# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 21:16:27 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  37  21  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  OC    -1  -0.634  -4.5980  -3.1227   0.1536
 BXK  CAO  C  C      0   0.411  -4.5455  -1.8865   0.3290
 BXK  OAG  O  O      0  -0.610  -5.4236  -1.1812   0.8640
 BXK  CAJ  C  CH2    0  -0.582  -3.2708  -1.1916  -0.1821
 BXK  CAK  C  CH2    0  -0.445  -3.1533   0.2893   0.1439
 BXK  CAU  C  CH1    0  -0.067  -1.9133   0.9487  -0.4456
 BXK  CAQ  C  C      0   0.384  -1.9032   2.4634  -0.1571
 BXK  OAI  O  OC    -1  -0.623  -2.7031   3.1296  -0.8461
 BXK  OAE  O  O      0  -0.591  -1.1480   2.8757   0.7373
 BXK  OAN  O  O2     0  -0.496  -0.7819   0.2960   0.1293
 BXK  CAR  C  C      0   0.759   0.4067   0.5088  -0.4376
 BXK  OAF  O  O      0  -0.545   0.5716   1.1499  -1.4589
 BXK  N    N  NH1    0  -0.653   1.3794  -0.1525   0.2173
 BXK  CA   C  CH1    0  -0.199   2.7736   0.0464  -0.0984
 BXK  C    C  C      0   0.408   3.3258   1.4135   0.3780
 BXK  O    O  O     -1  -0.590   2.6200   2.0877   1.1454
 BXK  OXT  O  OC     0  -0.624   4.4627   1.7015  -0.0521
 BXK  CB   C  CH2    0  -0.440   3.5965  -1.0911   0.5070
 BXK  CG   C  CH1    0  -0.221   3.1951  -2.5015   0.0690
 BXK  CD2  C  CH3    0  -0.662   3.2696  -2.6734  -1.4442
 BXK  CD1  C  CH3    0  -0.652   4.0762  -3.5289   0.7733
 BXK  H2   H  HCH2   0   0.223  -2.4062  -1.7377   0.2061
 BXK  H3   H  HCH2   0   0.218  -3.2282  -1.3285  -1.2700
 BXK  H4   H  HCH2   0   0.221  -4.0193   0.8219  -0.2512
 BXK  H5   H  HCH2   0   0.211  -3.1675   0.4435   1.2275
 BXK  H6   H  HCH1   0   0.211  -1.9135   0.7932  -1.5299
 BXK  H8   H  HNH1   0   0.378   1.1590  -0.4999   1.1378
 BXK  H9   H  HCH1   0   0.230   2.8813   0.0070  -1.1854
 BXK  H11  H  HCH2   0   0.226   4.6443  -0.9237   0.2461
 BXK  H12  H  HCH2   0   0.220   3.5382  -1.0296   1.6010
 BXK  H13  H  HCH1   0   0.213   2.1605  -2.6817   0.3800
 BXK  H14  H  HCH3   0   0.211   4.2726  -2.4459  -1.8154
 BXK  H15  H  HCH3   0   0.225   3.0349  -3.6995  -1.7330
 BXK  H16  H  HCH3   0   0.228   2.5671  -2.0221  -1.9657
 BXK  H17  H  HCH3   0   0.222   4.0014  -3.4395   1.8589
 BXK  H18  H  HCH3   0   0.224   3.7925  -4.5477   0.5039
 BXK  H19  H  HCH3   0   0.211   5.1271  -3.3966   0.5034

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  deloc   1.241  0.020  1.241
 BXK  OAG  CAO  deloc   1.247  0.020  1.247
 BXK  CAQ  OAI  deloc   1.248  0.020  1.248
 BXK  CAQ  CAU  single  1.542  0.020  1.542
 BXK  CAO  OAC  deloc   1.250  0.020  1.250
 BXK  CAO  CAJ  single  1.539  0.020  1.539
 BXK  CAK  CAJ  single  1.521  0.020  1.521
 BXK  CAK  CAU  single  1.523  0.020  1.523
 BXK  CAU  OAN  single  1.427  0.020  1.427
 BXK  OAF  CAR  double  1.217  0.020  1.217
 BXK  OAN  CAR  single  1.334  0.020  1.334
 BXK  CAR  N    single  1.346  0.020  1.346
 BXK  N    CA   single  1.443  0.020  1.443
 BXK  CA   C    single  1.549  0.020  1.549
 BXK  CA   CB   single  1.529  0.020  1.529
 BXK  O    C    deloc   1.242  0.020  1.242
 BXK  C    OXT  deloc   1.249  0.020  1.249
 BXK  CD2  CG   single  1.525  0.020  1.525
