# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 23:23:42 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: (2R)-3-methylbutan-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H](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
 CDE  CDE  (2R)-3-methylbutan-2-amine  L-peptide  19  6  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CDE
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
 CDE  N     N  NH2   0  -0.795  -1.2593  -0.7862  -0.8462
 CDE  CA    C  CH1   0  -0.084  -0.3857   0.3682  -0.6683
 CDE  CB    C  CH1   0  -0.225   0.3845   0.4214   0.6700
 CDE  CG1   C  CH3   0  -0.664  -0.5723   0.5111   1.8555
 CDE  CG2   C  CH3   0  -0.671   1.3507  -0.7452   0.8536
 CDE  C     C  CH3   0  -0.660   0.5471   0.4667  -1.8688
 CDE  H     H  HNH2  0   0.344  -1.9220  -0.8511  -0.0839
 CDE  H2    H  HNH2  0   0.335  -0.7163  -1.6415  -0.8193
 CDE  HA    H  HCH1  0   0.216  -1.0350   1.2520  -0.6855
 CDE  HB    H  HCH1  0   0.209   0.9740   1.3461   0.6510
 CDE  HG11  H  HCH3  0   0.229  -0.0268   0.6460   2.7907
 CDE  HG12  H  HCH3  0   0.224  -1.2628   1.3501   1.7502
 CDE  HG13  H  HCH3  0   0.209  -1.1676  -0.3994   1.9623
 CDE  HG21  H  HCH3  0   0.209   0.8251  -1.7029   0.8697
 CDE  HG22  H  HCH3  0   0.229   2.1037  -0.7915   0.0660
 CDE  HG23  H  HCH3  0   0.230   1.8818  -0.6601   1.8030
 CDE  HC1   H  HCH3  0   0.229  -0.0222   0.5728  -2.7927
 CDE  HC2   H  HCH3  0   0.221   1.2129   1.3262  -1.7811
 CDE  HC3   H  HCH3  0   0.217   1.1701  -0.4250  -1.9678

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
 CDE  N    CA    single  1.458  0.019  1.458
 CDE  N    H     single  0.860  0.020  0.860
 CDE  N    H2    single  0.890  0.020  1.040
 CDE  CA   CB    single  1.521  0.033  1.521
 CDE  CA   C     single  1.525  0.021  1.525
 CDE  CA   HA    single  0.970  0.020  0.970
 CDE  CB   CG1   single  1.526  0.020  1.526
 CDE  CB   CG2   single  1.526  0.020  1.526
 CDE  CB   HB    single  0.970  0.020  1.090
 CDE  CG1  HG11  single  0.970  0.020  1.090
 CDE  CG1  HG12  single  0.970  0.020  1.090
 CDE  CG1  HG13  single  0.970  0.020  1.090
 CDE  CG2  HG21  single  0.970  0.020  1.090
 CDE  CG2  HG22  single  0.970  0.020  1.090
 CDE  CG2  HG23  single  0.970  0.020  1.090
 CDE  C    HC1   single  0.970  0.020  1.090
 CDE  C    HC2   single  0.970  0.020  1.090
 CDE  C    HC3   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
 CDE  H2    N    H     106.06  3.000
 CDE  H2    N    CA    110.11  3.000
 CDE  H     N    CA    114.00  3.000
 CDE  HA    CA   C     110.00  3.000
 CDE  HA    CA   CB    109.00  3.000
 CDE  C     CA   CB    110.50  1.500
 CDE  HA    CA   N     110.00  3.000
 CDE  C     CA   N     111.00  2.800
 CDE  CB    CA   N     110.40  1.500
 CDE  HB    CB   CG2   107.84  3.000
 CDE  HB    CB   CG1   107.51  3.000
 CDE  CG2   CB   CG1   110.39  3.000
 CDE  HB    CB   CA    106.38  3.000
 CDE  CG2   CB   CA    113.18  3.000
 CDE  CG1   CB   CA    111.25  3.000
 CDE  HG13  CG1  HG12  107.77  3.000
 CDE  HG13  CG1  HG11  106.95  3.000
 CDE  HG12  CG1  HG11  107.69  3.000
 CDE  HG13  CG1  CB    111.62  3.000
 CDE  HG12  CG1  CB    111.52  3.000
 CDE  HG11  CG1  CB    111.08  3.000
 CDE  HG23  CG2  HG22  107.19  3.000
 CDE  HG23  CG2  HG21  106.84  3.000
 CDE  HG22  CG2  HG21  107.80  3.000
 CDE  HG23  CG2  CB    110.69  3.000
 CDE  HG22  CG2  CB    112.50  3.000
 CDE  HG21  CG2  CB    111.55  3.000
 CDE  HC3   C    HC2   107.60  3.000
 CDE  HC3   C    HC1   107.48  3.000
 CDE  HC2   C    HC1   108.07  3.000
 CDE  HC3   C    CA    111.58  3.000
 CDE  HC2   C    CA    111.18  3.000
 CDE  HC1   C    CA    110.75  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
 CDE  Var_01  HG11  CG1  CB  CA  -174.49  30.0  3
 CDE  Var_02  HG21  CG2  CB  CA   -61.97  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
 CDE  chir_01  CA  N  CB  C  negativ

