# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 11:42:04 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (3R,4S)-4-amino-5-cyclohexyl-2,2-difluoro-3-hydroxy-N-methylpentanamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)C(F)(F)[C@H](O)[C@@H](N)CC1CCCCC1
#
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
 MI0  MI0  '(3R,4S)-4-amino-5-cyclohexyl-2,2-difluoro-3-hydroxy-N-methylpentanamide (non-preferred name)'  peptide  40  18  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MI0
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
 MI0  F1   F  F     0  -0.345   2.2212  -1.4136   0.6246
 MI0  F2   F  F     0  -0.343   1.8101  -1.3591  -1.5129
 MI0  N1   N  NH2   0  -0.830  -0.2454  -0.2107   1.6940
 MI0  N2   N  NH1   0  -0.620   4.4465  -0.1058   0.1680
 MI0  O1   O  OH1   0  -0.675   1.5015   1.4058   0.7073
 MI0  O2   O  O     0  -0.488   3.6189   0.7218  -1.7643
 MI0  C1   C  CH1   0  -0.152  -0.3036  -0.1205   0.2389
 MI0  C2   C  CH2   0  -0.420  -1.4371   0.7972  -0.2186
 MI0  C3   C  CH1   0  -0.251  -2.8490   0.3780   0.1919
 MI0  C4   C  CH2   0  -0.422  -3.2131  -1.0307  -0.2768
 MI0  C5   C  CH2   0  -0.409  -3.8644   1.3905  -0.3406
 MI0  C6   C  CH2   0  -0.428  -4.6451  -1.4040   0.0976
 MI0  C7   C  CH2   0  -0.432  -5.2938   1.0230   0.0421
 MI0  C8   C  CH2   0  -0.429  -5.6486  -0.3836  -0.4278
 MI0  C9   C  CH1   0  -0.064   1.0488   0.4787  -0.2318
 MI0  C10  C  CT    0   0.698   2.1316  -0.5740  -0.4488
 MI0  C11  C  C     0   0.431   3.4913   0.0743  -0.7378
 MI0  C12  C  CH3   0  -0.516   5.7594   0.4800   0.0167
 MI0  H1   H  HNH2  0   0.373  -1.1337   0.0057   2.1225
 MI0  H2   H  HOH1  0   0.446   1.0812   1.0907   1.5391
 MI0  H3   H  HCH1  0   0.251  -0.4529  -1.1015  -0.2234
 MI0  H4   H  HCH2  0   0.232  -1.2462   1.8115   0.1490
 MI0  H5   H  HCH2  0   0.231  -1.3957   0.8546  -1.3108
 MI0  H6   H  HCH1  0   0.207  -2.9298   0.3973   1.2879
 MI0  H7   H  HCH2  0   0.207  -3.0966  -1.0842  -1.3665
 MI0  H8   H  HCH2  0   0.230  -2.5235  -1.7655   0.1469
 MI0  H9   H  HCH2  0   0.225  -3.6194   2.3893   0.0324
 MI0  H10  H  HCH2  0   0.206  -3.7789   1.4381  -1.4332
 MI0  H11  H  HCH2  0   0.226  -4.8819  -2.3996  -0.2855
 MI0  H12  H  HCH2  0   0.208  -4.7293  -1.4650   1.1884
 MI0  H13  H  HCH2  0   0.208  -5.3994   1.0772   1.1315
 MI0  H14  H  HCH2  0   0.225  -5.9937   1.7522  -0.3737
 MI0  H15  H  HCH2  0   0.207  -5.6521  -0.4107  -1.5232
 MI0  H16  H  HCH2  0   0.225  -6.6598  -0.6474  -0.1083
 MI0  H17  H  HCH1  0   0.258   0.9112   0.9754  -1.1986
 MI0  H18  H  HCH3  0   0.257   6.3751   0.1588   0.8511
 MI0  H19  H  HCH3  0   0.246   6.2343   0.1559  -0.9089
 MI0  H20  H  HCH3  0   0.245   5.7135   1.5693   0.0182
