# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 11:36:52 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{S})-2-[[(2~{R})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]carbamoyloxy]pentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@@H](NC(=O)O[C@@H](CCC(O)=O)C(O)=O)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
 BXK  BXK  '(2~{S})-2-[[(2~{R})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]carbamoyloxy]pentanedioic acid'  ligand  40  21  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BXK
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
 BXK  OAC  O  OH1   0  -0.595  -4.5145  -3.1356  -0.0975
 BXK  CAO  C  C     0   0.554  -4.5005  -1.8431   0.2091
 BXK  OAG  O  O     0  -0.443  -5.3996  -1.2935   0.7949
 BXK  CAJ  C  CH2   0  -0.583  -3.2391  -1.1765  -0.2660
 BXK  CAK  C  CH2   0  -0.466  -3.1653   0.2915   0.1239
 BXK  CAU  C  CH1   0  -0.069  -1.9036   0.9508  -0.4231
 BXK  CAQ  C  C     0   0.522  -1.8601   2.4213  -0.0421
 BXK  OAI  O  OH1   0  -0.588  -2.6819   3.1313  -0.7972
 BXK  OAE  O  O     0  -0.423  -1.1916   2.8666   0.8513
 BXK  OAN  O  O2    0  -0.485  -0.7932   0.2895   0.1480
 BXK  CAR  C  C     0   0.780   0.4065   0.5445  -0.3940
 BXK  OAF  O  O     0  -0.510   0.5801   1.2991  -1.3266
 BXK  N    N  NH1   0  -0.664   1.3712  -0.1701   0.2086
 BXK  CA   C  CH1   0  -0.197   2.7494   0.0038  -0.1547
 BXK  C    C  C     0   0.550   3.2485   1.3773   0.2673
 BXK  O    O  O     0  -0.428   2.7165   2.0739   1.0904
 BXK  OXT  O  OH1   0  -0.592   4.3662   1.6970  -0.3697
 BXK  CB   C  CH2   0  -0.456   3.6058  -1.0867   0.4980
 BXK  CG   C  CH1   0  -0.234   3.2233  -2.5143   0.0962
 BXK  CD2  C  CH3   0  -0.665   3.3115  -2.7293  -1.4105
 BXK  CD1  C  CH3   0  -0.653   4.1193  -3.5003   0.8392
 BXK  H1   H  HOH1  0   0.480  -5.3350  -3.5420   0.2189
 BXK  H2   H  HCH2  0   0.292  -2.3887  -1.7358   0.1310
 BXK  H3   H  HCH2  0   0.288  -3.1874  -1.2883  -1.3539
 BXK  H4   H  HCH2  0   0.270  -4.0268   0.8257  -0.2789
 BXK  H5   H  HCH2  0   0.263  -3.1977   0.4040   1.2100
 BXK  H6   H  HCH1  0   0.286  -1.8915   0.8620  -1.5140
 BXK  H7   H  HOH1  0   0.489  -2.6864   4.0587  -0.5146
 BXK  H8   H  HNH1  0   0.408   1.1523  -0.6695   1.0573
 BXK  H9   H  HCH1  0   0.289   2.8516  -0.0718  -1.2404
 BXK  H10  H  HOH1  0   0.485   4.6965   2.5546  -0.0618
 BXK  H11  H  HCH2  0   0.256   4.6503  -0.9140   0.2284
 BXK  H12  H  HCH2  0   0.251   3.5416  -0.9851   1.5865
 BXK  H13  H  HCH1  0   0.226   2.1913  -2.7040   0.4091
 BXK  H14  H  HCH3  0   0.219   4.3134  -2.4981  -1.7814
 BXK  H15  H  HCH3  0   0.235   3.0945  -3.7674  -1.6653
 BXK  H16  H  HCH3  0   0.230   2.6013  -2.1104  -1.9607
 BXK  H17  H  HCH3  0   0.228   4.0340  -3.3798   1.9206
