# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 16:07:55 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2S)-2-amino-4-[1-(trans-4-hydroxycyclohexyl)-1H-1,2,3-triazol-4-yl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCc1cn(nn1)[C@H]2CC[C@H](O)CC2)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
 FOD  FOD  '(2S)-2-amino-4-[1-(trans-4-hydroxycyclohexyl)-1H-1,2,3-triazol-4-yl]butanoic acid'  L-peptide  39  19  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_FOD
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
 FOD  C5   C  CR5   0   0.169  -0.7215   1.0347  -0.2611
 FOD  C6   C  CR15  0  -0.107   0.4370   0.3948  -0.6242
 FOD  C7   C  CH1   0  -0.075   2.7527   0.4551   0.3868
 FOD  C8   C  CH2   0  -0.448   2.9331  -1.0382   0.6417
 FOD  N2   N  N     0  -0.326  -0.4452   1.7870   0.8266
 FOD  C9   C  CH2   0  -0.468   4.4125  -1.3740   0.7988
 FOD  C10  C  CH1   0   0.085   5.2081  -0.9344  -0.4208
 FOD  C11  C  CH2   0  -0.485   5.0124   0.5578  -0.6706
 FOD  C12  C  CH2   0  -0.448   3.5367   0.9017  -0.8429
 FOD  N3   N  N     0  -0.109   0.7978   1.6438   1.1403
 FOD  N4   N  NR5   0  -0.262   1.3452   0.8081   0.2777
 FOD  N    N  NH2   0  -0.785  -5.1506   1.1624  -0.8301
 FOD  CA   C  CH1   0  -0.217  -4.4137  -0.0679  -0.6396
 FOD  CB   C  CH2   0  -0.442  -3.0173   0.0826  -0.0064
 FOD  CG   C  CH2   0  -0.512  -2.0814   0.9383  -0.8597
 FOD  O2   O  OH1   0  -0.676   6.5627  -1.2634  -0.1971
 FOD  C    C  C     0   0.546  -5.2340  -1.0082   0.2200
 FOD  H1   H  HCR5  0   0.306   0.6576  -0.2883  -1.4270
 FOD  H12  H  HCH1  0   0.270   3.1114   1.0099   1.2574
 FOD  H3   H  HCH2  0   0.259   2.3813  -1.3328   1.5364
 FOD  H4   H  HCH2  0   0.233   2.5155  -1.6076  -0.1949
 FOD  H5   H  HCH2  0   0.227   4.8108  -0.8712   1.6865
 FOD  H6   H  HCH2  0   0.249   4.5290  -2.4482   0.9589
 FOD  H7   H  HCH1  0   0.191   4.8201  -1.4791  -1.2970
 FOD  H8   H  HCH2  0   0.228   5.4251   1.1195   0.1747
 FOD  H9   H  HCH2  0   0.245   5.5660   0.8676  -1.5614
 FOD  H10  H  HCH2  0   0.233   3.1437   0.4019  -1.7339
 FOD  H11  H  HCH2  0   0.259   3.4120   1.9751  -0.9967
 FOD  H    H  HNH2  0   0.346  -5.1575   1.7060   0.0247
 FOD  H2   H  HNH2  0   0.360  -4.6898   1.7330  -1.5262
 FOD  HA   H  HCH1  0   0.272  -4.2894  -0.5389  -1.6203
 FOD  HB1  H  HCH2  0   0.241  -3.1197   0.5307   0.9870
 FOD  HB2  H  HCH2  0   0.247  -2.5643  -0.9010   0.1360
 FOD  HG1  H  HCH2  0   0.247  -2.4959   1.9420  -0.9803
 FOD  HG2  H  HCH2  0   0.253  -2.0014   0.5062  -1.8598
 FOD  H21  H  HOH1  0   0.447   7.0736  -0.9698  -0.9579
 FOD  O    O  O     0  -0.439  -6.1349  -0.6669   0.9432
 FOD  HXT  H  HOH1  0   0.481  -5.3189  -2.8330   0.7204
 FOD  OXT  O  OH1   0  -0.594  -4.8169  -2.2652   0.1167

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
 FOD  C11  C12  single    1.525  0.020  1.525
