# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 22:39:47 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (2~{S})-2-[[(2~{S})-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
 CQB  CQB  '(2~{S})-2-[[(2~{S})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]carbamoyloxy]pentanedioic acid'  ligand  37  21  .  2021-08-07  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CQB
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
 CQB  OAC  O  OC    -1  -0.635  -4.8381  -2.4658   1.4411
 CQB  CAO  C  C      0   0.411  -4.6234  -1.2574   1.2050
 CQB  OAG  O  O      0  -0.609  -5.3367  -0.3002   1.5647
 CQB  CAJ  C  CH2    0  -0.582  -3.3567  -0.9493   0.3872
 CQB  CAK  C  CH2    0  -0.446  -3.0740   0.5248   0.1439
 CQB  CAU  C  CH1    0  -0.066  -1.8633   0.7769  -0.7446
 CQB  CAQ  C  C      0   0.388  -1.6894   2.2829  -1.0299
 CQB  OAI  O  O      0  -0.596  -0.7869   2.8858  -0.4259
 CQB  OAE  O  OC    -1  -0.620  -2.5182   2.7592  -1.8316
 CQB  OAN  O  O2     0  -0.496  -0.7311   0.2366  -0.0656
 CQB  CAR  C  C      0   0.758   0.4232   0.2029  -0.7325
 CQB  OAF  O  O      0  -0.544   0.5278   0.4191  -1.9252
 CQB  N    N  NH1    0  -0.650   1.4519  -0.0925   0.0861
 CQB  CA   C  CH1    0  -0.204   2.7180  -0.5308  -0.4509
 CQB  C    C  C      0   0.412   2.6510  -1.9368  -1.1011
 CQB  O    O  O     -1  -0.597   1.6129  -2.6007  -0.9379
 CQB  OXT  O  OC     0  -0.620   3.6742  -2.2774  -1.7297
 CQB  CB   C  CH2    0  -0.438   3.7760  -0.5026   0.6520
 CQB  CG   C  CH1    0  -0.221   3.9550   0.8449   1.3546
 CQB  CD2  C  CH3    0  -0.651   4.9985   0.7221   2.4606
 CQB  CD1  C  CH3    0  -0.660   4.3328   1.9583   0.3836
 CQB  H2   H  HCH2   0   0.225  -2.5061  -1.4236   0.8858
 CQB  H3   H  HCH2   0   0.217  -3.4439  -1.4666  -0.5763
 CQB  H4   H  HCH2   0   0.221  -3.9329   0.9871  -0.3437
 CQB  H5   H  HCH2   0   0.211  -2.9437   1.0498   1.0952
 CQB  H6   H  HCH1   0   0.211  -2.0088   0.2501  -1.6945
 CQB  H8   H  HNH1   0   0.375   1.2119  -0.4289   1.0061
 CQB  H9   H  HCH1   0   0.232   3.0141   0.1730  -1.2324
 CQB  H11  H  HCH2   0   0.219   3.5306  -1.2627   1.4049
 CQB  H12  H  HCH2   0   0.225   4.7286  -0.8089   0.2127
 CQB  H13  H  HCH1   0   0.213   3.0028   1.1183   1.8215
 CQB  H14  H  HCH3   0   0.211   5.9773   0.4611   2.0505
 CQB  H15  H  HCH3   0   0.223   5.1094   1.6620   3.0045
 CQB  H16  H  HCH3   0   0.222   4.7275  -0.0493   3.1841
 CQB  H17  H  HCH3   0   0.229   3.5609   2.1259  -0.3688
 CQB  H18  H  HCH3   0   0.224   4.4797   2.9016   0.9128
 CQB  H19  H  HCH3   0   0.210   5.2639   1.7243  -0.1389

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
 CQB  OAI  CAQ  deloc   1.242  0.020  1.242
 CQB  OAG  CAO  deloc   1.247  0.020  1.247
 CQB  CAQ  OAE  deloc   1.248  0.020  1.248
 CQB  CAQ  CAU  single  1.543  0.020  1.543
 CQB  CAO  OAC  deloc   1.250  0.020  1.250
 CQB  CAO  CAJ  single  1.539  0.020  1.539
 CQB  CAK  CAJ  single  1.521  0.020  1.521
 CQB  CAK  CAU  single  1.523  0.020  1.523
 CQB  CAU  OAN  single  1.426  0.020  1.426
 CQB  OAF  CAR  double  1.217  0.020  1.217
 CQB  CD2  CG   single  1.526  0.020  1.526
 CQB  OAN  CAR  single  1.333  0.020  1.333
 CQB  CAR  N    single  1.347  0.020  1.347
 CQB  CB   CG   single  1.530  0.020  1.530
 CQB  CB   CA   single  1.529  0.020  1.529
 CQB  CG   CD1  single  1.525  0.020  1.525
 CQB  N    CA   single  1.443  0.020  1.443
 CQB  CA   C    single  1.551  0.020  1.551
 CQB  C    O    deloc   1.243  0.020  1.243
 CQB  C    OXT  deloc   1.248  0.020  1.248
 CQB  CAJ  H2   single  0.970  0.020  1.090
 CQB  CAJ  H3   single  0.970  0.020  1.090
 CQB  CAK  H4   single  0.970  0.020  1.090
 CQB  CAK  H5   single  0.970  0.020  1.090