 MI0  H21  H  HNH1  0   0.415   4.2595  -0.6507   0.9924
 MI0  H22  H  HNH2  0   0.370   0.0188  -1.1345   2.0051

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
 MI0  F1   C10  single  1.366  0.020  1.366
 MI0  N1   C1   single  1.459  0.020  1.459
 MI0  N1   H1   single  0.890  0.020  1.040
 MI0  N2   C12  single  1.446  0.020  1.446
 MI0  N2   H21  single  0.860  0.020  1.020
 MI0  O1   C9   single  1.395  0.020  1.395
 MI0  O1   H2   single  0.850  0.020  0.980
 MI0  O2   C11  double  1.220  0.020  1.220
 MI0  C1   C9   single  1.552  0.020  1.552
 MI0  C1   C2   single  1.528  0.020  1.528
 MI0  C1   H3   single  0.970  0.020  1.090
 MI0  C2   H4   single  0.970  0.020  1.090
 MI0  C2   H5   single  0.970  0.020  1.090
 MI0  C3   C2   single  1.529  0.020  1.529
 MI0  C3   C4   single  1.529  0.020  1.529
 MI0  C3   C5   single  1.530  0.020  1.530
 MI0  C3   H6   single  0.970  0.020  1.090
 MI0  C4   H7   single  0.970  0.020  1.090
 MI0  C4   H8   single  0.970  0.020  1.090
 MI0  C5   H9   single  0.970  0.020  1.090
 MI0  C5   H10  single  0.970  0.020  1.090
 MI0  C6   C4   single  1.526  0.020  1.526
 MI0  C6   C8   single  1.525  0.020  1.525
 MI0  C6   H11  single  0.970  0.020  1.090
 MI0  C6   H12  single  0.970  0.020  1.090
 MI0  C7   C5   single  1.525  0.020  1.525
 MI0  C7   C8   single  1.525  0.020  1.525
 MI0  C7   H13  single  0.970  0.020  1.090
 MI0  C7   H14  single  0.970  0.020  1.090
 MI0  C8   H15  single  0.970  0.020  1.090
 MI0  C8   H16  single  0.970  0.020  1.090
 MI0  C9   H17  single  0.970  0.020  1.090
 MI0  C10  F2   single  1.361  0.020  1.361
 MI0  C10  C9   single  1.526  0.020  1.526
 MI0  C10  C11  single  1.534  0.020  1.534
 MI0  C11  N2   single  1.329  0.020  1.329
 MI0  C12  H18  single  0.970  0.020  1.090
 MI0  C12  H19  single  0.970  0.020  1.090
 MI0  C12  H20  single  0.970  0.020  1.090
 MI0  N1   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
 MI0  H22  N1   H1   107.19  3.000
 MI0  H22  N1   C1   111.98  3.000
 MI0  H1   N1   C1   112.02  3.000
 MI0  H21  N2   C12  118.30  3.000
 MI0  H21  N2   C11  119.91  3.000
 MI0  C12  N2   C11  121.78  3.000
 MI0  H2   O1   C9   102.58  3.000
 MI0  H3   C1   C9   109.68  3.000
 MI0  H3   C1   C2   108.09  3.000
 MI0  C9   C1   C2   108.88  3.000
 MI0  H3   C1   N1   111.79  3.000
 MI0  C2   C1   N1   111.42  3.000
 MI0  C9   C1   N1   106.95  3.000
 MI0  H5   C2   H4   106.24  3.000
 MI0  H5   C2   C3   108.50  3.000
 MI0  H4   C2   C3   108.94  3.000
 MI0  C3   C2   C1   116.09  3.000
 MI0  H5   C2   C1   107.59  3.000
 MI0  H4   C2   C1   109.04  3.000
 MI0  H6   C3   C5   106.66  3.000
 MI0  H6   C3   C4   107.72  3.000
 MI0  C5   C3   C4   110.19  3.000