 BXK  H18  H  HCH3  0   0.231   3.8533  -4.5302   0.5977
 BXK  H19  H  HCH3  0   0.217   5.1688  -3.3577   0.5705

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
 BXK  OAE  CAQ  double  1.201  0.020  1.201
 BXK  OAG  CAO  double  1.206  0.020  1.206
 BXK  CAQ  OAI  single  1.323  0.020  1.323
 BXK  CAQ  CAU  single  1.520  0.020  1.520
 BXK  CAO  OAC  single  1.329  0.020  1.329
 BXK  CAO  CAJ  single  1.504  0.020  1.504
 BXK  CAK  CAJ  single  1.521  0.020  1.521
 BXK  CAK  CAU  single  1.525  0.020  1.525
 BXK  CAU  OAN  single  1.413  0.020  1.413
 BXK  OAF  CAR  double  1.212  0.020  1.212
 BXK  OAN  CAR  single  1.341  0.020  1.341
 BXK  CAR  N    single  1.343  0.020  1.343
 BXK  N    CA   single  1.436  0.020  1.436
 BXK  CA   C    single  1.521  0.020  1.521
 BXK  CA   CB   single  1.532  0.020  1.532
 BXK  O    C    double  1.202  0.020  1.202
 BXK  C    OXT  single  1.326  0.020  1.326
 BXK  CD2  CG   single  1.525  0.020  1.525
 BXK  CB   CG   single  1.532  0.020  1.532
 BXK  CG   CD1  single  1.526  0.020  1.526
 BXK  OAC  H1   single  0.850  0.020  0.980
 BXK  CAJ  H2   single  0.970  0.020  1.090
 BXK  CAJ  H3   single  0.970  0.020  1.090
 BXK  CAK  H4   single  0.970  0.020  1.090
 BXK  CAK  H5   single  0.970  0.020  1.090
 BXK  CAU  H6   single  0.970  0.020  1.090
 BXK  OAI  H7   single  0.850  0.020  0.980
 BXK  N    H8   single  0.860  0.020  1.020
 BXK  CA   H9   single  0.970  0.020  1.090
 BXK  OXT  H10  single  0.850  0.020  0.980
 BXK  CB   H11  single  0.970  0.020  1.090
 BXK  CB   H12  single  0.970  0.020  1.090
 BXK  CG   H13  single  0.970  0.020  1.090
 BXK  CD2  H14  single  0.970  0.020  1.090
 BXK  CD2  H15  single  0.970  0.020  1.090
 BXK  CD2  H16  single  0.970  0.020  1.090
 BXK  CD1  H17  single  0.970  0.020  1.090
 BXK  CD1  H18  single  0.970  0.020  1.090
 BXK  CD1  H19  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
 BXK  H1   OAC  CAO  109.98  3.000
 BXK  CAJ  CAO  OAG  125.24  3.000
 BXK  CAJ  CAO  OAC  111.54  3.000
 BXK  OAG  CAO  OAC  123.22  3.000
 BXK  H3   CAJ  H2   105.78  3.000
 BXK  H3   CAJ  CAK  110.55  3.000
 BXK  H2   CAJ  CAK  111.30  3.000
 BXK  H3   CAJ  CAO  107.96  3.000
 BXK  H2   CAJ  CAO  108.14  3.000
 BXK  CAK  CAJ  CAO  112.81  3.000
 BXK  H5   CAK  H4   107.06  3.000
 BXK  H5   CAK  CAU  109.67  3.000
 BXK  H4   CAK  CAU  108.01  3.000
 BXK  H5   CAK  CAJ  110.66  3.000
 BXK  H4   CAK  CAJ  109.86  3.000
 BXK  CAU  CAK  CAJ  111.44  3.000
 BXK  H6   CAU  OAN  110.86  3.000
 BXK  H6   CAU  CAQ  109.15  3.000
 BXK  OAN  CAU  CAQ  109.21  3.000
 BXK  H6   CAU  CAK  109.37  3.000
 BXK  OAN  CAU  CAK  107.63  3.000
 BXK  CAQ  CAU  CAK  110.62  3.000
 BXK  OAE  CAQ  OAI  124.84  3.000
 BXK  OAI  CAQ  CAU  111.00  3.000
