 MYE  H32   C3   C2    109.34  3.000
 MYE  H31   C3   C2    109.06  3.000
 MYE  C4    C3   C2    112.70  3.000
 MYE  H42   C4   H41   106.39  3.000
 MYE  H42   C4   C5    108.57  3.000
 MYE  H41   C4   C5    109.44  3.000
 MYE  H42   C4   C3    109.50  3.000
 MYE  H41   C4   C3    109.93  3.000
 MYE  C5    C4   C3    112.79  3.000
 MYE  H5    C5   C26   105.07  3.000
 MYE  H5    C5   N6    106.49  3.000
 MYE  C26   C5   N6    108.20  3.000
 MYE  H5    C5   C4    109.17  3.000
 MYE  C26   C5   C4    114.24  3.000
 MYE  N6    C5   C4    113.09  3.000
 MYE  HN6   N6   C7    118.08  3.000
 MYE  HN6   N6   C5    117.33  3.000
 MYE  C7    N6   C5    123.98  3.000
 MYE  C9    C7   O8    121.56  3.000
 MYE  C9    C7   N6    114.28  3.000
 MYE  O8    C7   N6    124.10  3.000
 MYE  H9    C9   N14   108.50  3.000
 MYE  H9    C9   C10   109.19  3.000
 MYE  N14   C9   C10   111.06  3.000
 MYE  H9    C9   C7    108.86  3.000
 MYE  N14   C9   C7    110.54  3.000
 MYE  C10   C9   C7    108.65  3.000
 MYE  H102  C10  H101  106.27  3.000
 MYE  H102  C10  C11   110.00  3.000
 MYE  H101  C10  C11   107.31  3.000
 MYE  H102  C10  C9    108.63  3.000
 MYE  H101  C10  C9    107.37  3.000
 MYE  C11   C10  C9    116.73  3.000
 MYE  H11   C11  C13   107.09  3.000
 MYE  H11   C11  C12   106.48  3.000
 MYE  C13   C11  C12   110.99  3.000
 MYE  H11   C11  C10   104.79  3.000
 MYE  C13   C11  C10   112.19  3.000
 MYE  C12   C11  C10   114.66  3.000
 MYE  H123  C12  H122  108.04  3.000
 MYE  H123  C12  H121  107.36  3.000
 MYE  H122  C12  H121  107.27  3.000
 MYE  H123  C12  C11   112.24  3.000
 MYE  H122  C12  C11   111.53  3.000
 MYE  H121  C12  C11   110.19  3.000
 MYE  H133  C13  H132  107.72  3.000
 MYE  H133  C13  H131  107.73  3.000
 MYE  H132  C13  H131  107.04  3.000
 MYE  H133  C13  C11   111.59  3.000
 MYE  H132  C13  C11   110.61  3.000
 MYE  H131  C13  C11   111.94  3.000
 MYE  H14   N14  C15   118.92  3.000
 MYE  H14   N14  C9    118.46  3.000
 MYE  C15   N14  C9    119.89  3.000
 MYE  O17   C15  O16   124.14  3.000
 MYE  O17   C15  N14   111.38  3.000
 MYE  O16   C15  N14   124.46  3.000
 MYE  C18   O17  C15   116.62  3.000
 MYE  H182  C18  H181  108.10  3.000
 MYE  H182  C18  C19   110.40  3.000
 MYE  H181  C18  C19   110.70  3.000
 MYE  H182  C18  O17   110.24  3.000
 MYE  H181  C18  O17   110.36  3.000
 MYE  C19   C18  O17   107.05  3.000
 MYE  C25   C19  C20   118.75  3.000
 MYE  C25   C19  C18   120.22  3.000
 MYE  C20   C19  C18   121.03  3.000
 MYE  H20   C20  C21   118.95  3.000
 MYE  H20   C20  C19   119.93  3.000
 MYE  C21   C20  C19   121.12  3.000
 MYE  H21   C21  C22   121.22  3.000
 MYE  H21   C21  C20   119.84  3.000
 MYE  C22   C21  C20   118.93  3.000
 MYE  C24   C22  BR2   119.34  3.000
 MYE  C24   C22  C21   121.17  3.000
 MYE  BR2   C22  C21   119.48  3.000