 MI0  H6   C3   C2   109.32  3.000
 MI0  C5   C3   C2   109.76  3.000
 MI0  C4   C3   C2   112.97  3.000
 MI0  H8   C4   H7   106.57  3.000
 MI0  H8   C4   C6   109.41  3.000
 MI0  H7   C4   C6   109.35  3.000
 MI0  C6   C4   C3   111.94  3.000
 MI0  H8   C4   C3   110.51  3.000
 MI0  H7   C4   C3   108.91  3.000
 MI0  H10  C5   H9   106.41  3.000
 MI0  H10  C5   C7   109.48  3.000
 MI0  H9   C5   C7   110.15  3.000
 MI0  C7   C5   C3   112.05  3.000
 MI0  H10  C5   C3   108.88  3.000
 MI0  H9   C5   C3   109.70  3.000
 MI0  H12  C6   H11  106.35  3.000
 MI0  H12  C6   C8   109.25  3.000
 MI0  H11  C6   C8   110.26  3.000
 MI0  H12  C6   C4   109.26  3.000
 MI0  H11  C6   C4   109.88  3.000
 MI0  C8   C6   C4   111.67  3.000
 MI0  H14  C7   H13  106.47  3.000
 MI0  H14  C7   C8   110.44  3.000
 MI0  H13  C7   C8   109.25  3.000
 MI0  H14  C7   C5   110.12  3.000
 MI0  H13  C7   C5   109.14  3.000
 MI0  C8   C7   C5   111.29  3.000
 MI0  H16  C8   H15  106.46  3.000
 MI0  H16  C8   C7   110.36  3.000
 MI0  H15  C8   C7   109.37  3.000
 MI0  H16  C8   C6   110.29  3.000
 MI0  H15  C8   C6   109.27  3.000
 MI0  C7   C8   C6   110.98  3.000
 MI0  H17  C9   C10  106.04  3.000
 MI0  C10  C9   C1   113.27  3.000
 MI0  H17  C9   C1   109.46  3.000
 MI0  C10  C9   O1   108.90  3.000
 MI0  H17  C9   O1   109.48  3.000
 MI0  C1   C9   O1   109.58  3.000
 MI0  C11  C10  C9   111.37  3.000
 MI0  C11  C10  F2   107.81  3.000
 MI0  C9   C10  F2   109.98  3.000
 MI0  C11  C10  F1   110.47  3.000
 MI0  C9   C10  F1   111.04  3.000
 MI0  F2   C10  F1   105.98  3.000
 MI0  C10  C11  O2   118.39  3.000
 MI0  C10  C11  N2   116.85  3.000
 MI0  O2   C11  N2   124.76  3.000
 MI0  H20  C12  H19  108.46  3.000
 MI0  H20  C12  H18  108.57  3.000
 MI0  H19  C12  H18  108.53  3.000
 MI0  H20  C12  N2   111.50  3.000
 MI0  H19  C12  N2   111.36  3.000
 MI0  H18  C12  N2   108.35  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
 MI0  CONST_01  C12  N2   C11  O2      0.00   0.0  0
 MI0  CONST_02  C12  N2   C11  C10   180.00   0.0  0
 MI0  CONST_03  H21  N2   C11  O2    180.00   0.0  0
 MI0  Var_01    C8   C6   C4   C3     55.17  30.0  1
 MI0  Var_02    C8   C7   C5   C3    -55.82  30.0  1
 MI0  Var_03    C6   C8   C7   C5     54.98  30.0  1
 MI0  Var_04    O2   C11  C10  F1    171.06  30.0  3
 MI0  Var_05    H18  C12  N2   C11  -177.47  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
 MI0  chir_01  C1  N1  C9  C2   positiv
 MI0  chir_02  C3  C2  C4  C5   positiv
 MI0  chir_03  C9  O1  C1  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
 MI0  plan-1  N2   0.020
 MI0  plan-1  O2   0.020
 MI0  plan-1  C10  0.020
 MI0  plan-1  C11  0.020
 MI0  plan-1  C12  0.020
 MI0  plan-1  H21  0.020

