# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 21:30:48 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: methyl (2~{S})-2-azanyl-3-methyl-3-[(2-methylpropan-2-yl)oxycarbonylamino]butanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](N)C(C)(C)NC(=O)OC(C)(C)C
#
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
 A5U  A5U  'methyl (2~{S})-2-azanyl-3-methyl-3-[(2-methylpropan-2-yl)oxycarbonylamino]butanoate'  ligand  39  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A5U
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
 A5U  C10  C  CH3   0  -0.665  -1.3347   1.6688   1.4777
 A5U  C11  C  CT    0   0.194   3.4390  -0.4985   0.0510
 A5U  C12  C  C     0   0.591  -2.5876  -0.7716   0.0678
 A5U  C13  C  C     0   0.768   1.2441   0.5680   0.2479
 A5U  C14  C  CH3   0  -0.671   4.1914   0.7009  -0.5132
 A5U  C15  C  CH3   0  -0.660   3.8575  -1.7640  -0.6887
 A5U  C16  C  CH3   0  -0.673   3.6839  -0.6783   1.5451
 A5U  C17  C  CH3   0  -0.426  -2.1344  -3.0772  -0.1387
 A5U  C7   C  CT    0   0.119  -1.1312   1.3210   0.0031
 A5U  C8   C  CH1   0  -0.222  -2.3917   0.6023  -0.5714
 A5U  C9   C  CH3   0  -0.640  -0.8907   2.5955  -0.8073
 A5U  N5   N  NH1   0  -0.690  -0.0266   0.3775  -0.1766
 A5U  N6   N  NH2   0  -0.778  -3.5631   1.4357  -0.4431
 A5U  O1   O  O2    0  -0.507   2.0206  -0.4033  -0.2411
 A5U  O3   O  O     0  -0.446  -3.1834  -0.9580   1.0996
 A5U  O4   O  O     0  -0.511   1.6211   1.4647   0.9732
 A5U  H1   H  HCH3  0   0.235  -1.3786   0.7805   2.1062
 A5U  H2   H  HCH3  0   0.250  -0.5277   2.2977   1.8422
 A5U  H3   H  HCH3  0   0.229  -2.2592   2.2314   1.6035
 A5U  H4   H  HCH3  0   0.245   3.9228   1.6313  -0.0180
 A5U  H5   H  HCH3  0   0.233   5.2632   0.5498  -0.3790
 A5U  H6   H  HCH3  0   0.233   4.0054   0.8083  -1.5832
 A5U  H7   H  HCH3  0   0.237   3.6531  -1.6862  -1.7575
 A5U  H8   H  HCH3  0   0.230   4.9281  -1.9263  -0.5644
 A5U  H9   H  HCH3  0   0.237   3.3382  -2.6414  -0.2998
 A5U  H10  H  HCH3  0   0.234   3.0754  -1.4932   1.9410
 A5U  H11  H  HCH3  0   0.234   4.7298  -0.9430   1.7050
 A5U  H12  H  HCH3  0   0.246   3.4751   0.2225   2.1168
 A5U  H13  H  HCH3  0   0.241  -1.6354  -3.1608   0.8263
 A5U  H14  H  HCH3  0   0.242  -3.1707  -3.3987  -0.0389
 A5U  H15  H  HCH3  0   0.254  -1.6291  -3.7083  -0.8632
 A5U  H16  H  HCH1  0   0.279  -2.2104   0.4515  -1.6398
 A5U  H17  H  HCH3  0   0.236  -1.7267   3.2830  -0.6992
 A5U  H18  H  HCH3  0   0.237   0.0129   3.0973  -0.4624
 A5U  H19  H  HCH3  0   0.226  -0.7703   2.3676  -1.8680
 A5U  H20  H  HNH1  0   0.392  -0.1310  -0.3094  -0.9077
 A5U  H21  H  HNH2  0   0.364  -4.2894   1.1006  -1.0622
 A5U  H22  H  HNH2  0   0.352  -3.9406   1.3803   0.4941
 A5U  O2   O  O2    0  -0.452  -2.0516  -1.7460  -0.6530

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
 A5U  C17  O2   single  1.430  0.020  1.430
 A5U  C9   C7   single  1.529  0.020  1.529
 A5U  O2   C12  single  1.325  0.020  1.325
 A5U  O4   C13  double  1.213  0.020  1.213
 A5U  C15  C11  single  1.524  0.020  1.524
 A5U  C13  N5   single  1.353  0.020  1.353
 A5U  C13  O1   single  1.336  0.020  1.336
 A5U  N5   C7   single  1.464  0.020  1.464
 A5U  C7   C8   single  1.561  0.020  1.561
 A5U  C7   C10  single  1.529  0.020  1.529
 A5U  C12  C8   single  1.528  0.020  1.528
 A5U  C12  O3   double  1.206  0.020  1.206
 A5U  C8   N6   single  1.443  0.020  1.443
 A5U  C14  C11  single  1.524  0.020  1.524
 A5U  C11  O1   single  1.451  0.020  1.451
 A5U  C11  C16  single  1.525  0.020  1.525
 A5U  C10  H1   single  0.970  0.020  1.090
 A5U  C10  H2   single  0.970  0.020  1.090
 A5U  C10  H3   single  0.970  0.020  1.090
 A5U  C14  H4   single  0.970  0.020  1.090
 A5U  C14  H5   single  0.970  0.020  1.090
 A5U  C14  H6   single  0.970  0.020  1.090
 A5U  C15  H7   single  0.970  0.020  1.090
 A5U  C15  H8   single  0.970  0.020  1.090
 A5U  C15  H9   single  0.970  0.020  1.090
