# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:04:39 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: (2~{S})-2-azanyl-3-[ethyl(methyl)carbamoyl]oxy-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(C)C(=O)OC[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
 BXT  BXT  '(2~{S})-2-azanyl-3-[ethyl(methyl)carbamoyl]oxy-propanoic acid'  L-peptide  26  13  .  2019-03-22  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_BXT
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
 BXT  C2   C  CH3    0  -0.659  5.5105  131.9027  153.9740
 BXT  C4   C  CH2    0  -0.310  4.4819  132.8952  154.4953
 BXT  C5   C  CH3    0  -0.513  5.2601  135.0914  153.6201
 BXT  N    N  NH2    0  -0.817  2.8162  135.6960  148.3163
 BXT  CA   C  CH1    0  -0.239  3.6221  135.3739  149.4849
 BXT  C    C  C      0   0.417  4.6519  134.2669  149.1402
 BXT  O    O  O      0  -0.602  5.0844  134.2689  147.9705
 BXT  CB   C  CH2    0  -0.159  2.6642  134.9798  150.6015
 BXT  OG   O  O2     0  -0.482  3.3261  135.0106  151.8625
 BXT  C1   C  C      0   0.754  3.3682  133.9094  152.6113
 BXT  N3   N  NT     0  -0.478  4.2731  134.0276  153.6102
 BXT  O2   O  O      0  -0.529  2.6448  132.9438  152.4540
 BXT  H1   H  HCH3   0   0.228  5.6426  131.0862  154.6846
 BXT  H2   H  HCH3   0   0.227  5.1957  131.4727  153.0229
 BXT  H3   H  HCH3   0   0.226  6.4824  132.3762  153.8285
 BXT  H4   H  HCH2   0   0.239  4.7996  133.2868  155.4631
 BXT  H5   H  HCH2   0   0.247  3.5285  132.3968  154.6605
 BXT  H6   H  HCH3   0   0.241  5.8765  134.9798  154.5092
 BXT  H7   H  HCH3   0   0.232  5.9178  135.0583  152.7496
 BXT  H8   H  HCH3   0   0.243  4.7963  136.0759  153.6647
 BXT  H12  H  HCH1   0   0.208  4.2082  136.2401  149.8380
 BXT  H14  H  HCH2   0   0.218  1.8472  135.7051  150.6546
 BXT  H15  H  HCH2   0   0.224  2.2245  134.0021  150.4057
 BXT  OXT  O  OC    -1  -0.590  4.9888  133.4944  150.0575
 BXT  H9   H  HNH2   0   0.335  2.4753  136.6464  148.3779
 BXT  H10  H  HNH2   0   0.338  3.4172  135.6485  147.5041

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
 BXT  O   C    deloc   1.231  0.020  1.231
 BXT  N   CA   single  1.458  0.019  1.458
 BXT  C   CA   single  1.525  0.021  1.525
 BXT  CA  CB   single  1.530  0.020  1.530
 BXT  CB  OG   single  1.425  0.020  1.425
 BXT  OG  C1   single  1.332  0.020  1.332
 BXT  O2  C1   double  1.217  0.020  1.217
 BXT  C1  N3   single  1.353  0.020  1.353
 BXT  N3  C5   single  1.451  0.020  1.451
 BXT  N3  C4   single  1.452  0.020  1.452
 BXT  C2  C4   single  1.521  0.020  1.521
 BXT  C2  H1   single  0.970  0.020  1.090
 BXT  C2  H2   single  0.970  0.020  1.090
 BXT  C2  H3   single  0.970  0.020  1.090
 BXT  C4  H4   single  0.970  0.020  1.090
 BXT  C4  H5   single  0.970  0.020  1.090
 BXT  C5  H6   single  0.970  0.020  1.090
 BXT  C5  H7   single  0.970  0.020  1.090
 BXT  C5  H8   single  0.970  0.020  1.090
 BXT  N   H9   single  0.890  0.020  1.040
 BXT  N   H10  single  0.890  0.020  1.040
 BXT  CA  H12  single  0.970  0.020  1.090
 BXT  CB  H14  single  0.970  0.020  1.090
 BXT  CB  H15  single  0.970  0.020  1.090
 BXT  C   OXT  deloc   1.246  0.020  1.246

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
 BXT  H3   C2  H2   108.18  3.000
 BXT  H3   C2  H1   107.69  3.000
 BXT  H2   C2  H1   107.94  3.000
 BXT  H3   C2  C4   111.40  3.000
 BXT  H2   C2  C4   111.17  3.000
 BXT  H1   C2  C4   110.31  3.000
 BXT  H5   C4  H4   106.54  3.000
 BXT  H5   C4  N3   108.88  3.000
 BXT  H4   C4  N3   107.61  3.000
 BXT  H5   C4  C2   110.21  3.000
 BXT  H4   C4  C2   109.95  3.000
 BXT  N3   C4  C2   113.39  3.000
 BXT  H8   C5  H7   108.46  3.000
 BXT  H8   C5  H6   107.49  3.000
 BXT  H7   C5  H6   107.90  3.000
 BXT  H8   C5  N3   111.92  3.000
 BXT  H7   C5  N3   112.46  3.000
 BXT  H6   C5  N3   108.41  3.000
 BXT  H10  N   H9   107.06  3.000
 BXT  H10  N   CA   107.78  3.000
 BXT  H9   N   CA   110.22  3.000
 BXT  H12  CA  CB   107.61  3.000
 BXT  H12  CA  C    106.18  3.000
 BXT  CB   CA  C    110.10  1.900
 BXT  H12  CA  N    112.15  3.000
 BXT  CB   CA  N    110.50  1.700
 BXT  C    CA  N    111.00  2.800
 BXT  OXT  C   O    126.72  3.000
 BXT  OXT  C   CA   117.29  3.000
 BXT  O    C   CA   120.80  1.700
 BXT  H15  CB  H14  107.60  3.000
 BXT  H15  CB  OG   111.46  3.000
 BXT  H14  CB  OG   106.84  3.000
 BXT  H15  CB  CA   110.74  3.000
 BXT  H14  CB  CA   109.50  3.000
 BXT  OG   CB  CA   110.56  3.000
 BXT  C1   OG  CB   119.63  3.000
 BXT  O2   C1  N3   124.22  3.000
 BXT  N3   C1  OG   111.34  3.000
 BXT  O2   C1  OG   124.37  3.000
 BXT  C1   N3  C5   121.59  3.000
 BXT  C5   N3  C4   118.01  3.000
 BXT  C1   N3  C4   118.56  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
 BXT  Var_01  C1   N3  C4  C2    86.62  30.0  2
 BXT  Var_02  OG   C1  N3  C4  -177.82  30.0  2
 BXT  Var_03  H6   C5  N3  C4   -15.30  30.0  3
 BXT  Var_04  H14  CB  OG  C1   118.83  30.0  2
 BXT  Var_05  H1   C2  C4  N3   178.83  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
 BXT  chir_01  CA  N  C  CB  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
 BXT  plan-1  CA   0.020
 BXT  plan-1  C    0.020
 BXT  plan-1  O    0.020
 BXT  plan-1  OXT  0.020
 BXT  plan-2  OG   0.020
 BXT  plan-2  C1   0.020
 BXT  plan-2  N3   0.020
 BXT  plan-2  O2   0.020