 CQB  CAU  H6   single  0.970  0.020  1.090
 CQB  N    H8   single  0.890  0.020  1.040
 CQB  CA   H9   single  0.970  0.020  1.090
 CQB  CB   H11  single  0.970  0.020  1.090
 CQB  CB   H12  single  0.970  0.020  1.090
 CQB  CG   H13  single  0.970  0.020  1.090
 CQB  CD2  H14  single  0.970  0.020  1.090
 CQB  CD2  H15  single  0.970  0.020  1.090
 CQB  CD2  H16  single  0.970  0.020  1.090
 CQB  CD1  H17  single  0.970  0.020  1.090
 CQB  CD1  H18  single  0.970  0.020  1.090
 CQB  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
 CQB  CAJ  CAO  OAG  118.07  3.000
 CQB  CAJ  CAO  OAC  115.81  3.000
 CQB  OAG  CAO  OAC  126.12  3.000
 CQB  H3   CAJ  H2   104.93  3.000
 CQB  H3   CAJ  CAK  109.35  3.000
 CQB  H2   CAJ  CAK  110.41  3.000
 CQB  H3   CAJ  CAO  107.87  3.000
 CQB  H2   CAJ  CAO  108.12  3.000
 CQB  CAK  CAJ  CAO  115.60  3.000
 CQB  H5   CAK  H4   106.20  3.000
 CQB  H5   CAK  CAU  109.46  3.000
 CQB  H4   CAK  CAU  107.17  3.000
 CQB  H5   CAK  CAJ  110.37  3.000
 CQB  H4   CAK  CAJ  109.65  3.000
 CQB  CAU  CAK  CAJ  113.68  3.000
 CQB  H6   CAU  OAN  109.63  3.000
 CQB  H6   CAU  CAQ  108.90  3.000
 CQB  OAN  CAU  CAQ  111.61  3.000
 CQB  H6   CAU  CAK  108.70  3.000
 CQB  OAN  CAU  CAK  106.90  3.000
 CQB  CAQ  CAU  CAK  111.05  3.000
 CQB  OAE  CAQ  OAI  127.58  3.000
 CQB  OAE  CAQ  CAU  114.63  3.000
 CQB  OAI  CAQ  CAU  117.76  3.000
 CQB  CAR  OAN  CAU  117.29  3.000
 CQB  N    CAR  OAF  124.67  3.000
 CQB  N    CAR  OAN  111.26  3.000
 CQB  OAF  CAR  OAN  124.07  3.000
 CQB  H8   N    CA   116.54  3.000
 CQB  H8   N    CAR  116.47  3.000
 CQB  CA   N    CAR  120.68  3.000
 CQB  H9   CA   CB   108.46  3.000
 CQB  H9   CA   C    107.21  3.000
 CQB  CB   CA   C    110.44  3.000
 CQB  H9   CA   N    107.95  3.000
 CQB  C    CA   N    113.17  3.000
 CQB  CB   CA   N    109.46  3.000
 CQB  OXT  C    O    127.22  3.000
 CQB  OXT  C    CA   115.04  3.000
 CQB  O    C    CA   117.74  3.000
 CQB  H12  CB   H11  106.06  3.000
 CQB  H12  CB   CG   109.23  3.000
 CQB  H11  CB   CG   108.73  3.000
 CQB  H12  CB   CA   107.95  3.000
 CQB  H11  CB   CA   109.11  3.000
 CQB  CG   CB   CA   115.37  3.000
 CQB  H13  CG   CD1  107.73  3.000
 CQB  H13  CG   CD2  107.80  3.000
 CQB  CD1  CG   CD2  110.55  3.000
 CQB  H13  CG   CB   108.29  3.000
 CQB  CD1  CG   CB   112.31  3.000
 CQB  CD2  CG   CB   110.00  3.000
 CQB  H16  CD2  H15  107.66  3.000
 CQB  H16  CD2  H14  107.59  3.000
 CQB  H15  CD2  H14  107.56  3.000
 CQB  H16  CD2  CG   111.56  3.000
 CQB  H15  CD2  CG   111.19  3.000
 CQB  H14  CD2  CG   111.09  3.000
 CQB  H19  CD1  H18  107.59  3.000
 CQB  H19  CD1  H17  107.82  3.000
 CQB  H18  CD1  H17  107.27  3.000
 CQB  H19  CD1  CG   111.04  3.000
 CQB  H18  CD1  CG   110.83  3.000
 CQB  H17  CD1  CG   112.09  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
 CQB  Var_01  CAK  CAJ  CAO  OAC  -177.96  30.0  3
 CQB  Var_02  CAU  CAK  CAJ  CAO  -176.23  30.0  1
 CQB  Var_03  OAF  CAR  OAN  CAU   -11.02  30.0  3
 CQB  Var_04  CA   N    CAR  OAN   163.37  30.0  2
 CQB  Var_05  CD2  CG   CB   CA    177.96  30.0  3
 CQB  Var_06  H14  CD2  CG   CB     62.79  30.0  3
 CQB  Var_07  H17  CD1  CG   CB     61.66  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
 CQB  chir_01  CAU  CAQ  CAK  OAN  positiv
 CQB  chir_02  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
 CQB  plan-1  OAC  0.020
 CQB  plan-1  CAO  0.020
 CQB  plan-1  OAG  0.020
 CQB  plan-1  CAJ  0.020
 CQB  plan-2  CAU  0.020
 CQB  plan-2  CAQ  0.020
 CQB  plan-2  OAI  0.020
 CQB  plan-2  OAE  0.020
 CQB  plan-3  CA   0.020
 CQB  plan-3  C    0.020
 CQB  plan-3  O    0.020
 CQB  plan-3  OXT  0.020
 CQB  plan-4  OAN  0.020
 CQB  plan-4  CAR  0.020
 CQB  plan-4  OAF  0.020
 CQB  plan-4  N    0.020