 BXK  OAE  CAQ  CAU  124.13  3.000
 BXK  H7   OAI  CAQ  110.48  3.000
 BXK  CAR  OAN  CAU  116.79  3.000
 BXK  N    CAR  OAF  124.99  3.000
 BXK  N    CAR  OAN  111.10  3.000
 BXK  OAF  CAR  OAN  123.89  3.000
 BXK  H8   N    CA   118.75  3.000
 BXK  H8   N    CAR  119.01  3.000
 BXK  CA   N    CAR  120.76  3.000
 BXK  H9   CA   CB   108.76  3.000
 BXK  H9   CA   C    107.90  3.000
 BXK  CB   CA   C    109.94  3.000
 BXK  H9   CA   N    109.43  3.000
 BXK  CB   CA   N    110.03  3.000
 BXK  C    CA   N    110.74  3.000
 BXK  OXT  C    O    124.22  3.000
 BXK  OXT  C    CA   111.17  3.000
 BXK  O    C    CA   124.60  3.000
 BXK  H10  OXT  C    110.37  3.000
 BXK  H12  CB   H11  106.66  3.000
 BXK  H12  CB   CG   109.43  3.000
 BXK  H11  CB   CG   108.75  3.000
 BXK  H12  CB   CA   108.94  3.000
 BXK  H11  CB   CA   108.46  3.000
 BXK  CG   CB   CA   114.33  3.000
 BXK  H13  CG   CD1  107.60  3.000
 BXK  H13  CG   CD2  108.22  3.000
 BXK  CD1  CG   CD2  110.87  3.000
 BXK  H13  CG   CB   108.78  3.000
 BXK  CD1  CG   CB   109.15  3.000
 BXK  CD2  CG   CB   112.10  3.000
 BXK  H16  CD2  H15  107.01  3.000
 BXK  H16  CD2  H14  107.80  3.000
 BXK  H15  CD2  H14  107.72  3.000
 BXK  H16  CD2  CG   112.38  3.000
 BXK  H15  CD2  CG   110.71  3.000
 BXK  H14  CD2  CG   111.01  3.000
 BXK  H19  CD1  H18  107.64  3.000
 BXK  H19  CD1  H17  107.71  3.000
 BXK  H18  CD1  H17  107.73  3.000
 BXK  H19  CD1  CG   111.11  3.000
 BXK  H18  CD1  CG   111.05  3.000
 BXK  H17  CD1  CG   111.42  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
 BXK  CONST_01  H1   OAC  CAO  OAG     0.00   0.0  0
 BXK  CONST_02  H7   OAI  CAQ  CAU   180.00   0.0  0
 BXK  CONST_03  H10  OXT  C    CA    180.00   0.0  0
 BXK  Var_01    CAK  CAJ  CAO  OAC  -177.47  30.0  3
 BXK  Var_02    CAU  CAK  CAJ  CAO  -177.60  30.0  1
 BXK  Var_03    OAF  CAR  OAN  CAU     0.14  30.0  3
 BXK  Var_04    CA   N    CAR  OAN  -176.19  30.0  2
 BXK  Var_05    CD2  CG   CB   CA     58.33  30.0  3
 BXK  Var_06    H14  CD2  CG   CB     56.93  30.0  3
 BXK  Var_07    H17  CD1  CG   CB     58.22  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
 BXK  chir_01  CAU  CAQ  CAK  OAN  positiv
 BXK  chir_02  CA   N    C    CB   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
 BXK  plan-1  OAC  0.020
 BXK  plan-1  CAO  0.020
 BXK  plan-1  OAG  0.020
 BXK  plan-1  CAJ  0.020
 BXK  plan-1  H1   0.020
 BXK  plan-2  CAU  0.020
 BXK  plan-2  CAQ  0.020
 BXK  plan-2  OAI  0.020
 BXK  plan-2  OAE  0.020
 BXK  plan-2  H7   0.020
 BXK  plan-3  CA   0.020
 BXK  plan-3  C    0.020
 BXK  plan-3  O    0.020
 BXK  plan-3  OXT  0.020
 BXK  plan-3  H10  0.020
 BXK  plan-4  OAN  0.020
 BXK  plan-4  CAR  0.020
 BXK  plan-4  OAF  0.020
 BXK  plan-4  N    0.020

