# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 00:48:15 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: [(1~{S},3~{S})-3-carboxycyclohexyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+][C@H]1CCC[C@@H](C1)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
 VDK  VDK  '[(1~{S},3~{S})-3-carboxycyclohexyl]azanium'  peptide  23  10  .  2022-08-11  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_VDK
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
 VDK  C2   C  CH1    0  -0.119  17.7721  -32.6407  -0.3185
 VDK  C4   C  CH2    0  -0.432  16.9524  -31.7848   0.6321
 VDK  C5   C  CH2    0  -0.446  15.5125  -32.2886   0.6737
 VDK  C6   C  CH2    0  -0.411  14.9028  -32.3416  -0.7224
 VDK  C7   C  CH1    0  -0.404  15.7384  -33.2029  -1.6691
 VDK  N1   N  NT3    1  -0.787  19.1715  -32.1118  -0.3907
 VDK  C9   C  CH2    0  -0.412  17.1730  -32.6767  -1.7138
 VDK  C10  C  C      0   0.427  15.6505  -34.7209  -1.3466
 VDK  O11  O  O      0  -0.598  16.6771  -35.4030  -1.5415
 VDK  H1   H  HCH1   0   0.287  17.8690  -33.6540   0.0725
 VDK  H2   H  HCH2   0   0.252  17.3929  -31.7990   1.6324
 VDK  H3   H  HCH2   0   0.232  16.9688  -30.7456   0.2853
 VDK  H4   H  HCH2   0   0.237  14.9244  -31.6381   1.3238
 VDK  H5   H  HCH2   0   0.222  15.4875  -33.2835   1.1282
 VDK  H6   H  HCH2   0   0.209  14.8402  -31.3229  -1.1203
 VDK  H7   H  HCH2   0   0.227  13.8831  -32.7218  -0.6741
 VDK  H8   H  HCH1   0   0.244  15.3260  -33.0886  -2.6796
 VDK  H9   H  HNT3   0   0.469  19.6127  -32.0669   0.5291
 VDK  H10  H  HNT3   0   0.469  19.7653  -32.6976  -0.9798
 VDK  H12  H  HCH2   0   0.245  17.7854  -33.2935  -2.3725
 VDK  H13  H  HCH2   0   0.229  17.1748  -31.6596  -2.1220
 VDK  OXY  O  OC    -1  -0.600  14.5440  -35.1418  -0.9566
 VDK  H11  H  HNT3   0   0.462  19.1985  -31.1688  -0.7822

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
 VDK  C7   C9   single  1.529  0.020  1.529
 VDK  C7   C10  single  1.554  0.020  1.554
 VDK  C7   C6   single  1.528  0.020  1.528
 VDK  C9   C2   single  1.519  0.020  1.519
 VDK  C10  O11  deloc   1.248  0.020  1.248
 VDK  C6   C5   single  1.524  0.020  1.524
 VDK  N1   C2   single  1.498  0.020  1.498
 VDK  C2   C4   single  1.519  0.020  1.519
 VDK  C4   C5   single  1.526  0.020  1.526
 VDK  C2   H1   single  0.970  0.020  1.090
 VDK  C4   H2   single  0.970  0.020  1.090
 VDK  C4   H3   single  0.970  0.020  1.090
 VDK  C5   H4   single  0.970  0.020  1.090
 VDK  C5   H5   single  0.970  0.020  1.090
 VDK  C6   H6   single  0.970  0.020  1.090
 VDK  C6   H7   single  0.970  0.020  1.090
 VDK  C7   H8   single  0.970  0.020  1.090
 VDK  N1   H9   single  0.890  0.020  1.040
 VDK  N1   H10  single  0.890  0.020  1.040
 VDK  C9   H12  single  0.970  0.020  1.090
 VDK  C9   H13  single  0.970  0.020  1.090
 VDK  C10  OXY  deloc   1.246  0.020  1.246
 VDK  N1   H11  single  0.890  0.020  1.040

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
 VDK  H1   C2   C9   110.02  3.000
 VDK  H1   C2   N1   105.22  3.000
 VDK  C9   C2   N1   109.43  3.000
 VDK  H1   C2   C4   110.31  3.000
 VDK  N1   C2   C4   109.59  3.000
 VDK  C9   C2   C4   112.05  3.000
 VDK  H3   C4   H2   107.21  3.000
 VDK  H3   C4   C5   109.63  3.000
 VDK  H2   C4   C5   110.55  3.000
 VDK  H3   C4   C2   109.16  3.000
 VDK  H2   C4   C2   110.36  3.000
 VDK  C5   C4   C2   109.89  3.000
 VDK  H5   C5   H4   106.39  3.000
 VDK  H5   C5   C6   109.86  3.000
 VDK  H4   C5   C6   110.52  3.000
 VDK  H5   C5   C4   109.46  3.000
 VDK  H4   C5   C4   109.14  3.000
 VDK  C6   C5   C4   111.34  3.000
 VDK  H7   C6   H6   106.69  3.000
 VDK  H7   C6   C7   110.03  3.000
 VDK  H6   C6   C7   109.29  3.000
 VDK  H7   C6   C5   110.24  3.000
 VDK  H6   C6   C5   108.86  3.000
 VDK  C7   C6   C5   111.60  3.000
 VDK  H8   C7   C10  105.75  3.000
 VDK  H8   C7   C9   106.85  3.000
 VDK  C10  C7   C9   113.28  3.000
 VDK  H8   C7   C6   107.83  3.000
 VDK  C10  C7   C6   113.01  3.000
 VDK  C9   C7   C6   109.71  3.000
 VDK  H11  N1   H10  107.05  3.000
 VDK  H11  N1   H9   107.05  3.000
 VDK  H10  N1   H9   107.07  3.000
 VDK  H11  N1   C2   111.67  3.000
 VDK  H10  N1   C2   111.62  3.000
 VDK  H9   N1   C2   112.07  3.000
 VDK  H13  C9   H12  107.40  3.000
 VDK  H13  C9   C7   109.38  3.000
 VDK  H12  C9   C7   110.49  3.000
 VDK  H13  C9   C2   108.63  3.000
 VDK  H12  C9   C2   110.29  3.000
 VDK  C7   C9   C2   110.57  3.000
 VDK  OXY  C10  O11  126.48  3.000
 VDK  OXY  C10  C7   116.42  3.000
 VDK  O11  C10  C7   117.06  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
 VDK  Var_01  C6  C5  C4  C2  -55.15  30.0  1
 VDK  Var_02  C7  C6  C5  C4   56.29  30.0  1

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
 VDK  chir_01  C2  C9  N1   C4  negativ
 VDK  chir_02  C7  C9  C10  C6  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
 VDK  plan-1  C7   0.020
 VDK  plan-1  C10  0.020
 VDK  plan-1  O11  0.020
 VDK  plan-1  OXY  0.020