 FOD  C11  C10  single    1.526  0.020  1.526
 FOD  C12  C7   single    1.525  0.020  1.525
 FOD  N    CA   single    1.458  0.019  1.458
 FOD  O2   C10  single    1.412  0.020  1.412
 FOD  C6   N4   aromatic  1.345  0.020  1.345
 FOD  C6   C5   aromatic  1.372  0.020  1.372
 FOD  C10  C9   single    1.521  0.020  1.521
 FOD  C7   N4   single    1.455  0.020  1.455
 FOD  C7   C8   single    1.526  0.020  1.526
 FOD  N4   N3   aromatic  1.320  0.020  1.320
 FOD  CG   C5   single    1.489  0.020  1.489
 FOD  CG   CB   single    1.529  0.020  1.529
 FOD  C5   N2   aromatic  1.351  0.020  1.351
 FOD  OXT  C    single    1.328  0.020  1.328
 FOD  CA   CB   single    1.521  0.033  1.521
 FOD  CA   C    single    1.525  0.021  1.525
 FOD  C9   C8   single    1.525  0.020  1.525
 FOD  N3   N2   aromatic  1.290  0.020  1.290
 FOD  C6   H1   single    0.930  0.020  1.080
 FOD  C7   H12  single    0.970  0.020  1.090
 FOD  C8   H3   single    0.970  0.020  1.090
 FOD  C8   H4   single    0.970  0.020  1.090
 FOD  C9   H5   single    0.970  0.020  1.090
 FOD  C9   H6   single    0.970  0.020  1.090
 FOD  C10  H7   single    0.970  0.020  1.090
 FOD  C11  H8   single    0.970  0.020  1.090
 FOD  C11  H9   single    0.970  0.020  1.090
 FOD  C12  H10  single    0.970  0.020  1.090
 FOD  C12  H11  single    0.970  0.020  1.090
 FOD  N    H    single    0.860  0.020  0.860
 FOD  N    H2   single    0.890  0.020  1.040
 FOD  CA   HA   single    0.970  0.020  0.970
 FOD  CB   HB1  single    0.970  0.020  1.090
 FOD  CB   HB2  single    0.970  0.020  1.090
 FOD  CG   HG1  single    0.970  0.020  1.090
 FOD  CG   HG2  single    0.970  0.020  1.090
 FOD  O2   H21  single    0.850  0.020  0.980
 FOD  C    O    double    1.231  0.020  1.231
 FOD  OXT  HXT  single    0.850  0.020  0.980

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
 FOD  CG   C5   N2   123.13  3.000
 FOD  N2   C5   C6   107.46  3.000
 FOD  CG   C5   C6   129.37  3.000
 FOD  H1   C6   N4   123.81  3.000
 FOD  H1   C6   C5   131.76  3.000
 FOD  N4   C6   C5   104.43  3.000
 FOD  H12  C7   N4   104.72  3.000
 FOD  H12  C7   C12  108.96  3.000
 FOD  N4   C7   C12  111.45  3.000
 FOD  H12  C7   C8   108.96  3.000
 FOD  N4   C7   C8   111.37  3.000
 FOD  C12  C7   C8   111.13  3.000
 FOD  H4   C8   H3   107.04  3.000
 FOD  H4   C8   C9   109.52  3.000
 FOD  H3   C8   C9   110.27  3.000
 FOD  H4   C8   C7   109.65  3.000
 FOD  H3   C8   C7   109.96  3.000
 FOD  C9   C8   C7   110.33  3.000
 FOD  N3   N2   C5   109.33  3.000
 FOD  H6   C9   H5   107.09  3.000
 FOD  H6   C9   C10  110.24  3.000
 FOD  H5   C9   C10  109.08  3.000
 FOD  H6   C9   C8   109.58  3.000
 FOD  H5   C9   C8   109.58  3.000
 FOD  C10  C9   C8   111.17  3.000
 FOD  H7   C10  O2   110.40  3.000
 FOD  H7   C10  C11  107.94  3.000
 FOD  O2   C10  C11  112.14  3.000
 FOD  H7   C10  C9   108.08  3.000
