# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 12:05:08 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (4R)-4-aminohexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@@H](N)CCC(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
 VIG  VIG  '(4R)-4-aminohexanoic acid'  ligand  21  9  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VIG
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
 VIG  C1'   C  C      0   0.413   0.1254  -0.1308  -2.4921
 VIG  O1'   O  OC    -1  -0.635  -0.6162  -0.4318  -3.4521
 VIG  O2'   O  O      0  -0.608   1.3007   0.2769  -2.5710
 VIG  C1    C  CH2    0  -0.593  -0.4979  -0.2773  -1.0914
 VIG  C2    C  CH2    0  -0.397   0.4177   0.0326   0.0808
 VIG  C3    C  CH1    0  -0.085  -0.2340  -0.1788   1.4521
 VIG  C4    C  CH2    0  -0.406   0.7761   0.0764   2.5696
 VIG  C5    C  CH3    0  -0.659   0.2813  -0.3102   3.9550
 VIG  N3    N  NH2    0  -0.791  -1.4294   0.6259   1.6861
 VIG  H1C1  H  HCH2   0   0.216  -0.8865  -1.2986  -0.9956
 VIG  H1C2  H  HCH2   0   0.212  -1.3846   0.3664  -1.0638
 VIG  H2C1  H  HCH2   0   0.196   0.7750   1.0664   0.0150
 VIG  H2C2  H  HCH2   0   0.200   1.3083  -0.5998   0.0194
 VIG  H3    H  HCH1   0   0.200  -0.5462  -1.2296   1.5182
 VIG  H4C1  H  HCH2   0   0.204   1.0539   1.1368   2.5577
 VIG  H4C2  H  HCH2   0   0.213   1.6929  -0.4747   2.3413
 VIG  H5C1  H  HCH3   0   0.220   1.0415  -0.1201   4.7139
 VIG  H5C2  H  HCH3   0   0.219  -0.6108   0.2518   4.2288
 VIG  H5C3  H  HCH3   0   0.210   0.0302  -1.3721   4.0011
 VIG  H3N1  H  HNH2   0   0.328  -1.2042   1.6038   1.5344
 VIG  H3N2  H  HNH2   0   0.343  -2.1359   0.4004   0.9967

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
 VIG  C1'  O1'   deloc   1.250  0.020  1.250
 VIG  C1'  O2'   deloc   1.247  0.020  1.247
 VIG  C1'  C1    single  1.540  0.020  1.540
 VIG  C1   C2    single  1.519  0.020  1.519
 VIG  C1   H1C1  single  0.970  0.020  1.090
 VIG  C1   H1C2  single  0.970  0.020  1.090
 VIG  C2   C3    single  1.533  0.020  1.533
 VIG  C2   H2C1  single  0.970  0.020  1.090
 VIG  C2   H2C2  single  0.970  0.020  1.090
 VIG  C3   C4    single  1.528  0.020  1.528
 VIG  C3   N3    single  1.460  0.020  1.460
 VIG  C3   H3    single  0.970  0.020  1.090
 VIG  C4   C5    single  1.521  0.020  1.521
 VIG  C4   H4C1  single  0.970  0.020  1.090
 VIG  C4   H4C2  single  0.970  0.020  1.090
 VIG  C5   H5C1  single  0.970  0.020  1.090
 VIG  C5   H5C2  single  0.970  0.020  1.090
 VIG  C5   H5C3  single  0.970  0.020  1.090
 VIG  N3   H3N1  single  0.890  0.020  1.040
 VIG  N3   H3N2  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
 VIG  C1    C1'  O2'   118.05  3.000
 VIG  C1    C1'  O1'   115.82  3.000
 VIG  O2'   C1'  O1'   126.13  3.000
 VIG  H1C2  C1   H1C1  104.95  3.000
 VIG  H1C2  C1   C2    110.38  3.000
 VIG  H1C1  C1   C2    109.63  3.000
 VIG  H1C2  C1   C1'   107.12  3.000
 VIG  H1C1  C1   C1'   108.14  3.000
 VIG  C2    C1   C1'   116.00  3.000
 VIG  H2C2  C2   H2C1  106.06  3.000
 VIG  H2C2  C2   C3    108.46  3.000
 VIG  H2C1  C2   C3    108.81  3.000
 VIG  H2C2  C2   C1    109.23  3.000
 VIG  H2C1  C2   C1    110.03  3.000
 VIG  C3    C2   C1    113.94  3.000
 VIG  H3    C3   N3    106.56  3.000
 VIG  H3    C3   C4    107.68  3.000
 VIG  N3    C3   C4    109.39  3.000
 VIG  H3    C3   C2    107.86  3.000
 VIG  N3    C3   C2    114.55  3.000
 VIG  C4    C3   C2    110.50  3.000
 VIG  H4C2  C4   H4C1  105.82  3.000
 VIG  H4C2  C4   C5    109.56  3.000
 VIG  H4C1  C4   C5    109.77  3.000
 VIG  H4C2  C4   C3    108.50  3.000
 VIG  H4C1  C4   C3    108.73  3.000
 VIG  C5    C4   C3    114.12  3.000
 VIG  H5C3  C5   H5C2  107.62  3.000
 VIG  H5C3  C5   H5C1  107.48  3.000
 VIG  H5C2  C5   H5C1  107.82  3.000
 VIG  H5C3  C5   C4    111.12  3.000
 VIG  H5C2  C5   C4    111.36  3.000
 VIG  H5C1  C5   C4    111.26  3.000
 VIG  H3N2  N3   H3N1  105.53  3.000
 VIG  H3N2  N3   C3    109.84  3.000
 VIG  H3N1  N3   C3    109.00  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
 VIG  Var_01  C3    C2  C1   C1'  -177.83  30.0  3
 VIG  Var_02  C2    C1  C1'  O1'   177.58  30.0  3
 VIG  Var_03  H5C1  C5  C4   C3    179.32  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
 VIG  chir_01  C3  C2  C4  N3  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
 VIG  plan-1  C1'  0.020
 VIG  plan-1  O1'  0.020
 VIG  plan-1  O2'  0.020
 VIG  plan-1  C1   0.020

