# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 28 22:37:30 2022
#   Inital geometry file: a 44 line input string
#   Ligand name: (2~{R})-2-methyl-2-oxidanyl-butanenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@](C)(O)C#N
#
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
 5Z9  5Z9  "(2R)-2-methyl-2-oxidanyl-butanenitrile"  ligand  16  7  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_5Z9
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
 5Z9  N1  N  NS    0  -0.259  -33.0592  12.3818  66.5100
 5Z9  C1  C  CH3   0  -0.668  -32.1563   9.8783  69.1377
 5Z9  C2  C  CH2   0  -0.443  -33.4835   9.5723  68.4628
 5Z9  C3  C  CT    0   0.134  -34.3519  10.8041  68.1649
 5Z9  C4  C  CH3   0  -0.659  -35.6612  10.3916  67.4900
 5Z9  C5  C  CSP   0   0.130  -33.6169  11.6947  67.2438
 5Z9  O1  O  OH1   0  -0.652  -34.5783  11.5890  69.3109
 5Z9  H1  H  HCH3  0   0.241  -31.6128   8.9532  69.3264
 5Z9  H2  H  HCH3  0   0.230  -31.5185  10.5086  68.5160
 5Z9  H3  H  HCH3  0   0.229  -32.2954  10.3794  70.0948
 5Z9  H4  H  HCH2  0   0.253  -34.0824   8.9099  69.0953
 5Z9  H5  H  HCH2  0   0.245  -33.3171   9.0328  67.5279
 5Z9  H6  H  HCH3  0   0.254  -36.2162   9.7347  68.1616
 5Z9  H7  H  HCH3  0   0.256  -36.2792  11.2597  67.2637
 5Z9  H8  H  HCH3  0   0.247  -35.4746   9.8469  66.5654
 5Z9  H9  H  HOH1  0   0.461  -35.0579  11.0478  69.9499

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
 5Z9  N1  C5  triple  1.150  0.020  1.150
 5Z9  C5  C3  single  1.477  0.020  1.477
 5Z9  C4  C3  single  1.530  0.020  1.530
 5Z9  C3  C2  single  1.536  0.020  1.536
 5Z9  C3  O1  single  1.407  0.020  1.407
 5Z9  C2  C1  single  1.520  0.020  1.520
 5Z9  C1  H1  single  0.970  0.020  1.090
 5Z9  C1  H2  single  0.970  0.020  1.090
 5Z9  C1  H3  single  0.970  0.020  1.090
 5Z9  C2  H4  single  0.970  0.020  1.090
 5Z9  C2  H5  single  0.970  0.020  1.090
 5Z9  C4  H6  single  0.970  0.020  1.090
 5Z9  C4  H7  single  0.970  0.020  1.090
 5Z9  C4  H8  single  0.970  0.020  1.090
 5Z9  O1  H9  single  0.850  0.020  0.980

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
 5Z9  H3  C1  H2  108.03  3.000
 5Z9  H3  C1  H1  107.59  3.000
 5Z9  H2  C1  H1  107.32  3.000
 5Z9  H3  C1  C2  111.79  3.000
 5Z9  H2  C1  C2  111.94  3.000
 5Z9  H1  C1  C2  109.97  3.000
 5Z9  H5  C2  H4  106.21  3.000
 5Z9  H5  C2  C3  108.43  3.000
 5Z9  H4  C2  C3  106.74  3.000
 5Z9  H5  C2  C1  110.27  3.000
 5Z9  H4  C2  C1  110.06  3.000
 5Z9  C3  C2  C1  114.73  3.000
 5Z9  O1  C3  C5  104.57  3.000
 5Z9  O1  C3  C4  111.84  3.000
 5Z9  C5  C3  C4  108.26  3.000
 5Z9  O1  C3  C2  112.35  3.000
 5Z9  C4  C3  C2  110.68  3.000
 5Z9  C5  C3  C2  108.85  3.000
 5Z9  H8  C4  H7  108.62  3.000
 5Z9  H8  C4  H6  107.97  3.000
 5Z9  H7  C4  H6  108.61  3.000
 5Z9  H8  C4  C3  111.27  3.000
 5Z9  H7  C4  C3  111.25  3.000
 5Z9  H6  C4  C3  109.04  3.000
 5Z9  C3  C5  N1  180.00  3.000
 5Z9  H9  O1  C3  107.85  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
 5Z9  Var_01  H1  C1  C2  C3  179.11  30.0  3
 5Z9  Var_02  H2  C1  C2  C3  -61.69  30.0  3
 5Z9  Var_03  H3  C1  C2  C3   59.67  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
 5Z9  chir_01  C3  C4  C2  O1  positiv

