# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 19:16:10 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: 3-[(2,2-dimethylpropanoyl)amino]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C(=O)NC[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
 Z01  Z01  3-[(2,2-dimethylpropanoyl)amino]-L-alanine  L-peptide  28  13  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_Z01
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
 Z01  N     N  NH2    0  -0.794  15.2020  11.5816  29.6394
 Z01  CA    C  CH1    0  -0.253  16.0092  10.4741  29.1497
 Z01  CB    C  CH2    0  -0.245  15.5222   9.1759  29.7971
 Z01  N1    N  NH1    0  -0.635  15.4534   9.3526  31.2288
 Z01  C1    C  C      0   0.583  15.5028   8.3590  32.1270
 Z01  C     C  C      0   0.388  16.0528  10.2901  27.6095
 Z01  O     O  O      0  -0.611  16.8470   9.4206  27.1972
 Z01  O1    O  O      0  -0.498  15.6150   7.1841  31.7962
 Z01  C2    C  CT     0  -0.238  15.4388   8.7963  33.5985
 Z01  C23   C  CH3    0  -0.642  14.1658   9.6127  33.8544
 Z01  C21   C  CH3    0  -0.635  16.6714   9.6512  33.9223
 Z01  C22   C  CH3    0  -0.627  15.4302   7.5660  34.5013
 Z01  H     H  HNH2   0   0.344  15.6719  12.4537  29.4331
 Z01  HA    H  HCH1   0   0.226  17.0353  10.6395  29.4961
 Z01  H25   H  HCH2   0   0.216  14.5376   8.9066  29.3932
 Z01  H25A  H  HCH2   0   0.236  16.2046   8.3641  29.5534
 Z01  HN27  H  HNH1   0   0.388  15.2854  10.3058  31.5173
 Z01  H76   H  HCH3   0   0.234  14.0963   9.8625  34.9144
 Z01  H76A  H  HCH3   0   0.228  14.1520  10.5542  33.3035
 Z01  H76B  H  HCH3   0   0.234  13.2692   9.0518  33.5854
 Z01  H78   H  HCH3   0   0.231  16.6657   9.9241  34.9789
 Z01  H78A  H  HCH3   0   0.232  17.5966   9.1075  33.7237
 Z01  H78B  H  HCH3   0   0.229  16.6941  10.5763  33.3452
 Z01  H80   H  HCH3   0   0.222  15.3950   7.8824  35.5452
 Z01  H80A  H  HCH3   0   0.225  14.5618   6.9318  34.3187
 Z01  H80B  H  HCH3   0   0.226  16.3241   6.9558  34.3706
 Z01  H2    H  HNH2   0   0.332  14.3456  11.6125  29.0972
 Z01  OXT   O  OC    -1  -0.593  15.2938  11.0022  26.9262

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
 Z01  N    CA    single  1.458  0.019  1.458
 Z01  N    H     single  0.860  0.020  0.860
 Z01  CA   CB    single  1.521  0.033  1.521
 Z01  CA   C     single  1.525  0.021  1.525
 Z01  CA   HA    single  0.970  0.020  0.970
 Z01  CB   N1    single  1.444  0.020  1.444
 Z01  CB   H25   single  0.970  0.020  1.090
 Z01  CB   H25A  single  0.970  0.020  1.090
 Z01  N1   C1    single  1.340  0.020  1.340
 Z01  N1   HN27  single  0.860  0.020  1.020
 Z01  C1   O1    double  1.226  0.020  1.226
 Z01  C1   C2    single  1.536  0.020  1.536
 Z01  C    O     deloc   1.231  0.020  1.231
 Z01  C2   C23   single  1.534  0.020  1.534
 Z01  C2   C21   single  1.535  0.020  1.535
 Z01  C2   C22   single  1.526  0.020  1.526
 Z01  C23  H76   single  0.970  0.020  1.090
 Z01  C23  H76A  single  0.970  0.020  1.090
 Z01  C23  H76B  single  0.970  0.020  1.090