 BXK  CB   CG   single  1.530  0.020  1.530
 BXK  CG   CD1  single  1.526  0.020  1.526
 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  N    H8   single  0.890  0.020  1.040
 BXK  CA   H9   single  0.970  0.020  1.090
 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  CAJ  CAO  OAG  118.06  3.000
 BXK  CAJ  CAO  OAC  115.77  3.000
 BXK  OAG  CAO  OAC  126.16  3.000
 BXK  H3   CAJ  H2   105.00  3.000
 BXK  H3   CAJ  CAK  109.33  3.000
 BXK  H2   CAJ  CAK  110.42  3.000
 BXK  H3   CAJ  CAO  107.77  3.000
 BXK  H2   CAJ  CAO  108.15  3.000
 BXK  CAK  CAJ  CAO  115.62  3.000
 BXK  H5   CAK  H4   106.24  3.000
 BXK  H5   CAK  CAU  109.43  3.000
 BXK  H4   CAK  CAU  107.14  3.000
 BXK  H5   CAK  CAJ  110.39  3.000
 BXK  H4   CAK  CAJ  109.66  3.000
 BXK  CAU  CAK  CAJ  113.67  3.000
 BXK  H6   CAU  OAN  109.51  3.000
 BXK  H6   CAU  CAQ  108.95  3.000
 BXK  OAN  CAU  CAQ  111.63  3.000
 BXK  H6   CAU  CAK  108.76  3.000
 BXK  OAN  CAU  CAK  106.95  3.000
 BXK  CAQ  CAU  CAK  110.99  3.000
 BXK  OAE  CAQ  OAI  127.61  3.000
 BXK  OAI  CAQ  CAU  114.63  3.000
 BXK  OAE  CAQ  CAU  117.73  3.000
 BXK  CAR  OAN  CAU  117.54  3.000
 BXK  N    CAR  OAF  124.68  3.000
 BXK  N    CAR  OAN  111.02  3.000
 BXK  OAF  CAR  OAN  124.15  3.000
 BXK  H8   N    CA   117.28  3.000
 BXK  H8   N    CAR  117.09  3.000
 BXK  CA   N    CAR  121.59  3.000
 BXK  H9   CA   CB   108.29  3.000
 BXK  H9   CA   C    107.61  3.000
 BXK  CB   CA   C    110.05  3.000
 BXK  H9   CA   N    107.92  3.000
 BXK  CB   CA   N    109.32  3.000
 BXK  C    CA   N    113.49  3.000
 BXK  OXT  C    O    127.23  3.000
 BXK  OXT  C    CA   114.95  3.000
 BXK  O    C    CA   117.81  3.000
 BXK  H12  CB   H11  106.28  3.000
 BXK  H12  CB   CG   108.85  3.000
 BXK  H11  CB   CG   108.92  3.000
 BXK  H12  CB   CA   108.93  3.000
 BXK  H11  CB   CA   107.92  3.000
 BXK  CG   CB   CA   115.54  3.000
 BXK  H13  CG   CD1  107.68  3.000
 BXK  H13  CG   CD2  108.02  3.000
 BXK  CD1  CG   CD2  110.73  3.000
 BXK  H13  CG   CB   108.55  3.000
 BXK  CD1  CG   CB   109.70  3.000
 BXK  CD2  CG   CB   112.03  3.000
 BXK  H16  CD2  H15  107.24  3.000
 BXK  H16  CD2  H14  107.71  3.000
 BXK  H15  CD2  H14  107.64  3.000
 BXK  H16  CD2  CG   112.07  3.000
 BXK  H15  CD2  CG   110.99  3.000
 BXK  H14  CD2  CG   110.99  3.000
 BXK  H19  CD1  H18  107.58  3.000
 BXK  H19  CD1  H17  107.55  3.000
 BXK  H18  CD1  H17  107.70  3.000
 BXK  H19  CD1  CG   111.08  3.000
 BXK  H18  CD1  CG   111.38  3.000
 BXK  H17  CD1  CG   111.36  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  Var_01  CAK  CAJ  CAO  OAC  -174.70  30.0  3
 BXK  Var_02  CAU  CAK  CAJ  CAO  -176.91  30.0  1
 BXK  Var_03  OAF  CAR  OAN  CAU    -4.99  30.0  3
 BXK  Var_04  CA   N    CAR  OAN  -172.21  30.0  2
 BXK  Var_05  CD2  CG   CB   CA     57.89  30.0  3
 BXK  Var_06  H14  CD2  CG   CB     57.14  30.0  3
 BXK  Var_07  H17  CD1  CG   CB     57.99  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-2  CAU  0.020
 BXK  plan-2  CAQ  0.020
 BXK  plan-2  OAI  0.020
 BXK  plan-2  OAE  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-4  OAN  0.020
 BXK  plan-4  CAR  0.020
 BXK  plan-4  OAF  0.020
 BXK  plan-4  N    0.020