 MYE  H24   C24  C25   119.88  3.000
 MYE  H24   C24  C22   121.19  3.000
 MYE  C25   C24  C22   118.93  3.000
 MYE  H25   C25  C24   118.85  3.000
 MYE  H25   C25  C19   120.05  3.000
 MYE  C24   C25  C19   121.10  3.000
 MYE  H26   C26  O27   121.51  3.000
 MYE  H26   C26  C5    113.70  3.000
 MYE  O27   C26  C5    124.78  3.000
 MYE  H13   C1   H12   107.59  3.000
 MYE  H13   C1   H11A  107.73  3.000
 MYE  H12   C1   H11A  107.46  3.000
 MYE  H13   C1   C2    111.63  3.000
 MYE  H12   C1   C2    111.19  3.000
 MYE  H11A  C1   C2    111.04  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
 MYE  CONST_01  C22   C21  C20  C19     0.00   0.0  0
 MYE  CONST_02  C22   C24  C25  C19     0.00   0.0  0
 MYE  CONST_03  C24   C25  C19  C20     0.00   0.0  0
 MYE  CONST_04  C24   C22  C21  C20     0.00   0.0  0
 MYE  CONST_05  C25   C19  C20  C21     0.00   0.0  0
 MYE  CONST_06  C25   C24  C22  C21     0.00   0.0  0
 MYE  CONST_07  C21   C20  C19  C18   180.00   0.0  0
 MYE  CONST_08  C24   C25  C19  C18   180.00   0.0  0
 MYE  CONST_09  BR2   C22  C21  C20   180.00   0.0  0
 MYE  CONST_10  C25   C24  C22  BR2   180.00   0.0  0
 MYE  CONST_11  H21   C21  C20  C19   180.00   0.0  0
 MYE  CONST_12  H24   C24  C25  C19   180.00   0.0  0
 MYE  CONST_13  H25   C25  C19  C20   180.00   0.0  0
 MYE  CONST_14  H20   C20  C21  C22   180.00   0.0  0
 MYE  CONST_15  O8    C7   N6   C5      0.00   0.0  0
 MYE  CONST_16  C9    C7   N6   C5    180.00   0.0  0
 MYE  CONST_17  HN6   N6   C7   O8    180.00   0.0  0
 MYE  Var_01    C20   C19  C18  O17  -100.95  30.0  2
 MYE  Var_02    C19   C18  O17  C15   179.76  30.0  3
 MYE  Var_03    C5    C4   C3   C2    179.67  30.0  3
 MYE  Var_04    C1    C2   C3   C4    179.59  30.0  1
 MYE  Var_05    C12   C11  C10  C9     70.50  30.0  3
 MYE  Var_06    O16   C15  N14  C9     -7.94  30.0  2
 MYE  Var_07    H11A  C1   C2   C3    -60.05  30.0  3
 MYE  Var_08    H121  C12  C11  C10   169.17  30.0  3
 MYE  Var_09    H131  C13  C11  C10    70.52  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
 MYE  chir_01  C5  C4   N6  C26  positiv
 MYE  chir_02  C9  N14  C7  C10  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
 MYE  plan-1  C18  0.020
 MYE  plan-1  C19  0.020
 MYE  plan-1  C20  0.020
 MYE  plan-1  C21  0.020
 MYE  plan-1  C22  0.020
 MYE  plan-1  BR2  0.020
 MYE  plan-1  C24  0.020
 MYE  plan-1  C25  0.020
 MYE  plan-1  H20  0.020
 MYE  plan-1  H21  0.020
 MYE  plan-1  H24  0.020
 MYE  plan-1  H25  0.020
 MYE  plan-2  C5   0.020
 MYE  plan-2  N6   0.020
 MYE  plan-2  C7   0.020
 MYE  plan-2  O8   0.020
 MYE  plan-2  C9   0.020
 MYE  plan-2  HN6  0.020
 MYE  plan-3  N14  0.020
 MYE  plan-3  C15  0.020
 MYE  plan-3  O16  0.020
 MYE  plan-3  O17  0.020
 MYE  plan-4  C5   0.020
 MYE  plan-4  C26  0.020
 MYE  plan-4  O27  0.020
 MYE  plan-4  H26  0.020