 FOD  O2   C10  C9   107.91  3.000
 FOD  C11  C10  C9   110.30  3.000
 FOD  H9   C11  H8   107.01  3.000
 FOD  H9   C11  C12  109.51  3.000
 FOD  H8   C11  C12  109.64  3.000
 FOD  H9   C11  C10  110.22  3.000
 FOD  H8   C11  C10  109.08  3.000
 FOD  C12  C11  C10  111.30  3.000
 FOD  H11  C12  H10  107.06  3.000
 FOD  H11  C12  C11  110.38  3.000
 FOD  H10  C12  C11  109.66  3.000
 FOD  H11  C12  C7   110.05  3.000
 FOD  H10  C12  C7   109.76  3.000
 FOD  C11  C12  C7   109.90  3.000
 FOD  N4   N3   N2   108.12  3.000
 FOD  N3   N4   C7   120.38  3.000
 FOD  N3   N4   C6   110.66  3.000
 FOD  C7   N4   C6   128.96  3.000
 FOD  H2   N    H    106.34  3.000
 FOD  H2   N    CA   109.78  3.000
 FOD  H    N    CA   114.00  3.000
 FOD  HA   CA   C    110.00  3.000
 FOD  HA   CA   CB   109.00  3.000
 FOD  C    CA   CB   110.50  1.500
 FOD  HA   CA   N    110.00  3.000
 FOD  C    CA   N    111.00  2.800
 FOD  CB   CA   N    110.40  1.500
 FOD  HB2  CB   HB1  106.81  3.000
 FOD  HB2  CB   CG   108.85  3.000
 FOD  HB1  CB   CG   109.56  3.000
 FOD  HB2  CB   CA   109.97  3.000
 FOD  HB1  CB   CA   109.16  3.000
 FOD  CG   CB   CA   112.35  3.000
 FOD  HG2  CG   HG1  106.87  3.000
 FOD  HG2  CG   CB   109.54  3.000
 FOD  HG1  CG   CB   110.09  3.000
 FOD  HG2  CG   C5   109.08  3.000
 FOD  HG1  CG   C5   109.36  3.000
 FOD  CB   CG   C5   111.78  3.000
 FOD  H21  O2   C10  108.24  3.000
 FOD  O    C    OXT  123.34  3.000
 FOD  O    C    CA   120.80  1.700
 FOD  OXT  C    CA   120.80  1.700
 FOD  HXT  OXT  C    110.08  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
 FOD  CONST_01  N3   N4   C6   C5     0.00   0.0  0
 FOD  CONST_02  N4   N3   N2   C5     0.00   0.0  0
 FOD  CONST_03  N2   N3   N4   C6     0.00   0.0  0
 FOD  CONST_04  N3   N2   C5   C6     0.00   0.0  0
 FOD  CONST_05  N4   C6   C5   N2     0.00   0.0  0
 FOD  CONST_06  C7   N4   C6   C5   180.00   0.0  0
 FOD  CONST_07  N2   N3   N4   C7   180.00   0.0  0
 FOD  CONST_08  CG   C5   N2   N3   180.00   0.0  0
 FOD  CONST_09  CG   C5   C6   N4   180.00   0.0  0
 FOD  CONST_10  H1   C6   N4   C7     0.00   0.0  0
 FOD  CONST_11  HXT  OXT  C    CA   180.00   0.0  0
 FOD  Var_01    C10  C11  C12  C7    57.09  30.0  1
 FOD  Var_02    C10  C9   C8   C7   -56.66  30.0  1
 FOD  Var_03    CB   CG   C5   C6   103.55  30.0  2
 FOD  Var_04    CA   CB   CG   C5  -177.94  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
 FOD  chir_01  C7   C12  N4  C8   negativ
 FOD  chir_02  C10  O2   C9  C11  negativ
 FOD  chir_03  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
 FOD  plan-1  C5   0.020
 FOD  plan-1  C6   0.020
 FOD  plan-1  C7   0.020
 FOD  plan-1  N2   0.020
 FOD  plan-1  N3   0.020
 FOD  plan-1  N4   0.020
 FOD  plan-1  CG   0.020
 FOD  plan-1  H1   0.020
 FOD  plan-2  CA   0.020
 FOD  plan-2  C    0.020
 FOD  plan-2  O    0.020
 FOD  plan-2  HXT  0.020
 FOD  plan-2  OXT  0.020