 Z01  C21  H78   single  0.970  0.020  1.090
 Z01  C21  H78A  single  0.970  0.020  1.090
 Z01  C21  H78B  single  0.970  0.020  1.090
 Z01  C22  H80   single  0.970  0.020  1.090
 Z01  C22  H80A  single  0.970  0.020  1.090
 Z01  C22  H80B  single  0.970  0.020  1.090
 Z01  N    H2    single  0.890  0.020  1.040
 Z01  C    OXT   deloc   1.245  0.020  1.245

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
 Z01  H2    N    H     104.89  3.000
 Z01  H2    N    CA    108.16  3.000
 Z01  H     N    CA    114.00  3.000
 Z01  HA    CA   C     109.00  3.000
 Z01  HA    CA   CB    109.00  3.000
 Z01  C     CA   CB    110.50  1.500
 Z01  HA    CA   N     110.00  3.000
 Z01  C     CA   N     111.00  2.800
 Z01  CB    CA   N     110.40  1.500
 Z01  H25A  CB   H25   107.28  3.000
 Z01  H25A  CB   N1    110.08  3.000
 Z01  H25   CB   N1    110.61  3.000
 Z01  H25A  CB   CA    109.79  3.000
 Z01  H25   CB   CA    109.74  3.000
 Z01  N1    CB   CA    109.32  3.000
 Z01  HN27  N1   C1    120.95  3.000
 Z01  HN27  N1   CB    113.99  3.000
 Z01  C1    N1   CB    124.88  3.000
 Z01  C2    C1   O1    122.35  3.000
 Z01  C2    C1   N1    115.43  3.000
 Z01  O1    C1   N1    122.21  3.000
 Z01  OXT   C    O     127.26  3.000
 Z01  OXT   C    CA    117.37  3.000
 Z01  O     C    CA    120.80  1.700
 Z01  C22   C2   C21   109.20  3.000
 Z01  C22   C2   C23   109.01  3.000
 Z01  C21   C2   C23   109.57  3.000
 Z01  C22   C2   C1    109.72  3.000
 Z01  C21   C2   C1    109.10  3.000
 Z01  C23   C2   C1    110.23  3.000
 Z01  H76B  C23  H76A  107.98  3.000
 Z01  H76B  C23  H76   107.74  3.000
 Z01  H76A  C23  H76   106.98  3.000
 Z01  H76B  C23  C2    111.54  3.000
 Z01  H76A  C23  C2    112.69  3.000
 Z01  H76   C23  C2    109.68  3.000
 Z01  H78B  C21  H78A  107.98  3.000
 Z01  H78B  C21  H78   107.48  3.000
 Z01  H78A  C21  H78   107.77  3.000
 Z01  H78B  C21  C2    112.19  3.000
 Z01  H78A  C21  C2    111.40  3.000
 Z01  H78   C21  C2    109.84  3.000
 Z01  H80B  C22  H80A  107.90  3.000
 Z01  H80B  C22  H80   107.66  3.000
 Z01  H80A  C22  H80   107.64  3.000
 Z01  H80B  C22  C2    112.07  3.000
 Z01  H80A  C22  C2    111.98  3.000
 Z01  H80   C22  C2    109.41  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
 Z01  CONST_01  O1    C1   N1  CB     0.00   0.0  0
 Z01  CONST_02  C2    C1   N1  CB   180.00   0.0  0
 Z01  CONST_03  HN27  N1   C1  O1   180.00   0.0  0
 Z01  Var_01    C1    N1   CB  CA  -156.80  30.0  3
 Z01  Var_02    C23   C2   C1  N1    56.98  30.0  3
 Z01  Var_03    H76   C23  C2  C1   176.30  30.0  3
 Z01  Var_04    H78   C21  C2  C1  -176.99  30.0  3
 Z01  Var_05    H80   C22  C2  C1   179.43  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
 Z01  chir_01  CA  N  CB  C  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
 Z01  plan-1  CB    0.020
 Z01  plan-1  N1    0.020
 Z01  plan-1  C1    0.020
 Z01  plan-1  O1    0.020
 Z01  plan-1  C2    0.020
 Z01  plan-1  HN27  0.020
 Z01  plan-2  CA    0.020
 Z01  plan-2  C     0.020
 Z01  plan-2  O     0.020
 Z01  plan-2  OXT   0.020

