# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 18:11:50 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S)-2-amino-4-methylpentane-1,1-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](N)C(O)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
 LOL  LOL  (2S)-2-amino-4-methylpentane-1,1-diol  peptide  24  9  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LOL
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
 LOL  CD1   C  CH3   0  -0.648  -3.1505  -0.5217  -0.8055
 LOL  CD2   C  CH3   0  -0.661  -2.2494   0.0199   1.4711
 LOL  CG    C  CH1   0  -0.240  -2.0512   0.1988  -0.0312
 LOL  CB    C  CH2   0  -0.401  -0.6810  -0.2991  -0.4952
 LOL  N     N  NH2   0  -0.788   0.5187   1.8141   0.1310
 LOL  CA    C  CH1   0  -0.193   0.5168   0.3602   0.1975
 LOL  C     C  CH1   0   0.300   1.8349  -0.1607  -0.3834
 LOL  O     O  OH1   0  -0.664   2.8809   0.3699   0.3711
 LOL  OXT   O  OH1   0  -0.664   1.8876  -1.5590  -0.4323
 LOL  HD11  H  HCH3  0   0.223  -3.0427  -0.3730  -1.8816
 LOL  HD12  H  HCH3  0   0.212  -3.1200  -1.5978  -0.6169
 LOL  HD13  H  HCH3  0   0.225  -4.1402  -0.1628  -0.5179
 LOL  HD21  H  HCH3  0   0.215  -2.1202  -1.0262   1.7606
 LOL  HD22  H  HCH3  0   0.226  -1.5440   0.6120   2.0569
 LOL  HD23  H  HCH3  0   0.228  -3.2530   0.3250   1.7713
 LOL  HG    H  HCH1  0   0.207  -2.1343   1.2674  -0.2617
 LOL  HB3   H  HCH2  0   0.211  -0.6440  -1.3822  -0.3446
 LOL  HB2   H  HCH2  0   0.213  -0.5966  -0.1396  -1.5776
 LOL  H     H  HNH2  0   0.335   0.3998   2.1110  -0.8321
 LOL  H2    H  HNH2  0   0.350  -0.2857   2.1782   0.6262
 LOL  HA    H  HCH1  0   0.230   0.5032   0.0865   1.2607
 LOL  HC    H  HCH1  0   0.191   1.9108   0.1522  -1.4343
 LOL  HO    H  HOH1  0   0.451   3.7098   0.1846  -0.0827
 LOL  HXT   H  HOH1  0   0.444   1.7023  -1.9100   0.4470

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
 LOL  CD1  CG    single  1.526  0.020  1.526
 LOL  CD1  HD11  single  0.970  0.020  1.090
 LOL  CD1  HD12  single  0.970  0.020  1.090
 LOL  CD1  HD13  single  0.970  0.020  1.090
 LOL  CD2  CG    single  1.526  0.020  1.526
 LOL  CD2  HD21  single  0.970  0.020  1.090
 LOL  CD2  HD22  single  0.970  0.020  1.090
 LOL  CD2  HD23  single  0.970  0.020  1.090
 LOL  CG   CB    single  1.530  0.020  1.530
 LOL  CG   HG    single  0.970  0.020  1.090
 LOL  CB   CA    single  1.521  0.033  1.521
 LOL  CB   HB3   single  0.970  0.020  1.090
 LOL  CB   HB2   single  0.970  0.020  1.090
 LOL  N    CA    single  1.458  0.019  1.458
 LOL  N    H     single  0.860  0.020  0.860
 LOL  N    H2    single  0.890  0.020  1.040
 LOL  CA   C     single  1.525  0.021  1.525
 LOL  CA   HA    single  0.970  0.020  0.970
 LOL  C    O     single  1.231  0.020  1.231
 LOL  C    OXT   single  1.400  0.020  1.400
 LOL  C    HC    single  0.970  0.020  1.090
 LOL  O    HO    single  0.850  0.020  0.980
 LOL  OXT  HXT   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
 LOL  HD13  CD1  HD12  107.68  3.000
 LOL  HD13  CD1  HD11  107.73  3.000
 LOL  HD12  CD1  HD11  107.54  3.000
 LOL  HD13  CD1  CG    111.37  3.000
 LOL  HD12  CD1  CG    110.94  3.000
 LOL  HD11  CD1  CG    111.39  3.000
 LOL  HD23  CD2  HD22  107.17  3.000
 LOL  HD23  CD2  HD21  107.67  3.000
 LOL  HD22  CD2  HD21  107.50  3.000
 LOL  HD23  CD2  CG    110.95  3.000
 LOL  HD22  CD2  CG    112.39  3.000
 LOL  HD21  CD2  CG    110.95  3.000
 LOL  HG    CG   CB    108.75  3.000
 LOL  HG    CG   CD2   108.15  3.000
 LOL  CB    CG   CD2   112.13  3.000
 LOL  HG    CG   CD1   107.40  3.000
 LOL  CB    CG   CD1   109.74  3.000
 LOL  CD2   CG   CD1   110.53  3.000
 LOL  HB2   CB   HB3   106.08  3.000
 LOL  HB2   CB   CA    108.85  3.000
 LOL  HB3   CB   CA    109.71  3.000
 LOL  HB2   CB   CG    108.71  3.000
 LOL  HB3   CB   CG    108.10  3.000
 LOL  CA    CB   CG    115.02  3.000
 LOL  H2    N    H     105.43  3.000
 LOL  H2    N    CA    109.63  3.000
 LOL  H     N    CA    114.00  3.000
 LOL  HA    CA   C     110.00  3.000
 LOL  HA    CA   N     110.00  3.000
 LOL  C     CA   N     111.00  2.800
 LOL  HA    CA   CB    109.00  3.000
 LOL  C     CA   CB    110.50  1.500
 LOL  N     CA   CB    110.40  1.500
 LOL  HC    C    OXT   104.38  3.000
 LOL  HC    C    O     110.92  3.000
 LOL  OXT   C    O     111.75  3.000
 LOL  HC    C    CA    108.98  3.000
 LOL  OXT   C    CA    112.67  3.000
 LOL  O     C    CA    120.80  1.700
 LOL  HO    O    C     108.51  3.000
 LOL  HXT   OXT  C     108.92  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
 LOL  Var_01  CA    CB   CG  CD1  179.36  30.0  3
 LOL  Var_02  HD21  CD2  CG  CD1   65.85  30.0  3
 LOL  Var_03  HD11  CD1  CG  CD2  177.96  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
 LOL  chir_01  CA  CB  N  C  positiv