 A5U  C16  H10  single  0.970  0.020  1.090
 A5U  C16  H11  single  0.970  0.020  1.090
 A5U  C16  H12  single  0.970  0.020  1.090
 A5U  C17  H13  single  0.970  0.020  1.090
 A5U  C17  H14  single  0.970  0.020  1.090
 A5U  C17  H15  single  0.970  0.020  1.090
 A5U  C8   H16  single  0.970  0.020  1.090
 A5U  C9   H17  single  0.970  0.020  1.090
 A5U  C9   H18  single  0.970  0.020  1.090
 A5U  C9   H19  single  0.970  0.020  1.090
 A5U  N5   H20  single  0.890  0.020  1.040
 A5U  N6   H21  single  0.890  0.020  1.040
 A5U  N6   H22  single  0.890  0.020  1.040

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
 A5U  H3   C10  H2   107.02  3.000
 A5U  H3   C10  H1   108.68  3.000
 A5U  H2   C10  H1   107.97  3.000
 A5U  H3   C10  C7   109.99  3.000
 A5U  H2   C10  C7   110.89  3.000
 A5U  H1   C10  C7   112.12  3.000
 A5U  O1   C11  C16  111.22  3.000
 A5U  C16  C11  C15  109.48  3.000
 A5U  O1   C11  C15  103.01  3.000
 A5U  C16  C11  C14  112.10  3.000
 A5U  O1   C11  C14  110.88  3.000
 A5U  C15  C11  C14  109.76  3.000
 A5U  O3   C12  O2   123.47  3.000
 A5U  O3   C12  C8   124.07  3.000
 A5U  O2   C12  C8   112.44  3.000
 A5U  O4   C13  O1   125.12  3.000
 A5U  O1   C13  N5   109.18  3.000
 A5U  O4   C13  N5   125.69  3.000
 A5U  H6   C14  H5   107.56  3.000
 A5U  H6   C14  H4   108.67  3.000
 A5U  H5   C14  H4   107.77  3.000
 A5U  H6   C14  C11  110.87  3.000
 A5U  H5   C14  C11  109.30  3.000
 A5U  H4   C14  C11  112.50  3.000
 A5U  H9   C15  H8   107.88  3.000
 A5U  H9   C15  H7   108.50  3.000
 A5U  H8   C15  H7   107.84  3.000
 A5U  H9   C15  C11  111.34  3.000
 A5U  H8   C15  C11  109.75  3.000
 A5U  H7   C15  C11  111.40  3.000
 A5U  H12  C16  H11  107.95  3.000
 A5U  H12  C16  H10  108.71  3.000
 A5U  H11  C16  H10  107.47  3.000
 A5U  H12  C16  C11  112.75  3.000
 A5U  H11  C16  C11  109.05  3.000
 A5U  H10  C16  C11  110.73  3.000
 A5U  H15  C17  H14  109.41  3.000
 A5U  H15  C17  H13  109.47  3.000
 A5U  H14  C17  H13  109.39  3.000
 A5U  H15  C17  O2   105.91  3.000
 A5U  H14  C17  O2   111.27  3.000
 A5U  H13  C17  O2   111.32  3.000
 A5U  N5   C7   C9   110.70  3.000
 A5U  N5   C7   C8   105.52  3.000
 A5U  C9   C7   C8   108.41  3.000
 A5U  C8   C7   C10  110.63  3.000
 A5U  N5   C7   C10  111.44  3.000
 A5U  C9   C7   C10  110.03  3.000
 A5U  H16  C8   N6   107.51  3.000
 A5U  H16  C8   C7   106.80  3.000
 A5U  N6   C8   C7   110.91  3.000
 A5U  H16  C8   C12  107.81  3.000
 A5U  N6   C8   C12  112.21  3.000
 A5U  C7   C8   C12  111.32  3.000
 A5U  H19  C9   H18  108.19  3.000
 A5U  H19  C9   H17  108.26  3.000
 A5U  H18  C9   H17  108.35  3.000
 A5U  H19  C9   C7   110.99  3.000
 A5U  H18  C9   C7   110.28  3.000
 A5U  H17  C9   C7   110.69  3.000
 A5U  H20  N5   C7   116.74  3.000
 A5U  H20  N5   C13  114.87  3.000
 A5U  C7   N5   C13  125.40  3.000
 A5U  H22  N6   H21  106.31  3.000
 A5U  H22  N6   C8   110.70  3.000
 A5U  H21  N6   C8   109.70  3.000
 A5U  C13  O1   C11  122.82  3.000
 A5U  C17  O2   C12  117.74  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
 A5U  Var_01  C13  N5   C7   C10  -56.26  30.0  1
 A5U  Var_02  O4   C13  O1   C11    0.15  30.0  1
 A5U  Var_03  C15  C11  O1   C13  178.53  30.0  3
 A5U  Var_04  C8   C12  O2   C17  178.18  30.0  3
 A5U  Var_05  O4   C13  N5   C7     9.37  30.0  1
 A5U  Var_06  H17  C9   C7   C10  -58.22  30.0  3
 A5U  Var_07  H13  C17  O2   C12  -60.24  30.0  3
 A5U  Var_08  H7   C15  C11  C14  -59.13  30.0  3
 A5U  Var_09  H10  C16  C11  C14  175.57  30.0  3
 A5U  Var_10  H4   C14  C11  C15  179.79  30.0  3
 A5U  Var_11  H1   C10  C7   C8    67.74  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
 A5U  chir_01  C8  C7  C12  N6  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
 A5U  plan-1  C13  0.020
 A5U  plan-1  N5   0.020
 A5U  plan-1  O1   0.020
 A5U  plan-1  O4   0.020
 A5U  plan-2  C12  0.020
 A5U  plan-2  C8   0.020
 A5U  plan-2  O3   0.020
 A5U  plan-2  O2   0.020

